Psyllid ID: psy10486

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180---
Protein Sequence
MSSMNVNSSSSTLEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQASNNNNTSNTNNNTSHHGHHHHHIGHAVTNGGLKHHHQ
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccHHHHHccccccccccccccHHHHHHcccccccccccccccccccccccccccccccccHHHHHHHHHHccccccHHHHHHHHHHHHcccccHHHHHHccccHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mssmnvnsssstlewtgqvtvrkkrkpyskhqtLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQniewtgqvtvrkkrkpyskhqtLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQasnnnntsntnnntshhghhhhhighavtngglkhhhq
Flexible Loop (DISEMBL)
mssmnvnsssstlewtgqvtvrkkrkpyskhqtlelekEFLYNAYVSKQKRWELARSLMLTERQVKiwfqniewtgqvtvrkkrkpyskhqtlelekEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQASNNNNTSNTNNNTSHHGHHHHHIGHAVTNGGLKHHHQ
Low Complexity Region (SEG)
mssmnvnssssTLEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQAsnnnntsntnnntshhghhhhhighAVTNGGLKHHHQ
Disordered region (IsUnstruct)
********************************TLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQ******************************************************
Disordered Region (DISOPRED)
****************************SKHQTLELEKEFLYN********************************************SKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNR****************************************************
Disordered Region (DISEMBL)
**************WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRR*****************NNTSNTNN************GHAVTN********
Disordered Region (DISPRO)
************************RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWT****VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ*******************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSSMNVNSSSSTLEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQASNNNNTSNTNNNTSHHGHHHHHIGHAVTNGGLKHHHQ
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	183	2.2.26 [Sep-21-2011]
P09087	493	Homeobox protein abdomina	yes	N/A	0.355	0.131	0.923	5e-30
Q9YGT5	253	Homeobox protein Hox-A9b	yes	N/A	0.349	0.252	0.703	3e-20
Q9IA26	260	Homeobox protein Hox-A9 O	N/A	N/A	0.338	0.238	0.687	5e-20
Q1KKS9	273	Homeobox protein Hox-D9a	N/A	N/A	0.349	0.234	0.687	6e-20
P09631	271	Homeobox protein Hox-A9 O	yes	N/A	0.349	0.236	0.687	8e-20
Q1KKV1	346	Homeobox protein Hox-C10a	N/A	N/A	0.349	0.184	0.671	8e-20
P31310	416	Homeobox protein Hox-A10	no	N/A	0.349	0.153	0.656	9e-20
Q9PWM6	262	Homeobox protein Hox-D9a	no	N/A	0.349	0.244	0.687	9e-20
P31269	272	Homeobox protein Hox-A9 O	yes	N/A	0.349	0.235	0.687	9e-20
Q9PVR2	271	Homeobox protein Hox-D9 O	N/A	N/A	0.349	0.236	0.687	1e-19

>sp|P09087|ABDB_DROME Homeobox protein abdominal-B OS=Drosophila melanogaster GN=Abd-B PE=1 SV=3

 Score =  130 bits (327), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 60/65 (92%), Positives = 63/65 (96%)

Query: 73  EWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRR 132
           EWTGQV+VRKKRKPYSK QTLELEKEFL+NAYVSKQKRWELAR+L LTERQVKIWFQNRR
Sbjct: 380 EWTGQVSVRKKRKPYSKFQTLELEKEFLFNAYVSKQKRWELARNLQLTERQVKIWFQNRR 439

Query: 133 MKNKK 137
           MKNKK
Sbjct: 440 MKNKK 444

Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.
Drosophila melanogaster (taxid: 7227)

>sp|Q9YGT5|HXA9B_DANRE Homeobox protein Hox-A9b OS=Danio rerio GN=hoxa9b PE=2 SV=3

 Score = 97.8 bits (242), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 45/64 (70%), Positives = 53/64 (82%)

Query: 74  WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133
           W    + RKKR PY+KHQTLELEKEFL+N Y+S+ +R+E+AR L LTERQVKIWFQNRRM
Sbjct: 181 WLHAKSTRKKRCPYTKHQTLELEKEFLFNMYLSRDRRYEVARLLNLTERQVKIWFQNRRM 240

Query: 134 KNKK 137
           K KK
Sbjct: 241 KMKK 244

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

Danio rerio (taxid: 7955)

>sp|Q9IA26|HXA9_HETFR Homeobox protein Hox-A9 OS=Heterodontus francisci GN=HOXA9 PE=3 SV=1

 Score = 97.1 bits (240), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 44/64 (68%), Positives = 53/64 (82%)

Query: 74  WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133
           W    + RKKR PY+KHQTLELEKEFL+N Y+++ +R+E+AR L LTERQVKIWFQNRRM
Sbjct: 187 WLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRM 246

Query: 134 KNKK 137
           K KK
Sbjct: 247 KMKK 250

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

Heterodontus francisci (taxid: 7792)

>sp|Q1KKS9|HXD9A_TAKRU Homeobox protein Hox-D9a OS=Takifugu rubripes GN=hoxd9a PE=3 SV=1

 Score = 97.1 bits (240), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 44/64 (68%), Positives = 53/64 (82%)

Query: 74  WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133
           W    + RKKR PY+K+QTLELEKEFLYN Y+++ +R+E+AR L LTERQVKIWFQNRRM
Sbjct: 199 WIHARSTRKKRCPYTKYQTLELEKEFLYNMYLTRDRRYEVARILSLTERQVKIWFQNRRM 258

Query: 134 KNKK 137
           K KK
Sbjct: 259 KMKK 262

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|P09631|HXA9_MOUSE Homeobox protein Hox-A9 OS=Mus musculus GN=Hoxa9 PE=1 SV=2

 Score = 96.7 bits (239), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 44/64 (68%), Positives = 53/64 (82%)

Query: 74  WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133
           W    + RKKR PY+KHQTLELEKEFL+N Y+++ +R+E+AR L LTERQVKIWFQNRRM
Sbjct: 199 WLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRM 258

Query: 134 KNKK 137
           K KK
Sbjct: 259 KMKK 262

Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Required for induction of E-selectin and VCAM-1, on the endothelial cells surface at sites of inflammation.

Mus musculus (taxid: 10090)

>sp|Q1KKV1|HXCAA_TAKRU Homeobox protein Hox-C10a OS=Takifugu rubripes GN=hoxc10a PE=3 SV=1

 Score = 96.7 bits (239), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 43/64 (67%), Positives = 54/64 (84%)

Query: 74  WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133
           W    + RKKR PY+KHQTLELEKEFL+N Y+S+++R E++RS+ LT+RQVKIWFQNRRM
Sbjct: 266 WLKAKSGRKKRCPYTKHQTLELEKEFLFNMYLSRERRLEISRSINLTDRQVKIWFQNRRM 325

Query: 134 KNKK 137
           K KK
Sbjct: 326 KLKK 329

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|P31310|HXA10_MOUSE Homeobox protein Hox-A10 OS=Mus musculus GN=Hoxa10 PE=2 SV=4

 Score = 96.7 bits (239), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 42/64 (65%), Positives = 54/64 (84%)

Query: 74  WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133
           W    + RKKR PY+KHQTLELEKEFL+N Y+++++R E++RS+ LT+RQVKIWFQNRRM
Sbjct: 336 WLTAKSGRKKRCPYTKHQTLELEKEFLFNMYLTRERRLEISRSVHLTDRQVKIWFQNRRM 395

Query: 134 KNKK 137
           K KK
Sbjct: 396 KLKK 399

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 to the DNA sequence 5'-AA[AT]TTTTATTAC-3'.

Mus musculus (taxid: 10090)

>sp|Q9PWM6|HXD9A_DANRE Homeobox protein Hox-D9a OS=Danio rerio GN=hoxd9a PE=2 SV=2

 Score = 96.3 bits (238), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 44/64 (68%), Positives = 53/64 (82%)

Query: 74  WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133
           W    + RKKR PY+K+QTLELEKEFLYN Y+++ +R+E+AR L LTERQVKIWFQNRRM
Sbjct: 189 WIHARSTRKKRCPYTKYQTLELEKEFLYNMYLTRDRRYEVARILNLTERQVKIWFQNRRM 248

Query: 134 KNKK 137
           K KK
Sbjct: 249 KMKK 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.

Danio rerio (taxid: 7955)

>sp|P31269|HXA9_HUMAN Homeobox protein Hox-A9 OS=Homo sapiens GN=HOXA9 PE=1 SV=4

 Score = 96.3 bits (238), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 44/64 (68%), Positives = 53/64 (82%)

Query: 74  WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133
           W    + RKKR PY+KHQTLELEKEFL+N Y+++ +R+E+AR L LTERQVKIWFQNRRM
Sbjct: 200 WLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRM 259

Query: 134 KNKK 137
           K KK
Sbjct: 260 KMKK 263

Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Required for induction of E-selectin and VCAM-1, on the endothelial cells surface at sites of inflammation.

Homo sapiens (taxid: 9606)

>sp|Q9PVR2|HXD9_ORYLA Homeobox protein Hox-D9 OS=Oryzias latipes GN=hoxd9 PE=2 SV=1

 Score = 96.3 bits (238), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 44/64 (68%), Positives = 53/64 (82%)

Query: 74  WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133
           W    + RKKR PY+K+QTLELEKEFLYN Y+++ +R+E+AR L LTERQVKIWFQNRRM
Sbjct: 197 WIHARSTRKKRCPYTKYQTLELEKEFLYNMYLTRDRRFEVARILSLTERQVKIWFQNRRM 256

Query: 134 KNKK 137
           K KK
Sbjct: 257 KMKK 260

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

Oryzias latipes (taxid: 8090)

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	183
87474981	377	abdominal-B [Anopheles gambiae]	0.540	0.262	0.732	1e-33
158290044	377	AGAP004664-PA [Anopheles gambiae str. PE	0.540	0.262	0.732	1e-33
157124602	187	homeobox protein abdominal-B, putative [	0.601	0.588	0.681	1e-32
321475836	484	putative homeotic abdominal-B protein [D	0.387	0.146	0.915	3e-32
307213531	585	Homeobox protein abdominal-B [Harpegnath	0.404	0.126	0.891	4e-32
195038664	530	GH18073 [Drosophila grimshawi] gi|193894	0.535	0.184	0.754	4e-32
195107237	585	GI23752 [Drosophila mojavensis] gi|19391	0.535	0.167	0.754	6e-32
157124058	149	homeobox protein abdominal-B, putative [	0.601	0.738	0.681	6e-32
195394378	579	GJ10598 [Drosophila virilis] gi|19414253	0.398	0.126	0.904	8e-32
383849760	429	PREDICTED: uncharacterized protein LOC10	0.606	0.258	0.677	2e-31

>gi|87474981|gb|ABD38144.1| abdominal-B [Anopheles gambiae]

 Score =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 74/101 (73%), Positives = 89/101 (88%), Gaps = 2/101 (1%)

Query: 72  IEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNR 131
           +EWTG VTVRKKRKPYSK QTLELEKEFL+NAYVSKQKRWELAR+L LTERQVKIWFQNR
Sbjct: 262 LEWTGNVTVRKKRKPYSKFQTLELEKEFLFNAYVSKQKRWELARNLNLTERQVKIWFQNR 321

Query: 132 RMKNKKNTQRQAAQASNNNNTSNTNNNTSHHGHHH--HHIG 170
           RMKNKKN+QRQ+AQA++ ++ ++++++ S    HH  HHIG
Sbjct: 322 RMKNKKNSQRQSAQANSGSSNNSSSHSHSQAQPHHNPHHIG 362

Source: Anopheles gambiae

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158290044|ref|XP_311628.4| AGAP004664-PA [Anopheles gambiae str. PEST] gi|157018342|gb|EAA07262.4| AGAP004664-PA [Anopheles gambiae str. PEST]

 Score =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 74/101 (73%), Positives = 89/101 (88%), Gaps = 2/101 (1%)

Query: 72  IEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNR 131
           +EWTG VTVRKKRKPYSK QTLELEKEFL+NAYVSKQKRWELAR+L LTERQVKIWFQNR
Sbjct: 262 LEWTGNVTVRKKRKPYSKFQTLELEKEFLFNAYVSKQKRWELARNLNLTERQVKIWFQNR 321

Query: 132 RMKNKKNTQRQAAQASNNNNTSNTNNNTSHHGHHH--HHIG 170
           RMKNKKN+QRQ+AQA++ ++ ++++++ S    HH  HHIG
Sbjct: 322 RMKNKKNSQRQSAQANSGSSNNSSSHSHSQAQPHHNPHHIG 362

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157124602|ref|XP_001654126.1| homeobox protein abdominal-B, putative [Aedes aegypti] gi|108873932|gb|EAT38157.1| AAEL009933-PA [Aedes aegypti]

 Score =  144 bits (364), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 77/113 (68%), Positives = 95/113 (84%), Gaps = 3/113 (2%)

Query: 72  IEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNR 131
           +EWTG VTVRKKRKPYSK QTLELEKEFL+NAYVSKQKRWELAR+L LTERQVKIWFQNR
Sbjct: 74  LEWTGNVTVRKKRKPYSKFQTLELEKEFLFNAYVSKQKRWELARNLNLTERQVKIWFQNR 133

Query: 132 RMKNKKNTQRQAAQASNNNNTSNTNNNT---SHHGHHHHHIGHAVTNGGLKHH 181
           RMKNKKN+QRQ AQ++N++++++++N+    SHH  HH ++G  +   G K H
Sbjct: 134 RMKNKKNSQRQQAQSNNSSSSNSSHNHAQQQSHHNPHHLNLGLGMPLHGSKMH 186

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321475836|gb|EFX86798.1| putative homeotic abdominal-B protein [Daphnia pulex]

 Score =  143 bits (360), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 65/71 (91%), Positives = 69/71 (97%)

Query: 72  IEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNR 131
           +EWTGQVTVRKKRKPYSK QTLELEKEFL+NAYVSKQKRWELAR+L LTERQVKIWFQNR
Sbjct: 351 LEWTGQVTVRKKRKPYSKFQTLELEKEFLFNAYVSKQKRWELARNLNLTERQVKIWFQNR 410

Query: 132 RMKNKKNTQRQ 142
           RMKNKKN+QRQ
Sbjct: 411 RMKNKKNSQRQ 421

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307213531|gb|EFN88940.1| Homeobox protein abdominal-B [Harpegnathos saltator]

 Score =  142 bits (359), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 66/74 (89%), Positives = 70/74 (94%)

Query: 72  IEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNR 131
           +EWTGQVTVRKKRKPYSK QTLELEKEFL+NAYVSKQKRWELAR+L LTERQVKIWFQNR
Sbjct: 375 LEWTGQVTVRKKRKPYSKFQTLELEKEFLFNAYVSKQKRWELARNLNLTERQVKIWFQNR 434

Query: 132 RMKNKKNTQRQAAQ 145
           RMKNKKN+QRQ  Q
Sbjct: 435 RMKNKKNSQRQTQQ 448

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195038664|ref|XP_001990775.1| GH18073 [Drosophila grimshawi] gi|193894971|gb|EDV93837.1| GH18073 [Drosophila grimshawi]

 Score =  142 bits (359), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 77/102 (75%), Positives = 89/102 (87%), Gaps = 4/102 (3%)

Query: 73  EWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRR 132
           EWTGQV+VRKKRKPYSK QTLELEKEFL+NAYVSKQKRWELAR+L LTERQVKIWFQNRR
Sbjct: 417 EWTGQVSVRKKRKPYSKFQTLELEKEFLFNAYVSKQKRWELARNLQLTERQVKIWFQNRR 476

Query: 133 MKNKKNTQRQAAQASNNNNTSNTNNNT----SHHGHHHHHIG 170
           MKNKKN+QRQA Q +NNNN+S+ +N+      HH +HH ++G
Sbjct: 477 MKNKKNSQRQATQQNNNNNSSSNHNHAQAAQQHHNNHHLNLG 518

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195107237|ref|XP_001998220.1| GI23752 [Drosophila mojavensis] gi|193914814|gb|EDW13681.1| GI23752 [Drosophila mojavensis]

 Score =  142 bits (358), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 77/102 (75%), Positives = 89/102 (87%), Gaps = 4/102 (3%)

Query: 73  EWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRR 132
           EWTGQV+VRKKRKPYSK QTLELEKEFL+NAYVSKQKRWELAR+L LTERQVKIWFQNRR
Sbjct: 472 EWTGQVSVRKKRKPYSKFQTLELEKEFLFNAYVSKQKRWELARNLQLTERQVKIWFQNRR 531

Query: 133 MKNKKNTQRQAAQASNNNNTSNTNNNT----SHHGHHHHHIG 170
           MKNKKN+QRQA Q +NNNN+S+ +N+      HH +HH ++G
Sbjct: 532 MKNKKNSQRQATQQNNNNNSSSNHNHAQAAQQHHNNHHLNLG 573

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157124058|ref|XP_001660311.1| homeobox protein abdominal-B, putative [Aedes aegypti] gi|108874130|gb|EAT38355.1| AAEL009743-PA [Aedes aegypti]

 Score =  142 bits (358), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 77/113 (68%), Positives = 95/113 (84%), Gaps = 3/113 (2%)

Query: 72  IEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNR 131
           +EWTG VTVRKKRKPYSK QTLELEKEFL+NAYVSKQKRWELAR+L LTERQVKIWFQNR
Sbjct: 36  LEWTGNVTVRKKRKPYSKFQTLELEKEFLFNAYVSKQKRWELARNLNLTERQVKIWFQNR 95

Query: 132 RMKNKKNTQRQAAQASNNNNTSNTNNNT---SHHGHHHHHIGHAVTNGGLKHH 181
           RMKNKKN+QRQ AQ++N++++++++N+    SHH  HH ++G  +   G K H
Sbjct: 96  RMKNKKNSQRQQAQSNNSSSSNSSHNHAQQQSHHNPHHLNLGLGMPLHGSKMH 148

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195394378|ref|XP_002055822.1| GJ10598 [Drosophila virilis] gi|194142531|gb|EDW58934.1| GJ10598 [Drosophila virilis]

 Score =  142 bits (357), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 66/73 (90%), Positives = 70/73 (95%)

Query: 73  EWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRR 132
           EWTGQV+VRKKRKPYSK QTLELEKEFL+NAYVSKQKRWELAR+L LTERQVKIWFQNRR
Sbjct: 466 EWTGQVSVRKKRKPYSKFQTLELEKEFLFNAYVSKQKRWELARNLQLTERQVKIWFQNRR 525

Query: 133 MKNKKNTQRQAAQ 145
           MKNKKN+QRQA Q
Sbjct: 526 MKNKKNSQRQATQ 538

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383849760|ref|XP_003700505.1| PREDICTED: uncharacterized protein LOC100875666, partial [Megachile rotundata]

 Score =  140 bits (353), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 86/127 (67%), Positives = 95/127 (74%), Gaps = 16/127 (12%)

Query: 72  IEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNR 131
           +EWTGQVTVRKKRKPYSK QTLELEKEFL+NAYVSKQKRWELAR+L LTERQVKIWFQNR
Sbjct: 222 LEWTGQVTVRKKRKPYSKFQTLELEKEFLFNAYVSKQKRWELARNLNLTERQVKIWFQNR 281

Query: 132 RMKNKKNTQRQAAQASNNNNTSNTNNNTSHHG----HHHHHIGHAV------------TN 175
           RMKNKKN QRQ+ Q +NNNN +++ NN +HH     HHH   GHA              N
Sbjct: 282 RMKNKKNNQRQSQQQNNNNNNNSSANNANHHAATGSHHHPSAGHAPPSSHHVVAQAHHAN 341

Query: 176 GGLKHHH 182
           G  KHHH
Sbjct: 342 GSAKHHH 348

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	183
FB|FBgn0000015	493	Abd-B "Abdominal B" [Drosophil	0.398	0.148	0.904	9.8e-32
WB|WBGene00004024	275	php-3 [Caenorhabditis elegans	0.382	0.254	0.774	7.6e-25
UNIPROTKB|E1BQM6	250	HOXB9 "Uncharacterized protein	0.393	0.288	0.597	1.4e-20
ZFIN|ZDB-GENE-000823-2	253	hoxa9b "homeo box A9b" [Danio	0.371	0.268	0.681	3.5e-20
ZFIN|ZDB-GENE-990415-121	262	hoxd9a "homeo box D9a" [Danio	0.382	0.267	0.647	7.2e-20
UNIPROTKB|F1NE14	169	LOC100858551 "Uncharacterized	0.371	0.402	0.666	9.2e-20
UNIPROTKB|F1NJG5	254	LOC100858551 "Uncharacterized	0.371	0.267	0.666	9.2e-20
UNIPROTKB|Q98924	169	HOXA9 "Homeobox protein Hox-A9	0.371	0.402	0.666	9.2e-20
UNIPROTKB|E2R520	272	HOXA9 "Uncharacterized protein	0.371	0.25	0.666	9.2e-20
UNIPROTKB|D6RAR5	112	D6RAR5 "Uncharacterized protei	0.371	0.607	0.666	9.2e-20

FB|FBgn0000015 Abd-B "Abdominal B" [Drosophila melanogaster (taxid:7227)]

 Score = 348 (127.6 bits), Expect = 9.8e-32, P = 9.8e-32
 Identities = 66/73 (90%), Positives = 70/73 (95%)

Query:    73 EWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRR 132
             EWTGQV+VRKKRKPYSK QTLELEKEFL+NAYVSKQKRWELAR+L LTERQVKIWFQNRR
Sbjct:   380 EWTGQVSVRKKRKPYSKFQTLELEKEFLFNAYVSKQKRWELARNLQLTERQVKIWFQNRR 439

Query:   133 MKNKKNTQRQAAQ 145
             MKNKKN+QRQA Q
Sbjct:   440 MKNKKNSQRQANQ 452

GO:0005634 "nucleus" evidence=NAS;IDA

GO:0008406 "gonad development" evidence=NAS

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

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

GO:0007506 "gonadal mesoderm development" evidence=IMP

GO:0008354 "germ cell migration" evidence=IMP;TAS

GO:0007280 "pole cell migration" evidence=TAS

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

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

GO:0007494 "midgut development" evidence=TAS

GO:0008595 "anterior/posterior axis specification, embryo" evidence=NAS

GO:0007385 "specification of segmental identity, abdomen" evidence=IMP;NAS

GO:0035215 "genital disc development" evidence=TAS

GO:0045705 "negative regulation of salivary gland boundary specification" evidence=TAS

GO:0048071 "sex-specific pigmentation" evidence=TAS

GO:0009997 "negative regulation of cardioblast cell fate specification" evidence=IMP

GO:0045843 "negative regulation of striated muscle tissue development" evidence=IMP

GO:0007484 "imaginal disc-derived genitalia development" evidence=TAS

GO:0048066 "developmental pigmentation" evidence=NAS

GO:0007548 "sex differentiation" evidence=NAS

GO:0048087 "positive regulation of developmental pigmentation" evidence=NAS

GO:0007507 "heart development" evidence=NAS

GO:0007431 "salivary gland development" evidence=NAS

GO:0008584 "male gonad development" evidence=IMP

GO:0035263 "genital disc sexually dimorphic development" evidence=IMP

GO:0035225 "determination of genital disc primordium" evidence=IMP

GO:0035261 "external genitalia morphogenesis" evidence=IMP

GO:0030540 "female genitalia development" evidence=IMP

GO:0030539 "male genitalia development" evidence=IMP

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

GO:0048094 "male pigmentation" evidence=IDA

GO:0007424 "open tracheal system development" evidence=IMP

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

GO:0060439 "trachea morphogenesis" evidence=IMP

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

WB|WBGene00004024 php-3 [Caenorhabditis elegans (taxid:6239)]

 Score = 283 (104.7 bits), Expect = 7.6e-25, P = 7.6e-25
 Identities = 55/71 (77%), Positives = 60/71 (84%)

Query:    72 IEWTGQV-TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 130
             +EWT     +RKKRKPY+K QTLELEKEFLYN YVSKQKRWELA+ L LTERQVKIWFQN
Sbjct:   190 LEWTSSSHAMRKKRKPYTKAQTLELEKEFLYNTYVSKQKRWELAKYLHLTERQVKIWFQN 249

Query:   131 RRMKNKKNTQR 141
             RRMK+KK  QR
Sbjct:   250 RRMKDKKQKQR 260

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

UNIPROTKB|E1BQM6 HOXB9 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 223 (83.6 bits), Expect = 1.4e-20, Sum P(2) = 1.4e-20
 Identities = 43/72 (59%), Positives = 55/72 (76%)

Query:    74 WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133
             W    + RKKR PY+K+QTLELEKEFL+N Y+++ +R E+AR L L+ERQVKIWFQNRRM
Sbjct:   176 WLHARSSRKKRCPYTKYQTLELEKEFLFNMYLTRDRRHEVARLLNLSERQVKIWFQNRRM 235

Query:   134 KNKKNTQRQAAQ 145
             K KK  + Q  +
Sbjct:   236 KMKKMNKEQGKE 247

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

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

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

GO:0005739 "mitochondrion" evidence=IEA

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

GO:0030879 "mammary gland development" evidence=IEA

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

GO:0048706 "embryonic skeletal system development" evidence=IEA

GO:0060070 "canonical Wnt receptor signaling pathway" evidence=IEA

GO:0060326 "cell chemotaxis" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

ZFIN|ZDB-GENE-000823-2 hoxa9b "homeo box A9b" [Danio rerio (taxid:7955)]

 Score = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 47/69 (68%), Positives = 55/69 (79%)

Query:    74 WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133
             W    + RKKR PY+KHQTLELEKEFL+N Y+S+ +R+E+AR L LTERQVKIWFQNRRM
Sbjct:   181 WLHAKSTRKKRCPYTKHQTLELEKEFLFNMYLSRDRRYEVARLLNLTERQVKIWFQNRRM 240

Query:   134 KNKK-NTQR 141
             K KK N  R
Sbjct:   241 KMKKCNKDR 249

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

ZFIN|ZDB-GENE-990415-121 hoxd9a "homeo box D9a" [Danio rerio (taxid:7955)]

 Score = 236 (88.1 bits), Expect = 7.2e-20, P = 7.2e-20
 Identities = 46/71 (64%), Positives = 57/71 (80%)

Query:    74 WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133
             W    + RKKR PY+K+QTLELEKEFLYN Y+++ +R+E+AR L LTERQVKIWFQNRRM
Sbjct:   189 WIHARSTRKKRCPYTKYQTLELEKEFLYNMYLTRDRRYEVARILNLTERQVKIWFQNRRM 248

Query:   134 KNKK-NTQRQA 143
             K KK N +R +
Sbjct:   249 KMKKMNRERSS 259

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

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

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

UNIPROTKB|F1NE14 LOC100858551 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 235 (87.8 bits), Expect = 9.2e-20, P = 9.2e-20
 Identities = 46/69 (66%), Positives = 55/69 (79%)

Query:    74 WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133
             W    + RKKR PY+KHQTLELEKEFL+N Y+++ +R+E+AR L LTERQVKIWFQNRRM
Sbjct:    97 WLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRM 156

Query:   134 KNKK-NTQR 141
             K KK N  R
Sbjct:   157 KMKKINKDR 165

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

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

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

GO:0005667 "transcription factor complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

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

GO:0030879 "mammary gland development" evidence=IEA

GO:0035115 "embryonic forelimb morphogenesis" evidence=IEA

GO:0048706 "embryonic skeletal system development" evidence=IEA

GO:0060216 "definitive hemopoiesis" evidence=IEA

UNIPROTKB|F1NJG5 LOC100858551 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 235 (87.8 bits), Expect = 9.2e-20, P = 9.2e-20
 Identities = 46/69 (66%), Positives = 55/69 (79%)

Query:    74 WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133
             W    + RKKR PY+KHQTLELEKEFL+N Y+++ +R+E+AR L LTERQVKIWFQNRRM
Sbjct:   182 WLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRM 241

Query:   134 KNKK-NTQR 141
             K KK N  R
Sbjct:   242 KMKKINKDR 250

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

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

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

GO:0005667 "transcription factor complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

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

GO:0030879 "mammary gland development" evidence=IEA

GO:0035115 "embryonic forelimb morphogenesis" evidence=IEA

GO:0048706 "embryonic skeletal system development" evidence=IEA

GO:0060216 "definitive hemopoiesis" evidence=IEA

UNIPROTKB|Q98924 HOXA9 "Homeobox protein Hox-A9" [Gallus gallus (taxid:9031)]

 Score = 235 (87.8 bits), Expect = 9.2e-20, P = 9.2e-20
 Identities = 46/69 (66%), Positives = 55/69 (79%)

Query:    74 WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133
             W    + RKKR PY+KHQTLELEKEFL+N Y+++ +R+E+AR L LTERQVKIWFQNRRM
Sbjct:    97 WLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRM 156

Query:   134 KNKK-NTQR 141
             K KK N  R
Sbjct:   157 KMKKINKDR 165

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

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|E2R520 HOXA9 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 235 (87.8 bits), Expect = 9.2e-20, P = 9.2e-20
 Identities = 46/69 (66%), Positives = 55/69 (79%)

Query:    74 WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133
             W    + RKKR PY+KHQTLELEKEFL+N Y+++ +R+E+AR L LTERQVKIWFQNRRM
Sbjct:   200 WLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRM 259

Query:   134 KNKK-NTQR 141
             K KK N  R
Sbjct:   260 KMKKINKDR 268

GO:0060216 "definitive hemopoiesis" evidence=IEA

GO:0048706 "embryonic skeletal system development" evidence=IEA

GO:0042118 "endothelial cell activation" evidence=IEA

GO:0035115 "embryonic forelimb morphogenesis" evidence=IEA

GO:0030879 "mammary gland development" evidence=IEA

GO:0019899 "enzyme binding" evidence=IEA

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

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

GO:0005737 "cytoplasm" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

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

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

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

UNIPROTKB|D6RAR5 D6RAR5 "Uncharacterized protein" [Homo sapiens (taxid:9606)]

 Score = 235 (87.8 bits), Expect = 9.2e-20, P = 9.2e-20
 Identities = 46/69 (66%), Positives = 55/69 (79%)

Query:    74 WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133
             W    + RKKR PY+KHQTLELEKEFL+N Y+++ +R+E+AR L LTERQVKIWFQNRRM
Sbjct:    40 WLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRM 99

Query:   134 KNKK-NTQR 141
             K KK N  R
Sbjct:   100 KMKKINKDR 108

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

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

GO:0005634 "nucleus" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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	183
pfam00046	57	pfam00046, Homeobox, Homeobox domain	1e-21
smart00389	57	smart00389, HOX, Homeodomain	4e-18
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	5e-18
pfam00046	57	pfam00046, Homeobox, Homeobox domain	4e-17
smart00389	57	smart00389, HOX, Homeodomain	1e-14
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	4e-14
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	4e-08
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	9e-05

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

 Score = 82.9 bits (206), Expect = 1e-21
 Identities = 33/57 (57%), Positives = 41/57 (71%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           R+KR  ++  Q  ELEKEF  N Y S ++R ELA+ L LTERQVK+WFQNRR K K+
Sbjct: 1   RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57

Length = 57

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 73.8 bits (182), Expect = 4e-18
 Identities = 32/56 (57%), Positives = 41/56 (73%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK 136
           R+KR  ++  Q  ELEKEF  N Y S+++R ELA+ L L+ERQVK+WFQNRR K K
Sbjct: 2   RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

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

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

 Score = 73.4 bits (181), Expect = 5e-18
 Identities = 34/58 (58%), Positives = 43/58 (74%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138
           R+KR  ++  Q  ELEKEF  N Y S+++R ELA+ L LTERQVKIWFQNRR K K++
Sbjct: 1   RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58

Length = 59

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

 Score = 71.0 bits (175), Expect = 4e-17
 Identities = 29/50 (58%), Positives = 36/50 (72%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          R+KR  ++  Q  ELEKEF  N Y S ++R ELA+ L LTERQVK+WFQN
Sbjct: 1  RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQN 50

Length = 57

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 65.0 bits (159), Expect = 1e-14
 Identities = 28/50 (56%), Positives = 37/50 (74%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          R+KR  ++  Q  ELEKEF  N Y S+++R ELA+ L L+ERQVK+WFQN
Sbjct: 2  RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQN 51

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 = 63.4 bits (155), Expect = 4e-14
 Identities = 30/50 (60%), Positives = 37/50 (74%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          R+KR  ++  Q  ELEKEF  N Y S+++R ELA+ L LTERQVKIWFQN
Sbjct: 1  RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQN 50

Length = 59

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

 Score = 49.7 bits (119), Expect = 4e-08
 Identities = 24/65 (36%), Positives = 36/65 (55%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           + KR+  +  Q + LE+EF  N Y S   R +L+  L +  + V+IWFQN+R K KK   
Sbjct: 52  KSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRS 111

Query: 141 RQAAQ 145
            +  Q
Sbjct: 112 GKVEQ 116

Length = 156

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

 Score = 40.5 bits (95), Expect = 9e-05
 Identities = 19/50 (38%), Positives = 29/50 (58%)

Query: 22  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
           + KR+  +  Q + LE+EF  N Y S   R +L+  L +  + V+IWFQN
Sbjct: 52  KSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQN 101

Length = 156

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	183
KOG0490|consensus	235		99.75
KOG0484|consensus	125		99.72
KOG2251|consensus	228		99.68
KOG0850|consensus	245		99.66
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.66
KOG0488|consensus	309		99.65
KOG0484|consensus	125		99.64
KOG0487|consensus	308		99.64
KOG0488|consensus	309		99.64
KOG0489|consensus	261		99.64
KOG0843|consensus	197		99.64
KOG2251|consensus	228		99.63
KOG0842|consensus	307		99.63
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.63
KOG0850|consensus	245		99.63
KOG0494|consensus	332		99.61
KOG0843|consensus	197		99.61
KOG0487|consensus	308		99.59
KOG0489|consensus	261		99.59
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.59
KOG0494|consensus	332		99.58
KOG0842|consensus	307		99.58
KOG0848|consensus	317		99.58
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.56
KOG0492|consensus	246		99.55
KOG0848|consensus	317		99.55
KOG0492|consensus	246		99.53
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.52
COG5576	156	Homeodomain-containing transcription factor [Trans	99.52
KOG0485|consensus	268		99.5
KOG0491|consensus	194		99.5
KOG0485|consensus	268		99.5
KOG3802|consensus	398		99.48
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.48
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.48
KOG0493|consensus	342		99.47
KOG0486|consensus	351		99.45
KOG0486|consensus	351		99.43
KOG0491|consensus	194		99.4
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.39
KOG0483|consensus	198		99.38
COG5576	156	Homeodomain-containing transcription factor [Trans	99.38
KOG0844|consensus	408		99.36
KOG3802|consensus	398		99.35
KOG0483|consensus	198		99.35
KOG0844|consensus	408		99.35
KOG0493|consensus	342		99.35
KOG4577|consensus	383		99.29
KOG0847|consensus	288		99.23
KOG4577|consensus	383		99.15
KOG0849|consensus	354		99.04
KOG0490|consensus	235		98.94
KOG0849|consensus	354		98.91
KOG0775|consensus	304		98.85
KOG0847|consensus	288		98.83
KOG0775|consensus	304		98.76
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.74
KOG1168|consensus	385		98.63
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.6
KOG1168|consensus	385		98.54
KOG2252|consensus	558		98.5
KOG0774|consensus	334		98.43
KOG1146|consensus	1406		98.33
KOG0774|consensus	334		98.3
KOG2252|consensus	558		97.96
KOG3623|consensus	1007		97.66
KOG1146|consensus	1406		97.48
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	97.41
KOG0773|consensus	342		97.21
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	97.12
KOG0773|consensus	342		96.25
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	95.12
PF13551	112	HTH_29: Winged helix-turn helix	94.54
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	94.13
KOG3623|consensus	1007		94.05
cd00131	128	PAX Paired Box domain	93.91
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	93.52
smart00351	125	PAX Paired Box domain.	93.5
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	92.61
cd04763	68	HTH_MlrA-like Helix-Turn-Helix DNA binding domain	91.87
KOG3755|consensus	769		91.72
cd04764	67	HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding dom	91.56
PRK06424	144	transcription factor; Provisional	90.51
cd01106	103	HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain	90.37
cd01104	68	HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain	90.08
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	89.94
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	89.72
PF13443	63	HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3	89.29
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	88.93
PHA01976	67	helix-turn-helix protein	88.17
cd04765	99	HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding dom	86.96
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	86.46
COG3413	215	Predicted DNA binding protein [General function pr	86.4
cd04773	108	HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding	84.63
cd04768	96	HTH_BmrR-like Helix-Turn-Helix DNA binding domain	84.1
TIGR02047	127	CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional	84.04
PRK09726	88	antitoxin HipB; Provisional	83.97
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	83.8
cd01109	113	HTH_YyaN Helix-Turn-Helix DNA binding domain of th	83.31
smart00422	70	HTH_MERR helix_turn_helix, mercury resistance.	83.26
TIGR03070	58	couple_hipB transcriptional regulator, y4mF family	82.68
TIGR02044	127	CueR Cu(I)-responsive transcriptional regulator. T	82.28
TIGR02607	78	antidote_HigA addiction module antidote protein, H	81.99
COG3415	138	Transposase and inactivated derivatives [DNA repli	81.97
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	81.83
TIGR02043	131	ZntR Zn(II)-responsive transcriptional regulator.	81.81
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	81.7
PRK09706	135	transcriptional repressor DicA; Reviewed	81.46
PF09607	58	BrkDBD: Brinker DNA-binding domain; InterPro: IPR0	81.27
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	81.15
cd04767	120	HTH_HspR-like_MBC Helix-Turn-Helix DNA binding dom	81.14
cd04788	96	HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain	80.99
PF10668	60	Phage_terminase: Phage terminase small subunit; In	80.71
PF12844	64	HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_	80.34
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	80.28

>KOG0490|consensus

Probab=99.75  E-value=2.1e-18  Score=134.75  Aligned_cols=123  Identities=30%  Similarity=0.362  Sum_probs=112.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc-----------------
Q psy10486         18 QVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV-----------------   80 (183)
Q Consensus        18 ~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~-----------------   80 (183)
                      ..+.++.|+.|+..|+++|+..|..++||+...++.||..+++++..|++||+|+|++.++..                 
T Consensus        57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~~~~~~~~~~~~~~~~~  136 (235)
T KOG0490|consen   57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEERPLPEGENLPDLSGTAP  136 (235)
T ss_pred             hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhccccccccCCCCCCCCC
Confidence            567889999999999999999999999999999999999999999999999999999866433                 


Q ss_pred             -----------------cccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486         81 -----------------RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ  140 (183)
Q Consensus        81 -----------------rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~  140 (183)
                                       ++.++.+...++..+...|....+|+...++.|+..+|++...|++||+|+|.+.++...
T Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  137 PSASRDKLDKGPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             ccccccccccCCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence                             223457778899999999999999999999999999999999999999999999998877

>KOG0484|consensus

Probab=99.72  E-value=6.6e-18  Score=112.65  Aligned_cols=70  Identities=34%  Similarity=0.492  Sum_probs=64.2

Q ss_pred             cccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHHh
Q psy10486         77 QVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQA  146 (183)
Q Consensus        77 ~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~~  146 (183)
                      +++.++-|+.|+..|+.+|+..|...+||++-++++||..+.|++..|++||||||+|.||+.+......
T Consensus        14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~~   83 (125)
T KOG0484|consen   14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAKM   83 (125)
T ss_pred             HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHHh
Confidence            4567788999999999999999999999999999999999999999999999999999999997665543

>KOG2251|consensus

Probab=99.68  E-value=3.1e-17  Score=123.65  Aligned_cols=64  Identities=30%  Similarity=0.415  Sum_probs=60.8

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486         16 TGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        16 ~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~   79 (183)
                      ..+++.||+||.|+..|+++||+.|.++.|||...+++||.+|+|.+-+|++||.|||+|.+..
T Consensus        32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~q   95 (228)
T KOG2251|consen   32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQ   95 (228)
T ss_pred             ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHh
Confidence            6789999999999999999999999999999999999999999999999999999999996553

>KOG0850|consensus

Probab=99.66  E-value=4.8e-17  Score=123.23  Aligned_cols=65  Identities=40%  Similarity=0.463  Sum_probs=60.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486         17 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR   81 (183)
Q Consensus        17 ~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r   81 (183)
                      ...|.|++||.|+..||..|+.+|+.+.|+...||.+||..|||+..||+|||||||.|-|+..+
T Consensus       118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k  182 (245)
T KOG0850|consen  118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK  182 (245)
T ss_pred             CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence            44677899999999999999999999999999999999999999999999999999998776554

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.66  E-value=1e-16  Score=98.64  Aligned_cols=56  Identities=48%  Similarity=0.639  Sum_probs=53.0

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccc
Q psy10486         22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQ   77 (183)
Q Consensus        22 rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~   77 (183)
                      +++|+.||.+|+.+|++.|..++||+..+++.||..|||+..+|.+||+|+|.+.+
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k   56 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEK   56 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhC
Confidence            57899999999999999999999999999999999999999999999999987643

; 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 ....

>KOG0488|consensus

Probab=99.65  E-value=1.4e-16  Score=128.73  Aligned_cols=76  Identities=46%  Similarity=0.593  Sum_probs=68.1

Q ss_pred             ccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHHhcCCCCCC
Q psy10486         78 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQASNNNNTS  153 (183)
Q Consensus        78 ~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~~~~~~~~~  153 (183)
                      ++.++.|+.||.-|+..||..|++..|++..+|++||..|||+..||++||||||+|||++...........++.+
T Consensus       170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~~~~~~~~~~  245 (309)
T KOG0488|consen  170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGELLYQAGNSS  245 (309)
T ss_pred             cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhcccccccccc
Confidence            6778889999999999999999999999999999999999999999999999999999999988655555444443

>KOG0484|consensus

Probab=99.64  E-value=4.7e-17  Score=108.60  Aligned_cols=62  Identities=31%  Similarity=0.394  Sum_probs=58.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         17 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        17 ~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      ...++||-||.||..||.+||..|.++.||+.-.+++||.+|.|++..|++||||||+|-++
T Consensus        13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRK   74 (125)
T KOG0484|consen   13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRK   74 (125)
T ss_pred             HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHH
Confidence            45788999999999999999999999999999999999999999999999999999998543

>KOG0487|consensus

Probab=99.64  E-value=1.2e-16  Score=127.43  Aligned_cols=69  Identities=59%  Similarity=0.888  Sum_probs=63.7

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccccC
Q psy10486         16 TGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKR   84 (183)
Q Consensus        16 ~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r   84 (183)
                      ......||+|.-||..|+.+||+-|-.|.|++++.|.+|+..|+|+++||+|||||||.|.|+..+..+
T Consensus       230 ~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r  298 (308)
T KOG0487|consen  230 SSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR  298 (308)
T ss_pred             ccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence            455788999999999999999999999999999999999999999999999999999999998776444

>KOG0488|consensus

Probab=99.64  E-value=1.8e-16  Score=128.07  Aligned_cols=64  Identities=44%  Similarity=0.546  Sum_probs=59.6

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486         16 TGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        16 ~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~   79 (183)
                      ..+.|.|+.||.||+.||..||++|+...|++..+|++||..|||+..||++||||||.|+++.
T Consensus       167 ~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq  230 (309)
T KOG0488|consen  167 STPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQ  230 (309)
T ss_pred             CCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHH
Confidence            3457888999999999999999999999999999999999999999999999999999987753

>KOG0489|consensus

Probab=99.64  E-value=1.6e-16  Score=126.16  Aligned_cols=82  Identities=43%  Similarity=0.739  Sum_probs=71.2

Q ss_pred             hhhhhhhhccc-----cccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486         64 QVKIWFQNIEW-----TGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN  138 (183)
Q Consensus        64 qV~~WF~nrr~-----k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~  138 (183)
                      +|--|+.....     ......++.|+.||..|+.+||++|..|.|++...|.+||..|+|++.||+|||||||+||||.
T Consensus       138 ~~~p~~~~~~~~~~~~~~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~  217 (261)
T KOG0489|consen  138 QIYPWMKSTANYLSSSETGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKE  217 (261)
T ss_pred             ccccchhhhhcccccccccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHh
Confidence            67778876542     2223467889999999999999999999999999999999999999999999999999999999


Q ss_pred             HhHHHHH
Q psy10486        139 TQRQAAQ  145 (183)
Q Consensus       139 ~~~~~~~  145 (183)
                      .+.....
T Consensus       218 ~k~~~~~  224 (261)
T KOG0489|consen  218 NKAKSSQ  224 (261)
T ss_pred             hcccccc
Confidence            9776655

>KOG0843|consensus

Probab=99.64  E-value=5e-16  Score=113.61  Aligned_cols=65  Identities=43%  Similarity=0.650  Sum_probs=60.6

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQA  143 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~  143 (183)
                      ..++.|+.|+.+|+..|+..|+.++|....+|+.||..|+|++.||++||||||+|.||++...+
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~k  165 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQEDK  165 (197)
T ss_pred             CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHhh
Confidence            35567999999999999999999999999999999999999999999999999999999987753

>KOG2251|consensus

Probab=99.63  E-value=8e-16  Score=116.07  Aligned_cols=67  Identities=36%  Similarity=0.543  Sum_probs=63.5

Q ss_pred             ccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHH
Q psy10486         76 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQ  142 (183)
Q Consensus        76 ~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~  142 (183)
                      ..++.++.|+.|+-.|+++|+..|.+.+||+...+++||.+|+|.+.+|+|||+|||+|+|++++.+
T Consensus        33 ~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   33 GPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             cchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            4556788899999999999999999999999999999999999999999999999999999999876

>KOG0842|consensus

Probab=99.63  E-value=2.1e-16  Score=126.00  Aligned_cols=64  Identities=42%  Similarity=0.593  Sum_probs=59.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         17 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        17 ~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      .+.+.||.|..||..|+.+||.+|....|.+..||+.||..|+||+.||+|||||||.|.|+..
T Consensus       149 ~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~  212 (307)
T KOG0842|consen  149 GKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQ  212 (307)
T ss_pred             ccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhh
Confidence            3567778889999999999999999999999999999999999999999999999999977644

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.63  E-value=5.4e-16  Score=95.39  Aligned_cols=57  Identities=56%  Similarity=0.750  Sum_probs=54.5

Q ss_pred             cccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486         81 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK  137 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk  137 (183)
                      +++++.|+.+|+.+|+..|..++||+..+++.||..+||+..+|.+||+|+|.++|+
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            357889999999999999999999999999999999999999999999999999986

; 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 ....

>KOG0850|consensus

Probab=99.63  E-value=3.3e-16  Score=118.72  Aligned_cols=67  Identities=46%  Similarity=0.571  Sum_probs=63.1

Q ss_pred             ccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHH
Q psy10486         76 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQ  142 (183)
Q Consensus        76 ~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~  142 (183)
                      ..++.|+.|+.++.-|+..|...|+.++|+-..+|.+||..|||+-.||++||||||.|.||..+..
T Consensus       118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g  184 (245)
T KOG0850|consen  118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQG  184 (245)
T ss_pred             CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcC
Confidence            4457888999999999999999999999999999999999999999999999999999999999843

>KOG0494|consensus

Probab=99.61  E-value=7.2e-16  Score=118.62  Aligned_cols=65  Identities=29%  Similarity=0.343  Sum_probs=58.3

Q ss_pred             CCCCCC-CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccccc
Q psy10486         19 VTVRKK-RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKK   83 (183)
Q Consensus        19 ~~~rr~-r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~   83 (183)
                      .+.||. ||.||..|++.||+.|.+..|||.-.|+.||.++.|.+++|++||||||+|.+++.++-
T Consensus       138 k~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w  203 (332)
T KOG0494|consen  138 KKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW  203 (332)
T ss_pred             ccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence            334444 99999999999999999999999999999999999999999999999999988766543

>KOG0843|consensus

Probab=99.61  E-value=5.1e-16  Score=113.56  Aligned_cols=66  Identities=35%  Similarity=0.507  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccc
Q psy10486         17 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRK   82 (183)
Q Consensus        17 ~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr   82 (183)
                      ...+.+|.||.||.+||..||..|+.+.|..-.||+.||..|+|++.||++||||||-|.++...+
T Consensus        98 ~~~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e  163 (197)
T KOG0843|consen   98 RSMRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE  163 (197)
T ss_pred             cccCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence            344889999999999999999999999999999999999999999999999999999987765544

>KOG0487|consensus

Probab=99.59  E-value=4.2e-16  Score=124.40  Aligned_cols=69  Identities=65%  Similarity=0.974  Sum_probs=63.1

Q ss_pred             ccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHHh
Q psy10486         78 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQA  146 (183)
Q Consensus        78 ~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~~  146 (183)
                      +..||+|..+|+.|+.+||++|..|.|++...|.+|+..|+|+++||+|||||||.|.||..+......
T Consensus       233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r~~~  301 (308)
T KOG0487|consen  233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENRLKE  301 (308)
T ss_pred             cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhhccc
Confidence            346778999999999999999999999999999999999999999999999999999999997655443

>KOG0489|consensus

Probab=99.59  E-value=6.4e-16  Score=122.75  Aligned_cols=66  Identities=41%  Similarity=0.689  Sum_probs=60.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccccC
Q psy10486         19 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKR   84 (183)
Q Consensus        19 ~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r   84 (183)
                      ...||.||.||..||.+||+-|+-+.|.++..|.+||..|.|+++||+|||||||+|.|+..+...
T Consensus       157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~  222 (261)
T KOG0489|consen  157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS  222 (261)
T ss_pred             CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence            347899999999999999999999999999999999999999999999999999999887555443

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.59  E-value=2.6e-15  Score=91.68  Aligned_cols=51  Identities=14%  Similarity=0.333  Sum_probs=49.6

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCC----CCHHHHHHHHHHcCCChhhhhhhhhhc
Q psy10486         22 RKKRKPYSKHQTLELEKEFLYNAY----VSKQKRWELARSLMLTERQVKIWFQNI   72 (183)
Q Consensus        22 rr~r~~ft~~Ql~~Le~~F~~~~~----p~~~~~~~La~~l~l~~~qV~~WF~nr   72 (183)
                      +|.||.||.+|+..|+..|+.+.|    |+..++++||..|||++.+|++||+|-
T Consensus         2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~   56 (58)
T TIGR01565         2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNN   56 (58)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccC
Confidence            789999999999999999999999    999999999999999999999999993

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.

>KOG0494|consensus

Probab=99.58  E-value=1.4e-15  Score=117.04  Aligned_cols=67  Identities=34%  Similarity=0.429  Sum_probs=61.5

Q ss_pred             ccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHH
Q psy10486         76 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQ  142 (183)
Q Consensus        76 ~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~  142 (183)
                      .++++|..|+.||.-|+..||+.|...+||+...++.||..++|++++|+|||||||+||||.++..
T Consensus       137 kk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w  203 (332)
T KOG0494|consen  137 KKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW  203 (332)
T ss_pred             cccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence            3445556699999999999999999999999999999999999999999999999999999998765

>KOG0842|consensus

Probab=99.58  E-value=1.6e-15  Score=121.03  Aligned_cols=75  Identities=43%  Similarity=0.570  Sum_probs=67.2

Q ss_pred             cccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHHhcCCCC
Q psy10486         77 QVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQASNNNN  151 (183)
Q Consensus        77 ~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~~~~~~~  151 (183)
                      +.++||.|.-|+..|+.+||..|....|++..+|+.||..|.||+.||+|||||||-|+||+.+...........
T Consensus       150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~~~~  224 (307)
T KOG0842|consen  150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALLLAS  224 (307)
T ss_pred             cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcccCCC
Confidence            445666778899999999999999999999999999999999999999999999999999999888777665443

>KOG0848|consensus

Probab=99.58  E-value=3.6e-15  Score=115.24  Aligned_cols=65  Identities=51%  Similarity=0.778  Sum_probs=60.6

Q ss_pred             ccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHH
Q psy10486         78 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQ  142 (183)
Q Consensus        78 ~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~  142 (183)
                      ++..+.|.++|+-|.-+||++|..++|+++..+.+||.-|||+++||++||||||+|+||.+++.
T Consensus       197 RTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk  261 (317)
T KOG0848|consen  197 RTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK  261 (317)
T ss_pred             ecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence            34556788999999999999999999999999999999999999999999999999999999666

>smart00389 HOX Homeodomain

Probab=99.56  E-value=8.6e-15  Score=89.57  Aligned_cols=55  Identities=51%  Similarity=0.696  Sum_probs=51.4

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccc
Q psy10486         22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTG   76 (183)
Q Consensus        22 rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~   76 (183)
                      ++.|+.|+.+|+.+|+..|..++||+..++..||..+||+..+|..||+|+|.+.
T Consensus         1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~   55 (56)
T smart00389        1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKW   55 (56)
T ss_pred             CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhcc
Confidence            3567889999999999999999999999999999999999999999999988753

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

>KOG0492|consensus

Probab=99.55  E-value=3.7e-15  Score=111.27  Aligned_cols=68  Identities=44%  Similarity=0.652  Sum_probs=62.3

Q ss_pred             ccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHH
Q psy10486         76 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQA  143 (183)
Q Consensus        76 ~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~  143 (183)
                      +.+..|++|+.||..|+..||..|...+|+++.++.+++..|.|++.||++||||||+|.||.++.+.
T Consensus       140 Khk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~  207 (246)
T KOG0492|consen  140 KHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAEL  207 (246)
T ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHH
Confidence            34567788999999999999999999999999999999999999999999999999999999885443

>KOG0848|consensus

Probab=99.55  E-value=1e-15  Score=118.22  Aligned_cols=63  Identities=49%  Similarity=0.693  Sum_probs=58.6

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccccC
Q psy10486         22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKR   84 (183)
Q Consensus        22 rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r   84 (183)
                      -|.|.+||+.|..+||+.|+.+.|++...+.+||..|||+++||++||||||+|+++..++++
T Consensus       200 DKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~  262 (317)
T KOG0848|consen  200 DKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR  262 (317)
T ss_pred             cceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence            367889999999999999999999999999999999999999999999999999988776664

>KOG0492|consensus

Probab=99.53  E-value=5.5e-15  Score=110.38  Aligned_cols=61  Identities=43%  Similarity=0.602  Sum_probs=56.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486         19 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        19 ~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~   79 (183)
                      .+.|++||.||.+||..||..|...+|.+..|+.+++..|.|++.||++||||||+|.++.
T Consensus       142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRl  202 (246)
T KOG0492|consen  142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRL  202 (246)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHH
Confidence            4457889999999999999999999999999999999999999999999999999987653

>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=99.52  E-value=2.2e-14  Score=88.59  Aligned_cols=55  Identities=53%  Similarity=0.691  Sum_probs=51.8

Q ss_pred             CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccc
Q psy10486         23 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQ   77 (183)
Q Consensus        23 r~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~   77 (183)
                      +.+..|+..|+.+|++.|..++||+..++..||..+||+..+|..||+|+|.+.+
T Consensus         2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~   56 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLK   56 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHh
Confidence            5678999999999999999999999999999999999999999999999987654

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.52  E-value=1.1e-14  Score=106.53  Aligned_cols=100  Identities=26%  Similarity=0.301  Sum_probs=77.6

Q ss_pred             cCCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHH
Q psy10486         15 WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLE   94 (183)
Q Consensus        15 ~~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~   94 (183)
                      ..+....+++|++-|.+|+.+|+..|..++||+..++..|+..|||+++-|++||||+|++.++.....           
T Consensus        45 ~~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~-----------  113 (156)
T COG5576          45 QDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGK-----------  113 (156)
T ss_pred             ccCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccc-----------
Confidence            345567888999999999999999999999999999999999999999999999999999876544433           


Q ss_pred             HHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhh
Q psy10486         95 LEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRR  132 (183)
Q Consensus        95 Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR  132 (183)
                            ...++.. +-..++....+...++.+||.+..
T Consensus       114 ------~~~~~~~-e~~~~~~~~~~~~~~~~~~~~~~~  144 (156)
T COG5576         114 ------VEQRPGE-EEADLAKIGSLSTGQISIIETLEF  144 (156)
T ss_pred             ------hhccccc-ccccccccccccccchhhHHhhhc
Confidence                  2333333 334456666666667777775443

>KOG0485|consensus

Probab=99.50  E-value=1.4e-14  Score=108.89  Aligned_cols=67  Identities=43%  Similarity=0.598  Sum_probs=60.8

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQ  145 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~  145 (183)
                      ..++.|++|+..|+..||..|+...|++..++..||..|.|++.||++||||||.|||++-......
T Consensus       103 RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ea  169 (268)
T KOG0485|consen  103 RKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLEA  169 (268)
T ss_pred             ccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhhh
Confidence            3456688999999999999999999999999999999999999999999999999999998655443

>KOG0491|consensus

Probab=99.50  E-value=1.4e-14  Score=104.59  Aligned_cols=80  Identities=41%  Similarity=0.566  Sum_probs=70.5

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHHhcCCCCCCCCCCC
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQASNNNNTSNTNNN  158 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~~~~~~~~~~~~~~  158 (183)
                      ..++.|++|+..|+..|+..|+...|++..++.+||..|+|++.||+.||||||.|.||..+.......+.....++...
T Consensus        99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p~nS~~~t~~a~a~t  178 (194)
T KOG0491|consen   99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQPKNSNGVTQKASAPT  178 (194)
T ss_pred             HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCCCCCCcccccccCcc
Confidence            34566899999999999999999999999999999999999999999999999999999999888777666655555443

>KOG0485|consensus

Probab=99.50  E-value=1.4e-14  Score=108.93  Aligned_cols=63  Identities=41%  Similarity=0.553  Sum_probs=58.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486         17 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        17 ~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~   79 (183)
                      +..+.+|.||.|+..|+..||..|+...|.+..+|..||..|.|++.||++||||||.|.++.
T Consensus       100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq  162 (268)
T KOG0485|consen  100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQ  162 (268)
T ss_pred             cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHH
Confidence            445778889999999999999999999999999999999999999999999999999887653

>KOG3802|consensus

Probab=99.48  E-value=4.3e-15  Score=121.00  Aligned_cols=127  Identities=24%  Similarity=0.344  Sum_probs=101.2

Q ss_pred             ccCCCCCCCCCCCCCCHHHHHHHHHHhhhcCC----CCHHHHHHHHHHcCCChhh-hhhhhhhcccc-------------
Q psy10486         14 EWTGQVTVRKKRKPYSKHQTLELEKEFLYNAY----VSKQKRWELARSLMLTERQ-VKIWFQNIEWT-------------   75 (183)
Q Consensus        14 ~~~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~----p~~~~~~~La~~l~l~~~q-V~~WF~nrr~k-------------   75 (183)
                      .+....|+||-+.-||..++-.-...-.-+.|    +++.|...|.-+-.+..+- +..|...-...             
T Consensus       210 qFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALqLSFKNMCKLKPLL~KWLeEAes~~~~~~~~~~e~i~  289 (398)
T KOG3802|consen  210 QFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAESRESTGSPNSIEKIG  289 (398)
T ss_pred             HHHHHHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHhhccCHHHHhhhHHHHHHHHHHHhcccccCCCCCHHHhh
Confidence            33466888999999999998766655444444    7777766666555555544 35898764331             


Q ss_pred             ccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486         76 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ  140 (183)
Q Consensus        76 ~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~  140 (183)
                      ...++|++|+.|.......||.+|..|+.|+..++..||.+|+|....|+|||+|||.|.||...
T Consensus       290 a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  290 AQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             ccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            22256788999999999999999999999999999999999999999999999999999999887

>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=99.48  E-value=8.2e-14  Score=85.96  Aligned_cols=57  Identities=58%  Similarity=0.807  Sum_probs=53.4

Q ss_pred             ccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486         82 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN  138 (183)
Q Consensus        82 r~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~  138 (183)
                      +.+..++..++.+|+..|..++||+..++..||..+||+..+|++||+|+|.+.++.
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            456789999999999999999999999999999999999999999999999998763

>smart00389 HOX Homeodomain

Probab=99.48  E-value=6.2e-14  Score=85.73  Aligned_cols=55  Identities=56%  Similarity=0.794  Sum_probs=51.3

Q ss_pred             ccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHH
Q psy10486         82 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK  136 (183)
Q Consensus        82 r~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~r  136 (183)
                      +.++.+++.++.+|+..|..++||+..++..||..+||+..+|++||+|+|.+.+
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            4566799999999999999999999999999999999999999999999998753

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

>KOG0493|consensus

Probab=99.47  E-value=3.9e-14  Score=109.21  Aligned_cols=61  Identities=44%  Similarity=0.691  Sum_probs=57.4

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      ..+++|+.|+.+|+..|..+|..+.|++...+.+||.+|||.+.||++||||+|+|-||..
T Consensus       245 eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT  305 (342)
T KOG0493|consen  245 EEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST  305 (342)
T ss_pred             hhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence            4467799999999999999999999999999999999999999999999999999998865

>KOG0486|consensus

Probab=99.45  E-value=5.4e-14  Score=111.05  Aligned_cols=62  Identities=32%  Similarity=0.441  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486         20 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR   81 (183)
Q Consensus        20 ~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r   81 (183)
                      |+||.||.||.+||.+||..|.++.||++..+++||..++|++..|.+||.|||+|.++..+
T Consensus       111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrEr  172 (351)
T KOG0486|consen  111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRER  172 (351)
T ss_pred             hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhh
Confidence            77899999999999999999999999999999999999999999999999999999877554

>KOG0486|consensus

Probab=99.43  E-value=7.7e-14  Score=110.17  Aligned_cols=68  Identities=37%  Similarity=0.542  Sum_probs=63.9

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHHh
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQA  146 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~~  146 (183)
                      +.++.|+.|+..|+.+||..|.++.||++..+++||.-++|++..|++||+|||+||||.++.+..+.
T Consensus       111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ae~  178 (351)
T KOG0486|consen  111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAEL  178 (351)
T ss_pred             hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHHHHh
Confidence            56777899999999999999999999999999999999999999999999999999999998888443

>KOG0491|consensus

Probab=99.40  E-value=5e-14  Score=101.69  Aligned_cols=65  Identities=40%  Similarity=0.530  Sum_probs=59.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccccC
Q psy10486         20 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKR   84 (183)
Q Consensus        20 ~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r   84 (183)
                      +.++-||.|++.|+..|+++|+...|.+..++.+||..|+|++.||+.||||||+|.++-.++..
T Consensus        99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~  163 (194)
T KOG0491|consen   99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ  163 (194)
T ss_pred             HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence            44677999999999999999999999999999999999999999999999999999887666543

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.39  E-value=2.2e-13  Score=83.19  Aligned_cols=52  Identities=13%  Similarity=0.364  Sum_probs=49.6

Q ss_pred             cccCCCCChhHHHHHHHccccCCc----cCHHHHHHHHHHhCCChhhHHHHHhhhh
Q psy10486         81 RKKRKPYSKHQTLELEKEFLYNAY----VSKQKRWELARSLMLTERQVKIWFQNRR  132 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F~~~~~----p~~~~~~~La~~l~l~~~~V~~WF~nrR  132 (183)
                      ++.|+.||.+|+..|+..|+.+.|    |+..++++||..+||++.+|++||+|-+
T Consensus         2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            577999999999999999999999    9999999999999999999999999854

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.

>KOG0483|consensus

Probab=99.38  E-value=2.7e-13  Score=102.60  Aligned_cols=75  Identities=28%  Similarity=0.310  Sum_probs=61.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHH
Q psy10486         21 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLEL   95 (183)
Q Consensus        21 ~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~L   95 (183)
                      ..+++.+|+.+|+..||..|+...+.....+..||..|||.++||.+||||||++.+.+..-..-.+...++..|
T Consensus        50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l  124 (198)
T KOG0483|consen   50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESL  124 (198)
T ss_pred             cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHH
Confidence            457778999999999999999999999999999999999999999999999999887655444333333333333

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.38  E-value=6.1e-13  Score=97.41  Aligned_cols=68  Identities=35%  Similarity=0.542  Sum_probs=61.3

Q ss_pred             ccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHH
Q psy10486         78 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQ  145 (183)
Q Consensus        78 ~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~  145 (183)
                      ...+++|++.+.+|+.+|+..|+.++||+..++..|+..++|+++.|++||||+|++.|+........
T Consensus        49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~~~  116 (156)
T COG5576          49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQ  116 (156)
T ss_pred             CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccchhc
Confidence            34566788999999999999999999999999999999999999999999999999999988654433

>KOG0844|consensus

Probab=99.36  E-value=1.9e-13  Score=107.57  Aligned_cols=68  Identities=34%  Similarity=0.546  Sum_probs=61.3

Q ss_pred             ccCCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486         14 EWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR   81 (183)
Q Consensus        14 ~~~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r   81 (183)
                      .-...+-.||.||.||-+|+.-||+.|.+..|.++..|.+||..|+|.+..|++||||||+|.++.+-
T Consensus       174 a~sa~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl  241 (408)
T KOG0844|consen  174 ANSADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL  241 (408)
T ss_pred             ccCccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence            33455667999999999999999999999999999999999999999999999999999999876443

>KOG3802|consensus

Probab=99.35  E-value=7.5e-13  Score=108.04  Aligned_cols=66  Identities=30%  Similarity=0.344  Sum_probs=60.9

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486         16 TGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR   81 (183)
Q Consensus        16 ~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r   81 (183)
                      ..+.+.||+||.|......+||+.|..|+.|+.+|+..||..|+|..++|++||+|||.|.|+...
T Consensus       289 ~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  289 GAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             hccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            344588999999999999999999999999999999999999999999999999999999877554

>KOG0483|consensus

Probab=99.35  E-value=7.6e-13  Score=100.14  Aligned_cols=59  Identities=34%  Similarity=0.522  Sum_probs=55.4

Q ss_pred             cccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         81 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      ..++.+++.+|...|+..|+.+.++....+..||..|||.++||.+||||||++||.++
T Consensus        51 ~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq  109 (198)
T KOG0483|consen   51 KGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ  109 (198)
T ss_pred             ccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence            44567899999999999999999999999999999999999999999999999999876

>KOG0844|consensus

Probab=99.35  E-value=2e-13  Score=107.45  Aligned_cols=61  Identities=46%  Similarity=0.808  Sum_probs=58.6

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      ..++.|+.||.+|+..||++|-+..|.+...+.+||..|+|++..|++||||||.|+|++.
T Consensus       180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQR  240 (408)
T KOG0844|consen  180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQR  240 (408)
T ss_pred             HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhh
Confidence            5678899999999999999999999999999999999999999999999999999999986

>KOG0493|consensus

Probab=99.35  E-value=1.3e-12  Score=100.90  Aligned_cols=59  Identities=37%  Similarity=0.583  Sum_probs=55.0

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        22 rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      +|+||.||.+||+-|...|..+.|++...|.+||.+|||.+-||++||||.|+|-++..
T Consensus       247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT  305 (342)
T KOG0493|consen  247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST  305 (342)
T ss_pred             cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence            57899999999999999999999999999999999999999999999999999866533

>KOG4577|consensus

Probab=99.29  E-value=1.9e-12  Score=101.32  Aligned_cols=63  Identities=21%  Similarity=0.313  Sum_probs=58.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486         17 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        17 ~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~   79 (183)
                      +....+|+||.+|..||+.|..+|...+.|.+..|++|+..+||..+.|++||||||+|.++-
T Consensus       163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRL  225 (383)
T KOG4577|consen  163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRL  225 (383)
T ss_pred             cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhh
Confidence            345678999999999999999999999999999999999999999999999999999997653

>KOG0847|consensus

Probab=99.23  E-value=1.2e-11  Score=93.44  Aligned_cols=73  Identities=36%  Similarity=0.600  Sum_probs=64.1

Q ss_pred             cCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHHhcCCCCCCCC
Q psy10486         83 KRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQASNNNNTSNT  155 (183)
Q Consensus        83 ~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~~~~~~~~~~~  155 (183)
                      .+..|+-.|+..|+..|+...|+-.+++.+||..+|+++.+|++||||||+||||+...+...+..-.+..+.
T Consensus       170 srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmasakkkqds~ae  242 (288)
T KOG0847|consen  170 SRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMASAKKKQDSGAE  242 (288)
T ss_pred             cCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhhccccCCCccc
Confidence            3557999999999999999999999999999999999999999999999999999998887776554444333

>KOG4577|consensus

Probab=99.15  E-value=2.8e-11  Score=94.81  Aligned_cols=64  Identities=25%  Similarity=0.398  Sum_probs=60.1

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQ  142 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~  142 (183)
                      ..+++|+.++..|++.|..+|...+.|..+.++.|+.++||.-+.|++||||||+|+|+-.+..
T Consensus       166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDA  229 (383)
T KOG4577|consen  166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDA  229 (383)
T ss_pred             ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhc
Confidence            5678899999999999999999999999999999999999999999999999999999877544

>KOG0849|consensus

Probab=99.04  E-value=2.6e-10  Score=94.30  Aligned_cols=65  Identities=29%  Similarity=0.308  Sum_probs=59.3

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         16 TGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        16 ~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      ....+.++.||.|+..|++.|++.|+.++||+...++.||..+++++..|++||+|+|++.++..
T Consensus       171 ~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~  235 (354)
T KOG0849|consen  171 ALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH  235 (354)
T ss_pred             cccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence            45567788899999999999999999999999999999999999999999999999998766544

>KOG0490|consensus

Probab=98.94  E-value=4.2e-10  Score=87.83  Aligned_cols=63  Identities=33%  Similarity=0.360  Sum_probs=59.3

Q ss_pred             ccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486         78 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ  140 (183)
Q Consensus        78 ~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~  140 (183)
                      .+.++.|+.++..|+++|+..|...+||+...++.||..+++++..|++||+|+|++++++..
T Consensus        58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~  120 (235)
T KOG0490|consen   58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER  120 (235)
T ss_pred             ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence            355677889999999999999999999999999999999999999999999999999999886

>KOG0849|consensus

Probab=98.91  E-value=1.2e-09  Score=90.40  Aligned_cols=72  Identities=31%  Similarity=0.348  Sum_probs=62.6

Q ss_pred             hhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486         66 KIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ  140 (183)
Q Consensus        66 ~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~  140 (183)
                      ..|+.+..   ++..++.|+.|+..|+..|++.|+.++||+...++.||.++++++..|.+||+|+|+++++...
T Consensus       165 ~~~p~~~~---~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~  236 (354)
T KOG0849|consen  165 EEPPGYAL---QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR  236 (354)
T ss_pred             cccccccc---cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence            34554432   2345566899999999999999999999999999999999999999999999999999999994

>KOG0775|consensus

Probab=98.85  E-value=2e-09  Score=83.97  Aligned_cols=51  Identities=33%  Similarity=0.505  Sum_probs=45.9

Q ss_pred             hhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         89 KHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        89 ~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      ..-..+|...|..++||+..++.+||+.+||+..||-+||+|||.++|-..
T Consensus       185 ekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~  235 (304)
T KOG0775|consen  185 EKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAA  235 (304)
T ss_pred             HhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhcc
Confidence            334578999999999999999999999999999999999999999999333

>KOG0847|consensus

Probab=98.83  E-value=1.7e-09  Score=81.84  Aligned_cols=55  Identities=36%  Similarity=0.579  Sum_probs=51.2

Q ss_pred             CCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         24 KRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        24 ~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      .|-.|+-.|+..|+..|+.+.|+--+++.+||..+|+++-+|.+||||||-|.++
T Consensus       170 srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRK  224 (288)
T KOG0847|consen  170 SRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRK  224 (288)
T ss_pred             cCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhh
Confidence            3557999999999999999999999999999999999999999999999887655

>KOG0775|consensus

Probab=98.76  E-value=9.6e-09  Score=80.21  Aligned_cols=59  Identities=27%  Similarity=0.376  Sum_probs=50.8

Q ss_pred             CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccccCCC
Q psy10486         28 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKP   86 (183)
Q Consensus        28 ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~   86 (183)
                      |-+.-...|.+.|..++||+..++.+||+++||+..||.+||.|||.+.+....+.+..
T Consensus       183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~ak~~~~  241 (304)
T KOG0775|consen  183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAAAKNSSN  241 (304)
T ss_pred             hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhccccccCC
Confidence            55556789999999999999999999999999999999999999999887555544433

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

Probab=98.74  E-value=1.4e-08  Score=57.53  Aligned_cols=35  Identities=40%  Similarity=0.635  Sum_probs=29.3

Q ss_pred             ccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhH
Q psy10486        100 LYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMK  134 (183)
Q Consensus       100 ~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k  134 (183)
                      ..++||+..++..||..+||+..||.+||.|.|.+
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            35799999999999999999999999999998864

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

>KOG1168|consensus

Probab=98.63  E-value=7e-09  Score=81.57  Aligned_cols=62  Identities=27%  Similarity=0.401  Sum_probs=57.2

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ  140 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~  140 (183)
                      ..+++|+.+...+...||++|...+.|+.+.+..+|++|+|....|++||+|+|.|.||+..
T Consensus       308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~  369 (385)
T KOG1168|consen  308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR  369 (385)
T ss_pred             ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence            45677888999999999999999999999999999999999999999999999999998654

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

Probab=98.60  E-value=2.3e-08  Score=56.57  Aligned_cols=33  Identities=36%  Similarity=0.561  Sum_probs=27.5

Q ss_pred             hcCCCCHHHHHHHHHHcCCChhhhhhhhhhccc
Q psy10486         42 YNAYVSKQKRWELARSLMLTERQVKIWFQNIEW   74 (183)
Q Consensus        42 ~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~   74 (183)
                      .+|||+.+++..||..+||+..||..||-|.|.
T Consensus         7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRr   39 (40)
T PF05920_consen    7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARR   39 (40)
T ss_dssp             TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHc
Confidence            469999999999999999999999999999653

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

>KOG1168|consensus

Probab=98.54  E-value=1.7e-08  Score=79.46  Aligned_cols=60  Identities=23%  Similarity=0.285  Sum_probs=55.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         19 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        19 ~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      .-.+|+||.+-.-....||++|...+.|+.+.+..||++|.|....|++||.|.|.|.++
T Consensus       307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR  366 (385)
T KOG1168|consen  307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR  366 (385)
T ss_pred             cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence            445788999999999999999999999999999999999999999999999999987665

>KOG2252|consensus

Probab=98.50  E-value=1.4e-07  Score=80.18  Aligned_cols=56  Identities=21%  Similarity=0.219  Sum_probs=51.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccc
Q psy10486         20 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWT   75 (183)
Q Consensus        20 ~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k   75 (183)
                      ..+|+|.+||+.|.+.|.+.|..+++|+.++++.|+..|||....|.+||=|-|.+
T Consensus       419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRR  474 (558)
T KOG2252|consen  419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRR  474 (558)
T ss_pred             cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhh
Confidence            45677999999999999999999999999999999999999999999999995543

>KOG0774|consensus

Probab=98.43  E-value=1.4e-07  Score=73.30  Aligned_cols=64  Identities=38%  Similarity=0.576  Sum_probs=57.4

Q ss_pred             cccccCCCCChhHHHHHHHccc---cCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFL---YNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQ  142 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~---~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~  142 (183)
                      ..+++|+.|++.-.++|..+|.   .++||+.+.+++||++.+++..||.+||.|+|-+.+|..-..
T Consensus       187 darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~  253 (334)
T KOG0774|consen  187 DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKN  253 (334)
T ss_pred             HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhh
Confidence            3567788999999999999984   689999999999999999999999999999999999877433

>KOG1146|consensus

Probab=98.33  E-value=2.9e-06  Score=78.61  Aligned_cols=136  Identities=18%  Similarity=0.182  Sum_probs=116.3

Q ss_pred             CCCCCCccccCCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccc--------
Q psy10486          6 VNSSSSTLEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQ--------   77 (183)
Q Consensus         6 ~~~s~~~~~~~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~--------   77 (183)
                      +++..+. +++.+...+..+...-.+++.+|-..|..+..|+......|.-....+.+++..||.+-+.+..        
T Consensus       691 t~s~~g~-~~~~~~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~v~g~~  769 (1406)
T KOG1146|consen  691 TGSEVGG-GESLSPRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQVPGDV  769 (1406)
T ss_pred             CCCCCCC-CCCCCcccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhcccCCC
Confidence            3444444 6666667778888899999999999999999999999999988888899999999987532200        


Q ss_pred             --------------------------------------------------------------------------------
Q psy10486         78 --------------------------------------------------------------------------------   77 (183)
Q Consensus        78 --------------------------------------------------------------------------------   77 (183)
                                                                                                      
T Consensus       770 ~~c~l~~y~t~~kanfqlh~Ktdkh~qk~~~~~hikegg~a~~~~t~~la~~~~P~~l~cn~cd~~Tns~~~L~lh~~~~  849 (1406)
T KOG1146|consen  770 PSCKLKPYATNTKANFQLHNKTDKHVQKYQLRAHIKEGGPANEYPTKTLASGPNPVHLKCNACDTPTNSPEPLLLHTPPS  849 (1406)
T ss_pred             CcceecccccccchhhhhhcccchhhhccchhhhhhccCCccCCcchhhhcCCCccccccccccCCCCCccccccCCCCC
Confidence                                                                                            


Q ss_pred             ---------------------------------------------------ccccccCCCCChhHHHHHHHccccCCccC
Q psy10486         78 ---------------------------------------------------VTVRKKRKPYSKHQTLELEKEFLYNAYVS  106 (183)
Q Consensus        78 ---------------------------------------------------~~~rr~r~~~t~~q~~~Le~~F~~~~~p~  106 (183)
                                                                         ..++.+|+.++..|+..+...|....+|.
T Consensus       850 ~he~~~~~~ks~~~l~~~ls~~~~s~~~as~~~s~~~~~~~~s~~s~~~~~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~  929 (1406)
T KOG1146|consen  850 EHEGPEEIYKSLLSLACSLSAGDLSDSSASSLASPESPGGGPSGGSGVPDGMGRRAYRTQESDLQLKIIKACYEAQRTPT  929 (1406)
T ss_pred             ccccccccchhHHHHHHHhhccccccccccccccccCCCCCCCCCcccchhhhhhhhccchhHHHHHHHHHHHhhccCCh
Confidence                                                               05667889999999999999999999999


Q ss_pred             HHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHH
Q psy10486        107 KQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQ  142 (183)
Q Consensus       107 ~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~  142 (183)
                      ..+.+.|...+++..+.|.+||+|-|.+.++....+
T Consensus       930 ~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~  965 (1406)
T KOG1146|consen  930 MQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG  965 (1406)
T ss_pred             HHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence            999999999999999999999999999999988744

>KOG0774|consensus

Probab=98.30  E-value=5.2e-07  Score=70.22  Aligned_cols=55  Identities=36%  Similarity=0.507  Sum_probs=50.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhhhcccc
Q psy10486         21 VRKKRKPYSKHQTLELEKEFLY---NAYVSKQKRWELARSLMLTERQVKIWFQNIEWT   75 (183)
Q Consensus        21 ~rr~r~~ft~~Ql~~Le~~F~~---~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k   75 (183)
                      .+|+|..|+..-.++|..+|..   +|||+.+++++||...||+.-||.+||.|.|..
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIr  245 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIR  245 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceee
Confidence            4688999999999999999975   699999999999999999999999999996543

>KOG2252|consensus

Probab=97.96  E-value=1e-05  Score=69.17  Aligned_cols=56  Identities=23%  Similarity=0.267  Sum_probs=52.0

Q ss_pred             ccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHH
Q psy10486         80 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKN  135 (183)
Q Consensus        80 ~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~  135 (183)
                      .+++|.+|++.|...|...|+.+++|+.+..+.|+..|+|....|.+||-|-|.+.
T Consensus       420 ~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  420 TKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             CCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            35668899999999999999999999999999999999999999999999877664

>KOG3623|consensus

Probab=97.66  E-value=6.4e-05  Score=66.33  Aligned_cols=107  Identities=21%  Similarity=0.248  Sum_probs=77.5

Q ss_pred             HHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc-----------ccCCCCChhHHHHHHHcccc
Q psy10486         33 TLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR-----------KKRKPYSKHQTLELEKEFLY  101 (183)
Q Consensus        33 l~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r-----------r~r~~~t~~q~~~Le~~F~~  101 (183)
                      +..|.+.|..+..|+.++...+|...||+.+.|+.||++++.......+           +-++.....+-..|..+++.
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps~psg~~p~kv~sp~k~~dq~ql~~a~el  647 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPSQPSGERPVKVRSPIKEEDQQQLKQAYEL  647 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCccCCCCCCCccccCCCCccchhhhHhhhhc
Confidence            8899999999999999999999999999999999999998766322111           11233344444556666665


Q ss_pred             CCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486        102 NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus       102 ~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      +..++--+....+..+-..+..|.+||.+|+..-+...
T Consensus       648 q~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~p  685 (1007)
T KOG3623|consen  648 QASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMP  685 (1007)
T ss_pred             ccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCc
Confidence            55544444444455577777788999999988766554

>KOG1146|consensus

Probab=97.48  E-value=0.00011  Score=68.66  Aligned_cols=59  Identities=20%  Similarity=0.202  Sum_probs=55.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         20 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        20 ~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      .++++|+.+++.||.+|...|....||...+++.|...+++..+.|.+||+|-|.+.++
T Consensus       902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k  960 (1406)
T KOG1146|consen  902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKK  960 (1406)
T ss_pred             hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhh
Confidence            45788999999999999999999999999999999999999999999999998887655

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

Probab=97.41  E-value=0.00011  Score=44.18  Aligned_cols=41  Identities=24%  Similarity=0.358  Sum_probs=31.0

Q ss_pred             HHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhh
Q psy10486         92 TLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRR  132 (183)
Q Consensus        92 ~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR  132 (183)
                      +..|+..|....++.......|+.+.+|+..+|+.||..+.
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            34599999999999999999999999999999999997664

>KOG0773|consensus

Probab=97.21  E-value=0.0003  Score=58.17  Aligned_cols=109  Identities=26%  Similarity=0.283  Sum_probs=78.3

Q ss_pred             HHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccc--------------------------cc-------------
Q psy10486         37 EKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWT--------------------------GQ-------------   77 (183)
Q Consensus        37 e~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k--------------------------~~-------------   77 (183)
                      ...-..++||+..+...|+...+++..+|..||-|-++.                          ..             
T Consensus       113 ~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~  192 (342)
T KOG0773|consen  113 LEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSEE  192 (342)
T ss_pred             hhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhccccccccccccc
Confidence            344566789999898889999999999988999874322                          00             


Q ss_pred             --------------------------------------------ccccccCCCCChhHHHHHHHcc-c--cCCccCHHHH
Q psy10486         78 --------------------------------------------VTVRKKRKPYSKHQTLELEKEF-L--YNAYVSKQKR  110 (183)
Q Consensus        78 --------------------------------------------~~~rr~r~~~t~~q~~~Le~~F-~--~~~~p~~~~~  110 (183)
                                                                  ....+....+......+|.... +  ..+||+..++
T Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K  272 (342)
T KOG0773|consen  193 LLGESEQDDSEDESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEK  272 (342)
T ss_pred             ccccccccccccccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhc
Confidence                                                        0011223356666677777653 2  3679999999


Q ss_pred             HHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHH
Q psy10486        111 WELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQ  145 (183)
Q Consensus       111 ~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~  145 (183)
                      ..|+.++||+..||.+||.|.|.+.-+-.......
T Consensus       273 ~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~~~~  307 (342)
T KOG0773|consen  273 LMLAKQTGLSRPQVSNWFINARVRLWKPMIEEMYL  307 (342)
T ss_pred             cccchhcCCCcccCCchhhhcccccCCchHHHHHH
Confidence            99999999999999999999998866555443333

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

Probab=97.12  E-value=0.00046  Score=41.57  Aligned_cols=41  Identities=22%  Similarity=0.298  Sum_probs=31.2

Q ss_pred             HHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcc
Q psy10486         33 TLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIE   73 (183)
Q Consensus        33 l~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr   73 (183)
                      +..|+.+|....++.......|..+.+|+..||+.||-.+.
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=96.25  E-value=0.0045  Score=51.21  Aligned_cols=54  Identities=22%  Similarity=0.290  Sum_probs=46.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhhhccc
Q psy10486         21 VRKKRKPYSKHQTLELEKEFLY---NAYVSKQKRWELARSLMLTERQVKIWFQNIEW   74 (183)
Q Consensus        21 ~rr~r~~ft~~Ql~~Le~~F~~---~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~   74 (183)
                      ..++...|......+|++....   .+||+..++..||..+||+..||.+||.|.|.
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~  295 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARV  295 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhccc
Confidence            4455668999999999987433   48999999999999999999999999999553

>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=95.12  E-value=0.046  Score=32.64  Aligned_cols=46  Identities=22%  Similarity=0.356  Sum_probs=36.2

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhc
Q psy10486         22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNI   72 (183)
Q Consensus        22 rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nr   72 (183)
                      +++|+.+|.++...+-..++...     ....||..+|++..+|..|..|+
T Consensus         1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k   46 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK   46 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred             CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence            57889999999999999998877     34679999999999999999884

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.

>PF13551 HTH_29: Winged helix-turn helix

Probab=94.54  E-value=0.16  Score=34.44  Aligned_cols=80  Identities=20%  Similarity=0.216  Sum_probs=53.8

Q ss_pred             HHHHHHHHcCCChhhhhhhhhhcccccc-------ccccccCCCCChhHHHHHHHccccCC-----ccCHHHHHH-H-HH
Q psy10486         50 KRWELARSLMLTERQVKIWFQNIEWTGQ-------VTVRKKRKPYSKHQTLELEKEFLYNA-----YVSKQKRWE-L-AR  115 (183)
Q Consensus        50 ~~~~La~~l~l~~~qV~~WF~nrr~k~~-------~~~rr~r~~~t~~q~~~Le~~F~~~~-----~p~~~~~~~-L-a~  115 (183)
                      ...++|..+|++...|..|....+..+-       ....+++..+++++...|...+...+     ..+...... | ..
T Consensus        14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~   93 (112)
T PF13551_consen   14 TIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEE   93 (112)
T ss_pred             cHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHh
Confidence            3567999999999999999988655431       11122233389999999998888765     234444433 3 22


Q ss_pred             H--hCCChhhHHHHHh
Q psy10486        116 S--LMLTERQVKIWFQ  129 (183)
Q Consensus       116 ~--l~l~~~~V~~WF~  129 (183)
                      .  +.++...|..|+.
T Consensus        94 ~~~~~~s~~ti~r~L~  109 (112)
T PF13551_consen   94 EFGIDVSPSTIRRILK  109 (112)
T ss_pred             ccCccCCHHHHHHHHH
Confidence            2  3588888888875

>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=94.13  E-value=0.11  Score=31.04  Aligned_cols=46  Identities=22%  Similarity=0.369  Sum_probs=34.3

Q ss_pred             ccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhh
Q psy10486         82 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRR  132 (183)
Q Consensus        82 r~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR  132 (183)
                      ++|..+|-++-..+-..++...     ....||..+|++..+|..|..|+.
T Consensus         2 rkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~   47 (53)
T PF04218_consen    2 RKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD   47 (53)
T ss_dssp             SSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred             CCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence            5677888888888777787775     577899999999999999998754

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.

>KOG3623|consensus

Probab=94.05  E-value=0.074  Score=47.71  Aligned_cols=48  Identities=21%  Similarity=0.286  Sum_probs=44.8

Q ss_pred             HHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         92 TLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        92 ~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      +.+|.++|..|..|...+...+|...||+...|+.||.++++.....+
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            788999999999999999999999999999999999999998877655

>cd00131 PAX Paired Box domain

Probab=93.91  E-value=0.62  Score=33.04  Aligned_cols=101  Identities=10%  Similarity=0.029  Sum_probs=66.1

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc----ccCCCCChhHHHHHHHcccc
Q psy10486         26 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR----KKRKPYSKHQTLELEKEFLY  101 (183)
Q Consensus        26 ~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r----r~r~~~t~~q~~~Le~~F~~  101 (183)
                      ..||.+....+-..|+..     ....++|..+|++...|..|.+..+..+.-..+    ......+..+...+......
T Consensus        16 ~~lS~d~R~rIv~~~~~G-----~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~   90 (128)
T cd00131          16 RPLPDSIRQRIVELAQSG-----IRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQE   90 (128)
T ss_pred             CcCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHH
Confidence            357777777777777643     233468999999999999998875544321111    11234456666666666677


Q ss_pred             CCccCHHHHHHHHHHhCC-------ChhhHHHHHhhh
Q psy10486        102 NAYVSKQKRWELARSLML-------TERQVKIWFQNR  131 (183)
Q Consensus       102 ~~~p~~~~~~~La~~l~l-------~~~~V~~WF~nr  131 (183)
                      ++..+..+..++...-|+       +...|..||+++
T Consensus        91 ~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~  127 (128)
T cd00131          91 NPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK  127 (128)
T ss_pred             CCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence            877777776665334466       888888888653

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

Probab=93.52  E-value=0.14  Score=30.60  Aligned_cols=43  Identities=16%  Similarity=0.175  Sum_probs=35.8

Q ss_pred             CCHHHHHHHHHHhhhcCC--CCHHHHHHHHHHcCCChhhhhhhhh
Q psy10486         28 YSKHQTLELEKEFLYNAY--VSKQKRWELARSLMLTERQVKIWFQ   70 (183)
Q Consensus        28 ft~~Ql~~Le~~F~~~~~--p~~~~~~~La~~l~l~~~qV~~WF~   70 (183)
                      +|+.|.++|..+|+..-|  |-.....+||..||++..-|....+
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            588999999999999977  6666668899999999887765553

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

>smart00351 PAX Paired Box domain

Probab=93.50  E-value=1  Score=31.76  Aligned_cols=97  Identities=10%  Similarity=0.024  Sum_probs=62.8

Q ss_pred             CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc----cccCCCCChhHHHHHHHccccC
Q psy10486         27 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV----RKKRKPYSKHQTLELEKEFLYN  102 (183)
Q Consensus        27 ~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~----rr~r~~~t~~q~~~Le~~F~~~  102 (183)
                      .++.++...+-..|....     ...+||..+|++...|..|.+..+..+....    .......+..+...+......+
T Consensus        17 ~~s~~~R~riv~~~~~G~-----s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~   91 (125)
T smart00351       17 PLPDEERQRIVELAQNGV-----RPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQEN   91 (125)
T ss_pred             CCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHC
Confidence            478888777777776432     2347999999999999999886544322111    1123345556666666667788


Q ss_pred             CccCHHHHHHHHHHhCC-------ChhhHHHHH
Q psy10486        103 AYVSKQKRWELARSLML-------TERQVKIWF  128 (183)
Q Consensus       103 ~~p~~~~~~~La~~l~l-------~~~~V~~WF  128 (183)
                      +..+..+...+....|+       +...|..||
T Consensus        92 p~~t~~el~~~L~~~gv~~~~~~Ps~sti~~~l  124 (125)
T smart00351       92 PGIFAWEIRDRLLSEGVCDKDNVPSVSSINRIL  124 (125)
T ss_pred             CCCCHHHHHHHHHHcCCCcCCCCCChhhHHHhh
Confidence            88888776554435555       556666665

>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition

Probab=92.61  E-value=0.36  Score=33.74  Aligned_cols=91  Identities=19%  Similarity=0.142  Sum_probs=54.7

Q ss_pred             CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc-cccccCCCCChhHHHHHHHccccCCccC
Q psy10486         28 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV-TVRKKRKPYSKHQTLELEKEFLYNAYVS  106 (183)
Q Consensus        28 ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~-~~rr~r~~~t~~q~~~Le~~F~~~~~p~  106 (183)
                      ||.+-.+...+.++...     ...++|..++++...|..|+. +...+.. ...+.+..+.   ...|...-..++-.+
T Consensus         3 YS~DlR~rVl~~~~~g~-----s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~~k~r~~~Kid---~~~L~~~v~~~pd~t   73 (119)
T PF01710_consen    3 YSLDLRQRVLAYIEKGK-----SIREAAKRFGVSRNTVYRWLK-RKETGDLEPKPRGRKKID---RDELKALVEENPDAT   73 (119)
T ss_pred             CCHHHHHHHHHHHHccc-----hHHHHHHHhCcHHHHHHHHHH-hccccccccccccccccc---HHHHHHHHHHCCCcC
Confidence            44444555556666533     234689999999999999999 4444322 1112221332   344555545544333


Q ss_pred             HHHHHHHHHHhCCChhhHHHHHhh
Q psy10486        107 KQKRWELARSLMLTERQVKIWFQN  130 (183)
Q Consensus       107 ~~~~~~La~~l~l~~~~V~~WF~n  130 (183)
                      .   .+||..+||+...|-..++.
T Consensus        74 l---~Ela~~l~Vs~~ti~~~Lkr   94 (119)
T PF01710_consen   74 L---RELAERLGVSPSTIWRALKR   94 (119)
T ss_pred             H---HHHHHHcCCCHHHHHHHHHH
Confidence            3   36788999999988877743

This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].

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

Probab=91.87  E-value=1  Score=27.90  Aligned_cols=64  Identities=8%  Similarity=0.005  Sum_probs=42.4

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHH
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWF  128 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF  128 (183)
                      .++|+.+|++...|+.|...--.-...........|+..++..|..            . ......|++...|+.++
T Consensus         4 ~e~A~~~gVs~~tlr~ye~~~gl~~~~r~~~g~R~yt~~di~~l~~------------i-~~l~~~g~~l~~i~~~l   67 (68)
T cd04763           4 GEVALLTGIKPHVLRAWEREFGLLKPQRSDGGHRLFNDADIDRILE------------I-KRWIDNGVQVSKVKKLL   67 (68)
T ss_pred             HHHHHHHCcCHHHHHHHHHhcCCCCCCcCCCCCcccCHHHHHHHHH------------H-HHHHHcCCCHHHHHHHh
Confidence            4689999999999999976411111122234456788888887732            2 23445888888887765

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

>KOG3755|consensus

Probab=91.72  E-value=0.5  Score=41.68  Aligned_cols=100  Identities=21%  Similarity=0.183  Sum_probs=65.5

Q ss_pred             CCCCCCCCHHHHHHHHHH-hhhcCCCCHHH---HHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHH
Q psy10486         22 RKKRKPYSKHQTLELEKE-FLYNAYVSKQK---RWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEK   97 (183)
Q Consensus        22 rr~r~~ft~~Ql~~Le~~-F~~~~~p~~~~---~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~   97 (183)
                      .++|+.++.+-+.+|... -...-||+.+.   ...|+..+.+..+.+..-|+|.|.-.+.                  .
T Consensus       648 p~~~~~isge~~~~~qs~i~~~gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~~------------------~  709 (769)
T KOG3755|consen  648 PRKRTKISGEALGILQSFITDVGLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVKH------------------H  709 (769)
T ss_pred             ccccceecccchHHHHHHHHHhccCchhhcccccchhhhhhcccHHHHHHhhhcceeecch------------------h
Confidence            456777788888888766 34456888877   7889999999999999999996654332                  2


Q ss_pred             ccccCCccCHHHHHHHHHHh-------CCChhhHHHHHhhhhhHHHHHH
Q psy10486         98 EFLYNAYVSKQKRWELARSL-------MLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        98 ~F~~~~~p~~~~~~~La~~l-------~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      .|..+..+......+-.+..       ......|+.||++||.++++-.
T Consensus       710 w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k  758 (769)
T KOG3755|consen  710 WKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK  758 (769)
T ss_pred             heecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
Confidence            22222222222222211111       2256789999999999988754

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

Probab=91.56  E-value=0.89  Score=28.02  Aligned_cols=63  Identities=11%  Similarity=0.095  Sum_probs=41.9

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHH
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWF  128 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF  128 (183)
                      .++|+.+|++...|+.|-+.-..... .....+..|+.+++..|.            .... ....|++..+|+.+.
T Consensus         4 ~evA~~~gvs~~tlR~~~~~g~l~~~-~~~~g~R~y~~~~l~~l~------------~i~~-l~~~g~~l~~i~~~l   66 (67)
T cd04764           4 KEVSEIIGVKPHTLRYYEKEFNLYIP-RTENGRRYYTDEDIELLK------------KIKT-LLEKGLSIKEIKEIL   66 (67)
T ss_pred             HHHHHHHCcCHHHHHHHHHhcCCCCC-CCCCCceeeCHHHHHHHH------------HHHH-HHHCCCCHHHHHHHh
Confidence            46899999999999999765222221 223345678888888773            2222 344788888877664

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

>PRK06424 transcription factor; Provisional

Probab=90.51  E-value=3.7  Score=29.78  Aligned_cols=20  Identities=10%  Similarity=0.061  Sum_probs=17.6

Q ss_pred             HHHHHHcCCChhhhhhhhhh
Q psy10486         52 WELARSLMLTERQVKIWFQN   71 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~n   71 (183)
                      .+||..+|++...|..|..+
T Consensus       101 ~eLA~~iGvs~stIskiE~G  120 (144)
T PRK06424        101 ADLAAKIFERKNVIASIERG  120 (144)
T ss_pred             HHHHHHhCCCHHHHHHHHCC
Confidence            56999999999999999877

>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA

Probab=90.37  E-value=1.3  Score=30.01  Aligned_cols=67  Identities=10%  Similarity=0.101  Sum_probs=42.0

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNR  131 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nr  131 (183)
                      .++|+.+|++...|+.|...-..............|+..++..|...             .....+|++...|+.++...
T Consensus         4 ~eva~~~gvs~~tlR~ye~~Gll~~~~~~~~g~R~y~~~di~~l~~i-------------~~lr~~g~~l~~i~~~~~~~   70 (103)
T cd01106           4 GEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQI-------------LFLKELGFSLKEIKELLKDP   70 (103)
T ss_pred             HHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCceeeCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHHcC
Confidence            46899999999999999875332221112234567888888877433             22344566666666666443

Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip

>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA

Probab=90.08  E-value=1.9  Score=26.47  Aligned_cols=62  Identities=13%  Similarity=0.080  Sum_probs=37.8

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHH
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKI  126 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~  126 (183)
                      .++|..+|++...+..|-+.-..-...........++.+++..|...             ......|++...|+.
T Consensus         4 ~eva~~~gvs~~tlr~w~~~~g~~~~~r~~~~~r~yt~~~v~~l~~i-------------~~l~~~g~~l~~i~~   65 (68)
T cd01104           4 GAVARLTGVSPDTLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLI-------------RRLTSEGVRISQAAA   65 (68)
T ss_pred             HHHHHHHCcCHHHHHHHHHhCCCCCCCcCCCCCeecCHHHHHHHHHH-------------HHHHHCCCCHHHHHH
Confidence            46899999999999999864211111111223456888887777322             223346777666654

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

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

Probab=89.94  E-value=1.1  Score=27.58  Aligned_cols=65  Identities=14%  Similarity=0.128  Sum_probs=42.4

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN  130 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~n  130 (183)
                      .++|..+|++...|+.|=..---...+ .......|+.+.+..|            .....|.. .|++..+|+-++++
T Consensus         4 ~eva~~~gvs~~tlr~y~~~gll~~~~-~~~g~r~y~~~dv~~l------------~~i~~l~~-~G~sl~~I~~~l~~   68 (69)
T PF13411_consen    4 KEVAKLLGVSPSTLRYYEREGLLPPPR-DENGYRYYSEEDVERL------------REIKELRK-QGMSLEEIKKLLKQ   68 (69)
T ss_dssp             HHHHHHTTTTHHHHHHHHHTTSSTTBE-STTSSEEE-HHHHHHH------------HHHHHHHH-TTTHHHHHHHHH--
T ss_pred             HHHHHHHCcCHHHHHHHHHhcCccccc-ccCceeeccHHHHHHH------------HHHHHHHH-CcCCHHHHHHHHcc
Confidence            468999999999999997653322222 2334467888888877            33444444 88888888777653

>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)

Probab=89.72  E-value=0.9  Score=26.61  Aligned_cols=41  Identities=17%  Similarity=0.120  Sum_probs=31.0

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTER  122 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~  122 (183)
                      .+||..+|++...|..|..+                              ...|+......||..+|++..
T Consensus        13 ~~la~~~gis~~~i~~~~~g------------------------------~~~~~~~~~~~ia~~l~~~~~   53 (55)
T PF01381_consen   13 KELAEKLGISRSTISRIENG------------------------------KRNPSLDTLKKIAKALGVSPE   53 (55)
T ss_dssp             HHHHHHHTS-HHHHHHHHTT------------------------------SSTSBHHHHHHHHHHHTSEHH
T ss_pred             HHHHHHhCCCcchhHHHhcC------------------------------CCCCCHHHHHHHHHHHCCCHH
Confidence            57999999999999999977                              334666677777888777654

; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....

>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A

Probab=89.29  E-value=0.7  Score=27.98  Aligned_cols=45  Identities=13%  Similarity=0.130  Sum_probs=29.3

Q ss_pred             HHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhH
Q psy10486         51 RWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQV  124 (183)
Q Consensus        51 ~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V  124 (183)
                      ...||..+|++...|..|+.++                             ...++......||..+|++..++
T Consensus        13 ~~~La~~~gis~~tl~~~~~~~-----------------------------~~~~~~~~l~~ia~~l~~~~~el   57 (63)
T PF13443_consen   13 QKDLARKTGISRSTLSRILNGK-----------------------------PSNPSLDTLEKIAKALNCSPEEL   57 (63)
T ss_dssp             HHHHHHHHT--HHHHHHHHTTT----------------------------------HHHHHHHHHHHT--HHHC
T ss_pred             HHHHHHHHCcCHHHHHHHHhcc-----------------------------cccccHHHHHHHHHHcCCCHHHH
Confidence            4579999999999999999762                             12456677888888888887654

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

Probab=88.93  E-value=0.73  Score=27.51  Aligned_cols=42  Identities=17%  Similarity=0.167  Sum_probs=35.2

Q ss_pred             CChhHHHHHHHccccCCc--cCHHHHHHHHHHhCCChhhHHHHH
Q psy10486         87 YSKHQTLELEKEFLYNAY--VSKQKRWELARSLMLTERQVKIWF  128 (183)
Q Consensus        87 ~t~~q~~~Le~~F~~~~~--p~~~~~~~La~~l~l~~~~V~~WF  128 (183)
                      +|+.|..+|..+|+..-|  |-.....+||..+|++...|..-.
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~L   44 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHL   44 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHH
Confidence            578899999999887665  777788899999999998877655

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

>PHA01976 helix-turn-helix protein

Probab=88.17  E-value=1.7  Score=26.60  Aligned_cols=41  Identities=17%  Similarity=0.066  Sum_probs=33.1

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTER  122 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~  122 (183)
                      .+||..+|++...|..|..+                              ...|+......||..+|++..
T Consensus        19 ~~lA~~~gvs~~~v~~~e~g------------------------------~~~p~~~~l~~ia~~l~v~~~   59 (67)
T PHA01976         19 PELSRRAGVRHSLIYDFEAD------------------------------KRLPNLKTLLRLADALGVTLD   59 (67)
T ss_pred             HHHHHHhCCCHHHHHHHHcC------------------------------CCCCCHHHHHHHHHHHCcCHH
Confidence            56999999999999998865                              234667778888999998875

>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators

Probab=86.96  E-value=3.1  Score=28.04  Aligned_cols=69  Identities=17%  Similarity=0.055  Sum_probs=45.6

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNR  131 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nr  131 (183)
                      .++|..+|++...+..|-..--.-........+..|+.+++..|.            ....|....|++-..|+.+..+.
T Consensus         4 ~EvA~~~gVs~~tLR~ye~~~gli~p~r~~~g~R~Yt~~di~~l~------------~I~~llr~~G~~l~~i~~~l~~~   71 (99)
T cd04765           4 GEVAEILGLPPHVLRYWETEFPQLKPVKRAGGRRYYRPKDVELLL------------LIKHLLYEKGYTIEGAKQALKED   71 (99)
T ss_pred             HHHHHHHCcCHHHHHHHHHHcCCCCCcCCCCCCeeeCHHHHHHHH------------HHHHHHHHCCCCHHHHHHHHHhc
Confidence            468999999999999996541111111223346678888888773            23335567788888888877543


Q ss_pred             h
Q psy10486        132 R  132 (183)
Q Consensus       132 R  132 (183)
                      .
T Consensus        72 ~   72 (99)
T cd04765          72 G   72 (99)
T ss_pred             c
Confidence            3

Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

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

Probab=86.46  E-value=0.82  Score=28.77  Aligned_cols=47  Identities=23%  Similarity=0.395  Sum_probs=31.3

Q ss_pred             CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcc
Q psy10486         23 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIE   73 (183)
Q Consensus        23 r~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr   73 (183)
                      +.|+.||+++...+-..+....    .....+|..+||++..|..|-...+
T Consensus         2 ~~r~~ys~e~K~~~v~~~~~~g----~sv~~va~~~gi~~~~l~~W~~~~~   48 (76)
T PF01527_consen    2 RKRRRYSPEFKLQAVREYLESG----ESVSEVAREYGISPSTLYNWRKQYR   48 (76)
T ss_dssp             -SS----HHHHHHHHHHHHHHH----CHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCC----CceEeeecccccccccccHHHHHHh
Confidence            4578899998888777773322    4456799999999999999987654

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.

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

Probab=86.40  E-value=0.94  Score=34.92  Aligned_cols=45  Identities=11%  Similarity=0.155  Sum_probs=38.5

Q ss_pred             CCCHHHHHHHHHHhhhcCC--CCHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486         27 PYSKHQTLELEKEFLYNAY--VSKQKRWELARSLMLTERQVKIWFQN   71 (183)
Q Consensus        27 ~ft~~Ql~~Le~~F~~~~~--p~~~~~~~La~~l~l~~~qV~~WF~n   71 (183)
                      -+|+.|+++|..+|+...|  |-.-...+||+.||++.--+....++
T Consensus       155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRr  201 (215)
T COG3413         155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRR  201 (215)
T ss_pred             cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHH
Confidence            6999999999999999966  77777789999999998887765543

>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE

Probab=84.63  E-value=5.1  Score=27.37  Aligned_cols=47  Identities=13%  Similarity=0.087  Sum_probs=30.9

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHc
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKE   98 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~   98 (183)
                      .++|+.+|++...|..|-..---............|+..++..|...
T Consensus         4 ~eva~~~gvs~~tlR~ye~~Gll~p~~~~~~g~R~Y~~~dl~~l~~I   50 (108)
T cd04773           4 GELAHLLGVPPSTLRHWEKEGLLSPDREPETGYRVYDPSDVRDARLI   50 (108)
T ss_pred             HHHHHHHCcCHHHHHHHHHCCCCCCCcCCCCCceeeCHHHHHHHHHH
Confidence            47899999999999999875222111111123456888888877433

Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.

>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators

Probab=84.10  E-value=5.2  Score=26.66  Aligned_cols=66  Identities=15%  Similarity=0.093  Sum_probs=42.3

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN  130 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~n  130 (183)
                      .++|..+|++...|+.|-+.---..........+.++..++..|.             .......+|++-..|+-.+..
T Consensus         4 ~eva~~~gvs~~tLRyye~~Gll~p~~~~~~gyR~Y~~~~l~~l~-------------~I~~lr~~G~~l~~I~~~l~~   69 (96)
T cd04768           4 GEFAKLAGVSIRTLRHYDDIGLFKPAKIAENGYRYYSYAQLYQLQ-------------FILFLRELGFSLAEIKELLDT   69 (96)
T ss_pred             HHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCeeeCCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhc
Confidence            468999999999999999762222111122345678888887773             233355566666666666644

Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator

Probab=84.04  E-value=6.3  Score=27.76  Aligned_cols=46  Identities=11%  Similarity=0.075  Sum_probs=31.4

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHH
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEK   97 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~   97 (183)
                      .++|+.+|++.+.|..|-+.--...........+.++..++..|.-
T Consensus         4 ~e~a~~~gvs~~tlR~Ye~~GLl~~~~r~~~gyR~Y~~~~l~~l~~   49 (127)
T TIGR02047         4 GELAQKTGVSVETIRFYEKQGLLPPPARTDNNYRVYTVGHVERLAF   49 (127)
T ss_pred             HHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCCcCCHHHHHHHHH
Confidence            5789999999999999976532222222234566788888877743

This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.

>PRK09726 antitoxin HipB; Provisional

Probab=83.97  E-value=9.5  Score=24.88  Aligned_cols=63  Identities=17%  Similarity=0.131  Sum_probs=43.1

Q ss_pred             CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccC
Q psy10486         27 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVS  106 (183)
Q Consensus        27 ~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~  106 (183)
                      .++..++....+.+....-.+.   .+||..+|++...|..|..+                              ...|+
T Consensus         7 ~~~~~~l~~~lk~~R~~~gltq---~elA~~~gvs~~tis~~e~g------------------------------~~~ps   53 (88)
T PRK09726          7 IYSPTQLANAMKLVRQQNGWTQ---SELAKKIGIKQATISNFENN------------------------------PDNTT   53 (88)
T ss_pred             ccCHHHHHHHHHHHHHHcCCCH---HHHHHHHCcCHHHHHHHHCC------------------------------CCCCC
Confidence            4566666555555555555543   56999999999999998865                              22456


Q ss_pred             HHHHHHHHHHhCCChh
Q psy10486        107 KQKRWELARSLMLTER  122 (183)
Q Consensus       107 ~~~~~~La~~l~l~~~  122 (183)
                      ......||..+|++..
T Consensus        54 ~~~l~~ia~~lgv~~~   69 (88)
T PRK09726         54 LTTFFKILQSLELSMT   69 (88)
T ss_pred             HHHHHHHHHHcCCCcc
Confidence            6677777888887754

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

Probab=83.80  E-value=1.7  Score=24.63  Aligned_cols=44  Identities=14%  Similarity=0.055  Sum_probs=29.3

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHH
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELE   96 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le   96 (183)
                      .++|+.+|++...|..|.+.-.... .........|+.+++..|.
T Consensus         4 ~e~a~~~gv~~~tlr~~~~~g~l~~-~~~~~~~~~y~~~~v~~l~   47 (49)
T cd04761           4 GELAKLTGVSPSTLRYYERIGLLSP-ARTEGGYRLYSDADLERLR   47 (49)
T ss_pred             HHHHHHHCcCHHHHHHHHHCCCCCC-CcCCCCCEEeCHHHHHHhh
Confidence            5689999999999999986633221 1111234567877777664

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

>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB

Probab=83.31  E-value=6.5  Score=26.94  Aligned_cols=65  Identities=11%  Similarity=0.056  Sum_probs=40.2

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQ  129 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~  129 (183)
                      .++|+.+|++.+.|..|-+.---..........+.++..++..|.             .......+|++-..|+..+.
T Consensus         4 ~e~a~~~gvs~~tlr~ye~~gll~~~~r~~~gyR~Y~~~~l~~l~-------------~I~~lr~~G~sL~eI~~~l~   68 (113)
T cd01109           4 KEVAEKTGLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWLE-------------FIKCLRNTGMSIKDIKEYAE   68 (113)
T ss_pred             HHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCccCCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHH
Confidence            468999999999999997642221111112234568888887773             22334556666666666554

Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>smart00422 HTH_MERR helix_turn_helix, mercury resistance

Probab=83.26  E-value=3.9  Score=25.05  Aligned_cols=64  Identities=14%  Similarity=0.078  Sum_probs=39.7

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHH
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWF  128 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF  128 (183)
                      .++|+.+|++...|..|-..--.............|+..++..|.....            | ...|++...|...+
T Consensus         4 ~eva~~~gvs~~tlr~~~~~gli~~~~~~~~g~r~y~~~dl~~l~~i~~------------l-r~~g~~~~~i~~~l   67 (70)
T smart00422        4 GEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKR------------L-KELGFSLEEIKELL   67 (70)
T ss_pred             HHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCCEecCHHHHHHHHHHHH------------H-HHcCCCHHHHHHHH
Confidence            4689999999999999976422221111223345688888887744332            2 34677776665543

>TIGR03070 couple_hipB transcriptional regulator, y4mF family

Probab=82.68  E-value=4  Score=23.69  Aligned_cols=20  Identities=15%  Similarity=-0.080  Sum_probs=17.7

Q ss_pred             HHHHHHcCCChhhhhhhhhh
Q psy10486         52 WELARSLMLTERQVKIWFQN   71 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~n   71 (183)
                      .+||..+|++...|..|..+
T Consensus        19 ~~lA~~~gvs~~~vs~~e~g   38 (58)
T TIGR03070        19 ADLADLAGVGLRFIRDVENG   38 (58)
T ss_pred             HHHHHHhCCCHHHHHHHHCC
Confidence            57999999999999999866

Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.

>TIGR02044 CueR Cu(I)-responsive transcriptional regulator

Probab=82.28  E-value=6.3  Score=27.69  Aligned_cols=45  Identities=11%  Similarity=0.134  Sum_probs=30.6

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHH
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELE   96 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le   96 (183)
                      .++|+.+|++...|+.|-+.---..........+.|+.+++..|.
T Consensus         4 ~e~a~~~gvs~~tlRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~   48 (127)
T TIGR02044         4 GQVAKLTGLSSKMIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELR   48 (127)
T ss_pred             HHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHH
Confidence            478999999999999988652221111123446678888888774

This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.

>TIGR02607 antidote_HigA addiction module antidote protein, HigA family

Probab=81.99  E-value=5.7  Score=24.91  Aligned_cols=40  Identities=15%  Similarity=0.172  Sum_probs=31.4

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCCh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTE  121 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~  121 (183)
                      ..||..+|++...|..|..+                              ...|+......|+..+|++.
T Consensus        22 ~~lA~~~gis~~tis~~~~g------------------------------~~~~~~~~~~~l~~~l~v~~   61 (78)
T TIGR02607        22 RALAKALGVSRSTLSRIVNG------------------------------RRGITADMALRLAKALGTSP   61 (78)
T ss_pred             HHHHHHhCCCHHHHHHHHcC------------------------------CCCCCHHHHHHHHHHcCCCH
Confidence            56999999999999999866                              22355667778899998875

Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.

>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=81.97  E-value=4.1  Score=29.36  Aligned_cols=88  Identities=17%  Similarity=0.124  Sum_probs=58.7

Q ss_pred             HHHHHHHHcCCChhhhhhhhhhccccccc---c-ccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChh--h
Q psy10486         50 KRWELARSLMLTERQVKIWFQNIEWTGQV---T-VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTER--Q  123 (183)
Q Consensus        50 ~~~~La~~l~l~~~qV~~WF~nrr~k~~~---~-~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~--~  123 (183)
                      -+.++|..+|++...|..|....+-++-.   . .+.....++..|..+|........+-.......|..+.|+...  .
T Consensus        23 S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~wTl~~~~~~l~~e~gv~y~~~~  102 (138)
T COG3415          23 SCREAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKDWTLKELVEELGLEFGVWYHASA  102 (138)
T ss_pred             cHHHHHHHhCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhcccchHHHHHHHHhhhcCeEEeHHH
Confidence            34568999999999999999765543222   1 2222346888888888877766664444444666888887776  6


Q ss_pred             HHHHHhhhhhHHHH
Q psy10486        124 VKIWFQNRRMKNKK  137 (183)
Q Consensus       124 V~~WF~nrR~k~rk  137 (183)
                      |..+++.--..++|
T Consensus       103 v~~~l~~~GlsykK  116 (138)
T COG3415         103 VRRLLHELGLSYKK  116 (138)
T ss_pred             HHHHHHHcCCCcCC
Confidence            77777654444444

>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=81.83  E-value=3.8  Score=23.53  Aligned_cols=44  Identities=11%  Similarity=0.108  Sum_probs=32.1

Q ss_pred             CCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhH
Q psy10486         86 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMK  134 (183)
Q Consensus        86 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k  134 (183)
                      .+++.+..++...|..+     ....++|..+|++...|+.+...-..+
T Consensus         4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~k   47 (50)
T PF04545_consen    4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKK   47 (50)
T ss_dssp             TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHH
Confidence            46788888888888333     356789999999999999887544333

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 ....

>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator

Probab=81.81  E-value=6.6  Score=27.79  Aligned_cols=46  Identities=15%  Similarity=0.077  Sum_probs=30.7

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHH
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEK   97 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~   97 (183)
                      .++|+.+|++.+.++.|-+.---..........+.++..++..|.-
T Consensus         5 ~e~a~~~gvs~~tlR~Ye~~GLl~p~~r~~~gyR~Y~~~~l~~l~~   50 (131)
T TIGR02043         5 GELAKLCGVTSDTLRFYEKNGLIKPAGRTDSGYRLYTDEDQKRLRF   50 (131)
T ss_pred             HHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCceecCHHHHHHHHH
Confidence            4789999999999999986521111111223456788888877743

This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.

>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=81.70  E-value=2.6  Score=24.25  Aligned_cols=40  Identities=10%  Similarity=0.127  Sum_probs=30.0

Q ss_pred             CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486         27 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN   71 (183)
Q Consensus        27 ~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~n   71 (183)
                      .+++.+..+|..+|..    + ....++|..+|++...|..+...
T Consensus         4 ~L~~~er~vi~~~y~~----~-~t~~eIa~~lg~s~~~V~~~~~~   43 (50)
T PF04545_consen    4 QLPPREREVIRLRYFE----G-LTLEEIAERLGISRSTVRRILKR   43 (50)
T ss_dssp             TS-HHHHHHHHHHHTS----T--SHHHHHHHHTSCHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHhcC----C-CCHHHHHHHHCCcHHHHHHHHHH
Confidence            4788999999999922    2 33467999999999999877643

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 ....

>PRK09706 transcriptional repressor DicA; Reviewed

Probab=81.46  E-value=4  Score=28.94  Aligned_cols=20  Identities=15%  Similarity=0.441  Sum_probs=18.2

Q ss_pred             HHHHHHcCCChhhhhhhhhh
Q psy10486         52 WELARSLMLTERQVKIWFQN   71 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~n   71 (183)
                      .+||..+|++...|..|..+
T Consensus        22 ~~lA~~~gvs~~~is~~E~g   41 (135)
T PRK09706         22 RSLAKAVKVSHVSISQWERD   41 (135)
T ss_pred             HHHHHHhCCCHHHHHHHHcC
Confidence            57999999999999999977

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

Probab=81.27  E-value=4.3  Score=24.65  Aligned_cols=45  Identities=22%  Similarity=0.335  Sum_probs=23.6

Q ss_pred             CCCCCHH-HHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486         25 RKPYSKH-QTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN   71 (183)
Q Consensus        25 r~~ft~~-Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~n   71 (183)
                      |..|+.. -|.+++.+...+. .-... ..-|.++|++.++|+.|.+.
T Consensus         3 rrsy~~~FKL~Vv~~a~~~~n-c~~~~-RAaarkf~V~r~~Vr~W~kq   48 (58)
T PF09607_consen    3 RRSYTAEFKLKVVEYAEKDNN-CKGNQ-RAAARKFNVSRRQVRKWRKQ   48 (58)
T ss_dssp             -----HHHHHHHHHHHHH-TT-TTT-H-HHHHHHTTS-HHHHHHHHTT
T ss_pred             ccccChHHHHHHHHHHHHccc-hhhhH-HHHHHHhCccHHHHHHHHHH
Confidence            4455554 4455554444433 22222 24589999999999999865

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.

>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella

Probab=81.15  E-value=5.1  Score=20.15  Aligned_cols=39  Identities=15%  Similarity=0.118  Sum_probs=28.0

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhh
Q psy10486         26 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWF   69 (183)
Q Consensus        26 ~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF   69 (183)
                      ..++..+...+...|... +    ....+|..+|++...|..|.
T Consensus         4 ~~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~   42 (42)
T cd00569           4 PKLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             CcCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence            346777777777777533 2    34568999999999888874

The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D

>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators

Probab=81.14  E-value=7.2  Score=27.38  Aligned_cols=64  Identities=19%  Similarity=0.141  Sum_probs=45.5

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQ  129 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~  129 (183)
                      .++|+.+|++...+..|-+.---...  .+...+.|+..++..|            .....|...+|++...|+..+.
T Consensus         5 ~eVA~~~GVs~~TLR~wE~~GLl~p~--r~~G~R~Ys~~dv~rL------------~~I~~L~~e~G~~l~eI~~~L~   68 (120)
T cd04767           5 GVVAELLNIHPETLRIWERHGLIKPA--RRNGQRLYSNNDLKRL------------RFIKKLINEKGLNIAGVKQILS   68 (120)
T ss_pred             HHHHHHHCcCHHHHHHHHHCCCCCCc--CCCCcEEECHHHHHHH------------HHHHHHHHHcCCCHHHHHHHHH
Confidence            46899999999999999875222221  2345667888888887            3444555558888888887763

Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe

>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR

Probab=80.99  E-value=7.6  Score=25.85  Aligned_cols=65  Identities=17%  Similarity=0.107  Sum_probs=39.4

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQ  129 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~  129 (183)
                      .++|..+|++.+.|..|-..---............++.+++..|..             ......+|++-..|+..+.
T Consensus         4 ~eva~~~gvs~~tlR~ye~~Gll~p~~r~~~gyR~Y~~~~l~~l~~-------------I~~lr~~G~~l~eI~~~l~   68 (96)
T cd04788           4 GELARRTGLSVRTLHHYDHIGLLSPSQRTEGGHRLYDRADIRRLHQ-------------IIALRRLGFSLREIGRALD   68 (96)
T ss_pred             HHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCceeeCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHh
Confidence            4689999999999999986421111111123345688887777632             2234555666666655553

Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>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=80.71  E-value=1.5  Score=26.92  Aligned_cols=21  Identities=24%  Similarity=0.444  Sum_probs=17.9

Q ss_pred             HHHHHHHHhCCChhhHHHHHh
Q psy10486        109 KRWELARSLMLTERQVKIWFQ  129 (183)
Q Consensus       109 ~~~~La~~l~l~~~~V~~WF~  129 (183)
                      ....||..||+++.+|+.|=.
T Consensus        24 ~lkdIA~~Lgvs~~tIr~WK~   44 (60)
T PF10668_consen   24 KLKDIAEKLGVSESTIRKWKS   44 (60)
T ss_pred             cHHHHHHHHCCCHHHHHHHhh
Confidence            455789999999999999953

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 [].

>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B

Probab=80.34  E-value=5  Score=24.18  Aligned_cols=44  Identities=14%  Similarity=0.076  Sum_probs=30.8

Q ss_pred             HHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhH
Q psy10486         51 RWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQV  124 (183)
Q Consensus        51 ~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V  124 (183)
                      ...+|..+|++...|..|-.++                              ..|+......||..+|++...+
T Consensus        15 ~~~~a~~~~i~~~~i~~~e~g~------------------------------~~~~~~~l~~i~~~~~v~~~~l   58 (64)
T PF12844_consen   15 QKDLAEKLGISRSTISKIENGK------------------------------RKPSVSTLKKIAEALGVSLDEL   58 (64)
T ss_dssp             HHHHHHHHTS-HHHHHHHHTTS------------------------------S--BHHHHHHHHHHHTS-HHHH
T ss_pred             HHHHHHHHCcCHHHHHHHHCCC------------------------------cCCCHHHHHHHHHHhCCCHHHH
Confidence            4678999999999999888772                              2355566778889998887643

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

Probab=80.28  E-value=1.5  Score=27.52  Aligned_cols=44  Identities=27%  Similarity=0.407  Sum_probs=28.6

Q ss_pred             cCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhh
Q psy10486         83 KRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN  130 (183)
Q Consensus        83 ~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~n  130 (183)
                      .+..|++++...+-..+.    ........+|..+||++..|..|-+.
T Consensus         3 ~r~~ys~e~K~~~v~~~~----~~g~sv~~va~~~gi~~~~l~~W~~~   46 (76)
T PF01527_consen    3 KRRRYSPEFKLQAVREYL----ESGESVSEVAREYGISPSTLYNWRKQ   46 (76)
T ss_dssp             SS----HHHHHHHHHHHH----HHHCHHHHHHHHHTS-HHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHH----HCCCceEeeecccccccccccHHHHH
Confidence            456788887776655551    12346778999999999999999853

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	183
1puf_A	77	Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo		1e-19
2lp0_A	60	The Solution Structure Of Homeodomain-Protein Compl		1e-18
1ftz_A	70	Nuclear Magnetic Resonance Solution Structure Of Th		1e-14
1b8i_A	81	Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX		3e-14
1hom_A	68	Determination Of The Three-Dimensional Structure Of		1e-13
2r5y_A	88	Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO		2e-13
1ahd_P	68	Determination Of The Nmr Solution Structure Of An A		2e-13
9ant_A	62	Antennapedia Homeodomain-Dna Complex Length = 62		2e-13
1san_A	62	The Des(1-6)antennapedia Homeodomain: Comparison Of		6e-13
2h1k_A	63	Crystal Structure Of The Pdx1 Homeodomain In Comple		8e-13
2cra_A	70	Solution Structure Of The Homeobox Domain Of Human		4e-12
2ld5_A	67	Solution Nmr-Derived Complex Structure Of Hoxa13 Dn		6e-11
2l7z_A	73	Nmr Structure Of A13 Homedomain Length = 73		7e-11
1b72_A	97	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		1e-10
1jgg_A	60	Even-Skipped Homeodomain Complexed To At-Rich Dna L		2e-09
1ig7_A	58	Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58		2e-09
2m34_A	71	Nmr Structure Of The Homeodomain Transcription Fact		1e-08
2e1o_A	70	Solution Structure Of Rsgi Ruh-028, A Homeobox Doma		4e-08
2l9r_A	69	Solution Nmr Structure Of Homeobox Domain Of Homeob		8e-08
2djn_A	70	The Solution Structure Of The Homeobox Domain Of Hu		8e-08
3a03_A	56	Crystal Structure Of Hox11l1 Homeodomain Length = 5		1e-07
1ftt_A	68	Thyroid Transcription Factor 1 Homeodomain (Rattus		3e-07
3rkq_A	58	Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Lengt		4e-07
3a01_A	93	Crystal Structure Of Aristaless And Clawless Homeod		7e-07
3hdd_A	60	Engrailed Homeodomain Dna Complex Length = 60		8e-07
1nk2_P	77	VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES		1e-06
2dmt_A	80	Solution Structure Of The Homeobox Domain Of Homeob		1e-06
1hdd_C	61	Crystal Structure Of An Engrailed Homeodomain-Dna C		3e-06
1qry_A	80	Homeobox Protein Vnd (Ventral Nervous System Defect		3e-06
1p7j_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		6e-06
1p7i_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		6e-06
1enh_A	54	Structural Studies Of The Engrailed Homeodomain Len		1e-05
2hdd_A	61	Engrailed Homeodomain Q50k Variant Dna Complex Leng		1e-05
1du0_A	57	Engrailed Homeodomain Q50a Variant Dna Complex Leng		1e-05
1zq3_P	68	Nmr Solution Structure Of The Bicoid Homeodomain Bo		2e-05
2hos_A	63	Phage-selected Homeodomain Bound To Unmodified Dna		3e-05
1ztr_A	61	Solution Structure Of Engrailed Homeodomain L16a Mu		3e-05
1b8i_B	63	Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX		7e-05
2vi6_A	62	Crystal Structure Of The Nanog Homeodomain Length =		1e-04
1fjl_A	81	Homeodomain From The Drosophila Paired Protein Boun		1e-04
1b72_B	87	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		2e-04
2kt0_A	84	Solution Structure Of Human Stem Cell Transcription		3e-04
2p81_A	44	Engrailed Homeodomain Helix-Turn-Helix Motif Length		3e-04
1puf_B	73	Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo		4e-04
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		4e-04
1lfu_P	82	Nmr Solution Stucture Of The Extended Pbx Homeodoma		6e-04
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		7e-04
2m0c_A	75	Solution Nmr Structure Of Homeobox Domain Of Human		8e-04

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

Iteration: 1
 Score = 92.4 bits (228), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 45/70 (64%), Positives = 56/70 (80%)
Query: 74  WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133
           W    + RKKR PY+KHQTLELEKEFL+N Y+++ +R+E+AR L LTERQVKIWFQNRRM
Sbjct: 7   WLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRM 66
Query: 134 KNKKNTQRQA 143
           K KK  + +A
Sbjct: 67  KMKKINKDRA 76

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

Iteration: 1
 Score = 89.0 bits (219), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 51/57 (89%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           RKKR PY+K+QTLELEKEFL+N Y+++ +R+E+AR L LTERQVKIWFQNRRMK KK
Sbjct: 2   RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58

>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 = 75.9 bits (185), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 32/58 (55%), Positives = 51/58 (87%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138
           ++ R+ Y+++QTLELEKEF +N Y+++++R ++A +L L+ERQ+KIWFQNRRMK+KK+
Sbjct: 4   KRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKD 61

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

Iteration: 1
 Score = 74.7 bits (182), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 36/60 (60%), Positives = 49/60 (81%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           R+ R+ Y+++QTLELEKEF  N Y+++++R E+A +L LTERQ+KIWFQNRRMK KK  Q
Sbjct: 21  RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEIQ 80

>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 = 72.4 bits (176), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 49/57 (85%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           ++ R+ Y+++QTLELEKEF +N Y+++++R E+A +L LTERQ+KIWFQNRRMK KK
Sbjct: 3   KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 59

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

Iteration: 1
 Score = 72.0 bits (175), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 34/58 (58%), Positives = 49/58 (84%)
Query: 80  VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
            +++R  Y+++QTLELEKEF +N Y+++++R E+A +L LTERQ+KIWFQNRRMK KK
Sbjct: 28  TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 85

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

Iteration: 1
 Score = 71.6 bits (174), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 49/57 (85%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           ++ R+ Y+++QTLELEKEF +N Y+++++R E+A +L LTERQ+KIWFQNRRMK KK
Sbjct: 3   KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 59

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

Iteration: 1
 Score = 71.6 bits (174), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 34/54 (62%), Positives = 47/54 (87%)
Query: 84  RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           R+ Y+++QTLELEKEF +N Y+++++R E+A +L LTERQ+KIWFQNRRMK KK
Sbjct: 7   RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 60

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 33/51 (64%), Positives = 45/51 (88%)
Query: 87  YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           Y+++QTLELEKEF +N Y+++++R E+A +L LTERQ+KIWFQNRRMK KK
Sbjct: 3   YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 53

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

Iteration: 1
 Score = 69.7 bits (169), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 35/57 (61%), Positives = 44/57 (77%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           ++ R  Y++ Q LELEKEFL+N Y+S+ +R ELA  L LTER +KIWFQNRRMK KK
Sbjct: 4   KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60

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

Iteration: 1
 Score = 67.8 bits (164), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 45/60 (75%)
Query: 79  TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138
           + RKKR PYSK Q  ELE+E+  N +++K KR +++ +  L+ERQ+ IWFQNRR+K KK+
Sbjct: 6   SGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKS 65

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

Iteration: 1
 Score = 63.5 bits (153), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 31/57 (54%), Positives = 42/57 (73%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           RKKR PY+K Q  ELE+E+  N +++K KR  ++ +  L+ERQV IWFQNRR+K KK
Sbjct: 2   RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58

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

Iteration: 1
 Score = 63.2 bits (152), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 31/57 (54%), Positives = 42/57 (73%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           RKKR PY+K Q  ELE+E+  N +++K KR  ++ +  L+ERQV IWFQNRR+K KK
Sbjct: 8   RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64

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

Iteration: 1
 Score = 62.4 bits (150), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 30/51 (58%), Positives = 38/51 (74%)
Query: 87  YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           ++  Q  ELEKEF +N Y+S+ +R E+A +L L E QVKIWFQNRRMK KK
Sbjct: 41  FTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 29/58 (50%), Positives = 39/58 (67%)
Query: 80  VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           VR+ R  +++ Q   LEKEF    YVS+ +R ELA  L L E  +K+WFQNRRMK+K+
Sbjct: 1   VRRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 58

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 30/57 (52%), Positives = 38/57 (66%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           RK R P++  Q L LE++F    Y+S  +R E + SL LTE QVKIWFQNRR K K+
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 28/54 (51%), Positives = 38/54 (70%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMK 134
           R++R  ++  Q LELEKEF    Y+S  +R ++A +L L+E QVKIWFQNRR K
Sbjct: 8   RRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAK 61

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 27/48 (56%), Positives = 34/48 (70%)
Query: 87  YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMK 134
           +S  QT+ELEK+F    Y+S  +R  LA+ L L+ERQVK WFQNRR K
Sbjct: 14  FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAK 61

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 26/47 (55%), Positives = 35/47 (74%)
Query: 91  QTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           Q +ELE++F +  Y+S  +R  LA++L LTE QVKIWFQNRR K K+
Sbjct: 15  QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 29/58 (50%), Positives = 37/58 (63%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138
           RK R  YS  Q   L++ F    Y++  +R ELA SL LT+ QVKIWFQN+R K KK+
Sbjct: 8   RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKS 65

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 37/54 (68%)
Query: 86  PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT 139
            +S+ Q LELE+ FL   Y++  +R  LA++L +T+ QVK WFQNRR K ++ T
Sbjct: 3   SFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQT 56

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 40/65 (61%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           RK+R  +S+ Q  ELE+ F    Y+S  +R  LA  + LT  QVKIWFQN R K K+  +
Sbjct: 3   RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62
Query: 141 RQAAQ 145
            +AAQ
Sbjct: 63  DKAAQ 67

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 29/56 (51%), Positives = 36/56 (64%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK 136
           RK R  +S+ Q  ELE+ F    Y+S  +R +LA  L LT  QVKIWFQNRR K+K
Sbjct: 3   RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

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

Iteration: 1
 Score = 50.1 bits (118), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 44/75 (58%), Gaps = 9/75 (12%)
Query: 79  TVRKKRKP---YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMK- 134
           T  K++KP   +++ Q  ELEK F    Y++  +R  LAR L +T+ QVK WFQNRR K 
Sbjct: 13  TPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKW 72
Query: 135 -----NKKNTQRQAA 144
                 ++  +RQAA
Sbjct: 73  RRQTAEEREAERQAA 87

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

Iteration: 1
 Score = 50.1 bits (118), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 25/59 (42%), Positives = 40/59 (67%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT 139
           ++ R  +S  Q   L++EF  N Y+++++R +L+  L L E Q+KIWFQN+R K KK+T
Sbjct: 2   KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKST 60

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 36/57 (63%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           RK+R  ++K QT ELE+ F    Y+S  +R  LA  + LT  QVKIWFQN R K K+
Sbjct: 10  RKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/58 (46%), Positives = 38/58 (65%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138
           R+ R  +++ Q + LEK F    Y+S   R +LA SL L++ QVK W+QNRRMK KK+
Sbjct: 18  RRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKS 75

>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 = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 39/58 (67%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138
           ++ R  +S  Q   L++EF  N Y+++++R +L+  L L E Q+KIWFQN+R K KK+
Sbjct: 4   KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 61

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/57 (47%), Positives = 35/57 (61%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           RK+R  ++K QT ELE+ F    Y+S  +R  L   + LT  QVKIWFQN R K K+
Sbjct: 13  RKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKR 69

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 38/58 (65%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138
           ++ R  +S  Q   L++EF  N Y+++++R +L+  L L E Q+KIWFQN R K KK+
Sbjct: 2   KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKKS 59

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 38/58 (65%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138
           ++ R  +S  Q   L++EF  N Y+++++R +L+  L L E Q+KIWFQN R K KK+
Sbjct: 2   KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKKS 59

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/53 (41%), Positives = 35/53 (66%)
Query: 82  KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMK 134
           + R  +S  Q   L++EF  N Y+++++R +L+  L L E Q+KIWFQN+R K
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 39/58 (67%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138
           ++ R  +S  Q   L++EF  N Y+++++R +L+  L L E Q+KIWF+N+R K KK+
Sbjct: 4   KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKKS 61

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/57 (40%), Positives = 37/57 (64%)
Query: 82  KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138
           + R  +S  Q   L++EF  N Y+++++R +L+  L L E Q+KIWF N+R K KK+
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKKS 57

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/56 (39%), Positives = 34/56 (60%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK 136
           R+ R  ++  Q  ELE+ FL   Y++  +  +L+  L L   QVKIWF+NRR ++K
Sbjct: 3   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 38/59 (64%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT 139
           ++ R  +S  Q   L++EF  N Y+++++R +L+  L L E QVK WF+N R K KK+T
Sbjct: 5   KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKKST 63

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/54 (38%), Positives = 35/54 (64%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMK 134
           ++ R  +S  Q    ++EF  N Y+++++R +L+  L L E Q+KIWFQN+R K
Sbjct: 4   KRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 57

>pdb|1B8I|B Chain B, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX Length = 63

Iteration: 1
 Score = 43.5 bits (101), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 26/63 (41%), Positives = 38/63 (60%), Gaps = 5/63 (7%)
Query: 80  VRKKRKPYSKHQTLELEKEFLY----NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKN 135
            R+KR+ +SK Q  E+  E+ Y    N Y S++ + ELAR   +T  QV  WF N+R++ 
Sbjct: 1   ARRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRY 59
Query: 136 KKN 138
           KKN
Sbjct: 60  KKN 62

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/59 (42%), Positives = 36/59 (61%)
Query: 79  TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           T +K R  +S+ Q   L+  F    Y+S Q+  EL+  L L+ +QVK WFQN+RMK K+
Sbjct: 2   TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/57 (40%), Positives = 33/57 (57%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           R+ R  +S  Q  ELE+ F    Y     R ELA+   LTE ++++WFQNRR + +K
Sbjct: 19  RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK 75

>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Length = 87

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/63 (38%), Positives = 38/63 (60%), Gaps = 5/63 (7%)
Query: 80  VRKKRKPYSKHQTLELEKEFLY----NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKN 135
            R+KR+ ++K Q  E+  E+ Y    N Y S++ + ELA+   +T  QV  WF N+R++ 
Sbjct: 1   ARRKRRNFNK-QATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRY 59
Query: 136 KKN 138
           KKN
Sbjct: 60  KKN 62

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 35/60 (58%)
Query: 78  VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           V  +K R  +S  Q   L   F    Y+S Q+  EL+  L L+ +QVK WFQN+RMK+K+
Sbjct: 20  VKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKR 79

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/42 (47%), Positives = 31/42 (73%)
Query: 97  KEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138
           +EF  N Y+++++R +L+  L L E Q+KIWFQN+R K KK+
Sbjct: 3   REFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 44

>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To Dna Length = 73

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/63 (38%), Positives = 38/63 (60%), Gaps = 5/63 (7%)
Query: 80  VRKKRKPYSKHQTLELEKEFLY----NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKN 135
            R+KR+ ++K Q  E+  E+ Y    N Y S++ + ELA+   +T  QV  WF N+R++ 
Sbjct: 1   ARRKRRNFNK-QATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRY 59
Query: 136 KKN 138
           KKN
Sbjct: 60  KKN 62

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 31/54 (57%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMK 134
           R+ R  ++  Q  ELEK F    Y     R ELA  + LTE ++++WFQNRR K
Sbjct: 7   RRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAK 60

>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain Bound To Dna Length = 82

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/63 (38%), Positives = 38/63 (60%), Gaps = 5/63 (7%)
Query: 80  VRKKRKPYSKHQTLELEKEFLY----NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKN 135
            R+KR+ ++K Q  E+  E+ Y    N Y S++ + ELA+   +T  QV  WF N+R++ 
Sbjct: 2   ARRKRRNFNK-QATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRY 60
Query: 136 KKN 138
           KKN
Sbjct: 61  KKN 63

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 31/54 (57%)
Query: 84  RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           R  ++  Q  ELEK F    Y     R ELA  + LTE ++++WFQNRR K +K
Sbjct: 3   RTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56

>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 = 39.7 bits (91), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 31/54 (57%)
Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMK 134
           R+ R  ++ +Q  ELEK F    Y     R +LA    LTE +V++WFQNRR K
Sbjct: 10  RRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAK 63

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	183
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	1e-27
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	3e-22
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	1e-26
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	7e-21
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	3e-26
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	1e-20
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	5e-26
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	3e-20
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	1e-24
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	3e-19
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	9e-24
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	1e-18
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	1e-23
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	2e-18
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	1e-23
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	1e-18
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	2e-23
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	8e-20
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	4e-23
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	7e-18
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	5e-23
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	3e-17
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	9e-23
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	1e-17
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	1e-22
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	3e-17
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	2e-22
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	4e-17
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	2e-22
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	1e-17
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	2e-22
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	1e-16
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	2e-22
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	6e-17
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	3e-22
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	6e-17
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	4e-22
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	4e-16
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	6e-22
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	2e-17
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	9e-22
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	9e-17
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	2e-21
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	6e-17
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	4e-21
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	8e-17
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	3e-20
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	8e-15
1e3o_C	160	Octamer-binding transcription factor 1; transcript	2e-18
1e3o_C	160	Octamer-binding transcription factor 1; transcript	1e-14
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	4e-17
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	3e-11
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	6e-16
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	7e-11
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	2e-14
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	2e-10
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	7e-13
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	3e-08
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	1e-12
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	4e-09
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	1e-12
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	2e-09
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	2e-12
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	4e-08
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	2e-12
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	4e-08
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	1e-11
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	4e-08
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	5e-10
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	5e-06
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	8e-10
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	2e-06
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	9e-10
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	2e-06
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	1e-09
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	3e-05
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	3e-09
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	2e-05
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	5e-09
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	3e-06
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	5e-09
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	2e-05
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	1e-08
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	2e-05
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	1e-08
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	2e-05
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	2e-08
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	1e-05
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	3e-08
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	9e-05
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	5e-08
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	3e-04
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	5e-08
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	2e-05
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	8e-08
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	1e-04
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	1e-07
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	5e-05
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	1e-07
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	6e-05
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	2e-07
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	6e-05
1uhs_A	72	HOP, homeodomain only protein; structural genomics	3e-06
1uhs_A	72	HOP, homeodomain only protein; structural genomics	5e-04
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	1e-05
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	4e-05
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	7e-05
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	4e-04
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	6e-04
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	6e-04
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	7e-04

>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 = 98.4 bits (245), Expect = 1e-27
 Identities = 45/70 (64%), Positives = 56/70 (80%)

Query: 74  WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133
           W    + RKKR PY+KHQTLELEKEFL+N Y+++ +R+E+AR L LTERQVKIWFQNRRM
Sbjct: 7   WLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRM 66

Query: 134 KNKKNTQRQA 143
           K KK  + +A
Sbjct: 67  KMKKINKDRA 76

>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 = 84.1 bits (208), Expect = 3e-22
 Identities = 38/63 (60%), Positives = 49/63 (77%)

Query: 9  SSSTLEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIW 68
          ++    W    + RKKR PY+KHQTLELEKEFL+N Y+++ +R+E+AR L LTERQVKIW
Sbjct: 1  NNPAANWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIW 60

Query: 69 FQN 71
          FQN
Sbjct: 61 FQN 63

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

 Score = 95.7 bits (238), Expect = 1e-26
 Identities = 31/66 (46%), Positives = 44/66 (66%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           RKKR PY+K Q  ELE+E+  N +++K KR  ++ +  L+ERQV IWFQNRR+K KK   
Sbjct: 8   RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVIN 67

Query: 141 RQAAQA 146
           +    +
Sbjct: 68  KLKTTS 73

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

 Score = 80.7 bits (199), Expect = 7e-21
 Identities = 26/50 (52%), Positives = 36/50 (72%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          RKKR PY+K Q  ELE+E+  N +++K KR  ++ +  L+ERQV IWFQN
Sbjct: 8  RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQN 57

>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 = 94.5 bits (235), Expect = 3e-26
 Identities = 31/63 (49%), Positives = 44/63 (69%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           RKKR PYSK Q  ELE+E+  N +++K KR +++ +  L+ERQ+ IWFQNRR+K KK+  
Sbjct: 8   RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGP 67

Query: 141 RQA 143
              
Sbjct: 68  SSG 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 = 79.9 bits (197), Expect = 1e-20
 Identities = 26/50 (52%), Positives = 37/50 (74%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          RKKR PYSK Q  ELE+E+  N +++K KR +++ +  L+ERQ+ IWFQN
Sbjct: 8  RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQN 57

>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 = 93.6 bits (233), Expect = 5e-26
 Identities = 34/63 (53%), Positives = 51/63 (80%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           ++ R+ Y+++QTLELEKEF +N Y+++++R E+A +L LTERQ+KIWFQNRRMK KK  +
Sbjct: 3   KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 62

Query: 141 RQA 143
            + 
Sbjct: 63  TKG 65

>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 = 79.0 bits (195), Expect = 3e-20
 Identities = 28/50 (56%), Positives = 43/50 (86%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          ++ R+ Y+++QTLELEKEF +N Y+++++R E+A +L LTERQ+KIWFQN
Sbjct: 3  KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQN 52

>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 = 90.6 bits (225), Expect = 1e-24
 Identities = 36/60 (60%), Positives = 49/60 (81%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           R+ R+ Y+++QTLELEKEF  N Y+++++R E+A +L LTERQ+KIWFQNRRMK KK  Q
Sbjct: 21  RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEIQ 80

>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 = 76.8 bits (189), Expect = 3e-19
 Identities = 29/50 (58%), Positives = 42/50 (84%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          R+ R+ Y+++QTLELEKEF  N Y+++++R E+A +L LTERQ+KIWFQN
Sbjct: 21 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQN 70

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

 Score = 87.8 bits (218), Expect = 9e-24
 Identities = 35/57 (61%), Positives = 44/57 (77%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           ++ R  Y++ Q LELEKEFL+N Y+S+ +R ELA  L LTER +KIWFQNRRMK KK
Sbjct: 4   KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60

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

 Score = 74.7 bits (184), Expect = 1e-18
 Identities = 29/50 (58%), Positives = 38/50 (76%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          ++ R  Y++ Q LELEKEFL+N Y+S+ +R ELA  L LTER +KIWFQN
Sbjct: 4  KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQN 53

>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 = 87.4 bits (217), Expect = 1e-23
 Identities = 29/58 (50%), Positives = 39/58 (67%)

Query: 80  VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           VR+ R  +++ Q   LEKEF    YVS+ +R ELA  L L E  +K+WFQNRRMK+K+
Sbjct: 1   VRRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 58

>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 = 73.9 bits (182), Expect = 2e-18
 Identities = 24/51 (47%), Positives = 32/51 (62%)

Query: 21 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          VR+ R  +++ Q   LEKEF    YVS+ +R ELA  L L E  +K+WFQN
Sbjct: 1  VRRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQN 51

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

 Score = 88.4 bits (219), Expect = 1e-23
 Identities = 34/67 (50%), Positives = 50/67 (74%)

Query: 74  WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133
                  +++R  Y+++QTLELEKEF +N Y+++++R E+A +L LTERQ+KIWFQNRRM
Sbjct: 22  VNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRM 81

Query: 134 KNKKNTQ 140
           K KK  +
Sbjct: 82  KWKKEHK 88

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

 Score = 75.7 bits (186), Expect = 1e-18
 Identities = 29/64 (45%), Positives = 44/64 (68%)

Query: 8  SSSSTLEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKI 67
              T         +++R  Y+++QTLELEKEF +N Y+++++R E+A +L LTERQ+KI
Sbjct: 15 VHLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKI 74

Query: 68 WFQN 71
          WFQN
Sbjct: 75 WFQN 78

>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 = 88.0 bits (218), Expect = 2e-23
 Identities = 32/70 (45%), Positives = 43/70 (61%)

Query: 71  NIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 130
            +   G  +    R  ++  Q  ELEKEF +N Y+S+ +R E+A +L L E QVKIWFQN
Sbjct: 25  KVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQN 84

Query: 131 RRMKNKKNTQ 140
           RRMK KK  +
Sbjct: 85  RRMKQKKRER 94

>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 = 78.8 bits (194), Expect = 8e-20
 Identities = 27/71 (38%), Positives = 39/71 (54%)

Query: 1  MSSMNVNSSSSTLEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLML 60
          M        ++ +   G  +    R  ++  Q  ELEKEF +N Y+S+ +R E+A +L L
Sbjct: 14 MKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLEL 73

Query: 61 TERQVKIWFQN 71
           E QVKIWFQN
Sbjct: 74 NETQVKIWFQN 84

>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 = 86.3 bits (214), Expect = 4e-23
 Identities = 27/60 (45%), Positives = 39/60 (65%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           +  +  +S  QT+ELEK+F    Y+S  +R  LA+ L L+ERQVK WFQNRR K +++  
Sbjct: 8   KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGP 67

>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 = 72.8 bits (179), Expect = 7e-18
 Identities = 24/50 (48%), Positives = 33/50 (66%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          +  +  +S  QT+ELEK+F    Y+S  +R  LA+ L L+ERQVK WFQN
Sbjct: 8  KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQN 57

>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 = 86.3 bits (214), Expect = 5e-23
 Identities = 23/66 (34%), Positives = 38/66 (57%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           R+ R  ++  Q  ELE+ FL   Y++  +  +L+  L L   QVKIWF+NRR ++K  + 
Sbjct: 3   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 62

Query: 141 RQAAQA 146
           +   Q+
Sbjct: 63  QHKDQS 68

>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 = 71.3 bits (175), Expect = 3e-17
 Identities = 19/50 (38%), Positives = 29/50 (58%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          R+ R  ++  Q  ELE+ FL   Y++  +  +L+  L L   QVKIWF+N
Sbjct: 3  RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKN 52

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

 Score = 85.0 bits (211), Expect = 9e-23
 Identities = 30/57 (52%), Positives = 38/57 (66%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           RK R P++  Q L LE++F    Y+S  +R E + SL LTE QVKIWFQNRR K K+
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

 Score = 71.9 bits (177), Expect = 1e-17
 Identities = 26/50 (52%), Positives = 33/50 (66%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          RK R P++  Q L LE++F    Y+S  +R E + SL LTE QVKIWFQN
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQN 50

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

 Score = 86.1 bits (213), Expect = 1e-22
 Identities = 27/71 (38%), Positives = 39/71 (54%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           +K R  +++ Q  ELEK F    Y++  +R  LAR L +T+ QVK WFQNRR K ++ T 
Sbjct: 18  KKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTA 77

Query: 141 RQAAQASNNNN 151
            +        N
Sbjct: 78  EEREAERQAAN 88

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

 Score = 71.8 bits (176), Expect = 3e-17
 Identities = 22/50 (44%), Positives = 31/50 (62%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          +K R  +++ Q  ELEK F    Y++  +R  LAR L +T+ QVK WFQN
Sbjct: 18 KKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQN 67

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

 Score = 84.7 bits (210), Expect = 2e-22
 Identities = 27/62 (43%), Positives = 36/62 (58%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
                  S  Q +ELE++F +  Y+S  +R  LA++L LTE QVKIWFQNRR K K+   
Sbjct: 5   HHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQL 64

Query: 141 RQ 142
             
Sbjct: 65  SS 66

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

 Score = 70.8 bits (174), Expect = 4e-17
 Identities = 23/50 (46%), Positives = 31/50 (62%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
                 S  Q +ELE++F +  Y+S  +R  LA++L LTE QVKIWFQN
Sbjct: 5  HHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQN 54

>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 = 85.2 bits (211), Expect = 2e-22
 Identities = 27/60 (45%), Positives = 38/60 (63%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           R+ R  +++ Q + LEK F    Y+S   R +LA SL L++ QVK W+QNRRMK KK+  
Sbjct: 18  RRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGP 77

>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 = 72.5 bits (178), Expect = 1e-17
 Identities = 24/65 (36%), Positives = 35/65 (53%)

Query: 7  NSSSSTLEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVK 66
          + SS     T     R+ R  +++ Q + LEK F    Y+S   R +LA SL L++ QVK
Sbjct: 3  SGSSGGEPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVK 62

Query: 67 IWFQN 71
           W+QN
Sbjct: 63 TWYQN 67

>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 = 84.8 bits (210), Expect = 2e-22
 Identities = 28/67 (41%), Positives = 38/67 (56%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           RK+R  ++K QT ELE+ F    Y+S  +R  LA  + LT  QVKIWFQN R K K+   
Sbjct: 10  RKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQN 69

Query: 141 RQAAQAS 147
            +  +  
Sbjct: 70  EKGYEGH 76

>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 = 69.8 bits (171), Expect = 1e-16
 Identities = 25/50 (50%), Positives = 32/50 (64%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          RK+R  ++K QT ELE+ F    Y+S  +R  LA  + LT  QVKIWFQN
Sbjct: 10 RKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQN 59

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

 Score = 84.4 bits (209), Expect = 2e-22
 Identities = 29/62 (46%), Positives = 37/62 (59%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           RK R  YS  Q   L++ F    Y++  +R ELA SL LT+ QVKIWFQN+R K KK+  
Sbjct: 8   RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGP 67

Query: 141 RQ 142
             
Sbjct: 68  SS 69

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

 Score = 70.5 bits (173), Expect = 6e-17
 Identities = 25/50 (50%), Positives = 31/50 (62%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          RK R  YS  Q   L++ F    Y++  +R ELA SL LT+ QVKIWFQN
Sbjct: 8  RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQN 57

>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 = 83.9 bits (208), Expect = 3e-22
 Identities = 23/58 (39%), Positives = 39/58 (67%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138
           ++ R  +S  Q   L++EF  N Y+++++R +L+  L L E Q+KIWF+N+R K KK+
Sbjct: 4   KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKKS 61

>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 = 70.1 bits (172), Expect = 6e-17
 Identities = 19/50 (38%), Positives = 33/50 (66%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          ++ R  +S  Q   L++EF  N Y+++++R +L+  L L E Q+KIWF+N
Sbjct: 4  KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKN 53

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

 Score = 83.6 bits (207), Expect = 4e-22
 Identities = 30/65 (46%), Positives = 40/65 (61%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           RK+R  +S+ Q  ELE+ F    Y+S  +R  LA  + LT  QVKIWFQN R K K+  +
Sbjct: 3   RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62

Query: 141 RQAAQ 145
            +AAQ
Sbjct: 63  DKAAQ 67

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

 Score = 68.5 bits (168), Expect = 4e-16
 Identities = 24/50 (48%), Positives = 31/50 (62%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          RK+R  +S+ Q  ELE+ F    Y+S  +R  LA  + LT  QVKIWFQN
Sbjct: 3  RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQN 52

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

 Score = 83.0 bits (206), Expect = 6e-22
 Identities = 29/56 (51%), Positives = 36/56 (64%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK 136
           RK R  +S+ Q  ELE+ F    Y+S  +R +LA  L LT  QVKIWFQNRR K+K
Sbjct: 3   RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

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

 Score = 71.5 bits (176), Expect = 2e-17
 Identities = 25/50 (50%), Positives = 31/50 (62%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          RK R  +S+ Q  ELE+ F    Y+S  +R +LA  L LT  QVKIWFQN
Sbjct: 3  RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQN 52

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

 Score = 82.7 bits (205), Expect = 9e-22
 Identities = 24/57 (42%), Positives = 35/57 (61%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           +K R  +S+ Q   L+  F    Y+S Q+  EL+  L L+ +QVK WFQN+RMK K+
Sbjct: 4   QKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60

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

 Score = 69.6 bits (171), Expect = 9e-17
 Identities = 20/50 (40%), Positives = 29/50 (58%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          +K R  +S+ Q   L+  F    Y+S Q+  EL+  L L+ +QVK WFQN
Sbjct: 4  QKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQN 53

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

 Score = 82.5 bits (204), Expect = 2e-21
 Identities = 24/60 (40%), Positives = 35/60 (58%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           +K R  +S  Q   L   F    Y+S Q+  EL+  L L+ +QVK WFQN+RMK+K+  +
Sbjct: 23  QKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK 82

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

 Score = 71.0 bits (174), Expect = 6e-17
 Identities = 23/65 (35%), Positives = 32/65 (49%)

Query: 7  NSSSSTLEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVK 66
           +S +  E    V  +K R  +S  Q   L   F    Y+S Q+  EL+  L L+ +QVK
Sbjct: 8  ENSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVK 67

Query: 67 IWFQN 71
           WFQN
Sbjct: 68 TWFQN 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 = 81.1 bits (201), Expect = 4e-21
 Identities = 16/56 (28%), Positives = 31/56 (55%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK 136
            K +   S      LE+ F     ++ +++ E+A+   +T  QV++WF N+RM++K
Sbjct: 6   PKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61

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

 Score = 69.9 bits (172), Expect = 8e-17
 Identities = 13/50 (26%), Positives = 25/50 (50%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
           K +   S      LE+ F     ++ +++ E+A+   +T  QV++WF N
Sbjct: 6  PKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFIN 55

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

 Score = 78.5 bits (194), Expect = 3e-20
 Identities = 25/53 (47%), Positives = 37/53 (69%)

Query: 87  YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT 139
           +S+ Q LELE+ FL   Y++  +R  LA++L +T+ QVK WFQNRR K ++ T
Sbjct: 4   FSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQT 56

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

 Score = 64.6 bits (158), Expect = 8e-15
 Identities = 21/44 (47%), Positives = 31/44 (70%)

Query: 28 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          +S+ Q LELE+ FL   Y++  +R  LA++L +T+ QVK WFQN
Sbjct: 4  FSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQN 47

>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 = 76.5 bits (188), Expect = 2e-18
 Identities = 18/57 (31%), Positives = 30/57 (52%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           RKKR     +  + LEK F+ N   + +    +A  L + +  +++WF NRR K K+
Sbjct: 102 RKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 158

>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 = 66.9 bits (163), Expect = 1e-14
 Identities = 18/71 (25%), Positives = 34/71 (47%)

Query: 1   MSSMNVNSSSSTLEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLML 60
            SS++  S+ ++    G    RKKR     +  + LEK F+ N   + +    +A  L +
Sbjct: 81  DSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNM 140

Query: 61  TERQVKIWFQN 71
            +  +++WF N
Sbjct: 141 EKEVIRVWFSN 151

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

 Score = 73.5 bits (180), Expect = 4e-17
 Identities = 28/92 (30%), Positives = 36/92 (39%)

Query: 53  ELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWE 112
            L + L  T+          +   Q   RKKR          LE  FL     S  +   
Sbjct: 72  LLNKWLEETDSSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITG 131

Query: 113 LARSLMLTERQVKIWFQNRRMKNKKNTQRQAA 144
           LA SL L +  V++WF NRR K K+ T    A
Sbjct: 132 LADSLQLEKEVVRVWFCNRRQKEKRMTPAAGA 163

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

 Score = 58.1 bits (140), Expect = 3e-11
 Identities = 19/55 (34%), Positives = 23/55 (41%)

Query: 17  GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
            Q   RKKR          LE  FL     S  +   LA SL L +  V++WF N
Sbjct: 95  AQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCN 149

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

 Score = 67.8 bits (166), Expect = 6e-16
 Identities = 15/73 (20%), Positives = 30/73 (41%)

Query: 75  TGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMK 134
           +G       +   S  Q   L+  F  N +  + +   L +   L+ R+V+ WF +RR  
Sbjct: 3   SGSSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYH 62

Query: 135 NKKNTQRQAAQAS 147
            +     ++  +S
Sbjct: 63  CRNLKGSRSGPSS 75

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

 Score = 54.7 bits (132), Expect = 7e-11
 Identities = 12/56 (21%), Positives = 23/56 (41%)

Query: 16 TGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          +G       +   S  Q   L+  F  N +  + +   L +   L+ R+V+ WF +
Sbjct: 3  SGSSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSD 58

>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 = 66.2 bits (161), Expect = 2e-14
 Identities = 19/57 (33%), Positives = 30/57 (52%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           RK+R   S      LE+ F  ++  S Q+   +A  L L +  V++WF NRR + K+
Sbjct: 88  RKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 144

>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 = 55.8 bits (134), Expect = 2e-10
 Identities = 16/50 (32%), Positives = 25/50 (50%)

Query: 22  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
           RK+R   S      LE+ F  ++  S Q+   +A  L L +  V++WF N
Sbjct: 88  RKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCN 137

>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 = 60.4 bits (146), Expect = 7e-13
 Identities = 15/76 (19%), Positives = 34/76 (44%)

Query: 82  KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQR 141
           +K K  +  Q   L+  FL ++ ++ ++   L     LT R++  WF  ++       ++
Sbjct: 13  QKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEK 72

Query: 142 QAAQASNNNNTSNTNN 157
                SN  ++S  ++
Sbjct: 73  MEIDESNAGSSSGPSS 88

>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 = 48.1 bits (114), Expect = 3e-08
 Identities = 12/49 (24%), Positives = 23/49 (46%)

Query: 23 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          +K K  +  Q   L+  FL ++ ++ ++   L     LT R++  WF  
Sbjct: 13 QKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTE 61

>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens} Length = 151

 Score = 61.6 bits (149), Expect = 1e-12
 Identities = 17/57 (29%), Positives = 26/57 (45%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           RK+R  ++      L   F  N   + Q+  E+A+ L      V++WF NRR   K 
Sbjct: 94  RKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN 150

>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 = 52.0 bits (124), Expect = 4e-09
 Identities = 14/50 (28%), Positives = 23/50 (46%)

Query: 22  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
           RK+R  ++      L   F  N   + Q+  E+A+ L      V++WF N
Sbjct: 94  RKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSN 143

>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 = 59.3 bits (144), Expect = 1e-12
 Identities = 19/58 (32%), Positives = 30/58 (51%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138
           R  R  ++ +Q   L+  F  NAY    +  +L+  L L  R + +WFQN R K +K+
Sbjct: 8   RSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKS 65

>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 = 50.8 bits (122), Expect = 2e-09
 Identities = 16/50 (32%), Positives = 25/50 (50%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          R  R  ++ +Q   L+  F  NAY    +  +L+  L L  R + +WFQN
Sbjct: 8  RSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQN 57

>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 = 60.9 bits (147), Expect = 2e-12
 Identities = 21/86 (24%), Positives = 37/86 (43%)

Query: 54  LARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWEL 113
           L + +   +    +   +   T     ++KR          LE  FL +   S Q+   +
Sbjct: 70  LEKWVEEADNNENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHI 129

Query: 114 ARSLMLTERQVKIWFQNRRMKNKKNT 139
           A  L L +  V++WF NRR K K+++
Sbjct: 130 ANQLGLEKDVVRVWFSNRRQKGKRSS 155

>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 = 49.3 bits (117), Expect = 4e-08
 Identities = 18/69 (26%), Positives = 27/69 (39%)

Query: 3   SMNVNSSSSTLEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTE 62
             N N    +   T     ++KR          LE  FL +   S Q+   +A  L L +
Sbjct: 78  DNNENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEK 137

Query: 63  RQVKIWFQN 71
             V++WF N
Sbjct: 138 DVVRVWFSN 146

>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 = 58.8 bits (142), Expect = 2e-12
 Identities = 16/67 (23%), Positives = 26/67 (38%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
             K K  +  Q   LE  F  N     ++   L     +T R++  WF  RR K      
Sbjct: 8   PTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEET 67

Query: 141 RQAAQAS 147
           +++  +S
Sbjct: 68  KKSGPSS 74

>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 = 47.6 bits (113), Expect = 4e-08
 Identities = 12/50 (24%), Positives = 18/50 (36%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
            K K  +  Q   LE  F  N     ++   L     +T R++  WF  
Sbjct: 8  PTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSE 57

>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 = 56.9 bits (137), Expect = 1e-11
 Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 2/76 (2%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
            +K K  ++ Q   LE  FL +++ ++ +   L     L+ R++  WF  RR        
Sbjct: 14  PQKFKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDS--M 71

Query: 141 RQAAQASNNNNTSNTN 156
            QA   S  +  S  +
Sbjct: 72  EQAVLDSMGSGKSGPS 87

>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 = 48.1 bits (114), Expect = 4e-08
 Identities = 12/50 (24%), Positives = 24/50 (48%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
           +K K  ++ Q   LE  FL +++ ++ +   L     L+ R++  WF  
Sbjct: 14 PQKFKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSE 63

>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 = 52.9 bits (127), Expect = 5e-10
 Identities = 14/60 (23%), Positives = 33/60 (55%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           ++ R   +  Q   L +++L ++  +++    +A  + L +R V++WFQN R + +K+  
Sbjct: 18  KRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSGP 77

>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 = 41.7 bits (98), Expect = 5e-06
 Identities = 15/66 (22%), Positives = 34/66 (51%), Gaps = 3/66 (4%)

Query: 9  SSSTLEWTGQVTVRKKRKP---YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQV 65
          SS +   TG    ++ ++     +  Q   L +++L ++  +++    +A  + L +R V
Sbjct: 2  SSGSSGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVV 61

Query: 66 KIWFQN 71
          ++WFQN
Sbjct: 62 QVWFQN 67

>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 = 52.0 bits (125), Expect = 8e-10
 Identities = 14/60 (23%), Positives = 29/60 (48%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           ++ R   +  Q   L + F  N   S+++  E+A    L ++ +K WF+N   K +++  
Sbjct: 8   KRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGP 67

>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 = 42.7 bits (101), Expect = 2e-06
 Identities = 13/50 (26%), Positives = 25/50 (50%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          ++ R   +  Q   L + F  N   S+++  E+A    L ++ +K WF+N
Sbjct: 8  KRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRN 57

>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 = 51.7 bits (124), Expect = 9e-10
 Identities = 11/60 (18%), Positives = 24/60 (40%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
               +  +K Q   L+  FL + +    + + L     L   ++K WF + R + ++   
Sbjct: 5   HHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGIV 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 = 42.5 bits (100), Expect = 2e-06
 Identities = 10/50 (20%), Positives = 20/50 (40%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
              +  +K Q   L+  FL + +    + + L     L   ++K WF +
Sbjct: 5  HHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSD 54

>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 = 51.7 bits (124), Expect = 1e-09
 Identities = 19/72 (26%), Positives = 36/72 (50%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           ++ R  +  HQ   ++  F  N     +   +LA+   LT+R +++WFQN R K ++N  
Sbjct: 8   KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLL 67

Query: 141 RQAAQASNNNNT 152
           RQ     +  ++
Sbjct: 68  RQENGGVSGPSS 79

>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 = 39.7 bits (93), Expect = 3e-05
 Identities = 14/50 (28%), Positives = 26/50 (52%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          ++ R  +  HQ   ++  F  N     +   +LA+   LT+R +++WFQN
Sbjct: 8  KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQN 57

>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 = 50.2 bits (120), Expect = 3e-09
 Identities = 14/60 (23%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

Query: 82  KKRKPYSKHQTLELEKEFLYNA-YVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           K            LEK F+    Y  +++   L++ L  + R+++ WF++RR ++K +  
Sbjct: 10  KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSGP 69

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

 Score = 40.2 bits (94), Expect = 2e-05
 Identities = 11/50 (22%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 23 KKRKPYSKHQTLELEKEFLYNA-YVSKQKRWELARSLMLTERQVKIWFQN 71
          K            LEK F+    Y  +++   L++ L  + R+++ WF++
Sbjct: 10 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRH 59

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

 Score = 49.7 bits (119), Expect = 5e-09
 Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 1/59 (1%)

Query: 81  RKKRKPYSKHQTLELEKEFL-YNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138
            +     ++ Q   LE  F   N +        +A    LTE Q + WF+ R  + +++
Sbjct: 3   AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 61

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

 Score = 42.4 bits (100), Expect = 3e-06
 Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 1/51 (1%)

Query: 22 RKKRKPYSKHQTLELEKEFL-YNAYVSKQKRWELARSLMLTERQVKIWFQN 71
           +     ++ Q   LE  F   N +        +A    LTE Q + WF+ 
Sbjct: 3  AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQ 53

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

 Score = 49.7 bits (119), Expect = 5e-09
 Identities = 21/72 (29%), Positives = 38/72 (52%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           R++R  +++ Q   LE  F    Y     R E+A  + L E +V++WF+NRR K ++  Q
Sbjct: 8   RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQ 67

Query: 141 RQAAQASNNNNT 152
           +Q     +  ++
Sbjct: 68  QQQNGGQSGPSS 79

>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 = 40.1 bits (94), Expect = 2e-05
 Identities = 16/50 (32%), Positives = 27/50 (54%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          R++R  +++ Q   LE  F    Y     R E+A  + L E +V++WF+N
Sbjct: 8  RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKN 57

>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 = 49.0 bits (117), Expect = 1e-08
 Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 1/59 (1%)

Query: 81  RKKRKPYSKHQTLELEKEFL-YNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138
            + R   S      L+        Y  ++    L+  L L +  +  +FQN+R   K +
Sbjct: 8   PRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS 66

>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 = 40.6 bits (95), Expect = 2e-05
 Identities = 10/51 (19%), Positives = 18/51 (35%), Gaps = 1/51 (1%)

Query: 22 RKKRKPYSKHQTLELEKEFL-YNAYVSKQKRWELARSLMLTERQVKIWFQN 71
           + R   S      L+        Y  ++    L+  L L +  +  +FQN
Sbjct: 8  PRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQN 58

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

 Score = 50.6 bits (120), Expect = 1e-08
 Identities = 14/65 (21%), Positives = 25/65 (38%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           +K R  ++  Q   L   F  N   SK+ +  +++ L L    V  +F N R ++     
Sbjct: 98  KKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWL 157

Query: 141 RQAAQ 145
                
Sbjct: 158 EHHHH 162

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

 Score = 42.2 bits (98), Expect = 2e-05
 Identities = 13/50 (26%), Positives = 22/50 (44%)

Query: 22  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
           +K R  ++  Q   L   F  N   SK+ +  +++ L L    V  +F N
Sbjct: 98  KKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMN 147

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

 Score = 48.1 bits (115), Expect = 2e-08
 Identities = 21/58 (36%), Positives = 33/58 (56%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138
           R+ R  ++++Q   LE  F  N Y       +LA+ L L   +++IWFQNRR K K++
Sbjct: 2   RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRS 59

>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 = 40.4 bits (95), Expect = 1e-05
 Identities = 17/50 (34%), Positives = 27/50 (54%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          R+ R  ++++Q   LE  F  N Y       +LA+ L L   +++IWFQN
Sbjct: 2  RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQN 51

>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 = 47.3 bits (113), Expect = 3e-08
 Identities = 15/62 (24%), Positives = 28/62 (45%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
            + R   ++ Q   L   +  N       + +L     L+ R +++WFQN+R K+KK + 
Sbjct: 4   TRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI 63

Query: 141 RQ 142
             
Sbjct: 64  MM 65

>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 = 38.1 bits (89), Expect = 9e-05
 Identities = 11/50 (22%), Positives = 21/50 (42%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
           + R   ++ Q   L   +  N       + +L     L+ R +++WFQN
Sbjct: 4  TRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQN 53

>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 = 47.7 bits (113), Expect = 5e-08
 Identities = 22/88 (25%), Positives = 34/88 (38%), Gaps = 16/88 (18%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSL---------------MLTERQVK 125
           R  R  + K     +E  F  N Y  + KR E+A +                 +T  +V 
Sbjct: 8   RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVY 67

Query: 126 IWFQNRRMKNKKNTQRQAAQASNNNNTS 153
            WF NRR + K+     AA   ++  +S
Sbjct: 68  NWFANRRKEIKRR-ANIAAILESSGPSS 94

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

 Score = 37.7 bits (87), Expect = 3e-04
 Identities = 16/65 (24%), Positives = 23/65 (35%), Gaps = 15/65 (23%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSL---------------MLTERQVK 66
          R  R  + K     +E  F  N Y  + KR E+A +                 +T  +V 
Sbjct: 8  RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVY 67

Query: 67 IWFQN 71
           WF N
Sbjct: 68 NWFAN 72

>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 = 46.9 bits (112), Expect = 5e-08
 Identities = 22/58 (37%), Positives = 33/58 (56%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138
           R++R  ++  Q  +LE  F  N Y     R E+A    LTE +V++WF+NRR K +K 
Sbjct: 4   RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61

>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 = 40.0 bits (94), Expect = 2e-05
 Identities = 18/50 (36%), Positives = 28/50 (56%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          R++R  ++  Q  +LE  F  N Y     R E+A    LTE +V++WF+N
Sbjct: 4  RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKN 53

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

 Score = 46.6 bits (111), Expect = 8e-08
 Identities = 19/72 (26%), Positives = 37/72 (51%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           ++ R  +++ Q   LEKEF    Y     R  LA  + L E ++++WF NRR K ++  +
Sbjct: 8   QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 67

Query: 141 RQAAQASNNNNT 152
            +  +  +  ++
Sbjct: 68  LRNQRRQSGPSS 79

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

 Score = 38.1 bits (89), Expect = 1e-04
 Identities = 16/50 (32%), Positives = 26/50 (52%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          ++ R  +++ Q   LEKEF    Y     R  LA  + L E ++++WF N
Sbjct: 8  QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSN 57

>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 = 46.2 bits (110), Expect = 1e-07
 Identities = 23/57 (40%), Positives = 33/57 (57%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           R+ R  +S  Q  ELE+ F    Y     R ELA+   LTE ++++WFQNRR + +K
Sbjct: 19  RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK 75

>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 = 39.3 bits (92), Expect = 5e-05
 Identities = 20/50 (40%), Positives = 28/50 (56%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          R+ R  +S  Q  ELE+ F    Y     R ELA+   LTE ++++WFQN
Sbjct: 19 RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQN 68

>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 = 45.7 bits (109), Expect = 1e-07
 Identities = 22/55 (40%), Positives = 30/55 (54%)

Query: 84  RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138
              ++  Q  ELEK F    Y     R ELA  + LTE ++++WFQNRR K +K 
Sbjct: 3   HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

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

 Score = 38.4 bits (90), Expect = 6e-05
 Identities = 18/47 (38%), Positives = 25/47 (53%)

Query: 25 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
             ++  Q  ELEK F    Y     R ELA  + LTE ++++WFQN
Sbjct: 3  HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQN 49

>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 = 45.8 bits (109), Expect = 2e-07
 Identities = 20/58 (34%), Positives = 32/58 (55%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138
           R+ R  ++  Q   LE  F    Y     R +LAR + L E +V++WF+NRR K +++
Sbjct: 8   RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRS 65

>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 = 38.9 bits (91), Expect = 6e-05
 Identities = 17/50 (34%), Positives = 26/50 (52%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          R+ R  ++  Q   LE  F    Y     R +LAR + L E +V++WF+N
Sbjct: 8  RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKN 57

>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 = 42.4 bits (100), Expect = 3e-06
 Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 2/72 (2%)

Query: 81  RKKRKPYSKHQTLELEKEFL-YNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT 139
            +     ++ Q   LE  F   N +        +A    LTE Q + WF+ R  + +++ 
Sbjct: 2   SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS- 60

Query: 140 QRQAAQASNNNN 151
           +   ++  +  +
Sbjct: 61  EGLPSECRSVTD 72

>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 = 36.2 bits (84), Expect = 5e-04
 Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 1/51 (1%)

Query: 22 RKKRKPYSKHQTLELEKEFL-YNAYVSKQKRWELARSLMLTERQVKIWFQN 71
           +     ++ Q   LE  F   N +        +A    LTE Q + WF+ 
Sbjct: 2  SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQ 52

>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 = 40.6 bits (95), Expect = 1e-05
 Identities = 12/59 (20%), Positives = 24/59 (40%), Gaps = 1/59 (1%)

Query: 83  KRKPYSKHQTLELEKEFLYNA-YVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
                +      LEK F     +  +++   L++ L    R ++ WF+ RR + K +  
Sbjct: 3   SGSSGTAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPSGP 61

>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 = 40.2 bits (93), Expect = 4e-05
 Identities = 12/61 (19%), Positives = 23/61 (37%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
             K    +  Q   L+  F+   + S ++  +LA+   L    +  WF + R   K    
Sbjct: 26  TGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNL 85

Query: 141 R 141
           +
Sbjct: 86  K 86

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

 Score = 40.8 bits (94), Expect = 7e-05
 Identities = 16/77 (20%), Positives = 26/77 (33%), Gaps = 21/77 (27%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELAR---------------------SLML 119
           R+ R  +       L + +      SK++R  L                       S ++
Sbjct: 143 RRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLV 202

Query: 120 TERQVKIWFQNRRMKNK 136
           TE +V  WF NRR +  
Sbjct: 203 TEVRVYNWFANRRKEEA 219

>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration calorimetry, protein-DNA complex, transcription/DNA complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1akh_B* 1apl_C* 1yrn_B* Length = 83

 Score = 36.7 bits (85), Expect = 4e-04
 Identities = 17/76 (22%), Positives = 28/76 (36%), Gaps = 3/76 (3%)

Query: 79  TVRKKRKPYSKHQTLELEKEF---LYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKN 135
           T   +   ++K     LE  F   + N Y+  +    L ++  L+  Q+K W   RR K 
Sbjct: 1   TKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKE 60

Query: 136 KKNTQRQAAQASNNNN 151
           K  T         +  
Sbjct: 61  KTITIAPELADLLSGE 76

>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 = 37.9 bits (87), Expect = 6e-04
 Identities = 16/77 (20%), Positives = 26/77 (33%), Gaps = 21/77 (27%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELAR---------------------SLML 119
           R+ R  +       L + +      SK++R  L                       S ++
Sbjct: 116 RRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLV 175

Query: 120 TERQVKIWFQNRRMKNK 136
           TE +V  WF NRR +  
Sbjct: 176 TEVRVYNWFANRRKEEA 192

>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 = 36.1 bits (83), Expect = 6e-04
 Identities = 12/69 (17%), Positives = 25/69 (36%)

Query: 82  KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQR 141
              K  +K Q   L+  FL   +  ++   +L +   L   ++  WF + R   K    +
Sbjct: 5   SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLK 64

Query: 142 QAAQASNNN 150
                ++  
Sbjct: 65  WFRDNASGP 73

>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 = 36.0 bits (82), Expect = 7e-04
 Identities = 10/52 (19%), Positives = 24/52 (46%)

Query: 86  PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           P        LE+ +  +  + +    +L+++  L+ +QV  WF +R  +  +
Sbjct: 12  PPPPPDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSRLPQPAE 63

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	183
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.83
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.82
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.82
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.81
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.8
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.79
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.79
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.78
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.77
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.77
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.77
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.77
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.77
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.77
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.76
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.76
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.76
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.76
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.76
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.76
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.76
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.76
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.76
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.75
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.75
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.75
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.75
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.74
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.74
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.74
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.74
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.74
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.74
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.74
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.74
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.74
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.74
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.74
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.74
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.74
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.73
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.73
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.73
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.73
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.73
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.73
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.73
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.73
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.73
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.73
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.72
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.72
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.72
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.72
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.72
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.72
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.72
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.72
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.72
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.72
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.72
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.71
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.71
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.71
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.71
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.71
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.71
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.71
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.71
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.71
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.71
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.71
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.71
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.71
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.71
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.7
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.7
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.7
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.7
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.7
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.7
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.7
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.7
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.7
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.7
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.7
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.7
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.7
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.69
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.69
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.69
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.69
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.69
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.69
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.69
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.69
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.68
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.68
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.68
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.68
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.68
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.67
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.67
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.67
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.67
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.66
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.66
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.66
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.66
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.66
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.66
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.65
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.65
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.65
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.65
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.65
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.65
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.64
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.64
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.64
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.64
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.64
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.64
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.64
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.64
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.63
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.62
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.62
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.62
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.61
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.61
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.61
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.6
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.6
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.59
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.59
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.58
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.57
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.57
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.56
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.55
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.54
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.54
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.52
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.51
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.49
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.45
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.42
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.39
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.38
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.33
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.26
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.17
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.12
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.54
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	97.69
1u78_A	141	TC3 transposase, transposable element TC3 transpos	97.1
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	96.46
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	96.34
2k27_A	159	Paired box protein PAX-8; paired domain, solution	96.31
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	95.62
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	94.86
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	94.45
3kz3_A	80	Repressor protein CI; five helix bundle, DNA-bindi	91.61
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	90.32
3bs3_A	76	Putative DNA-binding protein; XRE-family, structur	89.8
2xi8_A	66	Putative transcription regulator; HTH DNA-binding	89.66
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	89.34
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	89.31
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	88.63
2b5a_A	77	C.BCLI; helix-turn-helix motif, gene regulation; 1	88.31
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	88.04
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	87.69
3b7h_A	78	Prophage LP1 protein 11; structural genomics, PSI2	87.27
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	86.64
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	85.75
2k9q_A	77	Uncharacterized protein; all helix, helix-turn-hel	85.62
2ewt_A	71	BLDD, putative DNA-binding protein; the DNA-bindin	85.51
3t76_A	88	VANU, transcriptional regulator vanug; structural	85.32
3s8q_A	82	R-M controller protein; protein-DNA complex, helix	85.1
1lmb_3	92	Protein (lambda repressor); protein-DNA complex, d	84.61
2ict_A	94	Antitoxin HIGA; helix-turn-helix, structural genom	83.92
3op9_A	114	PLI0006 protein; structural genomics, PSI-2, prote	83.11
2ofy_A	86	Putative XRE-family transcriptional regulator; tra	82.75
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	82.64
3g5g_A	99	Regulatory protein; transcriptional regulator, hel	82.57
1iuf_A	144	Centromere ABP1 protein; riken structural genomics	82.14
3lfp_A	98	CSP231I C protein; transcriptional regulator, DNA	81.57
3ivp_A	126	Putative transposon-related DNA-binding protein; A	80.98
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	80.82
3vk0_A	114	NHTF, transcriptional regulator; HTH motif, XRE tr	80.44
3qq6_A	78	HTH-type transcriptional regulator SINR; helix-tur	80.27
2eby_A	113	Putative HTH-type transcriptional regulator YBAQ;	80.12

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

Probab=99.83  E-value=2e-20  Score=123.31  Aligned_cols=75  Identities=31%  Similarity=0.333  Sum_probs=64.9

Q ss_pred             CCCCCCccccCCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486          6 VNSSSSTLEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus         6 ~~~s~~~~~~~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      .+++........+.+.++.|+.||..|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++..
T Consensus         7 ~~~~~~~~~~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   81 (84)
T 2kt0_A            7 AENSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQ   81 (84)
T ss_dssp             CCCSSCCCSCCCCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCC
T ss_pred             CCCCCCccCCCCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHh
Confidence            333344444556678889999999999999999999999999999999999999999999999999999877644

>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=99.82  E-value=2.5e-20  Score=121.76  Aligned_cols=68  Identities=32%  Similarity=0.395  Sum_probs=61.4

Q ss_pred             cccCCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         13 LEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        13 ~~~~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      .+.....+.++.|+.||.+|+.+||..|..++||+..++..||..|||++.+|++||+|||++.++..
T Consensus         9 ~~~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   76 (80)
T 2dmt_A            9 EPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSG   76 (80)
T ss_dssp             CSCCCCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCC
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhccc
Confidence            34445678889999999999999999999999999999999999999999999999999999876543

>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=99.82  E-value=4.7e-20  Score=120.26  Aligned_cols=64  Identities=11%  Similarity=0.151  Sum_probs=58.8

Q ss_pred             cCCCCCCCCCCCCCCHHHHHHHHHHhhh----cCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         15 WTGQVTVRKKRKPYSKHQTLELEKEFLY----NAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        15 ~~~~~~~rr~r~~ft~~Ql~~Le~~F~~----~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      .....+.+|.||.||.+|+.+|+..|+.    ++||+..++++||..|||++.+|++||+|+|+|.+.
T Consensus        11 ~~~~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           11 EAGGGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCCCCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            3445678899999999999999999999    999999999999999999999999999999998653

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

Probab=99.81  E-value=7.6e-20  Score=119.11  Aligned_cols=64  Identities=14%  Similarity=0.167  Sum_probs=58.2

Q ss_pred             ccCCCCCCCCCCCCCCHHHHHHHHHHhhh-----cCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         14 EWTGQVTVRKKRKPYSKHQTLELEKEFLY-----NAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        14 ~~~~~~~~rr~r~~ft~~Ql~~Le~~F~~-----~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      ......+.+|.||.||.+|+.+|+ .|..     ++||+..++++||..|||++.+|++||+|||++.+.
T Consensus        10 ~~~~~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           10 PSSSGGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCCCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            344556788999999999999999 7999     999999999999999999999999999999998653

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

Probab=99.80  E-value=5.3e-20  Score=120.20  Aligned_cols=67  Identities=18%  Similarity=0.233  Sum_probs=60.6

Q ss_pred             ccCCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         14 EWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        14 ~~~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      ....+.+.++.|+.||.+|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++..
T Consensus        10 ~~~~~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   76 (80)
T 2da3_A           10 GGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSG   76 (80)
T ss_dssp             CCCCCCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhc
Confidence            3445577889999999999999999999999999999999999999999999999999998876543

>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=99.79  E-value=1.3e-19  Score=122.61  Aligned_cols=84  Identities=38%  Similarity=0.553  Sum_probs=64.7

Q ss_pred             HcCCChhhhhhhhhhcccccc---------ccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHH
Q psy10486         57 SLMLTERQVKIWFQNIEWTGQ---------VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIW  127 (183)
Q Consensus        57 ~l~l~~~qV~~WF~nrr~k~~---------~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~W  127 (183)
                      .++++..+|..||++.|...+         ...++.|+.|+..|+.+|+..|..++||+..++.+||..+||++.+|++|
T Consensus         2 ~~~~~~~~~~~W~~~~r~~~~~~~~~~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vW   81 (97)
T 1b72_A            2 EPNTPTARTFDWMKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIW   81 (97)
T ss_dssp             ------CCCCGGGGC--------------------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHH
T ss_pred             CCCCCCcccccccccccCCCCCCCCCCCCCCCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHH
Confidence            357788889999999775432         24456789999999999999999999999999999999999999999999


Q ss_pred             HhhhhhHHHHHHh
Q psy10486        128 FQNRRMKNKKNTQ  140 (183)
Q Consensus       128 F~nrR~k~rk~~~  140 (183)
                      |+|||+|+|+..+
T Consensus        82 FqNRR~k~kk~~~   94 (97)
T 1b72_A           82 FQNRRMKQKKRER   94 (97)
T ss_dssp             HHHHHHHHHHHHT
T ss_pred             HHHHhHHHhHHhc
Confidence            9999999999865

>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=99.79  E-value=2.4e-19  Score=114.15  Aligned_cols=63  Identities=41%  Similarity=0.626  Sum_probs=58.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         18 QVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        18 ~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      ..+.+++|+.||..|+.+||..|..++||+..++..||..|||++.+|++||+|||++.++..
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~   66 (70)
T 2cra_A            4 GSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSG   66 (70)
T ss_dssp             SCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccC
Confidence            357789999999999999999999999999999999999999999999999999999876543

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

Probab=99.78  E-value=3.9e-19  Score=113.18  Aligned_cols=64  Identities=25%  Similarity=0.313  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         17 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        17 ~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      ...+.++.|+.||.+|+.+|+..|..++||+..++..||..|||++.+|++||+|+|++.++..
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2da2_A            3 SGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSG   66 (70)
T ss_dssp             CSCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhcc
Confidence            3457789999999999999999999999999999999999999999999999999999876543

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

Probab=99.77  E-value=4.8e-19  Score=112.74  Aligned_cols=63  Identities=40%  Similarity=0.470  Sum_probs=58.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         18 QVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        18 ~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      ..+.++.|+.||.+|+.+|+..|..++||+..++..||..|||++.+|++||+|+|++.++..
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2djn_A            4 GSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSG   66 (70)
T ss_dssp             CCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccC
Confidence            357789999999999999999999999999999999999999999999999999999876543

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

Probab=99.77  E-value=3.8e-19  Score=110.57  Aligned_cols=59  Identities=36%  Similarity=0.451  Sum_probs=51.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         20 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        20 ~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      +.++.|+.||..|+.+||..|..++||+..++..||..|||++.+|++||+|+|++.++
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   60 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR   60 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGG
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhh
Confidence            46788999999999999999999999999999999999999999999999999998765

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

Probab=99.77  E-value=5e-19  Score=112.64  Aligned_cols=61  Identities=28%  Similarity=0.409  Sum_probs=57.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486         19 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        19 ~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~   79 (183)
                      ...++.|+.||.+|+.+|+..|..++||+..++..||..|||++.+|++||+|+|++.++.
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~   65 (70)
T 2dmu_A            5 SSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRS   65 (70)
T ss_dssp             TSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehcccccccccccc
Confidence            4678899999999999999999999999999999999999999999999999999887653

>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=99.77  E-value=3.4e-19  Score=110.41  Aligned_cols=59  Identities=32%  Similarity=0.542  Sum_probs=51.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         20 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        20 ~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      ..++.|+.||..|+.+|+..|..++||+..++..||..|||++.+|++||+|+|++.++
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            2 AEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             -----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            45789999999999999999999999999999999999999999999999999987653

>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=99.77  E-value=4.2e-19  Score=113.02  Aligned_cols=63  Identities=21%  Similarity=0.257  Sum_probs=58.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         18 QVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        18 ~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      ..+.++.|+.||.+|+.+|+..|..++||+..++..||..|||++.+|++||+|+|++.++..
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2da1_A            4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSG   66 (70)
T ss_dssp             SCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhc
Confidence            357789999999999999999999999999999999999999999999999999999876543

>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=99.77  E-value=6.8e-19  Score=114.08  Aligned_cols=65  Identities=57%  Similarity=0.856  Sum_probs=59.2

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         16 TGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        16 ~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      ....+.++.|+.||..|+.+||..|..++||+..++..||..|||++.+|++||+|||++.++..
T Consensus         8 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   72 (77)
T 1puf_A            8 LHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKIN   72 (77)
T ss_dssp             CCCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhh
Confidence            34467788999999999999999999999999999999999999999999999999999876543

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

Probab=99.76  E-value=5.5e-19  Score=108.37  Aligned_cols=56  Identities=46%  Similarity=0.695  Sum_probs=53.6

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccc
Q psy10486         22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQ   77 (183)
Q Consensus        22 rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~   77 (183)
                      +++|+.||.+|+.+|+..|..++||+..++..||..|||++.+|++||+|+|++.+
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~k   56 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK   56 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhc
Confidence            57899999999999999999999999999999999999999999999999998764

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

Probab=99.76  E-value=1.1e-18  Score=112.01  Aligned_cols=65  Identities=42%  Similarity=0.649  Sum_probs=59.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccc
Q psy10486         18 QVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRK   82 (183)
Q Consensus        18 ~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr   82 (183)
                      ..+.++.|+.||..|+.+||..|..++||+..++..||..|||++.+|++||+|||++.++...+
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~   68 (73)
T 2l7z_A            4 MLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINK   68 (73)
T ss_dssp             SSCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHhcc
Confidence            35678999999999999999999999999999999999999999999999999999987765443

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

Probab=99.76  E-value=4.9e-19  Score=110.41  Aligned_cols=59  Identities=49%  Similarity=0.789  Sum_probs=53.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         20 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        20 ~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      ..++.|+.||..|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk   60 (63)
T 2h1k_A            2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK   60 (63)
T ss_dssp             ---CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhh
Confidence            46789999999999999999999999999999999999999999999999999988654

>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=99.76  E-value=7.7e-19  Score=110.52  Aligned_cols=60  Identities=18%  Similarity=0.263  Sum_probs=56.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486         20 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        20 ~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~   79 (183)
                      +.++.|+.||.+|+.+|+..|..++||+..++..||..+||++.+|++||+|+|++.++.
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   61 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR   61 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHH
Confidence            568899999999999999999999999999999999999999999999999999987653

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

Probab=99.76  E-value=8.9e-19  Score=114.35  Aligned_cols=63  Identities=25%  Similarity=0.350  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486         19 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR   81 (183)
Q Consensus        19 ~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r   81 (183)
                      .+.++.|+.||.+|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++..+
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~   67 (80)
T 2dms_A            5 SSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQ   67 (80)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHH
Confidence            577899999999999999999999999999999999999999999999999999998766544

>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=99.76  E-value=8.9e-19  Score=113.53  Aligned_cols=63  Identities=40%  Similarity=0.536  Sum_probs=58.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486         17 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        17 ~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~   79 (183)
                      .+.+.++.|+.||..|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++.
T Consensus         5 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~   67 (77)
T 1nk2_P            5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRA   67 (77)
T ss_dssp             CSCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhh
Confidence            446778899999999999999999999999999999999999999999999999999987653

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

Probab=99.76  E-value=2.9e-18  Score=111.89  Aligned_cols=70  Identities=27%  Similarity=0.474  Sum_probs=63.9

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHHhcC
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQASN  148 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~~~~  148 (183)
                      ..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..+........
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~~~~~~s   75 (80)
T 2cue_A            6 SGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQRRQS   75 (80)
T ss_dssp             SSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHCCS
T ss_pred             CCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhhhccCCC
Confidence            4567789999999999999999999999999999999999999999999999999999999777655443

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

Probab=99.76  E-value=6.3e-19  Score=115.33  Aligned_cols=63  Identities=32%  Similarity=0.392  Sum_probs=56.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486         17 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        17 ~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~   79 (183)
                      ...+.++.|+.||..|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++.
T Consensus        14 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~   76 (81)
T 1fjl_A           14 LKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ   76 (81)
T ss_dssp             ---CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhh
Confidence            456788999999999999999999999999999999999999999999999999999886653

>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=99.76  E-value=1.1e-18  Score=110.99  Aligned_cols=62  Identities=39%  Similarity=0.507  Sum_probs=57.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         19 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        19 ~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      ...++.|+.||.+|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++..
T Consensus         5 ~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~   66 (70)
T 2e1o_A            5 SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSG   66 (70)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCC
Confidence            46678899999999999999999999999999999999999999999999999998876543

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

Probab=99.75  E-value=9.2e-19  Score=114.28  Aligned_cols=62  Identities=26%  Similarity=0.375  Sum_probs=57.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         19 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        19 ~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      .+.++.|+.||..|+.+||..|..++||+..++..||..|||++.+|++||+|||++.++..
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   66 (80)
T 2cue_A            5 SSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREE   66 (80)
T ss_dssp             CSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHh
Confidence            46788999999999999999999999999999999999999999999999999999876543

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

Probab=99.75  E-value=9.7e-19  Score=110.69  Aligned_cols=62  Identities=31%  Similarity=0.523  Sum_probs=57.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486         20 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR   81 (183)
Q Consensus        20 ~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r   81 (183)
                      +.++.|+.||..|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++...
T Consensus         1 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~   62 (68)
T 1zq3_P            1 GPRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD   62 (68)
T ss_dssp             CCSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhc
Confidence            35789999999999999999999999999999999999999999999999999998765443

>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=99.75  E-value=1.5e-18  Score=113.32  Aligned_cols=62  Identities=23%  Similarity=0.338  Sum_probs=58.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         19 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        19 ~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      .+.++.|+.||.+|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++..
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   66 (80)
T 2dmq_A            5 SSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNL   66 (80)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHH
Confidence            56789999999999999999999999999999999999999999999999999999876644

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

Probab=99.75  E-value=1.1e-18  Score=107.81  Aligned_cols=57  Identities=40%  Similarity=0.658  Sum_probs=53.6

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        22 rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      ++.|+.||.+|+.+|+..|..++||+..++..||..|||++.+|++||+|+|++.++
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   58 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR   58 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHhHhhc
Confidence            688999999999999999999999999999999999999999999999999987654

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

Probab=99.74  E-value=1.6e-18  Score=113.34  Aligned_cols=62  Identities=47%  Similarity=0.709  Sum_probs=52.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486         18 QVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        18 ~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~   79 (183)
                      ....++.|+.||..|+.+||..|..++||+..++..||..|||++.+|++||+|||++.++.
T Consensus        17 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   78 (81)
T 1b8i_A           17 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE   78 (81)
T ss_dssp             -------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhh
Confidence            35678899999999999999999999999999999999999999999999999999986653

>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=99.74  E-value=1.3e-18  Score=107.78  Aligned_cols=58  Identities=22%  Similarity=0.297  Sum_probs=47.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccc
Q psy10486         19 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTG   76 (183)
Q Consensus        19 ~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~   76 (183)
                      .+.++.|+.||..|+.+|+..|..++||+..++..||..|||++.+|++||+|+|++.
T Consensus         3 ~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~   60 (61)
T 1akh_A            3 EKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS   60 (61)
T ss_dssp             ---------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhcc
Confidence            4678889999999999999999999999999999999999999999999999999864

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

Probab=99.74  E-value=2.9e-18  Score=114.95  Aligned_cols=66  Identities=33%  Similarity=0.467  Sum_probs=60.1

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486         16 TGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR   81 (183)
Q Consensus        16 ~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r   81 (183)
                      ..+.+.++.|+.||.+|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++...
T Consensus        12 ~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~   77 (93)
T 3a01_A           12 RTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTA   77 (93)
T ss_dssp             SCCCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhH
Confidence            345677889999999999999999999999999999999999999999999999999998776443

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

Probab=99.74  E-value=1.4e-18  Score=115.36  Aligned_cols=63  Identities=44%  Similarity=0.754  Sum_probs=53.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486         17 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        17 ~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~   79 (183)
                      ...+.++.|+.||..|+.+||..|..++||+..++..||..|||++.+|++||+|||++.++.
T Consensus        24 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~   86 (88)
T 2r5y_A           24 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   86 (88)
T ss_dssp             -------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhh
Confidence            345678999999999999999999999999999999999999999999999999999987653

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

Probab=99.74  E-value=3.2e-18  Score=110.32  Aligned_cols=64  Identities=33%  Similarity=0.381  Sum_probs=59.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486         18 QVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR   81 (183)
Q Consensus        18 ~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r   81 (183)
                      ..+.++.|+.||..|+.+|+..|..++||+..++..||..|||++.+|++||+|+|++.++..+
T Consensus         6 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r   69 (75)
T 2m0c_A            6 KGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRER   69 (75)
T ss_dssp             CSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHh
Confidence            4567888999999999999999999999999999999999999999999999999998776544

>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=99.74  E-value=1.4e-18  Score=109.97  Aligned_cols=61  Identities=46%  Similarity=0.775  Sum_probs=56.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486         21 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR   81 (183)
Q Consensus        21 ~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r   81 (183)
                      .++.|+.||..|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++..+
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~   62 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK   62 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhcc
Confidence            4688999999999999999999999999999999999999999999999999998776543

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

Probab=99.74  E-value=2.5e-18  Score=105.38  Aligned_cols=56  Identities=45%  Similarity=0.630  Sum_probs=53.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccc
Q psy10486         21 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTG   76 (183)
Q Consensus        21 ~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~   76 (183)
                      .++.|+.||..|+.+|+..|..++||+..++..||..|||++.+|++||+|+|++.
T Consensus         2 ~rr~Rt~~t~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~   57 (58)
T 3rkq_A            2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKS   57 (58)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhhccC
Confidence            46789999999999999999999999999999999999999999999999999864

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

Probab=99.74  E-value=2.1e-18  Score=109.12  Aligned_cols=61  Identities=39%  Similarity=0.576  Sum_probs=56.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486         21 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR   81 (183)
Q Consensus        21 ~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r   81 (183)
                      .++.|+.||..|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++..+
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~   62 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK   62 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhh
Confidence            4788999999999999999999999999999999999999999999999999998766443

>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=99.74  E-value=3.8e-18  Score=105.37  Aligned_cols=58  Identities=17%  Similarity=0.156  Sum_probs=54.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhh-cCCCCHHHHHHHHHHcCCChhhhhhhhhhcccc
Q psy10486         18 QVTVRKKRKPYSKHQTLELEKEFLY-NAYVSKQKRWELARSLMLTERQVKIWFQNIEWT   75 (183)
Q Consensus        18 ~~~~rr~r~~ft~~Ql~~Le~~F~~-~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k   75 (183)
                      ....+|.||.|+.+||.+|+..|+. ++||+.+.++.||..|||++++|++||||+|.-
T Consensus         4 ~~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~   62 (71)
T 1wi3_A            4 GSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYH   62 (71)
T ss_dssp             CCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceee
Confidence            4578899999999999999999999 999999999999999999999999999998864

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

Probab=99.74  E-value=2.2e-18  Score=108.74  Aligned_cols=60  Identities=28%  Similarity=0.371  Sum_probs=56.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         21 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        21 ~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      .++.|+.||.+|+.+|+..|..++||+..++..||..|||++.+|++||+|+|++.++..
T Consensus         1 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~   60 (67)
T 2k40_A            1 GRRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSH   60 (67)
T ss_dssp             CCCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSC
T ss_pred             CcCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhc
Confidence            478899999999999999999999999999999999999999999999999999876544

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

Probab=99.74  E-value=3.2e-18  Score=106.66  Aligned_cols=60  Identities=58%  Similarity=0.921  Sum_probs=56.0

Q ss_pred             ccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         80 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        80 ~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      .++.++.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   62 (63)
T 2h1k_A            3 NKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE   62 (63)
T ss_dssp             --CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhhc
Confidence            456789999999999999999999999999999999999999999999999999999864

>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=99.74  E-value=4.1e-18  Score=109.80  Aligned_cols=59  Identities=20%  Similarity=0.216  Sum_probs=54.5

Q ss_pred             CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486         23 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR   81 (183)
Q Consensus        23 r~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r   81 (183)
                      ++|+.||.+|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++..+
T Consensus         9 ~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (75)
T 2da5_A            9 TKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEET   67 (75)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSC
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhh
Confidence            56778999999999999999999999999999999999999999999999998766544

>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=99.74  E-value=8e-19  Score=111.07  Aligned_cols=62  Identities=29%  Similarity=0.415  Sum_probs=57.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486         20 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR   81 (183)
Q Consensus        20 ~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r   81 (183)
                      +.++.|+.||..|+.+|+..|..++||+..++..||..|||++.+|++||+|+|++.++..+
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~   63 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREE   63 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhh
Confidence            56889999999999999999999999999999999999999999999999999998765443

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

Probab=99.73  E-value=2.1e-18  Score=106.46  Aligned_cols=56  Identities=32%  Similarity=0.411  Sum_probs=49.8

Q ss_pred             CCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486         24 KRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        24 ~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~   79 (183)
                      .|+.||.+|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++.
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~   57 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ   57 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC--
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhh
Confidence            58999999999999999999999999999999999999999999999999987653

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

Probab=99.73  E-value=4.7e-18  Score=104.18  Aligned_cols=57  Identities=53%  Similarity=0.805  Sum_probs=54.6

Q ss_pred             cccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486         81 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK  137 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk  137 (183)
                      ++.++.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            356889999999999999999999999999999999999999999999999999987

>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=99.73  E-value=2.6e-18  Score=112.15  Aligned_cols=64  Identities=30%  Similarity=0.460  Sum_probs=59.5

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQ  142 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~  142 (183)
                      ..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|++...+
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~   69 (80)
T 2dmq_A            6 SGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQ   69 (80)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHHH
Confidence            4567789999999999999999999999999999999999999999999999999999987543

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

Probab=99.73  E-value=7.2e-18  Score=106.65  Aligned_cols=62  Identities=35%  Similarity=0.632  Sum_probs=58.4

Q ss_pred             ccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhH
Q psy10486         80 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQR  141 (183)
Q Consensus        80 ~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~  141 (183)
                      .++.++.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+....
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            45678999999999999999999999999999999999999999999999999999998754

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

Probab=99.73  E-value=1.8e-18  Score=112.93  Aligned_cols=64  Identities=31%  Similarity=0.483  Sum_probs=59.7

Q ss_pred             ccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhH
Q psy10486         78 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQR  141 (183)
Q Consensus        78 ~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~  141 (183)
                      ...++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|++...
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~   68 (80)
T 2dms_A            5 SSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQ   68 (80)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHc
Confidence            3466789999999999999999999999999999999999999999999999999999997754

>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=99.73  E-value=4.1e-18  Score=105.50  Aligned_cols=58  Identities=40%  Similarity=0.682  Sum_probs=53.0

Q ss_pred             ccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486         80 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK  137 (183)
Q Consensus        80 ~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk  137 (183)
                      .++.++.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+
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            4677899999999999999999999999999999999999999999999999999986

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

Probab=99.73  E-value=1.4e-18  Score=113.43  Aligned_cols=61  Identities=18%  Similarity=0.216  Sum_probs=57.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhc----CCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         18 QVTVRKKRKPYSKHQTLELEKEFLYN----AYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        18 ~~~~rr~r~~ft~~Ql~~Le~~F~~~----~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      ..+.++.|+.||.+|+.+|+..|..+    +||+..++.+||..|||++.+|++||+|+|++.++
T Consensus         5 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk   69 (80)
T 2da4_A            5 SSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRL   69 (80)
T ss_dssp             CCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhh
Confidence            46788999999999999999999999    99999999999999999999999999999988765

>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=99.73  E-value=4.5e-18  Score=108.87  Aligned_cols=57  Identities=18%  Similarity=0.239  Sum_probs=52.8

Q ss_pred             CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486         23 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        23 r~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~   79 (183)
                      ..|+.||.+|+.+|++.|..++||+..++++||..+||++.+|++||+|+|++.++.
T Consensus         5 ~~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~   61 (76)
T 2ecc_A            5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHH
Confidence            456779999999999999999999999999999999999999999999999886543

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

Probab=99.73  E-value=2.5e-18  Score=106.86  Aligned_cols=59  Identities=41%  Similarity=0.545  Sum_probs=52.9

Q ss_pred             ccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486         80 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN  138 (183)
Q Consensus        80 ~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~  138 (183)
                      .++.++.|+..|+.+|+..|..++||+..++.+||..+||++.+|++||+|||+++|+.
T Consensus         3 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A            3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             -----CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            45678999999999999999999999999999999999999999999999999999985

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

Probab=99.73  E-value=3.6e-18  Score=115.20  Aligned_cols=62  Identities=16%  Similarity=0.187  Sum_probs=53.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         17 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        17 ~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      .....+++|+.||..|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++
T Consensus        21 ~~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk   82 (96)
T 3nar_A           21 PKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKN   82 (96)
T ss_dssp             ------CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhh
Confidence            34566788999999999999999999999999999999999999999999999999988665

>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=99.72  E-value=1.2e-17  Score=108.18  Aligned_cols=63  Identities=68%  Similarity=1.063  Sum_probs=59.3

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQR  141 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~  141 (183)
                      ..++.++.|+..|+.+|+..|..++||+..++.+||..+||++.+|++||+|||+++|+..+.
T Consensus        12 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k~   74 (77)
T 1puf_A           12 STRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             TTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhhh
Confidence            456778999999999999999999999999999999999999999999999999999998764

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

Probab=99.72  E-value=6.1e-18  Score=104.39  Aligned_cols=58  Identities=48%  Similarity=0.812  Sum_probs=55.1

Q ss_pred             cccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486         81 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN  138 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~  138 (183)
                      ++.++.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|+|+++|++
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            5678999999999999999999999999999999999999999999999999999874

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

Probab=99.72  E-value=1.1e-17  Score=108.06  Aligned_cols=61  Identities=18%  Similarity=0.260  Sum_probs=55.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486         21 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR   81 (183)
Q Consensus        21 ~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r   81 (183)
                      ..+.|+.||.+|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++..+
T Consensus         8 ~~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~   68 (76)
T 2dn0_A            8 ASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKG   68 (76)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCS
T ss_pred             CCCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhcc
Confidence            3445899999999999999999999999999999999999999999999999998776443

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

Probab=99.72  E-value=2.7e-18  Score=113.60  Aligned_cols=65  Identities=20%  Similarity=0.330  Sum_probs=57.8

Q ss_pred             cCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHHhc
Q psy10486         83 KRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQAS  147 (183)
Q Consensus        83 ~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~~~  147 (183)
                      +...++..|+.+|+..|..++||+..++.+||..+||++.+|++||+|||+|++++.+.......
T Consensus        14 k~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~~~~~~~~   78 (89)
T 2ecb_A           14 KFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEIDES   78 (89)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCCCCCCC
T ss_pred             hhccCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHHHhhcccC
Confidence            34489999999999999999999999999999999999999999999999999987765543333

>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=99.72  E-value=1.3e-17  Score=107.97  Aligned_cols=64  Identities=44%  Similarity=0.625  Sum_probs=59.2

Q ss_pred             ccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhH
Q psy10486         78 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQR  141 (183)
Q Consensus        78 ~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~  141 (183)
                      ...++.++.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+....
T Consensus         7 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~   70 (77)
T 1nk2_P            7 NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNE   70 (77)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhcc
Confidence            3456678899999999999999999999999999999999999999999999999999987654

>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=99.72  E-value=9.3e-18  Score=107.42  Aligned_cols=58  Identities=21%  Similarity=0.272  Sum_probs=54.6

Q ss_pred             ccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         82 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        82 r~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      ..+..||.+|+.+|+..|..++||+..++++||..+||++.+|++||+|+|+++|+..
T Consensus         5 ~~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~   62 (76)
T 2ecc_A            5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ   62 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHH
Confidence            3466799999999999999999999999999999999999999999999999999864

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

Probab=99.72  E-value=6.3e-18  Score=104.30  Aligned_cols=58  Identities=38%  Similarity=0.546  Sum_probs=50.6

Q ss_pred             cCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486         83 KRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ  140 (183)
Q Consensus        83 ~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~  140 (183)
                      +|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..+
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~k   59 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK   59 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC----
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhcc
Confidence            4688999999999999999999999999999999999999999999999999998764

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

Probab=99.72  E-value=9.4e-18  Score=102.09  Aligned_cols=54  Identities=44%  Similarity=0.768  Sum_probs=51.0

Q ss_pred             CCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486         85 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN  138 (183)
Q Consensus        85 ~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~  138 (183)
                      +.|+..|+.+|+..|..++||+..++.+||..+||++.+|++||+|||+|+|++
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            468999999999999999999999999999999999999999999999999986

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

Probab=99.72  E-value=1e-17  Score=106.55  Aligned_cols=62  Identities=32%  Similarity=0.524  Sum_probs=58.0

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ  140 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~  140 (183)
                      ..++.++.|+..|+.+|+..|..++||+..++.+||..+||++.+|++||+|||+++|+...
T Consensus         6 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2dmu_A            6 SGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP   67 (70)
T ss_dssp             SSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTST
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccCC
Confidence            45677899999999999999999999999999999999999999999999999999998653

>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=99.72  E-value=3.9e-18  Score=115.24  Aligned_cols=64  Identities=41%  Similarity=0.596  Sum_probs=54.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         17 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        17 ~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      +....++.|+.||..|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++..
T Consensus        30 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   93 (97)
T 1b72_A           30 GLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRE   93 (97)
T ss_dssp             -------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHh
Confidence            4467788999999999999999999999999999999999999999999999999999876543

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

Probab=99.72  E-value=8e-18  Score=106.43  Aligned_cols=61  Identities=44%  Similarity=0.650  Sum_probs=57.6

Q ss_pred             ccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486         80 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ  140 (183)
Q Consensus        80 ~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~  140 (183)
                      .++.++.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..+
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~   62 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK   62 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhh
Confidence            3567899999999999999999999999999999999999999999999999999998764

>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=99.71  E-value=7e-18  Score=107.90  Aligned_cols=60  Identities=20%  Similarity=0.125  Sum_probs=55.5

Q ss_pred             CCCCCCCCHHHHHHHHHHhhh-cCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486         22 RKKRKPYSKHQTLELEKEFLY-NAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR   81 (183)
Q Consensus        22 rr~r~~ft~~Ql~~Le~~F~~-~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r   81 (183)
                      .+.|+.||..|+.+|+..|.. ++||+..++..||..|||++.+|++||+|||++.++...
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~~   62 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   62 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhcc
Confidence            578899999999999999996 999999999999999999999999999999998766443

>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=99.71  E-value=1.4e-17  Score=110.66  Aligned_cols=56  Identities=20%  Similarity=0.275  Sum_probs=51.6

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486         26 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR   81 (183)
Q Consensus        26 ~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r   81 (183)
                      ..||.+||.+|+..|..++||+..++..||..|||++.+|++||+|||++.++...
T Consensus        18 k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~   73 (89)
T 2dmp_A           18 KEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQ   73 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCS
T ss_pred             ccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhH
Confidence            44999999999999999999999999999999999999999999999988765443

>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=99.71  E-value=5.7e-18  Score=107.09  Aligned_cols=61  Identities=56%  Similarity=0.934  Sum_probs=57.5

Q ss_pred             ccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486         80 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ  140 (183)
Q Consensus        80 ~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~  140 (183)
                      .++.++.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+...
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~   62 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK   62 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhcc
Confidence            3567899999999999999999999999999999999999999999999999999999764

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

Probab=99.71  E-value=1.7e-17  Score=106.67  Aligned_cols=62  Identities=21%  Similarity=0.305  Sum_probs=57.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486         20 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR   81 (183)
Q Consensus        20 ~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r   81 (183)
                      ..++.|+.||.+|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++...
T Consensus         5 ~~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   66 (74)
T 2ly9_A            5 DSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKS   66 (74)
T ss_dssp             CCCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTTC
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhCc
Confidence            45788999999999999999999999999999999999999999999999999998776443

>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=99.71  E-value=1.5e-17  Score=108.75  Aligned_cols=63  Identities=37%  Similarity=0.539  Sum_probs=58.7

Q ss_pred             ccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486         78 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ  140 (183)
Q Consensus        78 ~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~  140 (183)
                      ...++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|++..
T Consensus        16 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~   78 (81)
T 1fjl_A           16 RKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   78 (81)
T ss_dssp             -CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhcc
Confidence            345677899999999999999999999999999999999999999999999999999999864

>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=99.71  E-value=6.5e-18  Score=107.47  Aligned_cols=61  Identities=51%  Similarity=0.813  Sum_probs=57.5

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      ..++.++.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~   66 (70)
T 2cra_A            6 SGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSG   66 (70)
T ss_dssp             CCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccC
Confidence            4567789999999999999999999999999999999999999999999999999999864

>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=99.71  E-value=8.5e-18  Score=109.65  Aligned_cols=62  Identities=44%  Similarity=0.618  Sum_probs=58.0

Q ss_pred             ccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         78 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        78 ~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      ...++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+|+|+..
T Consensus        15 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   76 (80)
T 2dmt_A           15 KKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSG   76 (80)
T ss_dssp             CCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhccc
Confidence            34567789999999999999999999999999999999999999999999999999999864

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

Probab=99.71  E-value=8.4e-18  Score=107.80  Aligned_cols=61  Identities=20%  Similarity=0.093  Sum_probs=55.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhh-cCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486         21 VRKKRKPYSKHQTLELEKEFLY-NAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR   81 (183)
Q Consensus        21 ~rr~r~~ft~~Ql~~Le~~F~~-~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r   81 (183)
                      ..+.|+.||.+|+.+|+..|.. ++||+..++..||..|||++.+|++||+|||++.++..+
T Consensus         2 ~~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~~   63 (73)
T 2hi3_A            2 SAQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   63 (73)
T ss_dssp             CCSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhcc
Confidence            3577899999999999999995 999999999999999999999999999999998766543

>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=99.71  E-value=6.1e-18  Score=124.20  Aligned_cols=62  Identities=24%  Similarity=0.378  Sum_probs=53.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         17 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        17 ~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      +..+.+|.|+.||..|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++
T Consensus        97 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr  158 (160)
T 1e3o_C           97 GLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR  158 (160)
T ss_dssp             -------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTS
T ss_pred             CCCCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhc
Confidence            34578899999999999999999999999999999999999999999999999999998664

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

Probab=99.71  E-value=1e-17  Score=104.70  Aligned_cols=59  Identities=29%  Similarity=0.321  Sum_probs=55.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHh---hhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         20 TVRKKRKPYSKHQTLELEKEF---LYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        20 ~~rr~r~~ft~~Ql~~Le~~F---~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      ..++.|+.|+..|+.+|+..|   ..++||+..++..||..+||++.+|++||+|+|++.++
T Consensus         2 ~~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A            2 SGHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             CCCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            467889999999999999999   99999999999999999999999999999999987653

>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=99.71  E-value=1.5e-17  Score=105.74  Aligned_cols=61  Identities=44%  Similarity=0.659  Sum_probs=57.3

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      ..++.++.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         6 ~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~   66 (70)
T 2e1o_A            6 SGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSG   66 (70)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCC
Confidence            3456788999999999999999999999999999999999999999999999999999875

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

Probab=99.71  E-value=7.1e-18  Score=102.64  Aligned_cols=53  Identities=40%  Similarity=0.630  Sum_probs=49.0

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         26 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        26 ~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      |.||.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||++.++
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr   54 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRR   54 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhhcc
Confidence            68999999999999999999999999999999999999999999999987654

>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=99.71  E-value=2.2e-17  Score=105.52  Aligned_cols=58  Identities=22%  Similarity=0.247  Sum_probs=55.5

Q ss_pred             ccCCCCChhHHHHHHHcccc-CCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         82 KKRKPYSKHQTLELEKEFLY-NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        82 r~r~~~t~~q~~~Le~~F~~-~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      +.++.|+..|+.+|+..|.. ++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         3 k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~   61 (72)
T 1uhs_A            3 EGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhc
Confidence            56889999999999999996 99999999999999999999999999999999999976

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

Probab=99.71  E-value=1.8e-17  Score=101.51  Aligned_cols=57  Identities=51%  Similarity=0.700  Sum_probs=54.0

Q ss_pred             ccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHH
Q psy10486         80 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK  136 (183)
Q Consensus        80 ~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~r  136 (183)
                      .++.++.|+..|+.+|+..|..++||+..++.+||..+||++.+|++||+|||+++|
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            356789999999999999999999999999999999999999999999999999975

>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=99.70  E-value=1.2e-17  Score=106.17  Aligned_cols=61  Identities=31%  Similarity=0.425  Sum_probs=57.5

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      ..++.++.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         6 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2da2_A            6 SGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSG   66 (70)
T ss_dssp             CSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhcc
Confidence            4567789999999999999999999999999999999999999999999999999999864

>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=99.70  E-value=6.2e-18  Score=106.94  Aligned_cols=62  Identities=35%  Similarity=0.537  Sum_probs=58.5

Q ss_pred             ccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhH
Q psy10486         80 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQR  141 (183)
Q Consensus        80 ~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~  141 (183)
                      .++.++.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..+.
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~~   64 (68)
T 1yz8_P            3 QRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEF   64 (68)
T ss_dssp             SSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhhc
Confidence            45678999999999999999999999999999999999999999999999999999998754

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

Probab=99.70  E-value=2.3e-17  Score=105.71  Aligned_cols=59  Identities=22%  Similarity=0.217  Sum_probs=56.0

Q ss_pred             cccCCCCChhHHHHHHHcccc-CCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         81 RKKRKPYSKHQTLELEKEFLY-NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F~~-~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      .+.++.|+..|+.+|+..|.. ++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~   62 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   62 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhc
Confidence            456889999999999999995 99999999999999999999999999999999999977

>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=99.70  E-value=1.4e-17  Score=108.58  Aligned_cols=62  Identities=23%  Similarity=0.389  Sum_probs=58.0

Q ss_pred             ccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         78 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        78 ~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      ...++.|+.|+.+|+.+|+..|..++||+..++.+||..+||++.+|++||+|||+++|+..
T Consensus        15 ~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   76 (80)
T 2da3_A           15 QRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSG   76 (80)
T ss_dssp             CCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhc
Confidence            34567789999999999999999999999999999999999999999999999999999864

>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=99.70  E-value=2e-17  Score=106.05  Aligned_cols=61  Identities=23%  Similarity=0.255  Sum_probs=56.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         18 QVTVRKKRKPYSKHQTLELEKEFLY---NAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        18 ~~~~rr~r~~ft~~Ql~~Le~~F~~---~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      ..+.++.|+.|+..|+.+|+..|..   ++||+..++..||..+||++.+|++||+|+|++.++
T Consensus         4 ~~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   67 (73)
T 1x2n_A            4 GSSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQ   67 (73)
T ss_dssp             CSSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhccc
Confidence            3567888999999999999999987   999999999999999999999999999999987654

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

Probab=99.70  E-value=1.1e-17  Score=106.35  Aligned_cols=61  Identities=48%  Similarity=0.627  Sum_probs=57.4

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      ..++.++.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2djn_A            6 SGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSG   66 (70)
T ss_dssp             CCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccC
Confidence            4567789999999999999999999999999999999999999999999999999998754

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

Probab=99.70  E-value=1.1e-17  Score=112.11  Aligned_cols=66  Identities=39%  Similarity=0.620  Sum_probs=60.2

Q ss_pred             ccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHH
Q psy10486         78 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQA  143 (183)
Q Consensus        78 ~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~  143 (183)
                      ...++.++.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+|+|+......
T Consensus        15 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~   80 (93)
T 3a01_A           15 PKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEER   80 (93)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC-
T ss_pred             CCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHHH
Confidence            345677899999999999999999999999999999999999999999999999999999875443

>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=99.70  E-value=1.2e-17  Score=105.05  Aligned_cols=60  Identities=25%  Similarity=0.390  Sum_probs=56.7

Q ss_pred             ccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         80 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        80 ~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      .++.++.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         3 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   62 (66)
T 1bw5_A            3 TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             CSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             CCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHHh
Confidence            467789999999999999999999999999999999999999999999999999998754

>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=99.70  E-value=1.3e-17  Score=103.28  Aligned_cols=58  Identities=28%  Similarity=0.428  Sum_probs=48.4

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK  136 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~r  136 (183)
                      ..++.++.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|+|+++|
T Consensus         4 k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            4 KSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             --------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            4567789999999999999999999999999999999999999999999999999875

>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=99.70  E-value=1.3e-17  Score=106.09  Aligned_cols=61  Identities=23%  Similarity=0.328  Sum_probs=57.6

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      ..++.++.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         6 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2da1_A            6 SGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSG   66 (70)
T ss_dssp             CCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhc
Confidence            4567789999999999999999999999999999999999999999999999999999864

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

Probab=99.70  E-value=1.9e-17  Score=106.08  Aligned_cols=61  Identities=51%  Similarity=0.782  Sum_probs=57.7

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      ..++.++.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   66 (73)
T 2l7z_A            6 EGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVI   66 (73)
T ss_dssp             CCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHh
Confidence            4567789999999999999999999999999999999999999999999999999999864

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

Probab=99.70  E-value=2.6e-17  Score=103.73  Aligned_cols=60  Identities=35%  Similarity=0.544  Sum_probs=56.7

Q ss_pred             cccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486         81 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ  140 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~  140 (183)
                      ++.++.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+...
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~   61 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR   61 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCC
T ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhch
Confidence            567899999999999999999999999999999999999999999999999999998653

>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=99.70  E-value=1.5e-17  Score=108.76  Aligned_cols=62  Identities=58%  Similarity=0.888  Sum_probs=54.6

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ  140 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~  140 (183)
                      ..++.|+.|+..|+.+|+..|..++||+..++.+||..+||++.+|++||+|||+|+|++.+
T Consensus        19 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   80 (81)
T 1b8i_A           19 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEIQ   80 (81)
T ss_dssp             -----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC-
T ss_pred             CCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhcc
Confidence            45677899999999999999999999999999999999999999999999999999998653

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

Probab=99.69  E-value=2e-17  Score=107.92  Aligned_cols=62  Identities=23%  Similarity=0.271  Sum_probs=57.8

Q ss_pred             ccccccCCCCChhHHHHHHHccccC----CccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         78 VTVRKKRKPYSKHQTLELEKEFLYN----AYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        78 ~~~rr~r~~~t~~q~~~Le~~F~~~----~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      ...++.|+.|+..|+.+|+..|..+    +||+..++.+||..+||++.+|++||+|||+|+|+..
T Consensus         6 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~~   71 (80)
T 2da4_A            6 SGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMG   71 (80)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhcc
Confidence            3456778999999999999999999    9999999999999999999999999999999999853

>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=99.69  E-value=2.3e-17  Score=105.76  Aligned_cols=60  Identities=33%  Similarity=0.469  Sum_probs=55.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHh---hhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         21 VRKKRKPYSKHQTLELEKEF---LYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        21 ~rr~r~~ft~~Ql~~Le~~F---~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      .++.|+.||..|+.+|+..|   ..++||+..++..||..+||++.+|++||+|+|++.++..
T Consensus         1 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~   63 (73)
T 1puf_B            1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccccc
Confidence            47889999999999999999   9999999999999999999999999999999998876543

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

Probab=99.69  E-value=9.1e-18  Score=110.51  Aligned_cols=63  Identities=40%  Similarity=0.547  Sum_probs=58.5

Q ss_pred             ccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486         78 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ  140 (183)
Q Consensus        78 ~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~  140 (183)
                      ...++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+|+|+..+
T Consensus        20 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k   82 (84)
T 2kt0_A           20 VKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK   82 (84)
T ss_dssp             SCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhh
Confidence            355677899999999999999999999999999999999999999999999999999998653

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

Probab=99.69  E-value=1.6e-17  Score=111.73  Aligned_cols=65  Identities=25%  Similarity=0.222  Sum_probs=59.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcC---------------CChhhhhhhhhhccccccccccc
Q psy10486         18 QVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLM---------------LTERQVKIWFQNIEWTGQVTVRK   82 (183)
Q Consensus        18 ~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~---------------l~~~qV~~WF~nrr~k~~~~~rr   82 (183)
                      ..+.++.|+.|+..|+.+||..|..++||+..+++.||..||               |++.+|++||+|||++.++..+.
T Consensus         4 ~~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~~   83 (95)
T 2cuf_A            4 GSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANI   83 (95)
T ss_dssp             SSCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhhc
Confidence            357789999999999999999999999999999999999999               99999999999999987765443

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

Probab=99.69  E-value=4.3e-17  Score=107.80  Aligned_cols=56  Identities=20%  Similarity=0.307  Sum_probs=51.9

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486         26 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR   81 (183)
Q Consensus        26 ~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r   81 (183)
                      ..||.+||.+||..|..++||+..++.+||..|||++.||++||+|||++.++...
T Consensus        16 k~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~   71 (89)
T 2ecb_A           16 KEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEE   71 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCS
T ss_pred             ccCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHH
Confidence            38999999999999999999999999999999999999999999999988765443

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

Probab=99.69  E-value=2e-17  Score=109.81  Aligned_cols=61  Identities=56%  Similarity=0.940  Sum_probs=55.2

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      ..++.|+.|+..|+.+|+..|..++||+..++.+||..+||++.+|++||+|||+++|+..
T Consensus        27 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   87 (88)
T 2r5y_A           27 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH   87 (88)
T ss_dssp             ----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhhc
Confidence            4567789999999999999999999999999999999999999999999999999999864

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

Probab=99.69  E-value=1.8e-17  Score=122.05  Aligned_cols=66  Identities=29%  Similarity=0.271  Sum_probs=50.6

Q ss_pred             cCCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         15 WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        15 ~~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      ...+.+.+|.|+.||..|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++..
T Consensus        93 ~~~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~  158 (164)
T 2xsd_C           93 IAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMT  158 (164)
T ss_dssp             -------------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSC
T ss_pred             ccccccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhcc
Confidence            345677889999999999999999999999999999999999999999999999999999876644

>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=99.69  E-value=2.9e-17  Score=101.32  Aligned_cols=55  Identities=22%  Similarity=0.323  Sum_probs=51.7

Q ss_pred             CCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         24 KRKPYSKHQTLELEKEFLY---NAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        24 ~r~~ft~~Ql~~Le~~F~~---~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      +|+.||.+|+.+|+..|..   ++||+..++..||..+||++.+|++||+|+|++.++
T Consensus         1 rr~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk   58 (60)
T 1k61_A            1 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             CCCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CcCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHccccc
Confidence            3689999999999999999   999999999999999999999999999999987653

>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=99.68  E-value=1.6e-17  Score=120.21  Aligned_cols=64  Identities=25%  Similarity=0.278  Sum_probs=54.1

Q ss_pred             cCCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         15 WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        15 ~~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      .....+.+|.|+.||..|+.+||..|..++||+..++..||..|||++.+|++||+|||++.++
T Consensus        81 ~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr  144 (146)
T 1au7_A           81 VGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR  144 (146)
T ss_dssp             --------CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTS
T ss_pred             cCCCCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhc
Confidence            3445677889999999999999999999999999999999999999999999999999988764

>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=99.68  E-value=2.7e-17  Score=105.97  Aligned_cols=60  Identities=25%  Similarity=0.320  Sum_probs=56.2

Q ss_pred             cccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486         81 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ  140 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~  140 (183)
                      ++++..+|..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|++..
T Consensus         8 ~~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (75)
T 2da5_A            8 PTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEET   67 (75)
T ss_dssp             SCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSC
T ss_pred             CCCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhh
Confidence            456778999999999999999999999999999999999999999999999999998764

>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=99.68  E-value=1.7e-17  Score=108.08  Aligned_cols=59  Identities=8%  Similarity=0.156  Sum_probs=55.6

Q ss_pred             cccccCCCCChhHHHHHHHcccc----CCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLY----NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK  137 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~----~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk  137 (183)
                      ..++.|+.|+..|+..|+..|..    ++||+..++++||..|||++.+|++||+|||+|+|+
T Consensus        16 ~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           16 IRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            45677899999999999999999    999999999999999999999999999999999874

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

Probab=99.68  E-value=6e-17  Score=100.26  Aligned_cols=53  Identities=21%  Similarity=0.436  Sum_probs=50.5

Q ss_pred             CChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         87 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        87 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      -+.+|+.+|+..|..++||+..++.+||..+||++.+|++||+|||+++|+..
T Consensus        11 ~~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg~   63 (66)
T 3nau_A           11 KTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGI   63 (66)
T ss_dssp             CCHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhccC
Confidence            47899999999999999999999999999999999999999999999999754

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

Probab=99.68  E-value=4.8e-17  Score=104.76  Aligned_cols=62  Identities=39%  Similarity=0.526  Sum_probs=58.2

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ  140 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~  140 (183)
                      ..++.++.|+..|+.+|+..|..++||+..++.+||..+||++.+|++||+|||+++|+..+
T Consensus         8 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r   69 (75)
T 2m0c_A            8 KKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRER   69 (75)
T ss_dssp             CCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHh
Confidence            45677899999999999999999999999999999999999999999999999999998654

>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=99.67  E-value=5.6e-17  Score=107.39  Aligned_cols=60  Identities=33%  Similarity=0.469  Sum_probs=54.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHh---hhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         21 VRKKRKPYSKHQTLELEKEF---LYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        21 ~rr~r~~ft~~Ql~~Le~~F---~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      .+|.|+.|+..|+.+|+..|   ..++||+..++..||..+||++.+|++||+|+|++.++..
T Consensus         1 ~rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~   63 (87)
T 1b72_B            1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (87)
T ss_dssp             --CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCG
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhcc
Confidence            36889999999999999999   8999999999999999999999999999999998876544

>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=99.67  E-value=6.8e-17  Score=106.99  Aligned_cols=67  Identities=37%  Similarity=0.563  Sum_probs=59.7

Q ss_pred             cccCCCCChhHHHHHHHcc---ccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHHhc
Q psy10486         81 RKKRKPYSKHQTLELEKEF---LYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQAS  147 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F---~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~~~  147 (183)
                      ++.++.|+..|+.+|+..|   ..++||+..++..||..+||++.+|++||+|+|+++|+..........
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~~~~~~   71 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEAN   71 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGGGHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhcccccccccc
Confidence            4678899999999999999   899999999999999999999999999999999999998755444433

>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=99.67  E-value=1e-16  Score=105.12  Aligned_cols=61  Identities=18%  Similarity=0.191  Sum_probs=56.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486         19 VTVRKKRKPYSKHQTLELEKEFLY---NAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        19 ~~~rr~r~~ft~~Ql~~Le~~F~~---~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~   79 (183)
                      .+.++.|+.|+.+|+.+|+..|..   ++||+..++..||..+||+..||.+||+|+|++.++.
T Consensus         5 ~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~   68 (83)
T 2dmn_A            5 SSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPD   68 (83)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHH
Confidence            467888999999999999999988   5999999999999999999999999999999886543

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

Probab=99.67  E-value=5.1e-17  Score=104.39  Aligned_cols=60  Identities=23%  Similarity=0.360  Sum_probs=56.7

Q ss_pred             ccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         80 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        80 ~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      .+..|+.|+..|+.+|+..|..++||+..++.+||..+||++.+|++||+|||+++|+..
T Consensus         6 ~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   65 (74)
T 2ly9_A            6 SFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSK   65 (74)
T ss_dssp             CCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTT
T ss_pred             CCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhC
Confidence            356688999999999999999999999999999999999999999999999999999865

>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=99.66  E-value=9.4e-17  Score=106.30  Aligned_cols=60  Identities=22%  Similarity=0.287  Sum_probs=55.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccc
Q psy10486         18 QVTVRKKRKPYSKHQTLELEKEFLY---NAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQ   77 (183)
Q Consensus        18 ~~~~rr~r~~ft~~Ql~~Le~~F~~---~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~   77 (183)
                      ..+.++.|+.|+.+|+.+|+..|..   ++||+..++..||..+||++.+|++||+|+|++.+
T Consensus        24 ~~~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k   86 (87)
T 1mnm_C           24 KSTKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK   86 (87)
T ss_dssp             EESSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHT
T ss_pred             cCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcc
Confidence            3456677999999999999999999   99999999999999999999999999999998754

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

Probab=99.66  E-value=7e-17  Score=109.04  Aligned_cols=64  Identities=22%  Similarity=0.192  Sum_probs=52.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHH------------------cC---CChhhhhhhhhhcccc
Q psy10486         17 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARS------------------LM---LTERQVKIWFQNIEWT   75 (183)
Q Consensus        17 ~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~------------------l~---l~~~qV~~WF~nrr~k   75 (183)
                      ...+.+|.|+.|+..|+.+||..|..++||+..++++||..                  ||   |++.+|++||+|||++
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            34577899999999999999999999999999999999999                  88   9999999999999997


Q ss_pred             ccccc
Q psy10486         76 GQVTV   80 (183)
Q Consensus        76 ~~~~~   80 (183)
                      .+...
T Consensus        85 ~k~k~   89 (99)
T 1lfb_A           85 EAFRH   89 (99)
T ss_dssp             TSCCC
T ss_pred             HHHhc
Confidence            65433

>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=99.66  E-value=6.4e-17  Score=103.67  Aligned_cols=61  Identities=39%  Similarity=0.607  Sum_probs=57.2

Q ss_pred             cccCCCCChhHHHHHHHcc---ccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhH
Q psy10486         81 RKKRKPYSKHQTLELEKEF---LYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQR  141 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F---~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~  141 (183)
                      ++.++.|+..|+.+|+..|   ..++||+..++..||..+||++.+|++||+|+|+++|+....
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~   65 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGK   65 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccccccc
Confidence            4678899999999999999   999999999999999999999999999999999999987644

>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=99.66  E-value=8.8e-17  Score=108.25  Aligned_cols=62  Identities=19%  Similarity=0.204  Sum_probs=57.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHc---------------------CCChhhhhhhhhhccccc
Q psy10486         18 QVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSL---------------------MLTERQVKIWFQNIEWTG   76 (183)
Q Consensus        18 ~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l---------------------~l~~~qV~~WF~nrr~k~   76 (183)
                      ..+.+|.|+.|+..|+.+|+..|+.++||+..++++||..|                     +|++.+|++||+|||++.
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            35788999999999999999999999999999999999999                     799999999999999876


Q ss_pred             ccc
Q psy10486         77 QVT   79 (183)
Q Consensus        77 ~~~   79 (183)
                      ++.
T Consensus        83 kr~   85 (102)
T 2da6_A           83 AFR   85 (102)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            543

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

Probab=99.66  E-value=1.1e-16  Score=98.60  Aligned_cols=55  Identities=29%  Similarity=0.398  Sum_probs=52.6

Q ss_pred             CCCCChhHHHHHHHcccc---CCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486         84 RKPYSKHQTLELEKEFLY---NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN  138 (183)
Q Consensus        84 r~~~t~~q~~~Le~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~  138 (183)
                      ++.|+..|+.+|+..|..   ++||+..++..||..+||++.+|++||+|+|+++|+.
T Consensus         2 r~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A            2 GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             cCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            578999999999999999   9999999999999999999999999999999999863

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

Probab=99.66  E-value=5.6e-17  Score=118.01  Aligned_cols=63  Identities=24%  Similarity=0.315  Sum_probs=58.6

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         16 TGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        16 ~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      ..+.+.+|.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++
T Consensus        88 ~~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           88 GEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             SSCCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            445678889999999999999999999999999999999999999999999999999988664

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

Probab=99.65  E-value=7.8e-17  Score=100.64  Aligned_cols=58  Identities=34%  Similarity=0.464  Sum_probs=54.8

Q ss_pred             ccccCCCCChhHHHHHHHcc---ccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486         80 VRKKRKPYSKHQTLELEKEF---LYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK  137 (183)
Q Consensus        80 ~rr~r~~~t~~q~~~Le~~F---~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk  137 (183)
                      .++.++.|+..|+.+|+..|   ..++||+..++..||..+||++.+|++||+|+|+++|+
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            45678899999999999999   99999999999999999999999999999999999876

>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=99.65  E-value=4.2e-17  Score=106.09  Aligned_cols=58  Identities=14%  Similarity=0.215  Sum_probs=54.2

Q ss_pred             cccccCCCCChhHHHHHHHcccc-----CCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLY-----NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK  137 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~-----~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk  137 (183)
                      ..++.|+.|+..|+..|+ .|..     ++||+..++++||..|||++.+|++||+|||+|+++
T Consensus        16 ~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           16 TTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            456778999999999999 7999     999999999999999999999999999999999874

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

Probab=99.65  E-value=7.7e-17  Score=104.06  Aligned_cols=60  Identities=22%  Similarity=0.333  Sum_probs=56.1

Q ss_pred             cccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486         81 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ  140 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~  140 (183)
                      ...++.|+..|+.+|+..|..++||+..++.+||..+||++.+|++||+|||+++|+...
T Consensus         9 ~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~   68 (76)
T 2dn0_A            9 SIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKG   68 (76)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCS
T ss_pred             CCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhcc
Confidence            345789999999999999999999999999999999999999999999999999998654

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

Probab=99.65  E-value=4.7e-17  Score=103.88  Aligned_cols=60  Identities=18%  Similarity=0.242  Sum_probs=55.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHh-hhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486         20 TVRKKRKPYSKHQTLELEKEF-LYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        20 ~~rr~r~~ft~~Ql~~Le~~F-~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~   79 (183)
                      -..+.|++++.+|+.+||..| ..++||+..++.+||..|||++.+|++||+|||++.++.
T Consensus         7 ~g~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~   67 (72)
T 2cqx_A            7 GGIKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPS   67 (72)
T ss_dssp             CCCCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCC
Confidence            445778889999999999999 999999999999999999999999999999999987643

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

Probab=99.65  E-value=2.1e-16  Score=106.32  Aligned_cols=63  Identities=30%  Similarity=0.366  Sum_probs=59.3

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhC---------------CChhhHHHHHhhhhhHHHHHHhH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLM---------------LTERQVKIWFQNRRMKNKKNTQR  141 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~---------------l~~~~V~~WF~nrR~k~rk~~~~  141 (183)
                      ..++.|+.|+..|+.+|+..|..++||+..++++||..++               |++.+|++||+|||+++|++...
T Consensus         6 ~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~~   83 (95)
T 2cuf_A            6 SGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANI   83 (95)
T ss_dssp             CCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhhc
Confidence            4567789999999999999999999999999999999999               99999999999999999998764

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

Probab=99.65  E-value=1.2e-16  Score=107.67  Aligned_cols=61  Identities=20%  Similarity=0.225  Sum_probs=56.1

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      ..++.|+.|+..|+.+|+..|..++||+..++.+||..+||++.+|++||+|||+|+|+..
T Consensus        24 ~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   84 (96)
T 3nar_A           24 GSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGN   84 (96)
T ss_dssp             ---CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTC
T ss_pred             CCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhc
Confidence            3456789999999999999999999999999999999999999999999999999999876

>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=99.64  E-value=6.5e-17  Score=107.43  Aligned_cols=60  Identities=25%  Similarity=0.335  Sum_probs=54.9

Q ss_pred             cCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHH
Q psy10486         83 KRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQ  142 (183)
Q Consensus        83 ~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~  142 (183)
                      +...+|..|+.+|+..|..++||+..++.+||..+||++.+|++||+|||+|+|++....
T Consensus        16 k~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~~~   75 (89)
T 2dmp_A           16 KFKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAV   75 (89)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCSCC
T ss_pred             ccccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhHhh
Confidence            344599999999999999999999999999999999999999999999999998876543

>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=99.64  E-value=6.6e-16  Score=103.98  Aligned_cols=67  Identities=21%  Similarity=0.260  Sum_probs=61.3

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHh---------------------CCChhhHHHHHhhhhhHHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSL---------------------MLTERQVKIWFQNRRMKNKK  137 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l---------------------~l~~~~V~~WF~nrR~k~rk  137 (183)
                      ..++.|+.|++.|+.+|+..|..++||+..++++||..+                     +|++.+|++||+|||+++++
T Consensus         5 ~~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k~kr   84 (102)
T 2da6_A            5 SSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEEAF   84 (102)
T ss_dssp             CSCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHHHHH
Confidence            456779999999999999999999999999999999999                     79999999999999999999


Q ss_pred             HHhHHHHH
Q psy10486        138 NTQRQAAQ  145 (183)
Q Consensus       138 ~~~~~~~~  145 (183)
                      +.+.....
T Consensus        85 ~~~~~~~~   92 (102)
T 2da6_A           85 RQKLAMDA   92 (102)
T ss_dssp             HHHHHHSS
T ss_pred             hhHhhhcc
Confidence            87766444

>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=99.64  E-value=1.9e-16  Score=103.89  Aligned_cols=57  Identities=19%  Similarity=0.256  Sum_probs=51.8

Q ss_pred             CCCCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         22 RKKRKPYSKHQTLELEKEFLY---NAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        22 rr~r~~ft~~Ql~~Le~~F~~---~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      .+.|++|+..|+.+|+..|..   ++||+..++..||..+||++.||++||+|+|++.++
T Consensus         3 ~krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk   62 (83)
T 1le8_B            3 PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKT   62 (83)
T ss_dssp             --CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHccccc
Confidence            355677999999999999999   999999999999999999999999999999987654

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

Probab=99.64  E-value=9e-17  Score=102.55  Aligned_cols=58  Identities=24%  Similarity=0.383  Sum_probs=53.9

Q ss_pred             cccCCCCChhHHHHHHHcc-ccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486         81 RKKRKPYSKHQTLELEKEF-LYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN  138 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F-~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~  138 (183)
                      .+.+.+++..|+.+|+..| ..++||+..++.+||..+||++.+|++||+|||+++|+.
T Consensus         9 ~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~   67 (72)
T 2cqx_A            9 IKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPS   67 (72)
T ss_dssp             CCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCC
Confidence            3456778999999999999 999999999999999999999999999999999999864

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

Probab=99.64  E-value=1.2e-16  Score=98.93  Aligned_cols=51  Identities=22%  Similarity=0.393  Sum_probs=47.8

Q ss_pred             CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         28 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        28 ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      -|.+|+.+|+..|..++||+..++.+||..|||+..+|++||+|||.+.++
T Consensus        11 ~~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kk   61 (66)
T 3nau_A           11 KTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR   61 (66)
T ss_dssp             CCHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhc
Confidence            368999999999999999999999999999999999999999999987653

>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=99.64  E-value=3.7e-16  Score=100.09  Aligned_cols=61  Identities=25%  Similarity=0.328  Sum_probs=56.6

Q ss_pred             cccccCCCCChhHHHHHHHcccc---CCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLY---NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      ..++.++.|+..|+.+|+..|..   ++||+..++++||..+||++.+|++||+|+|+++++..
T Consensus         6 ~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~   69 (73)
T 1x2n_A            6 SGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSG   69 (73)
T ss_dssp             SSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhccccc
Confidence            45667889999999999999976   99999999999999999999999999999999999864

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

Probab=99.64  E-value=2.7e-16  Score=98.06  Aligned_cols=53  Identities=25%  Similarity=0.251  Sum_probs=49.1

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         26 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        26 ~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      ..++.+|+.+||..|..++||+..++..||..|||++++|++||+|||++...
T Consensus         8 ~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~   60 (64)
T 2e19_A            8 QPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS   60 (64)
T ss_dssp             CCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSC
T ss_pred             CCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCC
Confidence            44568999999999999999999999999999999999999999999997654

>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=99.64  E-value=2.2e-16  Score=103.63  Aligned_cols=64  Identities=25%  Similarity=0.319  Sum_probs=56.9

Q ss_pred             ccCCCCChhHHHHHHHcccc---CCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHH
Q psy10486         82 KKRKPYSKHQTLELEKEFLY---NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQ  145 (183)
Q Consensus        82 r~r~~~t~~q~~~Le~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~  145 (183)
                      +.+++|+..|+.+|+..|..   ++||+..++..||..+||++.+|++||+|+|+++|+........
T Consensus         4 krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~~~~~~~   70 (83)
T 1le8_B            4 YRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITIAPELA   70 (83)
T ss_dssp             -CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSCCCHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHccccccccCHHHH
Confidence            34566999999999999999   99999999999999999999999999999999999976544433

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

Probab=99.63  E-value=3e-16  Score=99.08  Aligned_cols=55  Identities=42%  Similarity=0.616  Sum_probs=51.3

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         26 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        26 ~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      -.+|..|+.+||..|..++||+..++..||..|||++++|++||+|||++.++..
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~   63 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ   63 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSS
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhh
Confidence            4689999999999999999999999999999999999999999999999876543

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

Probab=99.62  E-value=1.7e-16  Score=100.25  Aligned_cols=55  Identities=49%  Similarity=0.739  Sum_probs=52.3

Q ss_pred             CCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         85 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        85 ~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      ..++..|+..|+..|..++||+..++.+||..+||++.+|++||+|||+|+|+..
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~   63 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ   63 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSS
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhh
Confidence            4579999999999999999999999999999999999999999999999999865

>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=99.62  E-value=5.4e-16  Score=95.76  Aligned_cols=57  Identities=19%  Similarity=0.190  Sum_probs=53.6

Q ss_pred             ccccccCCCCChhHHHHHHHcccc-CCccCHHHHHHHHHHhCCChhhHHHHHhhhhhH
Q psy10486         78 VTVRKKRKPYSKHQTLELEKEFLY-NAYVSKQKRWELARSLMLTERQVKIWFQNRRMK  134 (183)
Q Consensus        78 ~~~rr~r~~~t~~q~~~Le~~F~~-~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k  134 (183)
                      ...++.|+.|+.+|+.+|+.+|.. +.||+...++.||..+||++.+|++||||+|--
T Consensus         5 ~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~   62 (71)
T 1wi3_A            5 SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYH   62 (71)
T ss_dssp             CCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceee
Confidence            456788999999999999999999 999999999999999999999999999999964

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

Probab=99.62  E-value=2e-16  Score=106.81  Aligned_cols=67  Identities=24%  Similarity=0.254  Sum_probs=54.1

Q ss_pred             ccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHH------------------hC---CChhhHHHHHhhhhhH
Q psy10486         76 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARS------------------LM---LTERQVKIWFQNRRMK  134 (183)
Q Consensus        76 ~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~------------------l~---l~~~~V~~WF~nrR~k  134 (183)
                      .+++.++.|+.|+..|+.+|+..|..++||+..++++||..                  ||   |++.+|++||+|||++
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            34566788999999999999999999999999999999999                  88   9999999999999999


Q ss_pred             HHHHHhHH
Q psy10486        135 NKKNTQRQ  142 (183)
Q Consensus       135 ~rk~~~~~  142 (183)
                      ++++....
T Consensus        85 ~k~k~~~~   92 (99)
T 1lfb_A           85 EAFRHKLA   92 (99)
T ss_dssp             TSCCC---
T ss_pred             HHHhchhh
Confidence            87776544

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

Probab=99.61  E-value=4.6e-16  Score=96.96  Aligned_cols=54  Identities=24%  Similarity=0.247  Sum_probs=50.6

Q ss_pred             CCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486         84 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK  137 (183)
Q Consensus        84 r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk  137 (183)
                      ...++..|+.+|+..|..++||+..++.+||..+||++.+|++||+|||+|.++
T Consensus         7 ~~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~   60 (64)
T 2e19_A            7 GQPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS   60 (64)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSC
T ss_pred             CCCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCC
Confidence            445789999999999999999999999999999999999999999999998765

>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=99.61  E-value=3.5e-16  Score=96.89  Aligned_cols=51  Identities=24%  Similarity=0.345  Sum_probs=47.2

Q ss_pred             CChhHHHHHHHcc-ccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486         87 YSKHQTLELEKEF-LYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK  137 (183)
Q Consensus        87 ~t~~q~~~Le~~F-~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk  137 (183)
                      -...++.+|+..| ..+.||+..++.+||..|||++.||++||+|||+|+|+
T Consensus         7 ~~~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~   58 (64)
T 1x2m_A            7 GTAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   58 (64)
T ss_dssp             CSSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             CCchHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCC
Confidence            3467899999999 67999999999999999999999999999999999885

>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=99.61  E-value=9e-16  Score=101.55  Aligned_cols=57  Identities=28%  Similarity=0.388  Sum_probs=54.0

Q ss_pred             ccccCCCCChhHHHHHHHcccc---CCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHH
Q psy10486         80 VRKKRKPYSKHQTLELEKEFLY---NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK  136 (183)
Q Consensus        80 ~rr~r~~~t~~q~~~Le~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~r  136 (183)
                      .++.++.|+..|+.+|+..|..   ++||+..++..||..+||++.+|++||+|||+|+|
T Consensus        27 ~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k   86 (87)
T 1mnm_C           27 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK   86 (87)
T ss_dssp             SCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcc
Confidence            4456889999999999999999   99999999999999999999999999999999987

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

Probab=99.60  E-value=7e-16  Score=113.69  Aligned_cols=63  Identities=22%  Similarity=0.164  Sum_probs=53.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486         17 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        17 ~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~   79 (183)
                      ...+.+|.|+.||..|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++.
T Consensus        93 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~  155 (164)
T 2d5v_A           93 RGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDK  155 (164)
T ss_dssp             -------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhcccccc
Confidence            345678999999999999999999999999999999999999999999999999999887653

>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=99.60  E-value=1.5e-15  Score=99.62  Aligned_cols=62  Identities=19%  Similarity=0.245  Sum_probs=56.4

Q ss_pred             cccccCCCCChhHHHHHHHcccc---CCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLY---NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ  140 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~  140 (183)
                      ..++.++.|+..|+.+|+..|..   ++||+..++.+||..+||++.+|++||+|+|+++++...
T Consensus         6 ~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~   70 (83)
T 2dmn_A            6 SGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDML   70 (83)
T ss_dssp             CCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHT
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHH
Confidence            45667889999999999999876   699999999999999999999999999999999988654

>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=99.59  E-value=9.7e-16  Score=111.85  Aligned_cols=60  Identities=27%  Similarity=0.366  Sum_probs=56.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         19 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        19 ~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      .+.+|+|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.++
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr  153 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKR  153 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC
T ss_pred             cCCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccccC
Confidence            567888999999999999999999999999999999999999999999999999987654

>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=99.59  E-value=8.9e-16  Score=95.06  Aligned_cols=49  Identities=18%  Similarity=0.247  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHh-hhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         30 KHQTLELEKEF-LYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        30 ~~Ql~~Le~~F-~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      ..|+.+||+.| ..+.||+..++.+||..|||+++||++||+|||++.+.
T Consensus         9 ~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~   58 (64)
T 1x2m_A            9 AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   58 (64)
T ss_dssp             SCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             chHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCC
Confidence            45899999999 67999999999999999999999999999999998764

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

Probab=99.58  E-value=7.3e-16  Score=113.43  Aligned_cols=121  Identities=24%  Similarity=0.293  Sum_probs=80.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChh-------hhhhhhhhcccc-----------ccccc
Q psy10486         19 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTER-------QVKIWFQNIEWT-----------GQVTV   80 (183)
Q Consensus        19 ~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~-------qV~~WF~nrr~k-----------~~~~~   80 (183)
                      .+.+|-+.-||..++........-+.|.-... .. -+.|+++..       .+..|...-...           .....
T Consensus        22 fk~~ri~lg~tQ~~vg~alg~l~g~~~Sqtti-~r-FE~l~ls~kn~~klkPlL~~wl~eae~~~~~~~~~~~~~~~~~~   99 (164)
T 2xsd_C           22 FKQRRIKLGFTQADVGLALGTLYGNVFSQTTI-CR-FEALQLSFKNMCKLKPLLNKWLEETDSSSGSPTNLDKIAAQGRK   99 (164)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHH-HH-HHTTCSBHHHHHHHHHHHHHHHHHHCC-----------------
T ss_pred             HHHHHhhcCCcccccccccccccCCCcCcchh-hh-hhccCCCHHHHHHcchhHHHHHhhhccccCCCcccccccccccC
Confidence            44555666788888776655555454433211 11 234555432       245677653211           12355


Q ss_pred             cccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhH
Q psy10486         81 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQR  141 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~  141 (183)
                      ++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+|+|++...
T Consensus       100 rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~  160 (164)
T 2xsd_C          100 RKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTPA  160 (164)
T ss_dssp             ------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC-
T ss_pred             CCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhccCC
Confidence            6778999999999999999999999999999999999999999999999999999997654

>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=99.57  E-value=1.7e-15  Score=109.44  Aligned_cols=111  Identities=23%  Similarity=0.307  Sum_probs=75.7

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChh-------hhhhhhhhcccc---------ccccccccCCCCCh
Q psy10486         26 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTER-------QVKIWFQNIEWT---------GQVTVRKKRKPYSK   89 (183)
Q Consensus        26 ~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~-------qV~~WF~nrr~k---------~~~~~rr~r~~~t~   89 (183)
                      ..||..++......-.-+.|. -..... .+.++|+..       .+..|+..-...         .....++.|+.|+.
T Consensus        19 lg~tQ~~vg~al~~l~g~~~S-qtti~r-fe~l~ls~knm~kLkPlL~~wl~e~e~~~~~~~~~~~~~~~~rr~Rt~ft~   96 (146)
T 1au7_A           19 LGYTQTNVGEALAAVHGSEFS-QTTICR-FENLQLSFKNACKLKAILSKWLEEAEQVGALYNEKVGANERKRKRRTTISI   96 (146)
T ss_dssp             HTCCHHHHHHHHHHTTSSCCC-HHHHHH-HHTTCSBHHHHHHHHHHHHHHHHHCCC----------------CCCCCCCH
T ss_pred             ccCcHHhhhhhcchhccCCCC-cchHHH-HhccCCChHHHHhcchHHHHHHHHhhcccCccCcccCCCCCCCCCCcCccH
Confidence            346666655333332233332 222211 355666642       245677653211         22345677899999


Q ss_pred             hHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486         90 HQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN  138 (183)
Q Consensus        90 ~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~  138 (183)
                      .|+.+|+..|..++||+..++..||..+||++.+|++||+|||+|+|++
T Consensus        97 ~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           97 AAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             HHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            9999999999999999999999999999999999999999999999874

>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=99.57  E-value=2.1e-15  Score=110.68  Aligned_cols=60  Identities=30%  Similarity=0.488  Sum_probs=54.5

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN  138 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~  138 (183)
                      ..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+|+||+
T Consensus       100 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C          100 RRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            456778999999999999999999999999999999999999999999999999999974

>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=99.56  E-value=2.7e-15  Score=109.09  Aligned_cols=60  Identities=28%  Similarity=0.435  Sum_probs=56.5

Q ss_pred             ccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486         78 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK  137 (183)
Q Consensus        78 ~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk  137 (183)
                      ...++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+|+||
T Consensus        91 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           91 SKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            345677889999999999999999999999999999999999999999999999999986

>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=99.55  E-value=5.4e-15  Score=107.88  Aligned_cols=115  Identities=21%  Similarity=0.277  Sum_probs=80.3

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhh-------hhhhhhhcccc-----------cccccccc
Q psy10486         22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQ-------VKIWFQNIEWT-----------GQVTVRKK   83 (183)
Q Consensus        22 rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~q-------V~~WF~nrr~k-----------~~~~~rr~   83 (183)
                      +|-+.-||..++......-.- +..+-..... -+.+.|+..-       ++.|+..-...           .....++.
T Consensus        22 ~ri~lg~tq~~vg~al~~l~G-~~~Sqtti~r-fE~l~ls~~nm~kLkPlL~~Wl~eae~~~~~~~~~~~~~~~~~~rr~   99 (155)
T 3l1p_A           22 KRITLGYTQADVGLTLGVLFG-KVFSQTTISR-FEALQLSLKNMSKLRPLLEKWVEEADNNENLQEISKSETLVQARKRK   99 (155)
T ss_dssp             HHHHTTCCHHHHHHHHHHHHS-CCCCHHHHHH-HHTTCSCHHHHHHHHHHHHHHHHHHTTCHHHHHSSCC---CCCSCCC
T ss_pred             hhheecccHHHHHHHHHhhcC-cccccccccc-cccccCChhhHhhcchHHHHHhhhhhcccCccccccccccccCCCCC
Confidence            334445677776655444332 2233233222 2456666432       45687542210           01245667


Q ss_pred             CCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486         84 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN  138 (183)
Q Consensus        84 r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~  138 (183)
                      |+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+|+|+.
T Consensus       100 Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A          100 RTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             CCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             CcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            8999999999999999999999999999999999999999999999999999974

>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=99.54  E-value=1.8e-15  Score=113.79  Aligned_cols=62  Identities=21%  Similarity=0.180  Sum_probs=53.0

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcC---------------------CChhhhhhhhhhccc
Q psy10486         16 TGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLM---------------------LTERQVKIWFQNIEW   74 (183)
Q Consensus        16 ~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~---------------------l~~~qV~~WF~nrr~   74 (183)
                      +...+.||.|+.|+..|+.+|+..|..++||+..++++||..+|                     |++.+|++||+|||+
T Consensus       110 ~~~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~  189 (194)
T 1ic8_A          110 LPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRK  189 (194)
T ss_dssp             -------CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHH
T ss_pred             cccccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhh
Confidence            34467789999999999999999999999999999999999999                     999999999999998


Q ss_pred             ccc
Q psy10486         75 TGQ   77 (183)
Q Consensus        75 k~~   77 (183)
                      +.+
T Consensus       190 ~~k  192 (194)
T 1ic8_A          190 EEA  192 (194)
T ss_dssp             HCC
T ss_pred             hhh
Confidence            754

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

Probab=99.54  E-value=4.2e-15  Score=93.49  Aligned_cols=58  Identities=26%  Similarity=0.282  Sum_probs=50.4

Q ss_pred             CCCChhHHHHHHHccc---cCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHH
Q psy10486         85 KPYSKHQTLELEKEFL---YNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQ  142 (183)
Q Consensus        85 ~~~t~~q~~~Le~~F~---~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~  142 (183)
                      ..|+.++..+|+..|.   .++||+..++.+||..+||++.+|++||+|+|+++++....+
T Consensus         3 g~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~   63 (67)
T 3k2a_A            3 GIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQ   63 (67)
T ss_dssp             ---CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC---
T ss_pred             CcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHHHH
Confidence            3689999999999999   999999999999999999999999999999999999865443

>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=99.52  E-value=8.7e-15  Score=92.02  Aligned_cols=52  Identities=25%  Similarity=0.252  Sum_probs=47.7

Q ss_pred             CCCHHHHHHHHHHhh---hcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         27 PYSKHQTLELEKEFL---YNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        27 ~ft~~Ql~~Le~~F~---~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      .|+.+|+.+|+..|.   .++||+..++..||..+||+..||++||+|+|++.++
T Consensus         4 ~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk   58 (67)
T 3k2a_A            4 IFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQ   58 (67)
T ss_dssp             --CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHS
T ss_pred             cCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhH
Confidence            799999999999999   9999999999999999999999999999999987654

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

Probab=99.51  E-value=1.2e-14  Score=110.46  Aligned_cols=65  Identities=20%  Similarity=0.186  Sum_probs=53.2

Q ss_pred             ccccCCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcC---------------------CChhhhhhhhh
Q psy10486         12 TLEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLM---------------------LTERQVKIWFQ   70 (183)
Q Consensus        12 ~~~~~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~---------------------l~~~qV~~WF~   70 (183)
                      +...+...+.||.|+.|+.+|+.+|+..|..++||+..++++||..+|                     |++.+|++||+
T Consensus       133 ~~~~~~~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFq  212 (221)
T 2h8r_A          133 ACSEPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFA  212 (221)
T ss_dssp             ---------CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHH
T ss_pred             cccccccCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhH
Confidence            334456678899999999999999999999999999999999999988                     89999999999


Q ss_pred             hccccc
Q psy10486         71 NIEWTG   76 (183)
Q Consensus        71 nrr~k~   76 (183)
                      |||+..
T Consensus       213 NRR~~~  218 (221)
T 2h8r_A          213 NRRKEE  218 (221)
T ss_dssp             HHHTTC
T ss_pred             Hhhhhh
Confidence            998753

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

Probab=99.49  E-value=1.3e-14  Score=106.84  Aligned_cols=63  Identities=24%  Similarity=0.222  Sum_probs=54.5

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQR  141 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~  141 (183)
                      ..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+....
T Consensus        96 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~~  158 (164)
T 2d5v_A           96 TPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWLE  158 (164)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC---
T ss_pred             CCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccCCC
Confidence            456778999999999999999999999999999999999999999999999999998876543

>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=99.45  E-value=5.7e-14  Score=87.33  Aligned_cols=46  Identities=17%  Similarity=0.236  Sum_probs=43.9

Q ss_pred             HHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccc
Q psy10486         30 KHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWT   75 (183)
Q Consensus        30 ~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k   75 (183)
                      ++|+.+|+++|..+++|+.+++..||..+||+.++|++||+|+|+.
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~   59 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVY   59 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhcccc
Confidence            5789999999999999999999999999999999999999998863

>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=99.42  E-value=7.6e-14  Score=104.88  Aligned_cols=59  Identities=25%  Similarity=0.288  Sum_probs=53.1

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhC---------------------CChhhHHHHHhhhhhHHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLM---------------------LTERQVKIWFQNRRMKNKK  137 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~---------------------l~~~~V~~WF~nrR~k~rk  137 (183)
                      ..++.|+.|++.|+.+|+..|..++||+..++++||..++                     |++.+|++||+|||++.+.
T Consensus       114 k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~~k~  193 (194)
T 1ic8_A          114 KGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAF  193 (194)
T ss_dssp             ---CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHHCC-
T ss_pred             cCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhhhhc
Confidence            4567788999999999999999999999999999999999                     9999999999999998764

>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=99.39  E-value=4.6e-13  Score=83.23  Aligned_cols=48  Identities=19%  Similarity=0.279  Sum_probs=45.1

Q ss_pred             CChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhH
Q psy10486         87 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMK  134 (183)
Q Consensus        87 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k  134 (183)
                      .-++|+.+|+++|..+++|+.+++..||..+||+...|++||+|+|+.
T Consensus        12 ~~k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~   59 (71)
T 2da7_A           12 PYKDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVY   59 (71)
T ss_dssp             SSTHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhcccc
Confidence            347899999999999999999999999999999999999999999973

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

Probab=99.38  E-value=7.3e-13  Score=86.94  Aligned_cols=57  Identities=28%  Similarity=0.293  Sum_probs=52.3

Q ss_pred             CCChhHHHHHHHcccc---CCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHH
Q psy10486         86 PYSKHQTLELEKEFLY---NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQ  142 (183)
Q Consensus        86 ~~t~~q~~~Le~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~  142 (183)
                      .++.++..+|...|..   ++||+..++.+||..+||++.||.+||+|+|.+.++.....
T Consensus        11 ~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~~~   70 (89)
T 2lk2_A           11 MLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRK   70 (89)
T ss_dssp             CCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHHHh
Confidence            5788999999999976   99999999999999999999999999999999998876544

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

Probab=99.33  E-value=8.9e-13  Score=86.54  Aligned_cols=53  Identities=26%  Similarity=0.221  Sum_probs=49.2

Q ss_pred             CCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         26 KPYSKHQTLELEKEFLY---NAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        26 ~~ft~~Ql~~Le~~F~~---~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      ..|+.+++.+|+..|..   ++||+.+++.+||..+||++.||.+||+|+|.+.++
T Consensus        10 ~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk   65 (89)
T 2lk2_A           10 HMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLP   65 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhh
Confidence            57999999999999988   999999999999999999999999999999877543

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

Probab=99.26  E-value=3.5e-12  Score=96.91  Aligned_cols=59  Identities=25%  Similarity=0.331  Sum_probs=52.6

Q ss_pred             cccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhC---------------------CChhhHHHHHhhhhhHH
Q psy10486         77 QVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLM---------------------LTERQVKIWFQNRRMKN  135 (183)
Q Consensus        77 ~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~---------------------l~~~~V~~WF~nrR~k~  135 (183)
                      ++..++.|+.|++.|+.+|+..|..++||+..++++||..+|                     |++.+|++||+|||+..
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            345677888999999999999999999999999999999987                     89999999999999863

>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=99.17  E-value=1.8e-11  Score=101.54  Aligned_cols=56  Identities=21%  Similarity=0.299  Sum_probs=51.9

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccc
Q psy10486         22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQ   77 (183)
Q Consensus        22 rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~   77 (183)
                      ++.++.|+..|+..|+..|+.++||+..+|++||..+||+++||++||+|||.+.+
T Consensus       366 ~~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          366 TAAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            34567899999999999999999999999999999999999999999999998753

>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=99.12  E-value=2e-11  Score=101.23  Aligned_cols=56  Identities=27%  Similarity=0.414  Sum_probs=52.3

Q ss_pred             cccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHH
Q psy10486         81 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK  136 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~r  136 (183)
                      ++.+..++..|+..|+..|..++||+..++++||..+||++.||++||+|||+|+|
T Consensus       366 ~~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          366 TAAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            34567899999999999999999999999999999999999999999999999875

>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=98.54  E-value=8e-09  Score=56.31  Aligned_cols=24  Identities=63%  Similarity=0.926  Sum_probs=20.2

Q ss_pred             hhHHHHHhhhhhHHHHHHhHHHHH
Q psy10486        122 RQVKIWFQNRRMKNKKNTQRQAAQ  145 (183)
Q Consensus       122 ~~V~~WF~nrR~k~rk~~~~~~~~  145 (183)
                      .||++||+|||+|+|++.......
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~~~~   24 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFNDARD   24 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHHTTT
T ss_pred             CCceeccHHHHHHHHHHhHHHHHH
Confidence            489999999999999999875433

>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=97.69  E-value=4e-06  Score=45.55  Aligned_cols=19  Identities=47%  Similarity=0.672  Sum_probs=15.6

Q ss_pred             hhhhhhhhhcccccccccc
Q psy10486         63 RQVKIWFQNIEWTGQVTVR   81 (183)
Q Consensus        63 ~qV~~WF~nrr~k~~~~~r   81 (183)
                      +||++||+|||+|.++...
T Consensus         1 rQVkIWFQNRRaK~Kk~~~   19 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVF   19 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHH
T ss_pred             CCceeccHHHHHHHHHHhH
Confidence            5899999999999776443

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=97.10  E-value=0.005  Score=42.65  Aligned_cols=99  Identities=15%  Similarity=0.217  Sum_probs=65.6

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCcc
Q psy10486         26 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYV  105 (183)
Q Consensus        26 ~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p  105 (183)
                      ..++.++...+...+...  .+   ..++|..||++...|..|+......+..........+++++...+... ..++..
T Consensus         5 ~~~s~~~r~~i~~~~~~G--~s---~~~ia~~lgis~~Tv~r~~~~~~~~g~~~~~gr~~~l~~~~~~~i~~~-~~~~~~   78 (141)
T 1u78_A            5 SALSDTERAQLDVMKLLN--VS---LHEMSRKISRSRHCIRVYLKDPVSYGTSKRAPRRKALSVRDERNVIRA-ASNSCK   78 (141)
T ss_dssp             CCCCHHHHHHHHHHHHTT--CC---HHHHHHHHTCCHHHHHHHHHSGGGTTCCCCCCCCCSSCHHHHHHHHHH-HHHCCC
T ss_pred             ccCCHHHHHHHHHHHHcC--CC---HHHHHHHHCcCHHHHHHHHHcccccCCcCCCCCCCcCCHHHHHHHHHH-HhCCCC
Confidence            568888887777777543  22   356899999999999999976443322211222335777777666555 334444


Q ss_pred             CHHHHHHHHHHhC--CChhhHHHHHhhhhh
Q psy10486        106 SKQKRWELARSLM--LTERQVKIWFQNRRM  133 (183)
Q Consensus       106 ~~~~~~~La~~l~--l~~~~V~~WF~nrR~  133 (183)
                      +.   .+|+..+|  ++...|..|+.....
T Consensus        79 s~---~~i~~~lg~~~s~~tV~r~l~~~g~  105 (141)
T 1u78_A           79 TA---RDIRNELQLSASKRTILNVIKRSGV  105 (141)
T ss_dssp             CH---HHHHHHTTCCSCHHHHHHHHHHTC-
T ss_pred             CH---HHHHHHHCCCccHHHHHHHHHHCCC
Confidence            44   35677778  799999999976554

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

Probab=96.46  E-value=0.0091  Score=36.71  Aligned_cols=39  Identities=21%  Similarity=0.294  Sum_probs=36.9

Q ss_pred             HHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhc
Q psy10486         34 LELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNI   72 (183)
Q Consensus        34 ~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nr   72 (183)
                      ++|+.+|.....+..+....|+.+.+|+..||+.||-.+
T Consensus        19 e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~k   57 (70)
T 2ys9_A           19 QPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSR   57 (70)
T ss_dssp             HHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             hHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHhc
Confidence            789999999999999999999999999999999999653

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

Probab=96.34  E-value=0.003  Score=38.90  Aligned_cols=44  Identities=18%  Similarity=0.248  Sum_probs=39.3

Q ss_pred             CChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhh
Q psy10486         87 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN  130 (183)
Q Consensus        87 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~n  130 (183)
                      .++.-.+.|..+|.....+.......|+.+.+|+..+|+.||..
T Consensus        13 ~~p~~~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~   56 (70)
T 2ys9_A           13 PPPPDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDS   56 (70)
T ss_dssp             CCCCCCHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCCCcchHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHh
Confidence            34455688999999999999999999999999999999999953

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens}

Probab=96.31  E-value=0.16  Score=35.83  Aligned_cols=100  Identities=11%  Similarity=0.035  Sum_probs=64.2

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc---c-ccccCCCCChhHHHHHHHcccc
Q psy10486         26 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV---T-VRKKRKPYSKHQTLELEKEFLY  101 (183)
Q Consensus        26 ~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~---~-~rr~r~~~t~~q~~~Le~~F~~  101 (183)
                      ..|+.++...+...+...  .+   ..++|..+|++...|..|+...+..+..   . ..+....++.+....+......
T Consensus        24 ~~~s~e~r~~ii~l~~~G--~s---~~~IA~~lgis~~TV~rwl~r~~~~G~~~~~~r~gr~~~~~~~~~~~~I~~~~~~   98 (159)
T 2k27_A           24 RPLPEVVRQRIVDLAHQG--VR---PCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPKVVEKIGDYKRQ   98 (159)
T ss_dssp             CSSCHHHHHHHHHHHHHT--CC---HHHHHHHHTCCSHHHHHHHCCSSTTSCCCCCCCCCCCCCCCCTTHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHcC--CC---HHHHHHHHCcCHHHHHHHHHHHHhcCCccCCCCCCCCCCCCCHHHHHHHHHHHHH
Confidence            468888887777777543  22   3468999999999999999764432211   1 1112345777777777777666


Q ss_pred             CCccCHHHHHH-HHHH------hCCChhhHHHHHhh
Q psy10486        102 NAYVSKQKRWE-LARS------LMLTERQVKIWFQN  130 (183)
Q Consensus       102 ~~~p~~~~~~~-La~~------l~l~~~~V~~WF~n  130 (183)
                      ++..+..+... |...      ..++...|..|...
T Consensus        99 ~~~~s~~~i~~~l~~~~~~~~~~~~S~sTV~r~L~~  134 (159)
T 2k27_A           99 NPTMFAWEIRDRLLAEGVCDNDTVPSVSSINRIIRT  134 (159)
T ss_dssp             CSSSCHHHHHHHHHHHTCSCTTTSCCHHHHHHHHHH
T ss_pred             CccchHHHHHHHHHHhcccccCCccCHHHHHHHHHH
Confidence            66556554433 3222      24788999999853

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5

Probab=95.62  E-value=0.17  Score=33.77  Aligned_cols=99  Identities=10%  Similarity=0.017  Sum_probs=63.0

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc---cccc-cCCCCChhHHHHHHHcccc
Q psy10486         26 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV---TVRK-KRKPYSKHQTLELEKEFLY  101 (183)
Q Consensus        26 ~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~---~~rr-~r~~~t~~q~~~Le~~F~~  101 (183)
                      ..|+.++...+...+... + +   ..++|..+|++...|..|+...+..+..   .... ....+++++...+......
T Consensus        16 ~~~s~~~r~~i~~~~~~g-~-s---~~~ia~~lgis~~Tv~~w~~~~~~~g~~~~~~~~g~~~~~l~~~~~~~i~~~~~~   90 (128)
T 1pdn_C           16 RPLPNNIRLKIVEMAADG-I-R---PCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYKRS   90 (128)
T ss_dssp             SCCCHHHHHHHHHHHHTT-C-C---HHHHHHHHTCCHHHHHHHHHHHHHHCCSSCCCCSCCCCCSSCSTHHHHHHHTTTT
T ss_pred             CcCCHHHHHHHHHHHHcC-C-C---HHHHHHHHCcCHHHHHHHHHHHHhhCCcccccCCCCCCCcCCHHHHHHHHHHHHh
Confidence            358888877777766532 2 3   3468999999999999999764332211   1111 2345777777788877776


Q ss_pred             CCccCHHHHHHHHHHhC-------CChhhHHHHHh
Q psy10486        102 NAYVSKQKRWELARSLM-------LTERQVKIWFQ  129 (183)
Q Consensus       102 ~~~p~~~~~~~La~~l~-------l~~~~V~~WF~  129 (183)
                      ++..+..+........|       ++...|..|..
T Consensus        91 ~~~~s~~~i~~~l~~~g~~~~~~~~s~~tv~r~l~  125 (128)
T 1pdn_C           91 SPGMFSWEIREKLIREGVCDRSTAPSVSAISRLVR  125 (128)
T ss_dssp             CTTCCHHHHHHHHHHTSSSCSTTCCCHHHHHHHC-
T ss_pred             CcchHHHHHHHHHHHcCCccccCCcCHHHHHHHHH
Confidence            66666554433222227       48888988875

>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=94.86  E-value=0.4  Score=32.52  Aligned_cols=105  Identities=15%  Similarity=0.083  Sum_probs=65.9

Q ss_pred             CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccc---------ccccccCCCCChhHHH
Q psy10486         23 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQ---------VTVRKKRKPYSKHQTL   93 (183)
Q Consensus        23 r~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~---------~~~rr~r~~~t~~q~~   93 (183)
                      ++|..||.++...+...+..+.....   .++|..+|++...|..|..++..-..         ...++.+....++.-.
T Consensus         3 ~~r~~~t~e~K~~iv~~~~~~g~~~~---~~~A~~~gvs~stl~~~~~~~~~~~~~~~~~~~~~~~~kr~r~~~~~~~E~   79 (131)
T 1hlv_A            3 PKRRQLTFREKSRIIQEVEENPDLRK---GEIARRFNIPPSTLSTILKNKRAILASERKYGVASTCRKTNKLSPYDKLEG   79 (131)
T ss_dssp             CSSCCCCHHHHHHHHHHHHHCTTSCH---HHHHHHHTCCHHHHHHHHHTHHHHHHHHHHHGGGGGTCCCCCCCTTHHHHH
T ss_pred             CcceeCCHHHHHHHHHHHHHCCCCcH---HHHHHHhCCCHHHHHHHHhchhhhcchhhhccccchhhcccCCCCCHHHHH
Confidence            35789999999888888766665553   35899999999999999987543211         1123344556666666


Q ss_pred             HHHHcccc----CCccCHHHHHH----HHHHhCCChh-hHHHHHhh
Q psy10486         94 ELEKEFLY----NAYVSKQKRWE----LARSLMLTER-QVKIWFQN  130 (183)
Q Consensus        94 ~Le~~F~~----~~~p~~~~~~~----La~~l~l~~~-~V~~WF~n  130 (183)
                      .|...+..    +--++.....+    |+..+|++.. --..|+.+
T Consensus        80 ~L~~Wi~~~~~~g~pvs~~~I~~kA~~i~~~~g~~~f~~S~gWl~~  125 (131)
T 1hlv_A           80 LLIAWFQQIRAAGLPVKGIILKEKALRIAEELGMDDFTASNGWLDR  125 (131)
T ss_dssp             HHHHHHHHHGGGTCCCCHHHHHHHHHHHHHHHTCTTCCCCHHHHHH
T ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHhCCCCCCCCHHHHHH
Confidence            66666532    22345544433    5666676532 22566644

>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A

Probab=94.45  E-value=0.48  Score=32.90  Aligned_cols=101  Identities=11%  Similarity=0.031  Sum_probs=64.3

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc---c-ccccCCCCChhHHHHHHHcccc
Q psy10486         26 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV---T-VRKKRKPYSKHQTLELEKEFLY  101 (183)
Q Consensus        26 ~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~---~-~rr~r~~~t~~q~~~Le~~F~~  101 (183)
                      ..|+.++.......+...  .+   ..++|..+|++...|..|....+..+..   . ..+....++.+....+......
T Consensus        31 ~~~s~e~r~~iv~~~~~G--~s---~~~iA~~lgis~~TV~rw~~~~~~~G~~~~~~r~gr~~~~~~~~~~~~I~~~~~~  105 (149)
T 1k78_A           31 RPLPDVVRQRIVELAHQG--VR---PCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVATPKVVEKIAEYKRQ  105 (149)
T ss_dssp             SCCCHHHHHHHHHHHHTT--CC---HHHHHHHHTCCHHHHHHHHHHHHHHSCCCCCCCCCCCCSSSCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHcC--CC---HHHHHHHHCcCHHHHHHHHHHHHHcCCCCccCCCCCCCCCCCHHHHHHHHHHHHh
Confidence            468888877777777532  23   3568999999999999998764332211   1 1112345778777777777766


Q ss_pred             CCccCHHHHHH-HHHHh----C--CChhhHHHHHhhh
Q psy10486        102 NAYVSKQKRWE-LARSL----M--LTERQVKIWFQNR  131 (183)
Q Consensus       102 ~~~p~~~~~~~-La~~l----~--l~~~~V~~WF~nr  131 (183)
                      ++..+..+... |....    |  ++...|..|....
T Consensus       106 ~~~~s~~~i~~~l~~~~~~~~g~~~S~sTV~r~L~~~  142 (149)
T 1k78_A          106 NPTMFAWEIRDRLLAERVCDNDTVPSVSSINRIIRTK  142 (149)
T ss_dssp             CTTCCHHHHHHHHHHTTSSCTTTSCCHHHHHHHHHCC
T ss_pred             CcchhHHHHHHHHHHhcccccCCCcCHHHHHHHHHHH
Confidence            65555544333 22211    5  7889999998643

>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda}

Probab=91.61  E-value=0.42  Score=29.40  Aligned_cols=47  Identities=13%  Similarity=0.070  Sum_probs=36.6

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHH
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWF  128 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF  128 (183)
                      .+||..+|++...|..|..+                              ...|+......||..+|++...+.-|+
T Consensus        29 ~~lA~~~gvs~~~is~~e~g------------------------------~~~~~~~~~~~ia~~l~v~~~~l~~~l   75 (80)
T 3kz3_A           29 ESVADKMGMGQSAVAALFNG------------------------------INALNAYNAALLAKILKVSVEEFSPSI   75 (80)
T ss_dssp             HHHHHHTTSCHHHHHHHHTT------------------------------SSCCCHHHHHHHHHHHTSCGGGTCHHH
T ss_pred             HHHHHHhCcCHHHHHHHHcC------------------------------CCCCCHHHHHHHHHHhCCCHHHHhHHH
Confidence            56999999999999999866                              223556677788888888887776665

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii}

Probab=90.32  E-value=0.74  Score=27.61  Aligned_cols=42  Identities=21%  Similarity=0.320  Sum_probs=32.9

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQ  123 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~  123 (183)
                      .+||..+|++...|..|..+                              ...|+......||..+|++...
T Consensus        25 ~~lA~~~gis~~~is~~e~g------------------------------~~~~~~~~l~~ia~~l~v~~~~   66 (73)
T 3omt_A           25 LWLTETLDKNKTTVSKWCTN------------------------------DVQPSLETLFDIAEALNVDVRE   66 (73)
T ss_dssp             HHHHHHTTCCHHHHHHHHTT------------------------------SSCCCHHHHHHHHHHHTSCGGG
T ss_pred             HHHHHHHCcCHHHHHHHHcC------------------------------CCCCCHHHHHHHHHHHCcCHHH
Confidence            56999999999999999866                              2236667777888888887753

>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis}

Probab=89.80  E-value=0.8  Score=27.45  Aligned_cols=41  Identities=22%  Similarity=0.218  Sum_probs=31.5

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTER  122 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~  122 (183)
                      .+||..+|++...|..|..+                              ...|+......||..+|++..
T Consensus        27 ~~lA~~~gis~~~i~~~e~g------------------------------~~~~~~~~l~~ia~~l~~~~~   67 (76)
T 3bs3_A           27 RWLAEQMGKSENTISRWCSN------------------------------KSQPSLDMLVKVAELLNVDPR   67 (76)
T ss_dssp             HHHHHHHTCCHHHHHHHHTT------------------------------SSCCCHHHHHHHHHHHTSCGG
T ss_pred             HHHHHHHCcCHHHHHHHHcC------------------------------CCCCCHHHHHHHHHHHCcCHH
Confidence            56999999999999999866                              223556667778888888764

>2xi8_A Putative transcription regulator; HTH DNA-binding motif; HET: GOL; 1.21A {Enterococcus faecalis} PDB: 2gzu_A 1utx_A* 2xj3_A 2xiu_A

Probab=89.66  E-value=0.82  Score=26.45  Aligned_cols=41  Identities=22%  Similarity=0.027  Sum_probs=30.3

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTER  122 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~  122 (183)
                      .+||..+|++...|..|..+.                              ..|+......|+..+|++..
T Consensus        18 ~~lA~~~gis~~~i~~~e~g~------------------------------~~~~~~~l~~i~~~l~~~~~   58 (66)
T 2xi8_A           18 SELAALLEVSRQTINGIEKNK------------------------------YNPSLQLALKIAYYLNTPLE   58 (66)
T ss_dssp             HHHHHHHTSCHHHHHHHHTTS------------------------------CCCCHHHHHHHHHHTTSCHH
T ss_pred             HHHHHHHCcCHHHHHHHHcCC------------------------------CCCCHHHHHHHHHHHCcCHH
Confidence            569999999999999998661                              22455566677777777664

>2r1j_L Repressor protein C2; protein-DNA complex, helix-turn-helix, DNA-binding, transcription, transcription regulation; 1.53A {Enterobacteria phage P22} SCOP: a.35.1.2 PDB: 3jxb_C 3jxc_L 3jxd_L

Probab=89.34  E-value=0.79  Score=26.72  Aligned_cols=42  Identities=10%  Similarity=0.204  Sum_probs=30.9

Q ss_pred             HHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChh
Q psy10486         51 RWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTER  122 (183)
Q Consensus        51 ~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~  122 (183)
                      ..+||..+|++...|..|..+                              ...|+......|+..+|++..
T Consensus        21 ~~~lA~~~gis~~~i~~~e~g------------------------------~~~~~~~~l~~i~~~l~~~~~   62 (68)
T 2r1j_L           21 QAALGKMVGVSNVAISQWERS------------------------------ETEPNGENLLALSKALQCSPD   62 (68)
T ss_dssp             HHHHHHHHTSCHHHHHHHHTT------------------------------SSCCBHHHHHHHHHHTTSCHH
T ss_pred             HHHHHHHHCCCHHHHHHHHcC------------------------------CCCCCHHHHHHHHHHhCCCHH
Confidence            356999999999999999866                              222445566677888887764

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

Probab=89.31  E-value=0.55  Score=27.32  Aligned_cols=46  Identities=22%  Similarity=0.410  Sum_probs=32.2

Q ss_pred             CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486         25 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN   71 (183)
Q Consensus        25 r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~n   71 (183)
                      |..||++....+...+... ........++|..+||+...|..|...
T Consensus         3 r~~ys~efK~~~~~~~~~g-~s~~~~~~~vA~~~gIs~~tl~~W~~~   48 (59)
T 2glo_A            3 RRIFTPHFKLQVLESYRND-NDCKGNQRATARKYNIHRRQIQKWLQC   48 (59)
T ss_dssp             CCCCCHHHHHHHHHHHHHC-TTTTTCHHHHHHHTTSCHHHHHHHHTT
T ss_pred             CCcCCHHHHHHHHHHHHcC-CCcchHHHHHHHHHCcCHHHHHHHHHH
Confidence            5679998877665555443 221112457999999999999999754

>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=88.63  E-value=1  Score=26.91  Aligned_cols=41  Identities=10%  Similarity=0.197  Sum_probs=31.3

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTER  122 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~  122 (183)
                      .+||..+|++...|..|..+                              ...|+......||..+|++..
T Consensus        22 ~~lA~~~gis~~~i~~~e~g------------------------------~~~~~~~~l~~ia~~l~~~~~   62 (76)
T 1adr_A           22 AALGKMVGVSNVAISQWERS------------------------------ETEPNGENLLALSKALQCSPD   62 (76)
T ss_dssp             HHHHHHHTSCHHHHHHHHTT------------------------------SSCCCHHHHHHHHHHTTSCHH
T ss_pred             HHHHHHHCcCHHHHHHHHcC------------------------------CCCCCHHHHHHHHHHHCcCHH
Confidence            56999999999999999865                              223556667778888888764

>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3

Probab=88.31  E-value=1  Score=27.06  Aligned_cols=42  Identities=14%  Similarity=0.038  Sum_probs=31.8

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQ  123 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~  123 (183)
                      .+||..+|++...|..|..+                              ...|+......||..+|++...
T Consensus        27 ~~lA~~~gis~~~i~~~e~g------------------------------~~~~~~~~l~~la~~l~~~~~~   68 (77)
T 2b5a_A           27 EELADLAGLHRTYISEVERG------------------------------DRNISLINIHKICAALDIPAST   68 (77)
T ss_dssp             HHHHHHHTCCHHHHHHHHTT------------------------------CSCCBHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHCCCHHHHHHHHCC------------------------------CCCCCHHHHHHHHHHhCcCHHH
Confidence            56999999999999999865                              2235566777788888887654

>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3

Probab=88.04  E-value=1.1  Score=26.60  Aligned_cols=41  Identities=24%  Similarity=-0.006  Sum_probs=30.0

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTER  122 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~  122 (183)
                      .+||..+|++...|..|..++                              ..|+......|+..+|++..
T Consensus        30 ~~lA~~~gis~~~i~~~e~g~------------------------------~~~~~~~l~~l~~~l~~~~~   70 (74)
T 1y7y_A           30 ETLAFLSGLDRSYVGGVERGQ------------------------------RNVSLVNILKLATALDIEPR   70 (74)
T ss_dssp             HHHHHHHTCCHHHHHHHHTTC------------------------------SCCBHHHHHHHHHHTTSCGG
T ss_pred             HHHHHHHCcCHHHHHHHHCCC------------------------------CCCCHHHHHHHHHHhCcCHH
Confidence            569999999999999888661                              23455566677777777664

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656}

Probab=87.69  E-value=1.2  Score=28.14  Aligned_cols=41  Identities=20%  Similarity=0.274  Sum_probs=33.2

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTER  122 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~  122 (183)
                      .+||..+|++...|..|..+                              ...|+......||..+|++..
T Consensus        26 ~~lA~~~gis~~~is~~e~G------------------------------~~~p~~~~l~~ia~~l~v~~~   66 (94)
T 2kpj_A           26 LEIAKSIGVSPQTFNTWCKG------------------------------IAIPRMGKVQALADYFNINKS   66 (94)
T ss_dssp             HHHHHHHTCCHHHHHHHHTT------------------------------SCCCCHHHHHHHHHHHTCCTH
T ss_pred             HHHHHHHCcCHHHHHHHHhC------------------------------CCCCCHHHHHHHHHHHCcCHH
Confidence            56999999999999999866                              233566778889999999874

>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1}

Probab=87.27  E-value=1.4  Score=26.51  Aligned_cols=43  Identities=12%  Similarity=0.074  Sum_probs=32.3

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQ  123 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~  123 (183)
                      .+||..+|++...|..|..+++                             ..|+......||..+|++...
T Consensus        24 ~~lA~~~gis~~~i~~~e~g~~-----------------------------~~~~~~~l~~ia~~l~~~~~~   66 (78)
T 3b7h_A           24 NRVATLAGLNQSTVNAMFEGRS-----------------------------KRPTITTIRKVCGTLGISVHD   66 (78)
T ss_dssp             HHHHHHHTCCHHHHHHHHCTTC-----------------------------CCCCHHHHHHHHHHHTCCHHH
T ss_pred             HHHHHHHCcCHHHHHHHHcCCC-----------------------------CCCCHHHHHHHHHHcCCCHHH
Confidence            5699999999999999986611                             135666777888888887643

>3f6w_A XRE-family like protein; helix-turn-helix, DNA binding protein, xenobiotic response E family of transcriptional regulators; HET: MSE BTB; 1.85A {Pseudomonas syringae PV}

Probab=86.64  E-value=1.6  Score=26.71  Aligned_cols=43  Identities=14%  Similarity=-0.004  Sum_probs=32.7

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhH
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQV  124 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V  124 (183)
                      .+||..+|++...|..|-.+                              ...|+......||..+|++...+
T Consensus        31 ~elA~~~gis~~~is~~e~g------------------------------~~~~~~~~l~~l~~~l~~~~~~l   73 (83)
T 3f6w_A           31 KELAARLGRPQSFVSKTENA------------------------------ERRLDVIEFMDFCRGIGTDPYAL   73 (83)
T ss_dssp             HHHHHHHTSCHHHHHHHHTT------------------------------SSCCCHHHHHHHHHHHTCCHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHCC------------------------------CCCCCHHHHHHHHHHcCCCHHHH
Confidence            56899999999999888866                              22356677788888888887543

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

Probab=85.75  E-value=2.5  Score=26.53  Aligned_cols=45  Identities=13%  Similarity=0.286  Sum_probs=33.1

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486         22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN   71 (183)
Q Consensus        22 rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~n   71 (183)
                      ++.+..|+.++.......+...  .+   ..++|..+||+...|..|...
T Consensus        17 ~~~~~~ys~e~k~~~v~~~~~g--~s---~~~iA~~~gIs~sTl~rW~k~   61 (87)
T 2elh_A           17 KRPLRSLTPRDKIHAIQRIHDG--ES---KASVARDIGVPESTLRGWCKN   61 (87)
T ss_dssp             SSCCSSCCHHHHHHHHHHHHHT--CC---HHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHCC--CC---HHHHHHHHCcCHHHHHHHHHH
Confidence            4556789999866665666432  22   347899999999999999865

>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}

Probab=85.62  E-value=1.6  Score=26.33  Aligned_cols=43  Identities=14%  Similarity=0.000  Sum_probs=31.8

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhH
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQV  124 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V  124 (183)
                      .+||..+|++...|..|-.+                              ...|+......||..+|++...+
T Consensus        19 ~~lA~~~gis~~~i~~~e~g------------------------------~~~p~~~~l~~ia~~l~v~~~~l   61 (77)
T 2k9q_A           19 KSVAEEMGISRQQLCNIEQS------------------------------ETAPVVVKYIAFLRSKGVDLNAL   61 (77)
T ss_dssp             HHHHHHHTSCHHHHHHHHTC------------------------------CSCCHHHHHHHHHHHTTCCHHHH
T ss_pred             HHHHHHhCCCHHHHHHHHcC------------------------------CCCCCHHHHHHHHHHhCcCHHHH
Confidence            56999999999999888865                              12245566777888888887654

>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor}

Probab=85.51  E-value=2.2  Score=25.05  Aligned_cols=42  Identities=14%  Similarity=0.041  Sum_probs=30.8

Q ss_pred             HHHHHHcC--CChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhh
Q psy10486         52 WELARSLM--LTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQ  123 (183)
Q Consensus        52 ~~La~~l~--l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~  123 (183)
                      .+||..+|  ++...|..|-.+                              ...|+......||..+|++...
T Consensus        25 ~~lA~~~g~~is~~~i~~~e~g------------------------------~~~~~~~~l~~la~~l~v~~~~   68 (71)
T 2ewt_A           25 HGVEEKSQGRWKAVVVGSYERG------------------------------DRAVTVQRLAELADFYGVPVQE   68 (71)
T ss_dssp             HHHHHHTTTSSCHHHHHHHHHT------------------------------CSCCCHHHHHHHHHHHTSCGGG
T ss_pred             HHHHHHHCCcCCHHHHHHHHCC------------------------------CCCCCHHHHHHHHHHHCcCHHH
Confidence            46899999  888888888865                              2235666777788888877643

>3s8q_A R-M controller protein; protein-DNA complex, helix-turn-helix; HET: DNA; 2.10A {Enterobacter SP} SCOP: a.35.1.0 PDB: 3clc_A* 3ufd_A*

Probab=85.10  E-value=1.8  Score=26.36  Aligned_cols=42  Identities=12%  Similarity=0.016  Sum_probs=32.1

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQ  123 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~  123 (183)
                      .+||..+|++...|..|-.+                              ...|+......||..+|++...
T Consensus        28 ~~lA~~~gis~~~i~~~e~g------------------------------~~~~~~~~l~~ia~~l~v~~~~   69 (82)
T 3s8q_A           28 EDLAYKSNLDRTYISGIERN------------------------------SRNLTIKSLELIMKGLEVSDVV   69 (82)
T ss_dssp             HHHHHHHTCCHHHHHHHHTT------------------------------CCCCBHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHhCcCHHHHHHHHCC------------------------------CCCCCHHHHHHHHHHHCcCHHH
Confidence            46899999999999888866                              2245667778888888888753

>1lmb_3 Protein (lambda repressor); protein-DNA complex, double helix, transcription/DNA complex; HET: DNA; 1.80A {Enterobacteria phage lambda} SCOP: a.35.1.2 PDB: 1lrp_A 1rio_A 1lli_A*

Probab=84.61  E-value=2  Score=26.78  Aligned_cols=42  Identities=14%  Similarity=0.104  Sum_probs=31.0

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQ  123 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~  123 (183)
                      .+||..+|++...|..|..+                              ...|+......||..+|++...
T Consensus        34 ~~lA~~~gis~~~is~~e~g------------------------------~~~~~~~~l~~ia~~l~v~~~~   75 (92)
T 1lmb_3           34 ESVADKMGMGQSGVGALFNG------------------------------INALNAYNAALLAKILKVSVEE   75 (92)
T ss_dssp             HHHHHHHTSCHHHHHHHHTT------------------------------SSCCCHHHHHHHHHHHTSCGGG
T ss_pred             HHHHHHHCcCHHHHHHHHcC------------------------------CCCCCHHHHHHHHHHHCCCHHH
Confidence            56999999999999988866                              1235556667777777777654

>2ict_A Antitoxin HIGA; helix-turn-helix, structural genomics, PSI-2, protein struct initiative, northeast structural genomics consortium, NESG; 1.63A {Escherichia coli} SCOP: a.35.1.3 PDB: 2icp_A

Probab=83.92  E-value=2.6  Score=26.45  Aligned_cols=45  Identities=13%  Similarity=0.292  Sum_probs=35.3

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQ  129 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~  129 (183)
                      .+||..+|++...|..|..+                              ...|+......|+..+|++.   .+||.
T Consensus        25 ~~lA~~~gis~~~is~~e~g------------------------------~~~~~~~~~~~i~~~l~v~~---~~~l~   69 (94)
T 2ict_A           25 REFARAMEIAPSTASRLLTG------------------------------KAALTPEMAIKLSVVIGSSP---QMWLN   69 (94)
T ss_dssp             HHHHHHHTCCHHHHHHHHHT------------------------------SSCCCHHHHHHHHHHTCSCH---HHHHH
T ss_pred             HHHHHHhCCCHHHHHHHHcC------------------------------CCCCCHHHHHHHHHHHCcCH---HHHHH
Confidence            57999999999999999866                              22356667788899999876   46774

>3op9_A PLI0006 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, transcription regulat; HET: MSE; 1.90A {Listeria innocua}

Probab=83.11  E-value=2.5  Score=27.65  Aligned_cols=20  Identities=20%  Similarity=0.355  Sum_probs=17.6

Q ss_pred             HHHHHHcCCChhhhhhhhhh
Q psy10486         52 WELARSLMLTERQVKIWFQN   71 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~n   71 (183)
                      .+||..+|++...|..|-.+
T Consensus        26 ~~lA~~~gis~~~i~~~e~g   45 (114)
T 3op9_A           26 HQIAELLNVQTRTVAYYMSG   45 (114)
T ss_dssp             HHHHHHHTSCHHHHHHHHHT
T ss_pred             HHHHHHHCcCHHHHHHHHcC
Confidence            56999999999999999876

>2ofy_A Putative XRE-family transcriptional regulator; transcription regulator, structural genomics, PS protein structure initiative; 1.70A {Rhodococcus SP} SCOP: a.35.1.3

Probab=82.75  E-value=2.6  Score=25.90  Aligned_cols=44  Identities=14%  Similarity=-0.093  Sum_probs=33.4

Q ss_pred             HHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhh
Q psy10486         51 RWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQ  123 (183)
Q Consensus        51 ~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~  123 (183)
                      ..+||..+|++...|..|-.+++                             ..|+......||..+|++...
T Consensus        30 q~~lA~~~gis~~~is~~E~g~~-----------------------------~~p~~~~l~~ia~~l~v~~~~   73 (86)
T 2ofy_A           30 MVTVAFDAGISVETLRKIETGRI-----------------------------ATPAFFTIAAVARVLDLSLDD   73 (86)
T ss_dssp             HHHHHHHHTCCHHHHHHHHTTCC-----------------------------SSCBHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHhCCCHHHHHHHHcCCC-----------------------------CCCCHHHHHHHHHHhCCCHHH
Confidence            45899999999999998886611                             146667778889999888643

>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=82.64  E-value=3  Score=22.18  Aligned_cols=41  Identities=20%  Similarity=0.369  Sum_probs=29.8

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486         26 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN   71 (183)
Q Consensus        26 ~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~n   71 (183)
                      ..+++++...+...+...  .+   ..+||..||++...|..|...
T Consensus         4 ~~l~~~~~~~i~~~~~~g--~s---~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C            4 SALSDTERAQLDVMKLLN--VS---LHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             CCCCHHHHHHHHHHHHTT--CC---HHHHHHHHTCCHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHcC--CC---HHHHHHHHCcCHHHHHHHHhh
Confidence            357787776666666433  23   457999999999999999865

>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A

Probab=82.57  E-value=2.5  Score=27.20  Aligned_cols=43  Identities=12%  Similarity=0.017  Sum_probs=32.6

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhH
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQV  124 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V  124 (183)
                      .+||..+|++...|..|-.+                              ...|+......||..+|++...+
T Consensus        45 ~elA~~~gis~~~is~iE~G------------------------------~~~ps~~~l~~ia~~l~v~~~~l   87 (99)
T 3g5g_A           45 EDLAYKSNLDRTYISGIERN------------------------------SRNLTIKSLELIMKGLEVSDVVF   87 (99)
T ss_dssp             HHHHHHHTCCHHHHHHHHTT------------------------------CSCCBHHHHHHHHHHTTCCHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHCC------------------------------CCCCCHHHHHHHHHHHCcCHHHH
Confidence            56899999999888888765                              23466677888888888877543

>1iuf_A Centromere ABP1 protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; NMR {Schizosaccharomyces pombe} SCOP: a.4.1.7 a.4.1.7

Probab=82.14  E-value=6.1  Score=27.27  Aligned_cols=80  Identities=16%  Similarity=0.120  Sum_probs=51.5

Q ss_pred             CCCCCCCCHHHHHHHHHHh-hhcCCCCHHHHHHHHH-Hc--CCChhhhhhhhhhcccc----c--cccccccCCCCChhH
Q psy10486         22 RKKRKPYSKHQTLELEKEF-LYNAYVSKQKRWELAR-SL--MLTERQVKIWFQNIEWT----G--QVTVRKKRKPYSKHQ   91 (183)
Q Consensus        22 rr~r~~ft~~Ql~~Le~~F-~~~~~p~~~~~~~La~-~l--~l~~~qV~~WF~nrr~k----~--~~~~rr~r~~~t~~q   91 (183)
                      +++|..+|.+|...+...+ +.++-.+..+....|. .+  +++...|..|..++..-    .  ....++.+....++-
T Consensus         6 ~~~R~~lT~~qK~~i~~~~~~~~~~~~q~~la~wa~~~f~~~is~stis~ilk~k~~~l~~~~~~~~~~kr~r~~~~~~l   85 (144)
T 1iuf_A            6 KIKRRAITEHEKRALRHYFFQLQNRSGQQDLIEWFREKFGKDISQPSVSQILSSKYSYLDNTVEKPWDVKRNRPPKYPLL   85 (144)
T ss_dssp             CCSSSCCCSHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHSSCCSSSSTTHHHHHHHHHTTTSCSSSSSSSCCCCCSCHHH
T ss_pred             CCcCccCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHCCCCcHHHHHHHHhhHHHHhhhcccccccccCCCCCCCHHH
Confidence            5788999999999999999 7777777655444322 67  78888899998875321    0  112233344444554


Q ss_pred             HHHHHHcccc
Q psy10486         92 TLELEKEFLY  101 (183)
Q Consensus        92 ~~~Le~~F~~  101 (183)
                      -..|...|..
T Consensus        86 e~~L~~Wi~~   95 (144)
T 1iuf_A           86 EAALFEWQVQ   95 (144)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            4555555543

>3lfp_A CSP231I C protein; transcriptional regulator, DNA binding protein, helix-turn-H restriction-modification, transcription; 2.00A {Citrobacter SP} PDB: 3lis_A

Probab=81.57  E-value=3.5  Score=26.13  Aligned_cols=21  Identities=10%  Similarity=0.045  Sum_probs=17.7

Q ss_pred             HHHHHHHcCCChhh----hhhhhhh
Q psy10486         51 RWELARSLMLTERQ----VKIWFQN   71 (183)
Q Consensus        51 ~~~La~~l~l~~~q----V~~WF~n   71 (183)
                      ..+||..+|++...    |..|-.+
T Consensus        17 q~~lA~~~gis~~~~~~~is~~E~g   41 (98)
T 3lfp_A           17 QEKLGVLAGIDEASASARMNQYEKG   41 (98)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHhCCCcchhhhHHHHHHCC
Confidence            35799999999998    8888866

>3ivp_A Putative transposon-related DNA-binding protein; APC62618, clostridium diffic structural genomics, PSI-2, protein structure initiative; HET: PG4; 2.02A {Clostridium difficile}

Probab=80.98  E-value=3.1  Score=27.76  Aligned_cols=20  Identities=5%  Similarity=-0.019  Sum_probs=17.9

Q ss_pred             HHHHHHcCCChhhhhhhhhh
Q psy10486         52 WELARSLMLTERQVKIWFQN   71 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~n   71 (183)
                      .+||..+|++...|..|-.+
T Consensus        29 ~~lA~~~gis~~~is~~E~g   48 (126)
T 3ivp_A           29 EQVGAMIEIDPRYLTNIENK   48 (126)
T ss_dssp             HHHHHHHTCCHHHHHHHHHS
T ss_pred             HHHHHHhCcCHHHHHHHHCC
Confidence            56999999999999999977

>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=80.82  E-value=3.1  Score=27.91  Aligned_cols=49  Identities=20%  Similarity=0.259  Sum_probs=36.2

Q ss_pred             cCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhH
Q psy10486         83 KRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMK  134 (183)
Q Consensus        83 ~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k  134 (183)
                      ++..+|.++...+-..+..+..+..   .++|..+|++...|..|..++...
T Consensus         4 ~r~~~t~e~K~~iv~~~~~~g~~~~---~~~A~~~gvs~stl~~~~~~~~~~   52 (131)
T 1hlv_A            4 KRRQLTFREKSRIIQEVEENPDLRK---GEIARRFNIPPSTLSTILKNKRAI   52 (131)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSCH---HHHHHHHTCCHHHHHHHHHTHHHH
T ss_pred             cceeCCHHHHHHHHHHHHHCCCCcH---HHHHHHhCCCHHHHHHHHhchhhh
Confidence            4678999988777666644444443   367899999999999999765543

>3vk0_A NHTF, transcriptional regulator; HTH motif, XRE transcription factor, DNA binding protein; 1.88A {Neisseria meningitidis}

Probab=80.44  E-value=3.5  Score=27.05  Aligned_cols=42  Identities=21%  Similarity=0.074  Sum_probs=33.1

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQ  123 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~  123 (183)
                      .+||..+|++...|..|-.+                              ...|+......||..+|++...
T Consensus        38 ~elA~~~gis~~~is~~E~G------------------------------~~~p~~~~l~~ia~~l~v~~~~   79 (114)
T 3vk0_A           38 EELARQCGLDRTYVSAVERK------------------------------RWNIALSNIEKMAAALGVAAYQ   79 (114)
T ss_dssp             HHHHHHHTCCHHHHHHHTTT------------------------------CCCCCHHHHHHHHHHHTSCHHH
T ss_pred             HHHHHHHCcCHHHHHHHHcC------------------------------CCCCCHHHHHHHHHHhCCCHHH
Confidence            56999999999999988866                              2236677888899999988753

>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis}

Probab=80.27  E-value=3.4  Score=25.11  Aligned_cols=43  Identities=16%  Similarity=0.028  Sum_probs=32.1

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQ  123 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~  123 (183)
                      .+||..+|++...|..|-.+.                             ...|+......||..+|++...
T Consensus        27 ~elA~~~gis~~~is~~E~G~-----------------------------~~~p~~~~l~~ia~~l~v~~~~   69 (78)
T 3qq6_A           27 SELAEKAGVAKSYLSSIERNL-----------------------------QTNPSIQFLEKVSAVLDVSVHT   69 (78)
T ss_dssp             HHHHHHHTCCHHHHHHHHTTS-----------------------------CCCCBHHHHHHHHHHHTCCHHH
T ss_pred             HHHHHHHCcCHHHHHHHHcCC-----------------------------CCCCCHHHHHHHHHHHCcCHHH
Confidence            468999999998888887551                             1236667788889999987643

>2eby_A Putative HTH-type transcriptional regulator YBAQ; hypothetical protein, JW0472, structural genomics, NPPSFA; 2.25A {Escherichia coli}

Probab=80.12  E-value=3.8  Score=26.66  Aligned_cols=20  Identities=30%  Similarity=0.290  Sum_probs=17.6

Q ss_pred             HHHHHHcCCChhhhhhhhhh
Q psy10486         52 WELARSLMLTERQVKIWFQN   71 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~n   71 (183)
                      .+||..+|++...|..|..+
T Consensus        28 ~~lA~~~gis~~~is~~e~g   47 (113)
T 2eby_A           28 NELAELLHVHRNSVSALINN   47 (113)
T ss_dssp             HHHHHHHTSCHHHHHHHHTT
T ss_pred             HHHHHHHCcCHHHHHHHHcC
Confidence            56999999999999999866

---

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	183
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	8e-19
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	2e-14
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	3e-18
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	5e-14
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	2e-17
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	4e-13
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	3e-17
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	7e-13
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	5e-17
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	6e-13
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	2e-16
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	4e-13
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	7e-16
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	1e-10
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	2e-15
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	1e-10
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	3e-15
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	3e-11
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	1e-14
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	8e-12
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	2e-14
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	8e-11
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	2e-14
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	2e-14
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	1e-12
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	3e-14
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	1e-11
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	3e-14
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	3e-10
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	7e-14
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	2e-10
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	1e-13
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	2e-10
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	1e-13
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	2e-09
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	1e-13
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	2e-10
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	2e-13
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	2e-09
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	3e-13
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	2e-09
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	3e-13
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	1e-09
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	6e-13
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	5e-09
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	8e-13
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	7e-08
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	9e-13
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	2e-08
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	2e-12
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	3e-09
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	9e-12
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	3e-08
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	2e-10
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	4e-07
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	6e-10
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	7e-07
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	1e-08
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	2e-08
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	2e-05
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	3e-07
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	4e-04

>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 = 74.5 bits (183), Expect = 8e-19
 Identities = 45/70 (64%), Positives = 56/70 (80%)

Query: 74  WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133
           W    + RKKR PY+KHQTLELEKEFL+N Y+++ +R+E+AR L LTERQVKIWFQNRRM
Sbjct: 7   WLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRM 66

Query: 134 KNKKNTQRQA 143
           K KK  + +A
Sbjct: 67  KMKKINKDRA 76

>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 = 62.5 bits (152), Expect = 2e-14
 Identities = 38/63 (60%), Positives = 49/63 (77%)

Query: 9  SSSTLEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIW 68
          ++    W    + RKKR PY+KHQTLELEKEFL+N Y+++ +R+E+AR L LTERQVKIW
Sbjct: 1  NNPAANWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIW 60

Query: 69 FQN 71
          FQN
Sbjct: 61 FQN 63

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 56

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

 Score = 72.1 bits (177), Expect = 3e-18
 Identities = 34/54 (62%), Positives = 47/54 (87%)

Query: 84  RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           R+ Y+++QTLELEKEF +N Y+++++R E+A +L LTERQ+KIWFQNRRMK KK
Sbjct: 1   RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 54

>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 = 61.3 bits (149), Expect = 5e-14
 Identities = 28/47 (59%), Positives = 41/47 (87%)

Query: 25 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          R+ Y+++QTLELEKEF +N Y+++++R E+A +L LTERQ+KIWFQN
Sbjct: 1  RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQN 47

>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 = 70.6 bits (173), Expect = 2e-17
 Identities = 19/65 (29%), Positives = 34/65 (52%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           ++ R  +++ Q   LEKEF    Y     R  LA  + L E ++++WF NRR K ++  +
Sbjct: 2   QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 61

Query: 141 RQAAQ 145
            +  +
Sbjct: 62  LRNQR 66

>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 = 59.4 bits (144), Expect = 4e-13
 Identities = 16/50 (32%), Positives = 26/50 (52%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          ++ R  +++ Q   LEKEF    Y     R  LA  + L E ++++WF N
Sbjct: 2  QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSN 51

>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 = 69.5 bits (170), Expect = 3e-17
 Identities = 31/57 (54%), Positives = 43/57 (75%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           RKKR PYSK Q  ELE+E+  N +++K KR +++ +  L+ERQ+ IWFQNRR+K KK
Sbjct: 2   RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 58

>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 = 58.3 bits (141), Expect = 7e-13
 Identities = 26/50 (52%), Positives = 37/50 (74%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          RKKR PYSK Q  ELE+E+  N +++K KR +++ +  L+ERQ+ IWFQN
Sbjct: 2  RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQN 51

>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 = 69.1 bits (169), Expect = 5e-17
 Identities = 27/57 (47%), Positives = 38/57 (66%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           +  +  +S  QT+ELEK+F    Y+S  +R  LA+ L L+ERQVK WFQNRR K ++
Sbjct: 1   KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 57

>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 = 58.7 bits (142), Expect = 6e-13
 Identities = 24/50 (48%), Positives = 33/50 (66%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          +  +  +S  QT+ELEK+F    Y+S  +R  LA+ L L+ERQVK WFQN
Sbjct: 1  KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQN 50

>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 = 67.6 bits (165), Expect = 2e-16
 Identities = 22/53 (41%), Positives = 34/53 (64%)

Query: 82  KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMK 134
           + R  +S  Q   L++EF  N Y+++++R +L+  L L E Q+KIWFQN R K
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>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 = 59.1 bits (143), Expect = 4e-13
 Identities = 20/49 (40%), Positives = 32/49 (65%)

Query: 23 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          + R  +S  Q   L++EF  N Y+++++R +L+  L L E Q+KIWFQN
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQN 49

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 68

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

 Score = 66.5 bits (162), Expect = 7e-16
 Identities = 30/65 (46%), Positives = 40/65 (61%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           RK+R  +S+ Q  ELE+ F    Y+S  +R  LA  + LT  QVKIWFQN R K K+  +
Sbjct: 3   RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62

Query: 141 RQAAQ 145
            +AAQ
Sbjct: 63  DKAAQ 67

>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 = 52.6 bits (126), Expect = 1e-10
 Identities = 24/50 (48%), Positives = 31/50 (62%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          RK+R  +S+ Q  ELE+ F    Y+S  +R  LA  + LT  QVKIWFQN
Sbjct: 3  RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQN 52

>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 = 65.7 bits (160), Expect = 2e-15
 Identities = 23/66 (34%), Positives = 38/66 (57%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           R+ R  ++  Q  ELE+ FL   Y++  +  +L+  L L   QVKIWF+NRR ++K  + 
Sbjct: 2   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 61

Query: 141 RQAAQA 146
           +   Q+
Sbjct: 62  QHKDQS 67

>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 = 53.0 bits (127), Expect = 1e-10
 Identities = 19/50 (38%), Positives = 29/50 (58%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          R+ R  ++  Q  ELE+ FL   Y++  +  +L+  L L   QVKIWF+N
Sbjct: 2  RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKN 51

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

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

 Score = 64.6 bits (157), Expect = 3e-15
 Identities = 30/57 (52%), Positives = 38/57 (66%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           RK R P++  Q L LE++F    Y+S  +R E + SL LTE QVKIWFQNRR K K+
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>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 = 54.2 bits (130), Expect = 3e-11
 Identities = 26/50 (52%), Positives = 33/50 (66%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          RK R P++  Q L LE++F    Y+S  +R E + SL LTE QVKIWFQN
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQN 50

>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 = 63.2 bits (154), Expect = 1e-14
 Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 3/60 (5%)

Query: 81  RKKRKPYSKHQTLELEKEF---LYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           + KR    KH T  +       + + Y ++ ++ ++A    LT  QV  WF N R +  +
Sbjct: 3   KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQ 62

>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 = 8e-12
 Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 3/53 (5%)

Query: 22 RKKRKPYSKHQTLELEKEF---LYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          + KR    KH T  +       + + Y ++ ++ ++A    LT  QV  WF N
Sbjct: 3  KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFIN 55

>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 = 62.9 bits (153), Expect = 2e-14
 Identities = 15/59 (25%), Positives = 28/59 (47%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT 139
            + R   ++ Q   L   +  N       + +L     L+ R +++WFQN+R K+KK +
Sbjct: 4   TRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS 62

>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 = 53.3 bits (128), Expect = 8e-11
 Identities = 11/50 (22%), Positives = 21/50 (42%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
           + R   ++ Q   L   +  N       + +L     L+ R +++WFQN
Sbjct: 4  TRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQN 53

>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 = 63.1 bits (153), Expect = 2e-14
 Identities = 21/82 (25%), Positives = 29/82 (35%), Gaps = 15/82 (18%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELAR---------------SLMLTERQVK 125
           R  R  + K     +E  F  N Y  + KR E+A                   +T  +V 
Sbjct: 1   RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVY 60

Query: 126 IWFQNRRMKNKKNTQRQAAQAS 147
            WF NRR + K+     A   S
Sbjct: 61  NWFANRRKEIKRRANIAAILES 82

>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 = 62.2 bits (151), Expect = 2e-14
 Identities = 13/49 (26%), Positives = 21/49 (42%)

Query: 84  RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRR 132
           R  ++  Q   L   F  N   SK+ +  +++ L L    V  +F N R
Sbjct: 2   RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>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 = 57.2 bits (138), Expect = 1e-12
 Identities = 12/47 (25%), Positives = 20/47 (42%)

Query: 25 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          R  ++  Q   L   F  N   SK+ +  +++ L L    V  +F N
Sbjct: 2  RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMN 48

>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 = 62.7 bits (152), Expect = 3e-14
 Identities = 32/67 (47%), Positives = 42/67 (62%)

Query: 71  NIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 130
            +   G  +    R  ++  Q  ELEKEF +N Y+S+ +R E+A +L L E QVKIWFQN
Sbjct: 18  KVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQN 77

Query: 131 RRMKNKK 137
           RRMK KK
Sbjct: 78  RRMKQKK 84

>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 = 56.2 bits (135), Expect = 1e-11
 Identities = 27/71 (38%), Positives = 39/71 (54%)

Query: 1  MSSMNVNSSSSTLEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLML 60
          M        ++ +   G  +    R  ++  Q  ELEKEF +N Y+S+ +R E+A +L L
Sbjct: 7  MKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLEL 66

Query: 61 TERQVKIWFQN 71
           E QVKIWFQN
Sbjct: 67 NETQVKIWFQN 77

>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 = 61.8 bits (150), Expect = 3e-14
 Identities = 27/56 (48%), Positives = 37/56 (66%)

Query: 82  KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           + R  +++ Q   LEKEF    YVS+ +R ELA  L L E  +K+WFQNRRMK+K+
Sbjct: 1   RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 56

>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 = 51.4 bits (123), Expect = 3e-10
 Identities = 22/49 (44%), Positives = 30/49 (61%)

Query: 23 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          + R  +++ Q   LEKEF    YVS+ +R ELA  L L E  +K+WFQN
Sbjct: 1  RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQN 49

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 58

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

 Score = 61.1 bits (148), Expect = 7e-14
 Identities = 18/56 (32%), Positives = 29/56 (51%)

Query: 82  KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           K+R   S      LE+ F  ++  S Q+   +A  L L +  V++WF NRR + K+
Sbjct: 1   KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 56

>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 = 51.8 bits (124), Expect = 2e-10
 Identities = 15/49 (30%), Positives = 24/49 (48%)

Query: 23 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          K+R   S      LE+ F  ++  S Q+   +A  L L +  V++WF N
Sbjct: 1  KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCN 49

>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 = 60.7 bits (147), Expect = 1e-13
 Identities = 22/57 (38%), Positives = 33/57 (57%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           R++R  ++  Q  +LE  F  N Y     R E+A    LTE +V++WF+NRR K +K
Sbjct: 2   RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 58

>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 = 51.9 bits (124), Expect = 2e-10
 Identities = 18/50 (36%), Positives = 28/50 (56%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          R++R  ++  Q  +LE  F  N Y     R E+A    LTE +V++WF+N
Sbjct: 2  RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKN 51

>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 = 60.1 bits (146), Expect = 1e-13
 Identities = 12/52 (23%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 88  SKHQTLELEKEFL-YNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138
           +      LEK F     +  +++   L++ L    R ++ WF+ RR + K +
Sbjct: 1   TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPS 52

>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 = 49.3 bits (118), Expect = 2e-09
 Identities = 9/44 (20%), Positives = 19/44 (43%), Gaps = 1/44 (2%)

Query: 29 SKHQTLELEKEFL-YNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          +      LEK F     +  +++   L++ L    R ++ WF+ 
Sbjct: 1  TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQ 44

>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 = 60.2 bits (146), Expect = 1e-13
 Identities = 14/56 (25%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 82  KKRKPYSKHQTLELEKEFL-YNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK 136
           K            LEK F+    Y  +++   L++ L  + R+++ WF++RR ++K
Sbjct: 3   KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 59

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

 Score = 52.1 bits (125), Expect = 2e-10
 Identities = 11/50 (22%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 23 KKRKPYSKHQTLELEKEFL-YNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          K            LEK F+    Y  +++   L++ L  + R+++ WF++
Sbjct: 3  KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRH 52

>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 = 60.2 bits (146), Expect = 2e-13
 Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 3/60 (5%)

Query: 83  KRKPYSKHQTLELEKEF---LYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT 139
           +   ++K     LE  F   + N Y+  +    L ++  L+  Q+K W  NRR K K  T
Sbjct: 1   RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTIT 60

>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 = 49.4 bits (118), Expect = 2e-09
 Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 3/51 (5%)

Query: 24 KRKPYSKHQTLELEKEF---LYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          +   ++K     LE  F   + N Y+  +    L ++  L+  Q+K W  N
Sbjct: 1  RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSN 51

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 77

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

 Score = 60.1 bits (145), Expect = 3e-13
 Identities = 28/62 (45%), Positives = 37/62 (59%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           RK+R  ++K QT ELE+ F    Y+S  +R  LA  + LT  QVKIWFQN R K K+   
Sbjct: 10  RKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQN 69

Query: 141 RQ 142
            +
Sbjct: 70  EK 71

>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 = 49.7 bits (118), Expect = 2e-09
 Identities = 25/50 (50%), Positives = 32/50 (64%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          RK+R  ++K QT ELE+ F    Y+S  +R  LA  + LT  QVKIWFQN
Sbjct: 10 RKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQN 59

>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 = 59.5 bits (144), Expect = 3e-13
 Identities = 23/60 (38%), Positives = 33/60 (55%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
           R+ R  +S  Q  ELE+ F    Y     R ELA+   LTE ++++WFQNRR + +K   
Sbjct: 3   RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT 62

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

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

 Score = 50.3 bits (120), Expect = 1e-09
 Identities = 20/50 (40%), Positives = 28/50 (56%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          R+ R  +S  Q  ELE+ F    Y     R ELA+   LTE ++++WFQN
Sbjct: 3  RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQN 52

>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 = 58.8 bits (142), Expect = 6e-13
 Identities = 14/68 (20%), Positives = 26/68 (38%), Gaps = 1/68 (1%)

Query: 81  RKKRKPYSKHQTLELEKEF-LYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT 139
            +     ++ Q   LE  F   N +        +A    LTE Q + WF+ R  + +++ 
Sbjct: 2   SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 61

Query: 140 QRQAAQAS 147
              +   S
Sbjct: 62  GLPSECRS 69

>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 = 48.4 bits (115), Expect = 5e-09
 Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 1/51 (1%)

Query: 22 RKKRKPYSKHQTLELEKEF-LYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
           +     ++ Q   LE  F   N +        +A    LTE Q + WF+ 
Sbjct: 2  SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQ 52

>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 = 59.0 bits (142), Expect = 8e-13
 Identities = 14/72 (19%), Positives = 31/72 (43%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
            +K K  +  Q   L+  FL ++ ++ ++   L     LT R++  WF  ++       +
Sbjct: 5   PQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEE 64

Query: 141 RQAAQASNNNNT 152
           +     SN  ++
Sbjct: 65  KMEIDESNAGSS 76

>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 = 45.5 bits (107), Expect = 7e-08
 Identities = 12/50 (24%), Positives = 23/50 (46%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
           +K K  +  Q   L+  FL ++ ++ ++   L     LT R++  WF  
Sbjct: 5  PQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTE 54

>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 = 58.4 bits (141), Expect = 9e-13
 Identities = 24/70 (34%), Positives = 40/70 (57%), Gaps = 3/70 (4%)

Query: 81  RKKRKPYSKHQTLELEK---EFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           R+KR+ ++K  T  L +     L N Y S++ + ELA+   +T  QV  WF N+R++ KK
Sbjct: 2   RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61

Query: 138 NTQRQAAQAS 147
           N  +   +A+
Sbjct: 62  NIGKFQEEAN 71

>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 = 46.9 bits (111), Expect = 2e-08
 Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 3/53 (5%)

Query: 22 RKKRKPYSKHQTLELEK---EFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          R+KR+ ++K  T  L +     L N Y S++ + ELA+   +T  QV  WF N
Sbjct: 2  RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGN 54

>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 = 57.2 bits (138), Expect = 2e-12
 Identities = 15/53 (28%), Positives = 30/53 (56%)

Query: 84  RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK 136
           +   S      LE+ F     ++ +++ E+A+   +T  QV++WF N+RM++K
Sbjct: 1   KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53

>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 = 48.7 bits (116), Expect = 3e-09
 Identities = 12/47 (25%), Positives = 24/47 (51%)

Query: 25 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          +   S      LE+ F     ++ +++ E+A+   +T  QV++WF N
Sbjct: 1  KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFIN 47

>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 = 55.8 bits (134), Expect = 9e-12
 Identities = 19/59 (32%), Positives = 29/59 (49%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT 139
           ++KR          LE  FL     S Q+   +A  L L +  V++WF NRR K K+++
Sbjct: 9   KRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRSS 67

>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 = 46.5 bits (110), Expect = 3e-08
 Identities = 15/50 (30%), Positives = 22/50 (44%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          ++KR          LE  FL     S Q+   +A  L L +  V++WF N
Sbjct: 9  KRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCN 58

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

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

 Score = 52.4 bits (125), Expect = 2e-10
 Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 1/59 (1%)

Query: 81  RKKRKPYSKHQTLELEKEFL-YNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138
            + R   S      L+        Y  ++    L+  L L +  +  +FQN+R   K +
Sbjct: 8   PRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS 66

>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 = 43.5 bits (102), Expect = 4e-07
 Identities = 10/51 (19%), Positives = 18/51 (35%), Gaps = 1/51 (1%)

Query: 22 RKKRKPYSKHQTLELEKEFL-YNAYVSKQKRWELARSLMLTERQVKIWFQN 71
           + R   S      L+        Y  ++    L+  L L +  +  +FQN
Sbjct: 8  PRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQN 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 = 50.7 bits (121), Expect = 6e-10
 Identities = 16/55 (29%), Positives = 28/55 (50%)

Query: 83  KRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137
           KR     +  + LEK F+ N   + +    +A  L + +  +++WF NRR K K+
Sbjct: 1   KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 55

>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 = 42.6 bits (100), Expect = 7e-07
 Identities = 12/48 (25%), Positives = 23/48 (47%)

Query: 24 KRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
          KR     +  + LEK F+ N   + +    +A  L + +  +++WF N
Sbjct: 1  KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSN 48

>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 = 1e-08
 Identities = 14/78 (17%), Positives = 24/78 (30%), Gaps = 21/78 (26%)

Query: 84  RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSL---------------------MLTER 122
           R  +       L + +      SK++R  L                         ++TE 
Sbjct: 1   RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 123 QVKIWFQNRRMKNKKNTQ 140
           +V  WF NRR +     +
Sbjct: 61  RVYNWFANRRKEEAFRHK 78

>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 = 47.3 bits (112), Expect = 2e-08
 Identities = 6/61 (9%), Positives = 17/61 (27%), Gaps = 4/61 (6%)

Query: 81  RKKRKPYSKHQTLELEKEFL----YNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK 136
           ++ R  ++  Q  ++                    +      +  + +KIW  N +    
Sbjct: 18  KRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGP 77

Query: 137 K 137
            
Sbjct: 78  S 78

>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 = 39.2 bits (91), Expect = 2e-05
 Identities = 9/68 (13%), Positives = 21/68 (30%), Gaps = 4/68 (5%)

Query: 8  SSSSTLEWTGQVTVRKKRKPYSKHQTLELEKEFL----YNAYVSKQKRWELARSLMLTER 63
           SS +   +   T ++ R  ++  Q  ++                    +      +  +
Sbjct: 4  GSSGSNPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQ 63

Query: 64 QVKIWFQN 71
           +KIW  N
Sbjct: 64 VLKIWMHN 71

>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 = 44.0 bits (103), Expect = 3e-07
 Identities = 12/62 (19%), Positives = 23/62 (37%)

Query: 81  RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140
               K  +K Q   L+  FL   +  ++   +L +   L   ++  WF + R   K    
Sbjct: 4   GSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQL 63

Query: 141 RQ 142
           + 
Sbjct: 64  KW 65

>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 = 35.5 bits (81), Expect = 4e-04
 Identities = 10/50 (20%), Positives = 20/50 (40%)

Query: 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71
              K  +K Q   L+  FL   +  ++   +L +   L   ++  WF +
Sbjct: 4  GSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGD 53

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	183
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.85
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.84
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.83
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.83
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.83
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.82
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.82
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.82
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.81
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.81
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.81
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.81
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.8
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.8
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.8
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.8
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.8
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.79
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.79
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.79
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.79
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.79
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.78
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.78
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.78
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.78
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.78
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.77
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.77
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.77
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.76
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.76
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.76
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.76
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.76
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.75
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.74
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.73
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.73
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.73
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.73
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.72
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.72
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.7
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.7
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.69
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.68
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.68
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.68
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.67
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.67
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.64
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.63
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.62
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.62
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.62
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.6
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.6
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.6
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.59
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.58
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.56
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.55
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.5
d1hlva1	66	DNA-binding domain of centromere binding protein B	93.35
d1hlva1	66	DNA-binding domain of centromere binding protein B	91.94
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	91.49
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	91.43
d1y7ya1	69	Restriction-modification controller protein C.AhdI	90.18
d1y9qa1	79	Probable transcriptional regulator VC1968, N-termi	90.05
d1b0na2	68	SinR repressor, DNA-binding domain {Bacillus subti	89.53
d2b5aa1	77	Regulatory protein C.BclI {Bacillus caldolyticus [	88.7
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	87.25
d2r1jl1	66	P22 C2 repressor, DNA-binding domain {Salmonella b	87.0
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	86.92
d2icta1	87	Antitoxin HigA {Escherichia coli [TaxId: 562]}	84.86
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	83.38
d1lmb3_	87	lambda C1 repressor, DNA-binding domain {Bacteriop	81.09
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	80.45

>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=99.85  E-value=5.5e-22  Score=119.63  Aligned_cols=57  Identities=46%  Similarity=0.715  Sum_probs=54.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccc
Q psy10486         21 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQ   77 (183)
Q Consensus        21 ~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~   77 (183)
                      ++++|+.||.+|+.+|+..|..++||+.+++++||..|||++.+|++||+|+|++.+
T Consensus         1 Grr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~k   57 (58)
T d2craa1           1 GRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK   57 (58)
T ss_dssp             CCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhcc
Confidence            478899999999999999999999999999999999999999999999999998765

>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=99.84  E-value=1.8e-21  Score=115.59  Aligned_cols=53  Identities=38%  Similarity=0.640  Sum_probs=51.3

Q ss_pred             CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccc
Q psy10486         23 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWT   75 (183)
Q Consensus        23 r~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k   75 (183)
                      |+|+.||++|+.+|+..|..++||+..++.+||..|||++++|++||+|||+|
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            57999999999999999999999999999999999999999999999999875

>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=99.83  E-value=2.9e-21  Score=116.80  Aligned_cols=57  Identities=46%  Similarity=0.671  Sum_probs=54.0

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        22 rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      ||+|+.||++|+.+|+..|..++||+..++.+||..|||++.+|++||+|+|++.++
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            578999999999999999999999999999999999999999999999999987653

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

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

Probab=99.83  E-value=4.7e-21  Score=121.99  Aligned_cols=65  Identities=58%  Similarity=0.939  Sum_probs=59.1

Q ss_pred             cCCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486         15 WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        15 ~~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~   79 (183)
                      .......+++|++||++|+.+|+..|..++||+..+++.||..|||++++|++||+|+|++.++.
T Consensus         7 ~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~   71 (77)
T d1pufa_           7 WLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKI   71 (77)
T ss_dssp             SCCCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCccCcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHH
Confidence            33445677889999999999999999999999999999999999999999999999999987653

>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=99.83  E-value=3.2e-21  Score=116.10  Aligned_cols=56  Identities=43%  Similarity=0.601  Sum_probs=53.3

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccc
Q psy10486         22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQ   77 (183)
Q Consensus        22 rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~   77 (183)
                      ++.|++||++|+.+|+..|..++||+.+++..||..|||++.+|++||+|+|++.+
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k~k   56 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR   56 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhhcc
Confidence            57899999999999999999999999999999999999999999999999998654

>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=99.82  E-value=7.6e-21  Score=121.16  Aligned_cols=65  Identities=38%  Similarity=0.506  Sum_probs=59.4

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         16 TGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        16 ~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      ..+.+.++.|+.||++|+.+|+..|..++||+..++++||..|||++.+|++||+|+|++.++..
T Consensus         4 g~p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   68 (77)
T d1vnda_           4 GLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ   68 (77)
T ss_dssp             CCSSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHh
Confidence            34467788899999999999999999999999999999999999999999999999999876544

>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=99.82  E-value=5e-21  Score=115.24  Aligned_cols=55  Identities=40%  Similarity=0.665  Sum_probs=52.8

Q ss_pred             CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccc
Q psy10486         23 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQ   77 (183)
Q Consensus        23 r~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~   77 (183)
                      |.|+.||++|+.+|+..|..++||+..++.+||..|||++.+|++||+|+|++.+
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~k   55 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDK   55 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhh
Confidence            5799999999999999999999999999999999999999999999999998765

>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=99.82  E-value=4.5e-21  Score=114.51  Aligned_cols=54  Identities=52%  Similarity=0.858  Sum_probs=51.7

Q ss_pred             CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         25 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        25 r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      ||.||++|+.+|+..|..++||+..++.+||..|||++++|++||+|||++.++
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk   54 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK   54 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhh
Confidence            799999999999999999999999999999999999999999999999987654

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

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

Probab=99.81  E-value=6.5e-21  Score=118.39  Aligned_cols=59  Identities=32%  Similarity=0.563  Sum_probs=55.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486         21 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        21 ~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~   79 (183)
                      ++|+|+.||++|+.+|+..|..++||+..++..||..|||++.+|++||+|+|++.++.
T Consensus         1 Prr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~   59 (67)
T d1zq3p1           1 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQ   59 (67)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhh
Confidence            46789999999999999999999999999999999999999999999999999987653

>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=99.81  E-value=5.5e-21  Score=124.73  Aligned_cols=64  Identities=41%  Similarity=0.607  Sum_probs=53.7

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486         16 TGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        16 ~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~   79 (183)
                      .+..+.++.|+.||++|+.+|+..|..++||+.+++++||..|||++++|++||+|+|++.++.
T Consensus        22 ~~~~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~   85 (88)
T d1b72a_          22 PGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKR   85 (88)
T ss_dssp             --------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHh
Confidence            3445668899999999999999999999999999999999999999999999999999987653

>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=99.81  E-value=1.4e-20  Score=116.28  Aligned_cols=59  Identities=34%  Similarity=0.446  Sum_probs=55.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         20 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        20 ~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      +.++.|+.||++|+.+|+..|..++||+..++..||..|||++.+|++||+|+|++.++
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk   59 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK   59 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHh
Confidence            46889999999999999999999999999999999999999999999999999988654

>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=99.81  E-value=1.1e-20  Score=113.85  Aligned_cols=57  Identities=54%  Similarity=0.881  Sum_probs=54.5

Q ss_pred             cccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486         81 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK  137 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk  137 (183)
                      ++.|+.||+.|+.+|+..|..++||+..++++||..+||++.+|++||+|||+|+||
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            567889999999999999999999999999999999999999999999999999875

>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=99.80  E-value=6.6e-20  Score=117.72  Aligned_cols=66  Identities=12%  Similarity=0.075  Sum_probs=58.0

Q ss_pred             cccCCCCCCCCCCCCCCHHHHHHHHHHhhh----cCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         13 LEWTGQVTVRKKRKPYSKHQTLELEKEFLY----NAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        13 ~~~~~~~~~rr~r~~ft~~Ql~~Le~~F~~----~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      .+.....+.+|.||.||.+|+++|++.|+.    ++||+.+++++||..|||+..+|++||+|+|++.+.
T Consensus         9 ~~~~~~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_           9 NPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCCCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            334444567889999999999999999987    799999999999999999999999999999987653

>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=99.80  E-value=1.8e-20  Score=116.67  Aligned_cols=58  Identities=28%  Similarity=0.409  Sum_probs=55.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         21 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        21 ~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      ++|.||.||++|+.+|+..|..++||+..+++.||..|||++.+|++||+|+|++.++
T Consensus         1 grR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr   58 (68)
T d2cuea1           1 GQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRR   58 (68)
T ss_dssp             SCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHh
Confidence            4678999999999999999999999999999999999999999999999999988664

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]}

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

Probab=99.80  E-value=3.3e-20  Score=110.71  Aligned_cols=55  Identities=62%  Similarity=1.010  Sum_probs=53.2

Q ss_pred             CCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486         84 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN  138 (183)
Q Consensus        84 r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~  138 (183)
                      |+.||+.|+.+|+..|..++||+..++.+||..|||++.+|++||+|||+|+|++
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            5789999999999999999999999999999999999999999999999999985

>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=99.80  E-value=4.6e-20  Score=111.45  Aligned_cols=57  Identities=53%  Similarity=0.805  Sum_probs=54.7

Q ss_pred             cccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486         81 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK  137 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk  137 (183)
                      +++|+.|++.|+.+|+..|..++||+..++.+||..+||++.+|++||+|+|+++||
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            356889999999999999999999999999999999999999999999999999987

>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=99.80  E-value=2.6e-20  Score=115.85  Aligned_cols=59  Identities=41%  Similarity=0.580  Sum_probs=55.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486         21 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        21 ~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~   79 (183)
                      .+|.|+.||+.|+.+|++.|..++||+..++.+||..|||++.+|++||+|+|.+.++.
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~   60 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ   60 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhc
Confidence            46889999999999999999999999999999999999999999999999999887653

>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=99.79  E-value=5.3e-20  Score=110.67  Aligned_cols=57  Identities=47%  Similarity=0.717  Sum_probs=54.5

Q ss_pred             cccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486         81 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK  137 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk  137 (183)
                      +++|+.||+.|+.+|+..|..++||+..+++.||..+||++.+|++||+|||+++||
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            356889999999999999999999999999999999999999999999999999986

>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=99.79  E-value=4.1e-20  Score=111.15  Aligned_cols=57  Identities=47%  Similarity=0.799  Sum_probs=54.4

Q ss_pred             ccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486         82 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN  138 (183)
Q Consensus        82 r~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~  138 (183)
                      +.|+.||+.|+.+|+..|..++||+..++.+||..+||++.+|++||+|+|+++|++
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            458899999999999999999999999999999999999999999999999999974

>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=99.79  E-value=7.6e-20  Score=113.15  Aligned_cols=60  Identities=18%  Similarity=0.263  Sum_probs=56.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486         20 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        20 ~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~   79 (183)
                      +.+|.|+.||++|+.+|+..|..++||+..+++.||..+||++.+|++||+|+|++.++.
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~   61 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR   61 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSC
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHH
Confidence            567899999999999999999999999999999999999999999999999999887653

>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=99.79  E-value=1.3e-20  Score=114.71  Aligned_cols=58  Identities=31%  Similarity=0.445  Sum_probs=54.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         21 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        21 ~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      ++|.||.||++|+.+|+..|..++||+..++..||..|||++.+|++||+|+|++.++
T Consensus         1 Qrr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   58 (60)
T d1yz8p1           1 QRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK   58 (60)
T ss_dssp             SSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHh
Confidence            4788999999999999999999999999999999999999999999999999987653

>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=99.79  E-value=1.2e-19  Score=112.55  Aligned_cols=61  Identities=36%  Similarity=0.652  Sum_probs=57.2

Q ss_pred             cccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhH
Q psy10486         81 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQR  141 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~  141 (183)
                      ++.|+.||+.|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|++...
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            4568899999999999999999999999999999999999999999999999999987643

>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=99.78  E-value=1.2e-19  Score=112.51  Aligned_cols=60  Identities=27%  Similarity=0.337  Sum_probs=56.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         19 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        19 ~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      ...+|.|+.|+++|+.+|+..|..++||+.++++.||..|||++.+|++||+|+|++.++
T Consensus         6 ~~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk   65 (67)
T d1ocpa_           6 QARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR   65 (67)
T ss_dssp             CCSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSS
T ss_pred             hccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhc
Confidence            455788999999999999999999999999999999999999999999999999988654

>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=99.78  E-value=1.6e-19  Score=114.81  Aligned_cols=64  Identities=67%  Similarity=1.055  Sum_probs=59.7

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQ  142 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~  142 (183)
                      ..++.|+.|++.|+.+|+..|..++||+..+++.||..+||++.+|++||+|+|+|+|+..+.+
T Consensus        12 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~~   75 (77)
T d1pufa_          12 STRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDR   75 (77)
T ss_dssp             TTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHHh
Confidence            4567789999999999999999999999999999999999999999999999999999987654

>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=99.78  E-value=9.9e-20  Score=107.86  Aligned_cols=52  Identities=23%  Similarity=0.343  Sum_probs=50.3

Q ss_pred             CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccc
Q psy10486         25 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTG   76 (183)
Q Consensus        25 r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~   76 (183)
                      |+.||++|+.+|+..|..++||+..++.+||..+||++.+|++||+|+|++.
T Consensus         1 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~   52 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS   52 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhcc
Confidence            7899999999999999999999999999999999999999999999999875

>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=99.78  E-value=2.1e-19  Score=110.90  Aligned_cols=61  Identities=38%  Similarity=0.567  Sum_probs=57.6

Q ss_pred             ccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486         80 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ  140 (183)
Q Consensus        80 ~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~  140 (183)
                      .++.|+.|+++|+.+|+..|..++||+..++..||..+||++.+|++||+|+|+++|++..
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~   62 (65)
T d1fjla_           2 QRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   62 (65)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhccc
Confidence            3567889999999999999999999999999999999999999999999999999998764

>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=99.78  E-value=1.4e-19  Score=113.42  Aligned_cols=60  Identities=20%  Similarity=0.112  Sum_probs=55.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhh-cCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         21 VRKKRKPYSKHQTLELEKEFLY-NAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        21 ~rr~r~~ft~~Ql~~Le~~F~~-~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      +++.|+.||.+|+.+|+..|.. ++||+..+++.||..|||++++|++||+|||++.++..
T Consensus         1 g~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~   61 (72)
T d1uhsa_           1 GSEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhcc
Confidence            3678999999999999999986 68999999999999999999999999999999876544

>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=99.77  E-value=3.9e-19  Score=110.54  Aligned_cols=63  Identities=30%  Similarity=0.526  Sum_probs=58.7

Q ss_pred             cccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHH
Q psy10486         81 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQA  143 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~  143 (183)
                      ++.|+.||++|+.+|+..|..++||+..+++.||..+||++.+|++||+|+|+++|+......
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~~~   64 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRN   64 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhhhhh
Confidence            467899999999999999999999999999999999999999999999999999998765543

>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=99.77  E-value=1.6e-19  Score=108.87  Aligned_cols=56  Identities=27%  Similarity=0.327  Sum_probs=53.3

Q ss_pred             CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         23 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        23 r~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      |.||.|+.+|+.+|+..|..++||+..++..||..|||++++|++||+|+|++.++
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr   56 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR   56 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHh
Confidence            57999999999999999999999999999999999999999999999999987654

>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=99.77  E-value=1.4e-19  Score=107.23  Aligned_cols=53  Identities=42%  Similarity=0.706  Sum_probs=50.9

Q ss_pred             ccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhH
Q psy10486         82 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMK  134 (183)
Q Consensus        82 r~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k  134 (183)
                      ++|+.||+.|+.+|+..|..++||+..++.+||..+||++.+|++||+|||+|
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            46889999999999999999999999999999999999999999999999986

>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=99.76  E-value=3.8e-19  Score=111.73  Aligned_cols=60  Identities=17%  Similarity=0.145  Sum_probs=55.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhh-hcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         19 VTVRKKRKPYSKHQTLELEKEFL-YNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        19 ~~~rr~r~~ft~~Ql~~Le~~F~-~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      ...++.|++||++|+.+|++.|. .++||+.++++.||..|||+.++|++||+|+|++.++
T Consensus         5 ~~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk   65 (71)
T d1wi3a_           5 SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             CCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhcc
Confidence            34578899999999999999997 5899999999999999999999999999999998664

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=99.76  E-value=5.2e-19  Score=110.83  Aligned_cols=59  Identities=22%  Similarity=0.242  Sum_probs=55.3

Q ss_pred             cccCCCCChhHHHHHHHcccc-CCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         81 RKKRKPYSKHQTLELEKEFLY-NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F~~-~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      +++++.||.+|+.+|+..|.. ++||+...+++||..+||++.+|++||+|||+++|+..
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~   61 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhcc
Confidence            467889999999999999986 78999999999999999999999999999999999864

>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=99.76  E-value=2.1e-19  Score=105.35  Aligned_cols=50  Identities=24%  Similarity=0.229  Sum_probs=48.7

Q ss_pred             CCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcc
Q psy10486         24 KRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIE   73 (183)
Q Consensus        24 ~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr   73 (183)
                      +|+.||++|+.+|+..|..++||+..++.+||..|||+.++|++||+|+|
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            58999999999999999999999999999999999999999999999976

>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=99.76  E-value=1.9e-19  Score=109.46  Aligned_cols=59  Identities=37%  Similarity=0.581  Sum_probs=56.1

Q ss_pred             cccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         81 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      ++.|+.|+++|+.+|+..|..++||+..++..||..+||++.+|++||+|+|+++|+++
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~~   60 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE   60 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhcC
Confidence            46789999999999999999999999999999999999999999999999999999863

>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=99.76  E-value=5.8e-19  Score=109.69  Aligned_cols=60  Identities=45%  Similarity=0.653  Sum_probs=56.9

Q ss_pred             ccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         80 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        80 ~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      .++.|+.||+.|+.+|+..|..++||+..++.+||..+||++.+|++||+|+|+++|+..
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~   61 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA   61 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhcc
Confidence            356789999999999999999999999999999999999999999999999999999865

>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=99.75  E-value=7.9e-19  Score=114.35  Aligned_cols=62  Identities=50%  Similarity=0.777  Sum_probs=56.0

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ  140 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~  140 (183)
                      ..++.|+.|++.|+.+|+..|..++||+..++++||..|||++.+|++||+|+|+++|++.+
T Consensus        26 ~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~~   87 (88)
T d1b72a_          26 SPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   87 (88)
T ss_dssp             ----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhcc
Confidence            34567889999999999999999999999999999999999999999999999999998764

>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=99.74  E-value=9.3e-19  Score=105.08  Aligned_cols=55  Identities=22%  Similarity=0.367  Sum_probs=52.3

Q ss_pred             CCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         24 KRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        24 ~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      +||.|+.+|+.+|+..|..++||+.+++..||..|||++.+|++||+|+|++.++
T Consensus         1 kRT~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk   55 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR   55 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTS
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHc
Confidence            5899999999999999999999999999999999999999999999999987654

>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=99.73  E-value=6.3e-19  Score=112.14  Aligned_cols=61  Identities=46%  Similarity=0.662  Sum_probs=56.6

Q ss_pred             cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      +.++.|+.||++|+.+|+..|..++||+..++++||..+||++.+|++||+|+|+|.|+..
T Consensus         8 k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   68 (77)
T d1vnda_           8 KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ   68 (77)
T ss_dssp             SSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHh
Confidence            4456788999999999999999999999999999999999999999999999999988654

>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=99.73  E-value=1.2e-18  Score=103.03  Aligned_cols=53  Identities=28%  Similarity=0.468  Sum_probs=50.9

Q ss_pred             CCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHH
Q psy10486         84 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK  136 (183)
Q Consensus        84 r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~r  136 (183)
                      |+.||++|+.+|+..|..++||+..++.+||..+||++.+|++||+|+|++.|
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            57899999999999999999999999999999999999999999999999864

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

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

Probab=99.73  E-value=9.8e-19  Score=112.75  Aligned_cols=58  Identities=28%  Similarity=0.280  Sum_probs=54.0

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcC---------------CChhhhhhhhhhcccccccc
Q psy10486         22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLM---------------LTERQVKIWFQNIEWTGQVT   79 (183)
Q Consensus        22 rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~---------------l~~~qV~~WF~nrr~k~~~~   79 (183)
                      ||.|+.||++|+.+||..|..++||+..++++||..+|               |++.+|++||+|||++.++.
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~   73 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRR   73 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHh
Confidence            68899999999999999999999999999999999875               99999999999999887653

>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=99.73  E-value=1.5e-18  Score=107.38  Aligned_cols=59  Identities=32%  Similarity=0.445  Sum_probs=55.7

Q ss_pred             ccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486         80 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN  138 (183)
Q Consensus        80 ~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~  138 (183)
                      .++.|+.|++.|+.+|+..|..++||+..++++||..+||++.+|++||+|+|+++|+.
T Consensus         8 ~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_           8 RKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             SSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            45678999999999999999999999999999999999999999999999999998863

>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=99.72  E-value=2.1e-18  Score=103.92  Aligned_cols=57  Identities=32%  Similarity=0.449  Sum_probs=54.2

Q ss_pred             ccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486         82 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN  138 (183)
Q Consensus        82 r~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~  138 (183)
                      +.|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.
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            458899999999999999999999999999999999999999999999999998864

>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=99.72  E-value=2.2e-18  Score=106.46  Aligned_cols=60  Identities=25%  Similarity=0.390  Sum_probs=56.3

Q ss_pred             ccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         80 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        80 ~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      .++.|+.|+++|+.+|+..|..++||+..+++.||..+||++.+|++||+|+|++.|+..
T Consensus         3 ~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~~   62 (66)
T d1bw5a_           3 TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             CSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             CCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHHH
Confidence            456789999999999999999999999999999999999999999999999999988753

>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=99.70  E-value=6.8e-18  Score=101.23  Aligned_cols=56  Identities=29%  Similarity=0.488  Sum_probs=53.7

Q ss_pred             cCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486         83 KRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN  138 (183)
Q Consensus        83 ~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~  138 (183)
                      +|+.|+++|..+|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.
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            47899999999999999999999999999999999999999999999999999874

>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=99.70  E-value=8.3e-18  Score=108.32  Aligned_cols=60  Identities=32%  Similarity=0.408  Sum_probs=56.1

Q ss_pred             cccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhC---------------CChhhHHHHHhhhhhHHHHHHh
Q psy10486         81 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLM---------------LTERQVKIWFQNRRMKNKKNTQ  140 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~---------------l~~~~V~~WF~nrR~k~rk~~~  140 (183)
                      ++.|+.|+++|+.+|+..|..++||+..++++||..+|               |++.+|++||+|||+++|++..
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~   75 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRAN   75 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhh
Confidence            46789999999999999999999999999999999875               9999999999999999999764

>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=99.69  E-value=1.6e-17  Score=105.52  Aligned_cols=56  Identities=20%  Similarity=0.286  Sum_probs=50.3

Q ss_pred             CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486         25 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV   80 (183)
Q Consensus        25 r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~   80 (183)
                      +..+|.+|+.+|+..|..++||+..+++.||..|||++++|++||+|+|++.+...
T Consensus         8 ~k~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~   63 (76)
T d2ecba1           8 FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE   63 (76)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCC
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHh
Confidence            34469999999999999999999999999999999999999999999998754433

>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=99.68  E-value=5.4e-18  Score=107.73  Aligned_cols=59  Identities=20%  Similarity=0.356  Sum_probs=53.3

Q ss_pred             cCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhH
Q psy10486         83 KRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQR  141 (183)
Q Consensus        83 ~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~  141 (183)
                      ++...|++|+.+|+..|..++||+..+++.||..+||++.+|++||+|+|++.++....
T Consensus         7 k~k~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~~   65 (76)
T d2ecba1           7 KFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEK   65 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhHh
Confidence            34557999999999999999999999999999999999999999999999887765543

>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=99.68  E-value=1.2e-17  Score=104.69  Aligned_cols=59  Identities=20%  Similarity=0.207  Sum_probs=54.8

Q ss_pred             cccccCCCCChhHHHHHHHccc-cCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFL-YNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK  137 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~-~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk  137 (183)
                      ..++.++.|+++|+.+|+..|. .++||+..+++.||..+||++.+|++||+|+|++.|+
T Consensus         6 ~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk   65 (71)
T d1wi3a_           6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             CCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             CCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhcc
Confidence            3457789999999999999997 5899999999999999999999999999999999876

>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=99.68  E-value=2.4e-17  Score=103.88  Aligned_cols=58  Identities=33%  Similarity=0.441  Sum_probs=53.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         21 VRKKRKPYSKHQTLELEKEFLY---NAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        21 ~rr~r~~ft~~Ql~~Le~~F~~---~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      .||+|+.||.+|+.+|+..|..   +|||+..+++.||..+||+..||.+||+|+|.+.++
T Consensus         1 ~rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~   61 (73)
T d1pufb_           1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   61 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcc
Confidence            3678999999999999999985   899999999999999999999999999999987654

>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=99.67  E-value=2e-17  Score=96.72  Aligned_cols=50  Identities=26%  Similarity=0.259  Sum_probs=48.6

Q ss_pred             cCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhh
Q psy10486         83 KRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRR  132 (183)
Q Consensus        83 ~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR  132 (183)
                      +|+.|++.|+.+|+..|..++||+..++.+||..+||++.+|++||+|+|
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            47899999999999999999999999999999999999999999999997

>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=99.67  E-value=4.3e-17  Score=103.52  Aligned_cols=56  Identities=18%  Similarity=0.249  Sum_probs=51.6

Q ss_pred             CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         23 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        23 r~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      ..+++||.+|+.+|++.|..++||+..++..||..|||+..+|++||+|+|++.++
T Consensus         5 s~~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~   60 (76)
T d2ecca1           5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH   60 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHh
Confidence            34567899999999999999999999999999999999999999999999987654

>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=99.64  E-value=7.3e-17  Score=102.44  Aligned_cols=54  Identities=22%  Similarity=0.204  Sum_probs=50.5

Q ss_pred             CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcC---------------------CChhhhhhhhhhccccccc
Q psy10486         25 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLM---------------------LTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        25 r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~---------------------l~~~qV~~WF~nrr~k~~~   78 (183)
                      |++||++|+.+|+..|+.++||+..+++.||..|+                     |++.+|++||+|||.+.+.
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr   75 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAF   75 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSC
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999994                     8999999999999988654

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

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

Probab=99.63  E-value=1.8e-16  Score=100.57  Aligned_cols=58  Identities=21%  Similarity=0.272  Sum_probs=53.9

Q ss_pred             ccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         82 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        82 r~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      ..++++|.+|+.+|+..|..++||+..++..||..+||++.+|++||+|+|+++|+..
T Consensus         5 s~~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~~   62 (76)
T d2ecca1           5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ   62 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhch
Confidence            3456789999999999999999999999999999999999999999999999998754

>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=99.62  E-value=1e-16  Score=94.13  Aligned_cols=50  Identities=24%  Similarity=0.367  Sum_probs=46.5

Q ss_pred             ChhHHHHHHHcccc-CCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486         88 SKHQTLELEKEFLY-NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK  137 (183)
Q Consensus        88 t~~q~~~Le~~F~~-~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk  137 (183)
                      |.+|..+|+..|.. ++||+..+++.||..+||++.+|++||+|||+++|+
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            46789999999976 689999999999999999999999999999999874

>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=99.62  E-value=8.7e-17  Score=94.42  Aligned_cols=50  Identities=18%  Similarity=0.242  Sum_probs=46.0

Q ss_pred             CHHHHHHHHHHhhh-cCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486         29 SKHQTLELEKEFLY-NAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV   78 (183)
Q Consensus        29 t~~Ql~~Le~~F~~-~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~   78 (183)
                      |.+|+.+||..|.. ++||+..+++.||..+||++++|++||+|||++.+.
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            56799999999986 799999999999999999999999999999987653

>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=99.62  E-value=3.7e-16  Score=98.34  Aligned_cols=59  Identities=39%  Similarity=0.595  Sum_probs=54.5

Q ss_pred             cccCCCCChhHHHHHHHccc---cCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486         81 RKKRKPYSKHQTLELEKEFL---YNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F~---~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      +++|+.|+++|+.+|+..|.   .++||+..++++||..+||+..+|++||+|+|++.++..
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~   63 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccc
Confidence            45688999999999999997   588999999999999999999999999999999988754

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

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

Probab=99.60  E-value=1.5e-16  Score=100.99  Aligned_cols=56  Identities=25%  Similarity=0.274  Sum_probs=51.9

Q ss_pred             CCCCChhHHHHHHHccccCCccCHHHHHHHHHHhC---------------------CChhhHHHHHhhhhhHHHHHH
Q psy10486         84 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLM---------------------LTERQVKIWFQNRRMKNKKNT  139 (183)
Q Consensus        84 r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~---------------------l~~~~V~~WF~nrR~k~rk~~  139 (183)
                      |..|+++|+.+|+..|+.++||+..+++.||..++                     |++.+|++||+|||++.+++.
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            46799999999999999999999999999999994                     899999999999999988653

>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=99.60  E-value=4.5e-16  Score=94.19  Aligned_cols=52  Identities=23%  Similarity=0.330  Sum_probs=47.7

Q ss_pred             CCCCHHHHHHHHHHhhhc---CCCCHHHHHHHHHHcCCChhhhhhhhhhcccccc
Q psy10486         26 KPYSKHQTLELEKEFLYN---AYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQ   77 (183)
Q Consensus        26 ~~ft~~Ql~~Le~~F~~~---~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~   77 (183)
                      .+||.+|+.+|+..|..+   |||+.++++.||..+||+..+|.+||+|+|.+.+
T Consensus         3 ~Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K   57 (60)
T d1k61a_           3 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK   57 (60)
T ss_dssp             CSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhccccc
Confidence            459999999999999875   7999999999999999999999999999987654

>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=99.60  E-value=6.4e-16  Score=94.03  Aligned_cols=55  Identities=25%  Similarity=0.332  Sum_probs=50.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhhhcccc
Q psy10486         21 VRKKRKPYSKHQTLELEKEFLY---NAYVSKQKRWELARSLMLTERQVKIWFQNIEWT   75 (183)
Q Consensus        21 ~rr~r~~ft~~Ql~~Le~~F~~---~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k   75 (183)
                      .+++|+.|+.+++.+|+..|..   +|||+.+++..||..+||+..||.+||+|+|.+
T Consensus         2 ~krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R   59 (62)
T d1x2na1           2 GKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRR   59 (62)
T ss_dssp             SCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHH
Confidence            3567889999999999999985   799999999999999999999999999998754

>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=99.59  E-value=2.1e-16  Score=101.11  Aligned_cols=59  Identities=12%  Similarity=0.130  Sum_probs=53.1

Q ss_pred             cccccCCCCChhHHHHHHHcccc----CCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486         79 TVRKKRKPYSKHQTLELEKEFLY----NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK  137 (183)
Q Consensus        79 ~~rr~r~~~t~~q~~~Le~~F~~----~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk  137 (183)
                      ..++.|+.||.+|+.+|+.+|+.    ++||+..++++||..|||++.+|++||+|+|.+.++
T Consensus        16 ~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          16 TTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            34567999999999999988875    899999999999999999999999999999987653

>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=99.58  E-value=2.4e-16  Score=94.95  Aligned_cols=55  Identities=20%  Similarity=0.326  Sum_probs=50.4

Q ss_pred             CCCCCCCHHHHHHHHHHhhh-cCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccc
Q psy10486         23 KKRKPYSKHQTLELEKEFLY-NAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQ   77 (183)
Q Consensus        23 r~r~~ft~~Ql~~Le~~F~~-~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~   77 (183)
                      +.++.|+.++..+||..|.. ++||+..+++.||..|||++++|++||+|+|++.+
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            56788999999999999986 68999999999999999999999999999998653

>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=99.56  E-value=8.8e-16  Score=92.38  Aligned_cols=54  Identities=24%  Similarity=0.423  Sum_probs=49.4

Q ss_pred             cCCCCChhHHHHHHHcccc-CCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHH
Q psy10486         83 KRKPYSKHQTLELEKEFLY-NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK  136 (183)
Q Consensus        83 ~r~~~t~~q~~~Le~~F~~-~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~r  136 (183)
                      .+..++.++..+|+..|.. ++||+..++++||..+||++.+|++||+|||+++|
T Consensus         4 ~~~~~k~~~~~iLE~~F~~~~~yPs~~~~~~LA~~lgls~~qV~~WFqNrR~k~r   58 (59)
T d2cqxa1           4 DSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK   58 (59)
T ss_dssp             CCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCccccHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccC
Confidence            4567788888999999986 68999999999999999999999999999999976

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

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

Probab=99.55  E-value=3.4e-15  Score=90.22  Aligned_cols=53  Identities=30%  Similarity=0.436  Sum_probs=48.7

Q ss_pred             CCCChhHHHHHHHcccc---CCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486         85 KPYSKHQTLELEKEFLY---NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK  137 (183)
Q Consensus        85 ~~~t~~q~~~Le~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk  137 (183)
                      .+|+++|+.+|+..|..   ++||+..+++.||..+||+..+|++||+|+|++.|+
T Consensus         3 ~Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           3 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             CSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            35999999999999965   479999999999999999999999999999998774

>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=99.50  E-value=2.1e-14  Score=87.21  Aligned_cols=56  Identities=27%  Similarity=0.360  Sum_probs=50.8

Q ss_pred             cccCCCCChhHHHHHHHcccc---CCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHH
Q psy10486         81 RKKRKPYSKHQTLELEKEFLY---NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK  136 (183)
Q Consensus        81 rr~r~~~t~~q~~~Le~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~r  136 (183)
                      ++++..|++++..+|+..|..   ++||+..++..||..+||+..+|++||+|+|.+..
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            455778999999999999974   88999999999999999999999999999998753

>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=93.35  E-value=0.12  Score=30.05  Aligned_cols=47  Identities=19%  Similarity=0.219  Sum_probs=40.5

Q ss_pred             CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhc
Q psy10486         23 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNI   72 (183)
Q Consensus        23 r~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nr   72 (183)
                      ++|..+|..+...+...|+..+..+.   .+||..+||..-.|..|..|+
T Consensus         3 ~kRk~LT~~eK~~ii~~~e~g~k~sq---~eIA~~fGv~~STvs~IlKnK   49 (66)
T d1hlva1           3 PKRRQLTFREKSRIIQEVEENPDLRK---GEIARRFNIPPSTLSTILKNK   49 (66)
T ss_dssp             CSSCCCCHHHHHHHHHHHHHCTTSCH---HHHHHHHTCCHHHHHHHHHTH
T ss_pred             cccccCCHHHHHHHHHHHHcCCcchH---HHHHHHhCCChhHHHHHHHHH
Confidence            34667999999999999999887664   459999999999999999984

>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=91.94  E-value=0.17  Score=29.32  Aligned_cols=48  Identities=19%  Similarity=0.276  Sum_probs=38.6

Q ss_pred             cCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhh
Q psy10486         83 KRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM  133 (183)
Q Consensus        83 ~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~  133 (183)
                      +|..+|..+...+-..|+.++...   ..++|..+||+...|..|.+|+..
T Consensus         4 kRk~LT~~eK~~ii~~~e~g~k~s---q~eIA~~fGv~~STvs~IlKnK~k   51 (66)
T d1hlva1           4 KRRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNKRA   51 (66)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTHHH
T ss_pred             ccccCCHHHHHHHHHHHHcCCcch---HHHHHHHhCCChhHHHHHHHHHHH
Confidence            355688888888888888886555   447899999999999999988543

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcription regulator CylR2
species: Enterococcus faecalis [TaxId: 1351]

Probab=91.49  E-value=0.21  Score=28.50  Aligned_cols=43  Identities=21%  Similarity=0.079  Sum_probs=35.0

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhH
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQV  124 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V  124 (183)
                      .+||..+|++...|..|-.+                              ...|+......||..+|++...+
T Consensus        18 ~elA~~~gis~~~is~~e~g------------------------------~~~p~~~~l~~ia~~l~v~~~~l   60 (66)
T d1utxa_          18 SELAALLEVSRQTINGIEKN------------------------------KYNPSLQLALKIAYYLNTPLEDI   60 (66)
T ss_dssp             HHHHHHHTSCHHHHHHHHTT------------------------------SCCCCHHHHHHHHHHTTSCHHHH
T ss_pred             HHHHHhcccCHHHHHHHHcC------------------------------CCCCCHHHHHHHHHHHCCCHHHH
Confidence            56899999999999999876                              34577788888999999887654

>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=91.43  E-value=0.28  Score=26.33  Aligned_cols=41  Identities=15%  Similarity=0.199  Sum_probs=34.5

Q ss_pred             CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhh
Q psy10486         25 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQ   70 (183)
Q Consensus        25 r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~   70 (183)
                      +..+|++|++.....+....  +   ..+||..+|++...|..||.
T Consensus         3 ~~~lt~~q~~~a~~l~~~G~--s---~~~iA~~~gVSr~TiYry~p   43 (47)
T d1ijwc_           3 PRAINKHEQEQISRLLEKGH--P---RQQLAIIFGIGVSTLYRYFP   43 (47)
T ss_dssp             CCSSCHHHHHHHHHHHHTTC--C---HHHHHHHHTCCHHHHHHHSC
T ss_pred             CCcCCHHHHHHHHHHHHCCC--C---HHHHHHHHCcCHHHHHhhCC
Confidence            34689999999999998653  2   45799999999999999984

>d1y7ya1 a.35.1.3 (A:5-73) Restriction-modification controller protein C.AhdI {Aeromonas hydrophila [TaxId: 644]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Restriction-modification controller protein C.AhdI
species: Aeromonas hydrophila [TaxId: 644]

Probab=90.18  E-value=0.3  Score=28.03  Aligned_cols=42  Identities=24%  Similarity=0.029  Sum_probs=33.0

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQ  123 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~  123 (183)
                      .+||..+|++...|..|-.+                              ...|+......||..+|++...
T Consensus        26 ~~lA~~~gis~~~i~~~E~g------------------------------~~~p~~~~l~~ia~~l~v~~~~   67 (69)
T d1y7ya1          26 ETLAFLSGLDRSYVGGVERG------------------------------QRNVSLVNILKLATALDIEPRE   67 (69)
T ss_dssp             HHHHHHHTCCHHHHHHHHTT------------------------------CSCCBHHHHHHHHHHTTSCGGG
T ss_pred             HHHHhHhCCCHHHHHHHHCC------------------------------CCCCCHHHHHHHHHHhCcCHHH
Confidence            45899999999888888765                              3347777888889998888764

>d1y9qa1 a.35.1.8 (A:4-82) Probable transcriptional regulator VC1968, N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Probable transcriptional regulator VC1968, N-terminal domain
domain: Probable transcriptional regulator VC1968, N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=90.05  E-value=0.32  Score=28.67  Aligned_cols=43  Identities=9%  Similarity=0.023  Sum_probs=34.4

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhH
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQV  124 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V  124 (183)
                      .+||..+|++...|..|..+                              ...|+......||..+|++...+
T Consensus        25 ~~lA~~~gis~~~i~~~E~g------------------------------~~~p~~~~l~~ia~~l~v~~~~l   67 (79)
T d1y9qa1          25 DATAQLTGVSKAMLGQIERG------------------------------ESSPTIATLWKIASGLEASFSAF   67 (79)
T ss_dssp             HHHHHHHSSCHHHHHHHHTT------------------------------CSCCCHHHHHHHHHHHTCCSGGG
T ss_pred             HHHHHHHCcchhHHHHHHcC------------------------------CCCCCHHHHHHHHHHHCCCHHHH
Confidence            56999999999999999976                              33477778888899998887543

>d1b0na2 a.35.1.3 (A:1-68) SinR repressor, DNA-binding domain {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: SinR repressor, DNA-binding domain
species: Bacillus subtilis [TaxId: 1423]

Probab=89.53  E-value=0.42  Score=27.26  Aligned_cols=44  Identities=16%  Similarity=0.041  Sum_probs=34.4

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhH
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQV  124 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V  124 (183)
                      .+||..+|++...|..|-.+.                             ...|+......||..+|++...+
T Consensus        18 ~~la~~~gis~~~i~~~E~g~-----------------------------~~~ps~~~l~~ia~~l~v~~~~l   61 (68)
T d1b0na2          18 SELAEKAGVAKSYLSSIERNL-----------------------------QTNPSIQFLEKVSAVLDVSVHTL   61 (68)
T ss_dssp             HHHHHHHTCCHHHHHHHHTTC-----------------------------CSCCCHHHHHHHHHHHTCCHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHcCC-----------------------------CCCCCHHHHHHHHHHHCCcHHHH
Confidence            568999999999999998661                             12367788888999999987543

>d2b5aa1 a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacillus caldolyticus [TaxId: 1394]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Regulatory protein C.BclI
species: Bacillus caldolyticus [TaxId: 1394]

Probab=88.70  E-value=0.43  Score=27.89  Aligned_cols=42  Identities=14%  Similarity=0.038  Sum_probs=33.3

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQ  123 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~  123 (183)
                      .+||..+|++...|..|..+                              ...|+......||..+|++...
T Consensus        27 ~~lA~~~gis~~~i~~~e~g------------------------------~~~p~~~~l~~ia~~l~v~~~~   68 (77)
T d2b5aa1          27 EELADLAGLHRTYISEVERG------------------------------DRNISLINIHKICAALDIPAST   68 (77)
T ss_dssp             HHHHHHHTCCHHHHHHHHTT------------------------------CSCCBHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHCCCHHHHHHHHcC------------------------------CCCCCHHHHHHHHHHhCCCHHH
Confidence            46899999999998888765                              3447777888899999988754

>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=87.25  E-value=0.34  Score=25.92  Aligned_cols=41  Identities=15%  Similarity=0.191  Sum_probs=34.0

Q ss_pred             CCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHh
Q psy10486         84 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQ  129 (183)
Q Consensus        84 r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~  129 (183)
                      +..+|++|+......+....     ...++|..+|++...|..||-
T Consensus         3 ~~~lt~~q~~~a~~l~~~G~-----s~~~iA~~~gVSr~TiYry~p   43 (47)
T d1ijwc_           3 PRAINKHEQEQISRLLEKGH-----PRQQLAIIFGIGVSTLYRYFP   43 (47)
T ss_dssp             CCSSCHHHHHHHHHHHHTTC-----CHHHHHHHHTCCHHHHHHHSC
T ss_pred             CCcCCHHHHHHHHHHHHCCC-----CHHHHHHHHCcCHHHHHhhCC
Confidence            34689999999988887653     366899999999999999983

>d2r1jl1 a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding domain {Salmonella bacteriophage P22 [TaxId: 10754]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: P22 C2 repressor, DNA-binding domain
species: Salmonella bacteriophage P22 [TaxId: 10754]

Probab=87.00  E-value=0.65  Score=26.17  Aligned_cols=41  Identities=10%  Similarity=0.197  Sum_probs=31.7

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTER  122 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~  122 (183)
                      .+||..+|++...|..|-.+                              ...|+......||..++++..
T Consensus        20 ~~lA~~~gvs~~~i~~~e~g------------------------------~~~p~~~~l~~ia~~l~v~~~   60 (66)
T d2r1jl1          20 AALGKMVGVSNVAISQWERS------------------------------ETEPNGENLLALSKALQCSPD   60 (66)
T ss_dssp             HHHHHHHTSCHHHHHHHHTT------------------------------SSCCBHHHHHHHHHHTTSCHH
T ss_pred             HHHHHHHCCCHHHHHHHHcC------------------------------CCCCCHHHHHHHHHHhCCCHH
Confidence            46999999999999999866                              233566677778888887764

>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=86.92  E-value=0.53  Score=28.47  Aligned_cols=47  Identities=17%  Similarity=0.163  Sum_probs=33.0

Q ss_pred             CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccc
Q psy10486         25 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEW   74 (183)
Q Consensus        25 r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~   74 (183)
                      |..||.+-....-..+....-.+   ..++|..|||+...|..|....+.
T Consensus         3 rk~Ys~EfK~~aV~l~~~~~g~s---~~~vA~~lGIs~~tl~~W~k~~~~   49 (89)
T d2jn6a1           3 TKTYSEEFKRDAVALYENSDGAS---LQQIANDLGINRVTLKNWIIKYGS   49 (89)
T ss_dssp             CCCCCHHHHHHHHHHHTTGGGSC---HHHHHHHHTSCHHHHHHHHHHHCC
T ss_pred             CCCCCHHHHHHHHHHHHHcCCCc---HHHHHHHHCCCHHHHHHHHHHHhh
Confidence            45799987766666554432222   245999999999999999876543

>d2icta1 a.35.1.3 (A:8-94) Antitoxin HigA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Antitoxin HigA
species: Escherichia coli [TaxId: 562]

Probab=84.86  E-value=1.1  Score=26.84  Aligned_cols=44  Identities=14%  Similarity=0.293  Sum_probs=35.4

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHH
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWF  128 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF  128 (183)
                      .+||..+|++...|..|-.+                              ...|+......||..+|++..   +|+
T Consensus        18 ~~LA~~lGvs~~~is~ie~g------------------------------~~~~s~~~~~kla~~lgvs~~---~~L   61 (87)
T d2icta1          18 REFARAMEIAPSTASRLLTG------------------------------KAALTPEMAIKLSVVIGSSPQ---MWL   61 (87)
T ss_dssp             HHHHHHHTCCHHHHHHHHHT------------------------------SSCCCHHHHHHHHHHTCSCHH---HHH
T ss_pred             HHHHHHHhhcHHHHHHHHHh------------------------------ccCCCHHHHHHHHHHHCcCHH---HHH
Confidence            56999999999999999877                              334666777889999998864   666

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

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

Probab=83.38  E-value=2.8  Score=26.77  Aligned_cols=88  Identities=11%  Similarity=0.029  Sum_probs=61.7

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc---cc-cccCCCCChhHHHHHHHcccc
Q psy10486         26 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV---TV-RKKRKPYSKHQTLELEKEFLY  101 (183)
Q Consensus        26 ~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~---~~-rr~r~~~t~~q~~~Le~~F~~  101 (183)
                      ..++.+.....-+.++...  +   ..++|..++++...|..|....+..+.-   .. .......+++....+......
T Consensus        15 rpLs~dlR~rIv~~~~~G~--s---~r~iA~~~~VS~~tV~k~l~r~~~~G~~~~~~~~~~rpr~~t~~~~~~I~~~~~~   89 (123)
T d1pdnc_          15 RPLPNNIRLKIVEMAADGI--R---PCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYKRS   89 (123)
T ss_dssp             SCCCHHHHHHHHHHHHTTC--C---HHHHHHHHTCCHHHHHHHHHHHHHHCCSSCCCCSCCCCCSSCSTHHHHHHHTTTT
T ss_pred             cCCCHHHHHHHHHHHHhcC--C---HHHHHHHHCcCHHHHHHHHHHHHccCCcCcCCCCCCCCCCCCHHHHHHHHHHHHh
Confidence            4577777777777776543  2   2369999999999999999887665332   11 112345788888999999999


Q ss_pred             CCccCHHHHHHHHHHhC
Q psy10486        102 NAYVSKQKRWELARSLM  118 (183)
Q Consensus       102 ~~~p~~~~~~~La~~l~  118 (183)
                      ++..+..+..+....-|
T Consensus        90 ~P~~t~~El~~~L~~eg  106 (123)
T d1pdnc_          90 SPGMFSWEIREKLIREG  106 (123)
T ss_dssp             CTTCCHHHHHHHHHHTS
T ss_pred             CCCccHHHHHHHHHHcC
Confidence            99988876655333433

>d1lmb3_ a.35.1.2 (3:) lambda C1 repressor, DNA-binding domain {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: lambda C1 repressor, DNA-binding domain
species: Bacteriophage lambda [TaxId: 10710]

Probab=81.09  E-value=1.6  Score=26.03  Aligned_cols=43  Identities=14%  Similarity=0.102  Sum_probs=32.4

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhH
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQV  124 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V  124 (183)
                      .+||..+|++...|..|-.+                              ...|+......||..+|++...+
T Consensus        29 ~~lA~~lgis~~~is~~E~g------------------------------~~~~s~~~l~~ia~~l~v~~~~~   71 (87)
T d1lmb3_          29 ESVADKMGMGQSGVGALFNG------------------------------INALNAYNAALLAKILKVSVEEF   71 (87)
T ss_dssp             HHHHHHHTSCHHHHHHHHTT------------------------------SSCCCHHHHHHHHHHHTSCGGGT
T ss_pred             HHHHHHhCccHHHHHHHHhc------------------------------cCCCcHHHHHHHHHHHCCCHHHH
Confidence            56899999999988888765                              33466677777888888887644

>d2a6ca1 a.35.1.13 (A:1-69) HTH-motif protein NE1354 {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: HTH-motif protein NE1354
species: Nitrosomonas europaea [TaxId: 915]

Probab=80.45  E-value=1.6  Score=24.80  Aligned_cols=42  Identities=17%  Similarity=0.124  Sum_probs=32.0

Q ss_pred             HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChh
Q psy10486         52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTER  122 (183)
Q Consensus        52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~  122 (183)
                      .+||..+|++...|..|..++                             ...|+......+|..||++..
T Consensus        23 ~elA~~~gv~~~~is~ie~g~-----------------------------~~~~s~~~L~~ia~~Lg~~i~   64 (69)
T d2a6ca1          23 FKAAELLGVTQPRVSDLMRGK-----------------------------IDLFSLESLIDMITSIGLKVE   64 (69)
T ss_dssp             HHHHHHHTSCHHHHHHHHTTC-----------------------------GGGCCHHHHHHHHHHTTCCCC
T ss_pred             HHHHHHHHcCHhHHHHHHccc-----------------------------ccchhHHHHHHHHHHhCCCcE
Confidence            469999999999999998651                             234666777788888887653