Psyllid ID: psy11996

---

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-------190-------200-------210-------220--
Protein Sequence
MSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNNPNLYTQYQTQGKSCTGRYQVRPITSPHGAYHGDLRYHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHLAT
Secondary Structure (PSIPRED)
ccccccccccccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHcccccHHHHHHcccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccccccccHHHHHHHHHHHcccccccHHHHHHHHHHHcccccccHHHHccccHHHHHHHccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHccHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHccHHHHHHcccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mstvnangetkrqrtSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMasmnnpnlytqyqtqgksctgryqvrpitsphgayhgdlryhwtnraplkyvkrgtvnangetkrqrtsYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASmnvipyhyhmsqpygnpyqfthlat
Flexible Loop (DISEMBL)
mstvnangetkrqrtsytryqtlelekefhfnryltrRRRIEIAHalclterqikiwFQNRRMKWKKEHKMASMNNPNLYTQYQTQGKSCTGRYQVRPITSPHGAYHGDLRYHWTnraplkyvkrgtvnangetkrqrtsytryqtlelekefhfnryltrRRRIEIAHalclterqikiwFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHLAT
Low Complexity Region (SEG)
MSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNNPNLYTQYQTQGKSCTGRYQVRPITSPHGAYHGDLRYHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHLAT
Disordered region (IsUnstruct)
****************YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK**********NLYTQYQTQGKSCTGRYQVRPITSPHGAYHGDLRYHWTNRAPLKYVKRGTVNAN******RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQF*****
Disordered Region (DISOPRED)
*****************TRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNNPNLYTQYQTQGKSCTGRYQVRPITSPHGAYHGDLRYHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM***********************************
Disordered Region (DISEMBL)
***************SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNNPNLYTQYQTQGKSCTGRYQVRPITSPHGAYHGDLRYHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHLAT
Disordered Region (DISPRO)
**************TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK**S****************************************************************RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK****************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNNPNLYTQYQTQGKSCTGRYQVRPITSPHGAYHGDLRYHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHLAT
Positional Conservation
no confident homologs detected

---

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	222	2.2.26 [Sep-21-2011]
P09077	417	Homeotic protein Sex comb	yes	N/A	0.472	0.251	0.739	5e-44
P15859	86	Homeobox protein H55 (Fra	no	N/A	0.387	1.0	0.921	6e-41
P17277	309	Homeobox protein Hox-A4 O	yes	N/A	0.391	0.281	0.704	2e-30
Q9IA11	252	Homeobox protein Hox-D5 O	N/A	N/A	0.315	0.277	0.857	3e-30
Q9PWD3	281	Homeobox protein Hox-A5 O	N/A	N/A	0.319	0.252	0.845	4e-30
Q1KKX9	319	Homeobox protein Hox-B5a	N/A	N/A	0.306	0.213	0.852	5e-30
A2D5Y4	270	Homeobox protein Hox-A5 O	N/A	N/A	0.310	0.255	0.840	7e-30
Q1KKX0	280	Homeobox protein Hox-B5b	N/A	N/A	0.310	0.246	0.826	8e-30
Q9IA23	275	Homeobox protein Hox-A5 O	N/A	N/A	0.306	0.247	0.867	9e-30
A2D5K9	270	Homeobox protein Hox-A5 O	N/A	N/A	0.310	0.255	0.840	1e-29

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

 Score =  177 bits (449), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 88/119 (73%), Positives = 94/119 (78%), Gaps = 14/119 (11%)

Query: 112 YHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 171
           Y W  R    ++   TVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL
Sbjct: 305 YPWMKRV---HLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 361

Query: 172 CLTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPY--------QFTHLAT 222
           CLTERQIKIWFQNRRMKWKKEHKMASMN++PYH     PYG+PY        QF HL+ 
Sbjct: 362 CLTERQIKIWFQNRRMKWKKEHKMASMNIVPYHM---GPYGHPYHQFDIHPSQFAHLSA 417

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

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

 Score =  167 bits (422), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 82/89 (92%), Positives = 85/89 (95%), Gaps = 3/89 (3%)

Query: 127 TVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR 186
           TVNANGE KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR
Sbjct: 1   TVNANGEVKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR 60

Query: 187 MKWKKEHKMASMNVIPYHYHMSQPYGNPY 215
           MKWKKEHKMASMN++P  YHMS PYG+PY
Sbjct: 61  MKWKKEHKMASMNIVP--YHMS-PYGHPY 86

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

Apis mellifera (taxid: 7460)

>sp|P17277|HXA4_CHICK Homeobox protein Hox-A4 OS=Gallus gallus GN=HOXA4 PE=2 SV=1

 Score =  132 bits (332), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 69/98 (70%), Positives = 75/98 (76%), Gaps = 11/98 (11%)

Query: 1   MSTVNAN---GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIW 57
           +STVN N   GE KR RT+YTR Q LELEKEFHFNRYLTRRRRIEIAH LCL+ERQ+KIW
Sbjct: 197 VSTVNPNYSGGEPKRSRTAYTRQQVLELEKEFHFNRYLTRRRRIEIAHTLCLSERQVKIW 256

Query: 58  FQNRRMKWKKEH-----KMASMNNPNLYTQ---YQTQG 87
           FQNRRMKWKK+H     KM S N P+L  Q    QTQG
Sbjct: 257 FQNRRMKWKKDHKLPNTKMRSSNQPSLGQQQAKAQTQG 294

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 sites in the 5'-flanking sequence of its coding region with various affinities. The consensus sequences of the high and low affinity binding sites are 5'-TAATGA[CG]-3' and 5'-CTAATTTT-3'.

Gallus gallus (taxid: 9031)

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

 Score =  131 bits (330), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 60/70 (85%), Positives = 66/70 (94%)

Query: 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
           E KR RT+YTRYQTLELEKEFH+NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK+
Sbjct: 176 EGKRTRTAYTRYQTLELEKEFHYNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKD 235

Query: 193 HKMASMNVIP 202
           +K+ S+NV P
Sbjct: 236 NKLKSINVSP 245

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

Heterodontus francisci (taxid: 7792)

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

 Score =  131 bits (329), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 60/71 (84%), Positives = 66/71 (92%)

Query: 130 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 189
           A  E KR RT+YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCL+ERQIKIWFQNRRMKW
Sbjct: 201 AGPEGKRARTAYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLSERQIKIWFQNRRMKW 260

Query: 190 KKEHKMASMNV 200
           KK++K+ SMN+
Sbjct: 261 KKDNKLKSMNM 271

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

Morone saxatilis (taxid: 34816)

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

 Score =  130 bits (328), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 58/68 (85%), Positives = 65/68 (95%)

Query: 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
           + KR RT+YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK+
Sbjct: 243 DGKRARTAYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKD 302

Query: 193 HKMASMNV 200
           +K+ SM++
Sbjct: 303 NKLKSMSL 310

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

Takifugu rubripes (taxid: 31033)

>sp|A2D5Y4|HXA5_LEMCA Homeobox protein Hox-A5 OS=Lemur catta GN=HOXA5 PE=3 SV=1

 Score =  130 bits (327), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 58/69 (84%), Positives = 65/69 (94%)

Query: 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
           E KR RT+YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCL+ERQIKIWFQNRRMKWKK+
Sbjct: 194 EGKRARTAYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLSERQIKIWFQNRRMKWKKD 253

Query: 193 HKMASMNVI 201
           +K+ SM++ 
Sbjct: 254 NKLKSMSMA 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. Also binds to its own promoter. Binds specifically to the motif 5'-CYYNATTA[TG]Y-3'.

Lemur catta (taxid: 9447)

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

 Score =  130 bits (327), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 57/69 (82%), Positives = 66/69 (95%)

Query: 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
           + KR RT+YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCL+ERQIKIWFQNRRMKWKK+
Sbjct: 204 DGKRARTAYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLSERQIKIWFQNRRMKWKKD 263

Query: 193 HKMASMNVI 201
           +K+ SM+++
Sbjct: 264 NKLKSMSLV 272

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

Takifugu rubripes (taxid: 31033)

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

 Score =  130 bits (326), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 59/68 (86%), Positives = 65/68 (95%)

Query: 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
           E KR RT+YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK+
Sbjct: 199 EGKRARTAYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKD 258

Query: 193 HKMASMNV 200
           +K+ SM++
Sbjct: 259 NKLKSMSM 266

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|A2D5K9|HXA5_LAGLA Homeobox protein Hox-A5 OS=Lagothrix lagotricha GN=HOXA5 PE=3 SV=1

 Score =  130 bits (326), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 58/69 (84%), Positives = 65/69 (94%)

Query: 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
           E KR RT+YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCL+ERQIKIWFQNRRMKWKK+
Sbjct: 194 EGKRARTAYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLSERQIKIWFQNRRMKWKKD 253

Query: 193 HKMASMNVI 201
           +K+ SM++ 
Sbjct: 254 NKLKSMSMA 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. Also binds to its own promoter. Binds specifically to the motif 5'-CYYNATTA[TG]Y-3'.

Lagothrix lagotricha (taxid: 9519)

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	222
344252749	222	Homeobox protein Hox-A5 [Cricetulus gris	0.734	0.734	0.572	1e-55
270065291	302	sex combs reduced [Oncopeltus fasciatus]	0.486	0.357	0.882	3e-51
224460203	338	sex combs reduced [Rhodnius prolixus]	0.486	0.319	0.864	5e-50
47213840	369	unnamed protein product [Tetraodon nigro	0.828	0.498	0.539	1e-47
383849607	373	PREDICTED: homeobox protein Hox-A5a-like	0.472	0.281	0.779	2e-44
86515396	312	cephalothorax [Tribolium castaneum] gi|1	0.472	0.336	0.779	3e-44
7229537	312	sex combs reduced Scr [Tribolium castane	0.472	0.336	0.779	3e-44
201023305	390	sex combs reduced [Nasonia vitripennis]	0.472	0.269	0.779	3e-44
31205335	372	AGAP004659-PA [Anopheles gambiae str. PE	0.450	0.268	0.830	3e-44
54607270	312	cephalothorax [Tribolium castaneum]	0.472	0.336	0.779	3e-44

>gi|344252749|gb|EGW08853.1| Homeobox protein Hox-A5 [Cricetulus griseus]

 Score =  221 bits (564), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 123/215 (57%), Positives = 139/215 (64%), Gaps = 52/215 (24%)

Query: 1   MSTVNANG-ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 59
           +S  N  G E KR RT+YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCL+ERQIKIWFQ
Sbjct: 33  ISHDNIGGPEGKRARTAYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLSERQIKIWFQ 92

Query: 60  NRRMKWKKEHKMASMNNPNLYTQYQTQGKSCTGRYQVRPITSPHGAYHGDLRYHWTNRAP 119
           NRRMKWKK++K+ SM NP                           +Y+G           
Sbjct: 93  NRRMKWKKDNKLKSMINP---------------------------SYNG----------- 114

Query: 120 LKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIK 179
                       GE KR RT+YTR Q LELEKEFHFNRYLTRRRRIEIAH LCL+ERQ+K
Sbjct: 115 ------------GEPKRSRTAYTRQQVLELEKEFHFNRYLTRRRRIEIAHTLCLSERQVK 162

Query: 180 IWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNP 214
           IWFQNRRMKWKK+HK+ +  +   +   S P G P
Sbjct: 163 IWFQNRRMKWKKDHKLPNTKMRSSN-PASAPAGPP 196

Source: Cricetulus griseus

Species: Cricetulus griseus

Genus: Cricetulus

Family: Cricetidae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

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

 Score =  207 bits (527), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 98/111 (88%), Positives = 101/111 (90%), Gaps = 3/111 (2%)

Query: 112 YHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 171
           Y W  R    ++ + TVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL
Sbjct: 195 YPWMKRV---HLGQSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 251

Query: 172 CLTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHLAT 222
           CLTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHL T
Sbjct: 252 CLTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHLTT 302

Source: Oncopeltus fasciatus

Species: Oncopeltus fasciatus

Genus: Oncopeltus

Family: Lygaeidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  203 bits (516), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 96/111 (86%), Positives = 100/111 (90%), Gaps = 3/111 (2%)

Query: 112 YHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 171
           Y W  R    ++ + TVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL
Sbjct: 231 YPWMKRV---HLGQSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 287

Query: 172 CLTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHLAT 222
           CLTERQIKIWFQNRRMKWKKE+KMASMNVIPYHYHMSQPY NPYQFTHL T
Sbjct: 288 CLTERQIKIWFQNRRMKWKKENKMASMNVIPYHYHMSQPYANPYQFTHLTT 338

Source: Rhodnius prolixus

Species: Rhodnius prolixus

Genus: Rhodnius

Family: Reduviidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|47213840|emb|CAG00644.1| unnamed protein product [Tetraodon nigroviridis]

 Score =  195 bits (495), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 115/213 (53%), Positives = 136/213 (63%), Gaps = 29/213 (13%)

Query: 11  KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
           +R R +YTRYQTLELEKEFHFNRYLTRRRRIEI+HALCLTERQIKIWFQNRRMK      
Sbjct: 156 RRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEISHALCLTERQIKIWFQNRRMKLGVYGC 215

Query: 71  MASMNN---PNL----YTQYQTQGKSCTGRYQVRPITSPHGAYHGDLRYHWTNRAPLKYV 123
              ++    PN        Y T G + +G ++      P   + G   Y++ N   L   
Sbjct: 216 AIIIHAWRYPNGSDYQLLNYGTNG-AVSGSFR-----DPGTMHSGSFGYNY-NGMDLTVN 268

Query: 124 KRGTVNANG---ETKRQRTSYTRYQ------------TLELEKEFHFNRYLTRRRRIEIA 168
           + GT    G   E  R      RY+            TLELEKEFHFNRYLTRRRRIEIA
Sbjct: 269 RTGTGGHFGAVREDARGFAPDARYRQTPNCALASPDPTLELEKEFHFNRYLTRRRRIEIA 328

Query: 169 HALCLTERQIKIWFQNRRMKWKKEHKMASMNVI 201
           HALCL+ERQIKIWFQNRRMKWKK++K+ SM+++
Sbjct: 329 HALCLSERQIKIWFQNRRMKWKKDNKLKSMSLV 361

Source: Tetraodon nigroviridis

Species: Tetraodon nigroviridis

Genus: Tetraodon

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

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

 Score =  184 bits (467), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 92/118 (77%), Positives = 98/118 (83%), Gaps = 13/118 (11%)

Query: 112 YHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 171
           Y W  R    ++ + TVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL
Sbjct: 262 YPWMKRV---HIGQSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 318

Query: 172 CLTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPY-------QFTHLAT 222
           CLTERQIKIWFQNRRMKWKKEHKMASMN++P  YHMS PYG+PY       QF HLAT
Sbjct: 319 CLTERQIKIWFQNRRMKWKKEHKMASMNIVP--YHMS-PYGHPYQFAPHPGQFAHLAT 373

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  184 bits (466), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 92/118 (77%), Positives = 98/118 (83%), Gaps = 13/118 (11%)

Query: 112 YHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 171
           Y W  R    ++ + TVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL
Sbjct: 201 YPWMKRV---HLGQSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 257

Query: 172 CLTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPY-------QFTHLAT 222
           CLTERQIKIWFQNRRMKWKKEHKMASMN++P  YHMS PYG+PY       QF HLAT
Sbjct: 258 CLTERQIKIWFQNRRMKWKKEHKMASMNIVP--YHMS-PYGHPYQFDLHPSQFAHLAT 312

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  184 bits (466), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 92/118 (77%), Positives = 98/118 (83%), Gaps = 13/118 (11%)

Query: 112 YHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 171
           Y W  R    ++ + TVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL
Sbjct: 201 YPWMKRV---HLGQSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 257

Query: 172 CLTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPY-------QFTHLAT 222
           CLTERQIKIWFQNRRMKWKKEHKMASMN++P  YHMS PYG+PY       QF HLAT
Sbjct: 258 CLTERQIKIWFQNRRMKWKKEHKMASMNIVP--YHMS-PYGHPYQFDLHPSQFAHLAT 312

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|201023305|ref|NP_001128396.1| sex combs reduced [Nasonia vitripennis]

 Score =  184 bits (466), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 92/118 (77%), Positives = 98/118 (83%), Gaps = 13/118 (11%)

Query: 112 YHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 171
           Y W  R    ++ + TVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL
Sbjct: 279 YPWMKRV---HIGQSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 335

Query: 172 CLTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPY-------QFTHLAT 222
           CLTERQIKIWFQNRRMKWKKEHKMASMN++P  YHMS PYG+PY       QF HLAT
Sbjct: 336 CLTERQIKIWFQNRRMKWKKEHKMASMNIVP--YHMS-PYGHPYQFAPHPGQFAHLAT 390

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|31205335|ref|XP_311616.1| AGAP004659-PA [Anopheles gambiae str. PEST] gi|3420834|gb|AAC31944.1| Sex combs reduced homeotic protein [Anopheles gambiae] gi|30177656|gb|EAA07257.2| AGAP004659-PA [Anopheles gambiae str. PEST]

 Score =  184 bits (466), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 88/106 (83%), Positives = 94/106 (88%), Gaps = 6/106 (5%)

Query: 112 YHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 171
           Y W  R    ++ + TVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL
Sbjct: 261 YPWMKRV---HIGQSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 317

Query: 172 CLTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQF 217
           CLTERQIKIWFQNRRMKWKKEHKMASMN++P  YHMS PYG+PYQF
Sbjct: 318 CLTERQIKIWFQNRRMKWKKEHKMASMNIVP--YHMS-PYGHPYQF 360

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  184 bits (466), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 92/118 (77%), Positives = 98/118 (83%), Gaps = 13/118 (11%)

Query: 112 YHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 171
           Y W  R    ++ + TVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL
Sbjct: 201 YPWMKRV---HLGQSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 257

Query: 172 CLTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPY-------QFTHLAT 222
           CLTERQIKIWFQNRRMKWKKEHKMASMN++P  YHMS PYG+PY       QF HLAT
Sbjct: 258 CLTERQIKIWFQNRRMKWKKEHKMASMNIVP--YHMS-PYGHPYQFDLHPSQFAHLAT 312

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	222
FB|FBgn0003339	417	Scr "Sex combs reduced" [Droso	0.450	0.239	0.813	6.7e-45
UNIPROTKB|F1NMG4	309	LOC100858374 "Uncharacterized	0.391	0.281	0.704	1e-29
UNIPROTKB|P17277	309	HOXA4 "Homeobox protein Hox-A4	0.391	0.281	0.704	1e-29
UNIPROTKB|P14840	245	HOXB4 "Homeobox protein Hox-B4	0.423	0.383	0.625	7.1e-29
UNIPROTKB|E2QT52	274	HOXB4 "Uncharacterized protein	0.427	0.346	0.625	9.1e-29
UNIPROTKB|F6UWC1	251	HOXB4 "Uncharacterized protein	0.427	0.378	0.625	9.1e-29
UNIPROTKB|F1RWG5	251	HOXB4 "Uncharacterized protein	0.427	0.378	0.625	9.1e-29
UNIPROTKB|F1N257	251	HOXB4 "Homeobox protein Hox-B4	0.427	0.378	0.625	9.1e-29
UNIPROTKB|Q08DG5	251	HOXB4 "Homeobox protein Hox-B4	0.427	0.378	0.625	9.1e-29
UNIPROTKB|P17483	251	HOXB4 "Homeobox protein Hox-B4	0.427	0.378	0.625	9.1e-29

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

 Score = 446 (162.1 bits), Expect = 6.7e-45, Sum P(2) = 6.7e-45
 Identities = 87/107 (81%), Positives = 92/107 (85%)

Query:   112 YHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 171
             Y W  R    ++   TVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL
Sbjct:   305 YPWMKRV---HLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 361

Query:   172 CLTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPY-QF 217
             CLTERQIKIWFQNRRMKWKKEHKMASMN++PYH  M  PYG+PY QF
Sbjct:   362 CLTERQIKIWFQNRRMKWKKEHKMASMNIVPYH--MG-PYGHPYHQF 405

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

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

GO:0005634 "nucleus" evidence=ISS;NAS

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

GO:0007494 "midgut development" evidence=TAS

GO:0007379 "segment specification" evidence=NAS

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

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

GO:0007548 "sex differentiation" evidence=TAS

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

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

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

GO:0042803 "protein homodimerization activity" evidence=IDA

UNIPROTKB|F1NMG4 LOC100858374 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 329 (120.9 bits), Expect = 1.0e-29, P = 1.0e-29
 Identities = 69/98 (70%), Positives = 75/98 (76%)

Query:     1 MSTVNAN---GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIW 57
             +STVN N   GE KR RT+YTR Q LELEKEFHFNRYLTRRRRIEIAH LCL+ERQ+KIW
Sbjct:   197 VSTVNPNYSGGEPKRSRTAYTRQQVLELEKEFHFNRYLTRRRRIEIAHTLCLSERQVKIW 256

Query:    58 FQNRRMKWKKEHK-----MASMNNPNLYTQY---QTQG 87
             FQNRRMKWKK+HK     M S N P+L  Q    QTQG
Sbjct:   257 FQNRRMKWKKDHKLPNTKMRSSNQPSLGQQQAKAQTQG 294

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

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

GO:0005634 "nucleus" evidence=IEA

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

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

UNIPROTKB|P17277 HOXA4 "Homeobox protein Hox-A4" [Gallus gallus (taxid:9031)]

 Score = 329 (120.9 bits), Expect = 1.0e-29, P = 1.0e-29
 Identities = 69/98 (70%), Positives = 75/98 (76%)

Query:     1 MSTVNAN---GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIW 57
             +STVN N   GE KR RT+YTR Q LELEKEFHFNRYLTRRRRIEIAH LCL+ERQ+KIW
Sbjct:   197 VSTVNPNYSGGEPKRSRTAYTRQQVLELEKEFHFNRYLTRRRRIEIAHTLCLSERQVKIW 256

Query:    58 FQNRRMKWKKEHK-----MASMNNPNLYTQY---QTQG 87
             FQNRRMKWKK+HK     M S N P+L  Q    QTQG
Sbjct:   257 FQNRRMKWKKDHKLPNTKMRSSNQPSLGQQQAKAQTQG 294

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|P14840 HOXB4 "Homeobox protein Hox-B4" [Gallus gallus (taxid:9031)]

 Score = 321 (118.1 bits), Expect = 7.1e-29, P = 7.1e-29
 Identities = 65/104 (62%), Positives = 78/104 (75%)

Query:     1 MSTVNAN---GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIW 57
             +STVN N   GE KR RT+YTR Q LELEKEFH+NRYLTRRRR+EIAH+LCL+ERQIKIW
Sbjct:   138 VSTVNPNYSGGEPKRSRTAYTRQQVLELEKEFHYNRYLTRRRRVEIAHSLCLSERQIKIW 197

Query:    58 FQNRRMKWKKEHKMASMNNPNLYTQYQTQGKSCTGRYQVRPITS 101
             FQNRRMKWKK+HK+     PN  T+ ++   S +   Q+ P  S
Sbjct:   198 FQNRRMKWKKDHKL-----PN--TKIRSNPSSSSASLQIPPAAS 234

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|E2QT52 HOXB4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 320 (117.7 bits), Expect = 9.1e-29, P = 9.1e-29
 Identities = 65/104 (62%), Positives = 76/104 (73%)

Query:   101 SP-HGAYHGDLRYHWTNRAPLKYVKRGTVNAN---GETKRQRTSYTRYQTLELEKEFHFN 156
             SP H A    + Y W     ++ V   TVN N   GE KR RT+YTR Q LELEKEFH+N
Sbjct:   137 SPSHSACKEPVVYPW-----MRKVHVSTVNPNYAGGEPKRSRTAYTRQQVLELEKEFHYN 191

Query:   157 RYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNV 200
             RYLTRRRR+EIAHALCL+ERQIKIWFQNRRMKWKK+HK+ +  +
Sbjct:   192 RYLTRRRRVEIAHALCLSERQIKIWFQNRRMKWKKDHKLPNTKI 235

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

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

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

UNIPROTKB|F6UWC1 HOXB4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 320 (117.7 bits), Expect = 9.1e-29, P = 9.1e-29
 Identities = 65/104 (62%), Positives = 76/104 (73%)

Query:   101 SP-HGAYHGDLRYHWTNRAPLKYVKRGTVNAN---GETKRQRTSYTRYQTLELEKEFHFN 156
             SP H A    + Y W     ++ V   TVN N   GE KR RT+YTR Q LELEKEFH+N
Sbjct:   130 SPSHSACKEPVVYPW-----MRKVHVSTVNPNYAGGEPKRSRTAYTRQQVLELEKEFHYN 184

Query:   157 RYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNV 200
             RYLTRRRR+EIAHALCL+ERQIKIWFQNRRMKWKK+HK+ +  +
Sbjct:   185 RYLTRRRRVEIAHALCLSERQIKIWFQNRRMKWKKDHKLPNTKI 228

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

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

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

UNIPROTKB|F1RWG5 HOXB4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 320 (117.7 bits), Expect = 9.1e-29, P = 9.1e-29
 Identities = 65/104 (62%), Positives = 76/104 (73%)

Query:   101 SP-HGAYHGDLRYHWTNRAPLKYVKRGTVNAN---GETKRQRTSYTRYQTLELEKEFHFN 156
             SP H A    + Y W     ++ V   TVN N   GE KR RT+YTR Q LELEKEFH+N
Sbjct:   130 SPSHSACKEPVVYPW-----MRKVHVSTVNPNYAGGEPKRSRTAYTRQQVLELEKEFHYN 184

Query:   157 RYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNV 200
             RYLTRRRR+EIAHALCL+ERQIKIWFQNRRMKWKK+HK+ +  +
Sbjct:   185 RYLTRRRRVEIAHALCLSERQIKIWFQNRRMKWKKDHKLPNTKI 228

GO:0005634 "nucleus" evidence=IEA

GO:2000738 "positive regulation of stem cell differentiation" evidence=IEA

GO:0060218 "hematopoietic stem cell differentiation" evidence=IEA

GO:0060216 "definitive hemopoiesis" evidence=IEA

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

GO:0048539 "bone marrow development" evidence=IEA

GO:0048536 "spleen development" evidence=IEA

GO:0048103 "somatic stem cell division" evidence=IEA

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

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

GO:0008283 "cell proliferation" evidence=IEA

GO:0002011 "morphogenesis of an epithelial sheet" evidence=IEA

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

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

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

UNIPROTKB|F1N257 HOXB4 "Homeobox protein Hox-B4" [Bos taurus (taxid:9913)]

 Score = 320 (117.7 bits), Expect = 9.1e-29, P = 9.1e-29
 Identities = 65/104 (62%), Positives = 76/104 (73%)

Query:   101 SP-HGAYHGDLRYHWTNRAPLKYVKRGTVNAN---GETKRQRTSYTRYQTLELEKEFHFN 156
             SP H A    + Y W     ++ V   TVN N   GE KR RT+YTR Q LELEKEFH+N
Sbjct:   130 SPSHSACKEPVVYPW-----MRKVHVSTVNPNYAGGEPKRSRTAYTRQQVLELEKEFHYN 184

Query:   157 RYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNV 200
             RYLTRRRR+EIAHALCL+ERQIKIWFQNRRMKWKK+HK+ +  +
Sbjct:   185 RYLTRRRRVEIAHALCLSERQIKIWFQNRRMKWKKDHKLPNTKI 228

GO:0005634 "nucleus" evidence=IEA

GO:2000738 "positive regulation of stem cell differentiation" evidence=IEA

GO:0060218 "hematopoietic stem cell differentiation" evidence=IEA

GO:0060216 "definitive hemopoiesis" evidence=IEA

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

GO:0048539 "bone marrow development" evidence=IEA

GO:0048536 "spleen development" evidence=IEA

GO:0048103 "somatic stem cell division" evidence=IEA

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

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

GO:0008283 "cell proliferation" evidence=IEA

GO:0002011 "morphogenesis of an epithelial sheet" evidence=IEA

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

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

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

UNIPROTKB|Q08DG5 HOXB4 "Homeobox protein Hox-B4" [Bos taurus (taxid:9913)]

 Score = 320 (117.7 bits), Expect = 9.1e-29, P = 9.1e-29
 Identities = 65/104 (62%), Positives = 76/104 (73%)

Query:   101 SP-HGAYHGDLRYHWTNRAPLKYVKRGTVNAN---GETKRQRTSYTRYQTLELEKEFHFN 156
             SP H A    + Y W     ++ V   TVN N   GE KR RT+YTR Q LELEKEFH+N
Sbjct:   130 SPSHSACKEPVVYPW-----MRKVHVSTVNPNYAGGEPKRSRTAYTRQQVLELEKEFHYN 184

Query:   157 RYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNV 200
             RYLTRRRR+EIAHALCL+ERQIKIWFQNRRMKWKK+HK+ +  +
Sbjct:   185 RYLTRRRRVEIAHALCLSERQIKIWFQNRRMKWKKDHKLPNTKI 228

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

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

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

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

UNIPROTKB|P17483 HOXB4 "Homeobox protein Hox-B4" [Homo sapiens (taxid:9606)]

 Score = 320 (117.7 bits), Expect = 9.1e-29, P = 9.1e-29
 Identities = 65/104 (62%), Positives = 76/104 (73%)

Query:   101 SP-HGAYHGDLRYHWTNRAPLKYVKRGTVNAN---GETKRQRTSYTRYQTLELEKEFHFN 156
             SP H A    + Y W     ++ V   TVN N   GE KR RT+YTR Q LELEKEFH+N
Sbjct:   130 SPSHSACKEPVVYPW-----MRKVHVSTVNPNYAGGEPKRSRTAYTRQQVLELEKEFHYN 184

Query:   157 RYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNV 200
             RYLTRRRR+EIAHALCL+ERQIKIWFQNRRMKWKK+HK+ +  +
Sbjct:   185 RYLTRRRRVEIAHALCLSERQIKIWFQNRRMKWKKDHKLPNTKI 228

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

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

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

GO:0002011 "morphogenesis of an epithelial sheet" evidence=IEA

GO:0008283 "cell proliferation" evidence=IEA

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

GO:0048103 "somatic stem cell division" evidence=IEA

GO:0048536 "spleen development" evidence=IEA

GO:0048539 "bone marrow development" evidence=IEA

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

GO:0060216 "definitive hemopoiesis" evidence=IEA

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

GO:0005634 "nucleus" evidence=NAS

GO:0007275 "multicellular organismal development" evidence=NAS

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

GO:2000738 "positive regulation of stem cell differentiation" evidence=IDA

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

GO:0060218 "hematopoietic stem cell differentiation" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P15859	SCR_APIME	No assigned EC number	0.9213	0.3873	1.0	no	N/A
P09077	SCR_DROME	No assigned EC number	0.7394	0.4729	0.2517	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	222
pfam00046	57	pfam00046, Homeobox, Homeobox domain	5e-24
pfam00046	57	pfam00046, Homeobox, Homeobox domain	5e-24
smart00389	57	smart00389, HOX, Homeodomain	1e-19
smart00389	57	smart00389, HOX, Homeodomain	1e-19
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	2e-19
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	2e-19
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	3e-07
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	3e-07

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

 Score = 89.8 bits (224), Expect = 5e-24
 Identities = 33/57 (57%), Positives = 42/57 (73%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          +R+RT++T  Q  ELEKEF  NRY +   R E+A  L LTERQ+K+WFQNRR KWK+
Sbjct: 1  RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57

Length = 57

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

 Score = 89.8 bits (224), Expect = 5e-24
 Identities = 33/57 (57%), Positives = 42/57 (73%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           +R+RT++T  Q  ELEKEF  NRY +   R E+A  L LTERQ+K+WFQNRR KWK+
Sbjct: 1   RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57

Length = 57

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 78.4 bits (194), Expect = 1e-19
 Identities = 33/57 (57%), Positives = 41/57 (71%)

Query: 10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 66
           +R+RTS+T  Q  ELEKEF  N Y +R  R E+A  L L+ERQ+K+WFQNRR KWK
Sbjct: 1  KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

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

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 78.4 bits (194), Expect = 1e-19
 Identities = 33/57 (57%), Positives = 41/57 (71%)

Query: 134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190
            +R+RTS+T  Q  ELEKEF  N Y +R  R E+A  L L+ERQ+K+WFQNRR KWK
Sbjct: 1   KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

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

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

 Score = 78.1 bits (193), Expect = 2e-19
 Identities = 33/59 (55%), Positives = 40/59 (67%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69
          +R+RT +T  Q  ELEKEF  N Y +R  R E+A  L LTERQ+KIWFQNRR K K+  
Sbjct: 1  RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59

Length = 59

>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 = 78.1 bits (193), Expect = 2e-19
 Identities = 33/59 (55%), Positives = 40/59 (67%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193
           +R+RT +T  Q  ELEKEF  N Y +R  R E+A  L LTERQ+KIWFQNRR K K+  
Sbjct: 1   RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59

Length = 59

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

 Score = 48.2 bits (115), Expect = 3e-07
 Identities = 24/58 (41%), Positives = 37/58 (63%), Gaps = 2/58 (3%)

Query: 11  KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68
           KR+RT  T  Q + LE+EF  N Y +   RI+++  L +  + ++IWFQN+R K KK+
Sbjct: 54  KRRRT--TDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKK 109

Length = 156

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

 Score = 48.2 bits (115), Expect = 3e-07
 Identities = 24/58 (41%), Positives = 37/58 (63%), Gaps = 2/58 (3%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
           KR+RT  T  Q + LE+EF  N Y +   RI+++  L +  + ++IWFQN+R K KK+
Sbjct: 54  KRRRT--TDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKK 109

Length = 156

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	222
KOG0484|consensus	125		99.81
KOG0490|consensus	235		99.8
KOG0850|consensus	245		99.73
KOG0489|consensus	261		99.72
KOG2251|consensus	228		99.71
KOG0850|consensus	245		99.7
KOG0484|consensus	125		99.69
KOG0489|consensus	261		99.69
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.69
KOG0842|consensus	307		99.67
KOG0843|consensus	197		99.67
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.67
KOG0488|consensus	309		99.66
KOG0488|consensus	309		99.66
KOG0842|consensus	307		99.66
KOG0485|consensus	268		99.65
KOG0843|consensus	197		99.65
KOG0494|consensus	332		99.64
KOG2251|consensus	228		99.63
KOG0485|consensus	268		99.6
KOG0492|consensus	246		99.59
KOG0487|consensus	308		99.57
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.56
KOG0487|consensus	308		99.56
KOG0492|consensus	246		99.56
KOG0848|consensus	317		99.56
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.54
KOG0494|consensus	332		99.54
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.54
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.53
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.52
KOG0493|consensus	342		99.52
KOG0848|consensus	317		99.51
KOG0491|consensus	194		99.5
KOG0493|consensus	342		99.49
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.49
KOG3802|consensus	398		99.48
KOG0844|consensus	408		99.45
KOG0491|consensus	194		99.45
KOG0486|consensus	351		99.45
COG5576	156	Homeodomain-containing transcription factor [Trans	99.43
KOG3802|consensus	398		99.42
KOG4577|consensus	383		99.42
COG5576	156	Homeodomain-containing transcription factor [Trans	99.4
KOG0844|consensus	408		99.39
KOG0483|consensus	198		99.37
KOG0483|consensus	198		99.35
KOG4577|consensus	383		99.35
KOG0847|consensus	288		99.33
KOG0486|consensus	351		99.31
KOG0847|consensus	288		99.3
KOG1168|consensus	385		99.02
KOG0849|consensus	354		99.02
KOG0775|consensus	304		98.96
KOG0775|consensus	304		98.96
KOG1168|consensus	385		98.95
KOG0490|consensus	235		98.93
KOG0849|consensus	354		98.84
KOG0774|consensus	334		98.78
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.74
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.67
KOG0774|consensus	334		98.51
KOG1146|consensus	1406		98.51
KOG2252|consensus	558		98.45
KOG2252|consensus	558		98.33
KOG0773|consensus	342		98.04
KOG1146|consensus	1406		98.0
KOG3623|consensus	1007		97.69
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	97.61
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	97.53
KOG0773|consensus	342		96.32
KOG3623|consensus	1007		96.13
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	95.39
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	94.41
KOG3755|consensus	769		92.12
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	87.79
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	85.78
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	84.03
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	83.86
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	80.99

>KOG0484|consensus

Probab=99.81  E-value=4.9e-20  Score=125.75  Aligned_cols=70  Identities=37%  Similarity=0.562  Sum_probs=64.9

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhcc
Q psy11996          5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASM   74 (222)
Q Consensus         5 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~   74 (222)
                      ...+++||-||+||..||..||..|.+.+||++..|++||.++.|++.+|++||||||+|.+++++....
T Consensus        12 ~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~   81 (125)
T KOG0484|consen   12 TEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIA   81 (125)
T ss_pred             hHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            3456789999999999999999999999999999999999999999999999999999999998876643

>KOG0490|consensus

Probab=99.80  E-value=2.1e-19  Score=145.80  Aligned_cols=157  Identities=29%  Similarity=0.337  Sum_probs=123.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhccCCCCcccccccC
Q psy11996          7 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNNPNLYTQYQTQ   86 (222)
Q Consensus         7 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~~~~~~~~~~~~~   86 (222)
                      ..++|+.|+.|+..|+.+|+..|+..+||+...++.||..+++++..|++||+|+|+++++.+........  ..     
T Consensus        57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~~~~~~~~--~~-----  129 (235)
T KOG0490|consen   57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEERPLPEGEN--LP-----  129 (235)
T ss_pred             hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhcccccccc--CC-----
Confidence            45678999999999999999999999999999999999999999999999999999999987650000000  00     


Q ss_pred             CCCCCCCcccCCCCCCCCCCCCCcccccccCCCccccccccccCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHH
Q psy11996         87 GKSCTGRYQVRPITSPHGAYHGDLRYHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIE  166 (222)
Q Consensus        87 ~~~~~~~~~~~p~~sp~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~  166 (222)
                               ......+..               .............+.++.++.+...|+..|...|..+++|+...+..
T Consensus       130 ---------~~~~~~~~~---------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~  185 (235)
T KOG0490|consen  130 ---------DLSGTAPPS---------------ASRDKLDKGPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQ  185 (235)
T ss_pred             ---------CCCCCCCcc---------------ccccccccCCCccccCCCccccccchhHhhhhcccCCCCCchhhHHH
Confidence                     000000000               00011112233446677899999999999999999999999999999


Q ss_pred             HHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996        167 IAHALCLTERQIKIWFQNRRMKWKKEHK  194 (222)
Q Consensus       167 la~~l~l~~~~V~~WF~nrR~k~kk~~~  194 (222)
                      |+..+|+....|++||+|+|.+.++...
T Consensus       186 l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  186 LAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             HHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            9999999999999999999999998765

>KOG0850|consensus

Probab=99.73  E-value=6.2e-18  Score=131.65  Aligned_cols=70  Identities=40%  Similarity=0.617  Sum_probs=64.9

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhcc
Q psy11996          5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASM   74 (222)
Q Consensus         5 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~   74 (222)
                      ..+++-|+.||.|+..||..|+..|+++.|+...||.+||+.|||+.+||+|||||||.|.||.++.+..
T Consensus       117 gk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~  186 (245)
T KOG0850|consen  117 GKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSG  186 (245)
T ss_pred             CCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCC
Confidence            4567789999999999999999999999999999999999999999999999999999999999885543

>KOG0489|consensus

Probab=99.72  E-value=1e-17  Score=137.55  Aligned_cols=87  Identities=64%  Similarity=1.016  Sum_probs=73.0

Q ss_pred             cccccccCCCccccccccccCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhH
Q psy11996        110 LRYHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW  189 (222)
Q Consensus       110 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~  189 (222)
                      .++||+......   .+.....+..+|.|+.||..|+.+||..|..|.|.+...|.+||..|.|+++||+|||||||+||
T Consensus       138 ~~~p~~~~~~~~---~~~~~~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~  214 (261)
T KOG0489|consen  138 QIYPWMKSTANY---LSSSETGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKW  214 (261)
T ss_pred             ccccchhhhhcc---cccccccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHH
Confidence            455555444332   12223345678999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhcccCC
Q psy11996        190 KKEHKMASMN  199 (222)
Q Consensus       190 kk~~~~~~~~  199 (222)
                      ||..+...+.
T Consensus       215 Kk~~k~~~~~  224 (261)
T KOG0489|consen  215 KKENKAKSSQ  224 (261)
T ss_pred             HHhhcccccc
Confidence            9999988877

>KOG2251|consensus

Probab=99.71  E-value=5.7e-17  Score=125.76  Aligned_cols=68  Identities=32%  Similarity=0.524  Sum_probs=64.1

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996          5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA   72 (222)
Q Consensus         5 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~   72 (222)
                      ...++.||.||+|+..|+.+||.+|.++.||+...+++||.+|+|.+.+|+|||+|||+|++++.+..
T Consensus        32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            45678899999999999999999999999999999999999999999999999999999999987764

>KOG0850|consensus

Probab=99.70  E-value=3.7e-17  Score=127.36  Aligned_cols=69  Identities=41%  Similarity=0.624  Sum_probs=63.7

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccC
Q psy11996        130 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASM  198 (222)
Q Consensus       130 ~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~  198 (222)
                      +..+.|+.||.++.-||..|...|++++|+-..||.+||+.|||+..||+|||||||.|.||..+.++.
T Consensus       118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~  186 (245)
T KOG0850|consen  118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSG  186 (245)
T ss_pred             CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCC
Confidence            345677889999999999999999999999999999999999999999999999999999999985443

>KOG0484|consensus

Probab=99.69  E-value=1.3e-17  Score=113.89  Aligned_cols=66  Identities=38%  Similarity=0.593  Sum_probs=61.8

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        130 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       130 ~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      ...+.++.|+.||..|+..|+..|...+||++-.+++||.++.|++..|++||||||+|.+|+++.
T Consensus        13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~   78 (125)
T KOG0484|consen   13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERA   78 (125)
T ss_pred             HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence            345678889999999999999999999999999999999999999999999999999999999665

>KOG0489|consensus

Probab=99.69  E-value=8.1e-17  Score=132.26  Aligned_cols=71  Identities=76%  Similarity=1.191  Sum_probs=65.4

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhccC
Q psy11996          5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMN   75 (222)
Q Consensus         5 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~~   75 (222)
                      ....+.||.||.||..||-+||+-|..|.|+++..|.++|..|.|+++||+|||||||+|+||..+.....
T Consensus       154 ~~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~  224 (261)
T KOG0489|consen  154 ETGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ  224 (261)
T ss_pred             cccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence            44566899999999999999999999999999999999999999999999999999999999987766544

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.69  E-value=8.3e-17  Score=102.04  Aligned_cols=57  Identities=53%  Similarity=0.704  Sum_probs=55.0

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996         11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus        11 ~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      |++|+.||.+|+..|+..|..++||+..+++.||..+||+..+|.+||+|+|.+.++
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            578999999999999999999999999999999999999999999999999999875

; 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 ....

>KOG0842|consensus

Probab=99.67  E-value=6.5e-17  Score=133.01  Aligned_cols=74  Identities=35%  Similarity=0.609  Sum_probs=67.7

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccCCCCCCC
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNVIPYH  204 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~~~~~~~  204 (222)
                      ..++||.|..|+..|+.+||+.|...+|++..||+.||..|.|+..||+|||||||.|+||.++...+......
T Consensus       150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~~~  223 (307)
T KOG0842|consen  150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALLLA  223 (307)
T ss_pred             cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcccCC
Confidence            33667788899999999999999999999999999999999999999999999999999999998887776644

>KOG0843|consensus

Probab=99.67  E-value=9.1e-17  Score=120.67  Aligned_cols=64  Identities=42%  Similarity=0.675  Sum_probs=60.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996          9 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA   72 (222)
Q Consensus         9 ~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~   72 (222)
                      +.||.||.||.+||..||..|+.+.|....+|+.||..|+|++.||++||||||.|.||.....
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~  164 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED  164 (197)
T ss_pred             CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence            6789999999999999999999999999999999999999999999999999999999976554

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.67  E-value=1.7e-16  Score=100.62  Aligned_cols=57  Identities=53%  Similarity=0.704  Sum_probs=54.8

Q ss_pred             CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996        135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  191 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk  191 (222)
                      ++.|+.|+.+|+.+|+..|..+++|+..+++.||..+||+..+|.+||+|+|.+.|+
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            467899999999999999999999999999999999999999999999999999886

; 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=99.66  E-value=1.4e-16  Score=133.12  Aligned_cols=67  Identities=42%  Similarity=0.747  Sum_probs=62.2

Q ss_pred             cCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        129 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       129 ~~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      ....+.++.|+.||..|+..||..|++.+|.+..+|..||..|||+..||++||||||+|||+....
T Consensus       167 ~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~  233 (309)
T KOG0488|consen  167 STPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE  233 (309)
T ss_pred             CCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence            3446778899999999999999999999999999999999999999999999999999999998554

>KOG0488|consensus

Probab=99.66  E-value=1.2e-16  Score=133.38  Aligned_cols=66  Identities=42%  Similarity=0.754  Sum_probs=62.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhh
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM   71 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~   71 (222)
                      ..+++|+.||.||..||..||+.|+...|++..+|.+||..|||+..||++||||||+|||+....
T Consensus       168 ~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~  233 (309)
T KOG0488|consen  168 TPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE  233 (309)
T ss_pred             CCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence            346788889999999999999999999999999999999999999999999999999999997654

>KOG0842|consensus

Probab=99.66  E-value=5.9e-17  Score=133.28  Aligned_cols=70  Identities=37%  Similarity=0.628  Sum_probs=64.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhccCCC
Q psy11996          8 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNNP   77 (222)
Q Consensus         8 ~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~~~~   77 (222)
                      .++||.|..||..|+.+||..|....|++..||+.||..|+||++||+|||||||.|.||..+...+...
T Consensus       151 ~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~  220 (307)
T KOG0842|consen  151 RKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEAL  220 (307)
T ss_pred             ccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcc
Confidence            3567778899999999999999999999999999999999999999999999999999999887766544

>KOG0485|consensus

Probab=99.65  E-value=9.4e-17  Score=123.82  Aligned_cols=65  Identities=45%  Similarity=0.797  Sum_probs=60.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhh
Q psy11996          7 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM   71 (222)
Q Consensus         7 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~   71 (222)
                      ++++||.||+|+..|+..||..|+...|++..+|..||+.|.|++.||++||||||.||||+...
T Consensus       101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa  165 (268)
T KOG0485|consen  101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA  165 (268)
T ss_pred             ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence            34788899999999999999999999999999999999999999999999999999999997543

>KOG0843|consensus

Probab=99.65  E-value=2e-16  Score=118.84  Aligned_cols=64  Identities=42%  Similarity=0.675  Sum_probs=60.9

Q ss_pred             CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcc
Q psy11996        133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA  196 (222)
Q Consensus       133 ~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~  196 (222)
                      +.+|.||.|+.+|+..||..|+.++|....+++.||..|+|++.||++||||||.|.||.....
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~  164 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED  164 (197)
T ss_pred             CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence            6788999999999999999999999999999999999999999999999999999999986654

>KOG0494|consensus

Probab=99.64  E-value=2.2e-16  Score=124.75  Aligned_cols=65  Identities=42%  Similarity=0.619  Sum_probs=59.7

Q ss_pred             CCCC-CCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhcc
Q psy11996         10 TKRQ-RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASM   74 (222)
Q Consensus        10 ~~r~-R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~   74 (222)
                      +||. ||.||..|+..||+.|++.+||+...|+-||..+.|.+++|++||||||+||||.++.-..
T Consensus       140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~  205 (332)
T KOG0494|consen  140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGG  205 (332)
T ss_pred             ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCc
Confidence            3444 9999999999999999999999999999999999999999999999999999998776543

>KOG2251|consensus

Probab=99.63  E-value=1.3e-15  Score=118.28  Aligned_cols=67  Identities=33%  Similarity=0.527  Sum_probs=62.9

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcc
Q psy11996        130 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA  196 (222)
Q Consensus       130 ~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~  196 (222)
                      ...+.+|.||.|+-.|+.+||.+|.+.+||+...+++||.+|+|.+.+|+|||+|||+|+|++++..
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            4457788999999999999999999999999999999999999999999999999999999998864

>KOG0485|consensus

Probab=99.60  E-value=2.8e-15  Score=115.69  Aligned_cols=65  Identities=45%  Similarity=0.797  Sum_probs=60.6

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      ...+|+.|++|+..|+..||..|+...|.+..++..||.+|.|++.||++||||||.|||++...
T Consensus       101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa  165 (268)
T KOG0485|consen  101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA  165 (268)
T ss_pred             ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence            44677889999999999999999999999999999999999999999999999999999998543

>KOG0492|consensus

Probab=99.59  E-value=1.4e-15  Score=116.57  Aligned_cols=65  Identities=42%  Similarity=0.654  Sum_probs=60.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhh
Q psy11996          7 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM   71 (222)
Q Consensus         7 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~   71 (222)
                      -+..|++||-||..||..||.-|...+|.++.++.+++..|.|++.||+|||||||+|.||....
T Consensus       141 hk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQea  205 (246)
T KOG0492|consen  141 HKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEA  205 (246)
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHH
Confidence            35568899999999999999999999999999999999999999999999999999999986443

>KOG0487|consensus

Probab=99.57  E-value=1.2e-15  Score=125.59  Aligned_cols=65  Identities=55%  Similarity=0.889  Sum_probs=61.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996          8 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA   72 (222)
Q Consensus         8 ~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~   72 (222)
                      +..||||--+|..|+.+||+-|..|.|++.+.|.+|++.|+|+++||+|||||||+|.||..+..
T Consensus       233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~  297 (308)
T KOG0487|consen  233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN  297 (308)
T ss_pred             cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence            56789999999999999999999999999999999999999999999999999999999987533

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.56  E-value=4e-15  Score=93.20  Aligned_cols=53  Identities=23%  Similarity=0.373  Sum_probs=50.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhCCC----CCHHHHHHHHHHhCCChHHHHHHhhcch
Q psy11996         10 TKRQRTSYTRYQTLELEKEFHFNRY----LTRRRRIEIAHALCLTERQIKIWFQNRR   62 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~~~~~----p~~~~~~~la~~~~l~~~~v~~WF~nrR   62 (222)
                      +||.||.||.+|+..|+..|..+.|    |+..++++||..+||++.+|++||+|-+
T Consensus         1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            3789999999999999999999999    9999999999999999999999999965

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

>KOG0487|consensus

Probab=99.56  E-value=4.9e-15  Score=122.04  Aligned_cols=64  Identities=56%  Similarity=0.905  Sum_probs=60.5

Q ss_pred             CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       132 ~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      ...||+|--+|+.|+.+||..|..|.|++.+.|-+|+..|+|+++||+|||||||+|.||..+.
T Consensus       233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re  296 (308)
T KOG0487|consen  233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRE  296 (308)
T ss_pred             cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhh
Confidence            4667888999999999999999999999999999999999999999999999999999998863

>KOG0492|consensus

Probab=99.56  E-value=3.8e-15  Score=114.26  Aligned_cols=65  Identities=42%  Similarity=0.655  Sum_probs=60.9

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996        130 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK  194 (222)
Q Consensus       130 ~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~  194 (222)
                      +....++.|+-||..|+..||..|...+|.+++++.+++..|.|++.||++||||||+|.||.+.
T Consensus       140 Khk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe  204 (246)
T KOG0492|consen  140 KHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE  204 (246)
T ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence            45567889999999999999999999999999999999999999999999999999999999754

>KOG0848|consensus

Probab=99.56  E-value=3.6e-15  Score=118.46  Aligned_cols=63  Identities=56%  Similarity=0.840  Sum_probs=59.0

Q ss_pred             CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcc
Q psy11996        134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA  196 (222)
Q Consensus       134 ~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~  196 (222)
                      +-+.|.++|+-|+.+||+.|..++|.++..+.+||..|||+++||+|||||||+|+||..|..
T Consensus       199 kDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk  261 (317)
T KOG0848|consen  199 KDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK  261 (317)
T ss_pred             ccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence            346788999999999999999999999999999999999999999999999999999987765

>smart00389 HOX Homeodomain

Probab=99.54  E-value=1.2e-14  Score=91.57  Aligned_cols=55  Identities=58%  Similarity=0.912  Sum_probs=51.9

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHH
Q psy11996         11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW   65 (222)
Q Consensus        11 ~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~   65 (222)
                      ++.|+.|+.+|+.+|+..|..++||+..++..||..+||+..+|+.||+|+|++.
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            3567889999999999999999999999999999999999999999999999864

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

>KOG0494|consensus

Probab=99.54  E-value=2.6e-14  Score=113.11  Aligned_cols=65  Identities=40%  Similarity=0.601  Sum_probs=59.8

Q ss_pred             CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhccc
Q psy11996        133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS  197 (222)
Q Consensus       133 ~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~  197 (222)
                      +.+..||.||..|+..||..|++.+||+...++.||.++.|.+..|++||||||+||||.++.-.
T Consensus       140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg  204 (332)
T KOG0494|consen  140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWG  204 (332)
T ss_pred             ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcC
Confidence            33445899999999999999999999999999999999999999999999999999999987744

>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=99.54  E-value=2.3e-14  Score=91.22  Aligned_cols=57  Identities=58%  Similarity=0.830  Sum_probs=53.9

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996         11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus        11 ~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      ++.|+.|+..|+.+|++.|..++||+..++..||..+||+..+|++||+|+|.+.++
T Consensus         1 ~~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~   57 (59)
T cd00086           1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR   57 (59)
T ss_pred             CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence            356789999999999999999999999999999999999999999999999998775

>smart00389 HOX Homeodomain

Probab=99.53  E-value=1.8e-14  Score=90.82  Aligned_cols=55  Identities=60%  Similarity=0.915  Sum_probs=51.7

Q ss_pred             CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHH
Q psy11996        136 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK  190 (222)
Q Consensus       136 ~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k  190 (222)
                      +.++.|+.+|+.+|+..|..++||+..++..||..+||+..+|.+||+|+|.+.+
T Consensus         2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~   56 (56)
T smart00389        2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK   56 (56)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence            4577899999999999999999999999999999999999999999999998753

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

>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=3.3e-14  Score=90.53  Aligned_cols=57  Identities=58%  Similarity=0.816  Sum_probs=53.7

Q ss_pred             CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996        136 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  192 (222)
Q Consensus       136 ~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~  192 (222)
                      +.+..++..++.+|+..|..++||+..++..||..+||+..+|.+||+|+|.+.++.
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            457889999999999999999999999999999999999999999999999998763

>KOG0493|consensus

Probab=99.52  E-value=1.2e-14  Score=115.14  Aligned_cols=64  Identities=53%  Similarity=0.759  Sum_probs=59.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH   69 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~   69 (222)
                      ....-||+||.||.+||..|+..|..+.|+....|.+||.+|||.+.||+|||||+|+|.||..
T Consensus       242 ~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT  305 (342)
T KOG0493|consen  242 SSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST  305 (342)
T ss_pred             ccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence            3445688999999999999999999999999999999999999999999999999999999843

>KOG0848|consensus

Probab=99.51  E-value=6.4e-15  Score=117.09  Aligned_cols=65  Identities=54%  Similarity=0.809  Sum_probs=59.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996          8 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA   72 (222)
Q Consensus         8 ~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~   72 (222)
                      +++-|.|.++|..|.-+||+.|.-++|+.+..+.+||..|||+++||+|||||||+|+||..+.+
T Consensus       197 RTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk  261 (317)
T KOG0848|consen  197 RTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK  261 (317)
T ss_pred             ecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence            34445688999999999999999999999999999999999999999999999999999876655

>KOG0491|consensus

Probab=99.50  E-value=1.2e-13  Score=102.39  Aligned_cols=70  Identities=41%  Similarity=0.621  Sum_probs=64.0

Q ss_pred             CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccCCCCC
Q psy11996        133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNVIP  202 (222)
Q Consensus       133 ~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~~~~~  202 (222)
                      ..++.|++|+..|+..|++.|+...|.+..++.+||..|+|++.||+.||||||+|.||..+.......+
T Consensus        99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p~nS~  168 (194)
T KOG0491|consen   99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQPKNSN  168 (194)
T ss_pred             HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCCCCCC
Confidence            4567799999999999999999999999999999999999999999999999999999998887654444

>KOG0493|consensus

Probab=99.49  E-value=2.8e-14  Score=113.05  Aligned_cols=62  Identities=53%  Similarity=0.746  Sum_probs=58.1

Q ss_pred             CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       134 ~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      -||.|+.||.+||..|+..|..+.|.+...+..||.+|||.+.||++||||+|+|.||-...
T Consensus       246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgs  307 (342)
T KOG0493|consen  246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGS  307 (342)
T ss_pred             hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCC
Confidence            46789999999999999999999999999999999999999999999999999999996443

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.49  E-value=3e-14  Score=89.24  Aligned_cols=52  Identities=23%  Similarity=0.379  Sum_probs=50.2

Q ss_pred             CCCCCcCCHHHHHHHHHhhhhcCC----CCHHHHHHHHHHcCCChhhHHHHHhhhh
Q psy11996        135 KRQRTSYTRYQTLELEKEFHFNRY----LTRRRRIEIAHALCLTERQIKIWFQNRR  186 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F~~~~~----p~~~~~~~la~~l~l~~~~V~~WF~nrR  186 (222)
                      ++.||.||.+|+..|+..|+.++|    |+..++++||..+||++.+|++||+|-+
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            688999999999999999999999    9999999999999999999999999965

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

>KOG3802|consensus

Probab=99.48  E-value=1.4e-14  Score=121.71  Aligned_cols=70  Identities=30%  Similarity=0.358  Sum_probs=64.0

Q ss_pred             CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccCCCC
Q psy11996        132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNVI  201 (222)
Q Consensus       132 ~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~~~~  201 (222)
                      +++||+||.|+...+..||.+|.+|+.|+.+|+..||++|+|.+++|+|||||||.|.||......+..+
T Consensus       292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~~~~~~~P  361 (398)
T KOG3802|consen  292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITPFPSAGSP  361 (398)
T ss_pred             ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCCCccCCCC
Confidence            3778899999999999999999999999999999999999999999999999999999998884444444

>KOG0844|consensus

Probab=99.45  E-value=1.8e-14  Score=116.46  Aligned_cols=70  Identities=47%  Similarity=0.690  Sum_probs=63.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhccC
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMN   75 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~~   75 (222)
                      +.+..||.||.||.+|+..||+.|-+..|-++..|++||..|+|++..|++||||||+|+||+.-...+.
T Consensus       177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaWP  246 (408)
T KOG0844|consen  177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAWP  246 (408)
T ss_pred             ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccCC
Confidence            4556799999999999999999999999999999999999999999999999999999999976554443

>KOG0491|consensus

Probab=99.45  E-value=8.4e-14  Score=103.16  Aligned_cols=64  Identities=45%  Similarity=0.711  Sum_probs=59.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhc
Q psy11996         10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS   73 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~   73 (222)
                      .++-||+|+..|+..|++.|+...|.+..++.+||..|+|+++||+.||||||+|-||..+...
T Consensus       100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~  163 (194)
T KOG0491|consen  100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ  163 (194)
T ss_pred             hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence            4677999999999999999999999999999999999999999999999999999999876554

>KOG0486|consensus

Probab=99.45  E-value=4.5e-14  Score=114.71  Aligned_cols=66  Identities=42%  Similarity=0.681  Sum_probs=62.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhc
Q psy11996          8 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS   73 (222)
Q Consensus         8 ~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~   73 (222)
                      .++||.||.||..||..||..|.++.||+...|+++|..++|++.+|++||+|||+||++++....
T Consensus       110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~  175 (351)
T KOG0486|consen  110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ  175 (351)
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence            367899999999999999999999999999999999999999999999999999999999876654

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.43  E-value=2.3e-13  Score=102.68  Aligned_cols=68  Identities=32%  Similarity=0.521  Sum_probs=62.0

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996          5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA   72 (222)
Q Consensus         5 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~   72 (222)
                      +.....+++|++.|.+|+.+|+..|..++||+...+..|+..++|+++-|++||||+|++.++....+
T Consensus        46 ~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~  113 (156)
T COG5576          46 DGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGK  113 (156)
T ss_pred             cCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccc
Confidence            34456788899999999999999999999999999999999999999999999999999999876544

>KOG3802|consensus

Probab=99.42  E-value=8.8e-14  Score=116.94  Aligned_cols=67  Identities=31%  Similarity=0.405  Sum_probs=62.5

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996          4 VNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus         4 ~~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      +.+..++||+||.|......+||++|.+|+.|+..|+..||.+|+|..++|+|||+|||.|.||...
T Consensus       288 i~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  288 IGAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             hhccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            4455588999999999999999999999999999999999999999999999999999999999655

>KOG4577|consensus

Probab=99.42  E-value=1.7e-13  Score=110.07  Aligned_cols=71  Identities=30%  Similarity=0.415  Sum_probs=65.4

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhcc
Q psy11996          4 VNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASM   74 (222)
Q Consensus         4 ~~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~   74 (222)
                      .+.....||+||++|..||+.|+..|...+.|.+..|+.|+.++||.-+.|++||||||+|.||-++.++-
T Consensus       161 l~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR  231 (383)
T KOG4577|consen  161 LEGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGR  231 (383)
T ss_pred             cccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcch
Confidence            45667789999999999999999999999999999999999999999999999999999999987776654

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.40  E-value=5.5e-13  Score=100.66  Aligned_cols=72  Identities=31%  Similarity=0.473  Sum_probs=64.0

Q ss_pred             cCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccCCC
Q psy11996        129 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNV  200 (222)
Q Consensus       129 ~~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~~~  200 (222)
                      +.....++.|...+.+|+.+|+..|..+++|+..++..|+..++|+++-|++||||+|++.|+....+....
T Consensus        46 ~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~~~~  117 (156)
T COG5576          46 DGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQR  117 (156)
T ss_pred             cCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccchhcc
Confidence            344566778889999999999999999999999999999999999999999999999999999877754443

>KOG0844|consensus

Probab=99.39  E-value=2.8e-14  Score=115.37  Aligned_cols=62  Identities=52%  Similarity=0.777  Sum_probs=59.0

Q ss_pred             CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996        132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH  193 (222)
Q Consensus       132 ~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~  193 (222)
                      ...+|.||.||.+|+..||+.|.+..|.+...+.+||..|+|.+.-|++||||||+|+|+++
T Consensus       179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQR  240 (408)
T KOG0844|consen  179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQR  240 (408)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhh
Confidence            35688999999999999999999999999999999999999999999999999999999974

>KOG0483|consensus

Probab=99.37  E-value=5.7e-13  Score=103.95  Aligned_cols=60  Identities=37%  Similarity=0.621  Sum_probs=55.7

Q ss_pred             CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996        134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH  193 (222)
Q Consensus       134 ~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~  193 (222)
                      ...+...|+.+|+..|+..|+...+.....+..||.+|||..+||.+||||||++||.++
T Consensus        50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq  109 (198)
T KOG0483|consen   50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ  109 (198)
T ss_pred             cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence            345567899999999999999999999999999999999999999999999999999874

>KOG0483|consensus

Probab=99.35  E-value=9e-13  Score=102.84  Aligned_cols=60  Identities=37%  Similarity=0.621  Sum_probs=55.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996         10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH   69 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~   69 (222)
                      ..+++.+|+.+|+..||..|+...+....++..||..|||.++||.+||||||+++|.+.
T Consensus        50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq  109 (198)
T KOG0483|consen   50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ  109 (198)
T ss_pred             cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence            455667899999999999999999999999999999999999999999999999999753

>KOG4577|consensus

Probab=99.35  E-value=9e-13  Score=105.96  Aligned_cols=70  Identities=30%  Similarity=0.427  Sum_probs=64.1

Q ss_pred             cccCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcc
Q psy11996        127 TVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA  196 (222)
Q Consensus       127 ~~~~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~  196 (222)
                      +.+..+..||+|+.||..|++.|+..|...+.|....++.|+.++||..+.|++||||||+|+|+-.|.+
T Consensus       160 ~l~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDA  229 (383)
T KOG4577|consen  160 ELEGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDA  229 (383)
T ss_pred             ccccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhc
Confidence            3445668899999999999999999999999999999999999999999999999999999999876543

>KOG0847|consensus

Probab=99.33  E-value=1.1e-12  Score=101.52  Aligned_cols=67  Identities=43%  Similarity=0.820  Sum_probs=62.5

Q ss_pred             cCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        129 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       129 ~~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      ...++.+..|..|+..|+..|+..|+..+|+-.+++.+||..+|+++.||++||||||.||||+...
T Consensus       162 ~kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa  228 (288)
T KOG0847|consen  162 NLNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA  228 (288)
T ss_pred             CcCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence            3567888889999999999999999999999999999999999999999999999999999998654

>KOG0486|consensus

Probab=99.31  E-value=9.8e-13  Score=107.03  Aligned_cols=65  Identities=43%  Similarity=0.689  Sum_probs=61.5

Q ss_pred             CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhccc
Q psy11996        133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS  197 (222)
Q Consensus       133 ~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~  197 (222)
                      +.++.|+.|+..|+..||..|.++.||+...+++||.-++|++..|++||+|||+||+|.+....
T Consensus       111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~  175 (351)
T KOG0486|consen  111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ  175 (351)
T ss_pred             hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence            45677899999999999999999999999999999999999999999999999999999988766

>KOG0847|consensus

Probab=99.30  E-value=2e-12  Score=100.14  Aligned_cols=66  Identities=42%  Similarity=0.813  Sum_probs=61.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhh
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM   71 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~   71 (222)
                      .+++++..|.+|+..|+..|+..|+...|+-..++.+||..+|+++.+|++||||||.||||+...
T Consensus       163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa  228 (288)
T KOG0847|consen  163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA  228 (288)
T ss_pred             cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence            456677788999999999999999999999999999999999999999999999999999997543

>KOG1168|consensus

Probab=99.02  E-value=4.9e-11  Score=96.13  Aligned_cols=63  Identities=32%  Similarity=0.451  Sum_probs=59.3

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996        130 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  192 (222)
Q Consensus       130 ~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~  192 (222)
                      ..+.+||+|+.+.......||.+|...+.|+.+.+..||++|+|.+..|++||||.|+|.||.
T Consensus       305 ~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm  367 (385)
T KOG1168|consen  305 PGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM  367 (385)
T ss_pred             CccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence            455778899999999999999999999999999999999999999999999999999999884

>KOG0849|consensus

Probab=99.02  E-value=9.5e-10  Score=94.11  Aligned_cols=65  Identities=34%  Similarity=0.601  Sum_probs=60.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      -+++.+|.||+|+.+|+..|++.|+.++||+...|+.||.++++++..|++||+|+|+++++...
T Consensus       172 ~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~  236 (354)
T KOG0849|consen  172 LQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR  236 (354)
T ss_pred             ccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence            45567888999999999999999999999999999999999999999999999999999999764

>KOG0775|consensus

Probab=98.96  E-value=3e-09  Score=85.42  Aligned_cols=49  Identities=31%  Similarity=0.405  Sum_probs=45.4

Q ss_pred             HHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996         19 RYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus        19 ~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      ..-...|.++|..++||+..++.+||+.+||+..||.+||+|||.++|-
T Consensus       185 ekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa  233 (304)
T KOG0775|consen  185 EKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA  233 (304)
T ss_pred             HhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence            3346789999999999999999999999999999999999999999983

>KOG0775|consensus

Probab=98.96  E-value=7.1e-10  Score=88.93  Aligned_cols=53  Identities=28%  Similarity=0.403  Sum_probs=48.3

Q ss_pred             CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996        141 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH  193 (222)
Q Consensus       141 ~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~  193 (222)
                      |-..-+.+|+++|..++||+..++.+||+.+||+..||-+||+|||+++|-..
T Consensus       183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~  235 (304)
T KOG0775|consen  183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAA  235 (304)
T ss_pred             hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhcc
Confidence            44557889999999999999999999999999999999999999999999543

>KOG1168|consensus

Probab=98.95  E-value=1.7e-10  Score=93.08  Aligned_cols=67  Identities=31%  Similarity=0.446  Sum_probs=62.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA   72 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~   72 (222)
                      .++.+||+||.+...+...||++|...+.|+.+.+..+|++|.|....|++||+|.|.|.||.....
T Consensus       305 ~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa  371 (385)
T KOG1168|consen  305 PGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSA  371 (385)
T ss_pred             CccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhh
Confidence            4567899999999999999999999999999999999999999999999999999999999965543

>KOG0490|consensus

Probab=98.93  E-value=8.6e-10  Score=89.33  Aligned_cols=64  Identities=31%  Similarity=0.343  Sum_probs=60.5

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK  194 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~  194 (222)
                      ..+.++.|+.|+..|+.+|+..|+.++||+...++.||..+++++..|++||+|+|+++++..+
T Consensus        57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~  120 (235)
T KOG0490|consen   57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER  120 (235)
T ss_pred             hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence            4467889999999999999999999999999999999999999999999999999999999875

>KOG0849|consensus

Probab=98.84  E-value=8e-09  Score=88.48  Aligned_cols=63  Identities=35%  Similarity=0.612  Sum_probs=59.1

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH  193 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~  193 (222)
                      ....++.|+.|+..|+..|+..|+.++||+...++.||.++++++..|.+||+|+|++++|..
T Consensus       173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~  235 (354)
T KOG0849|consen  173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH  235 (354)
T ss_pred             cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence            335566789999999999999999999999999999999999999999999999999999998

>KOG0774|consensus

Probab=98.78  E-value=1.1e-08  Score=81.63  Aligned_cols=60  Identities=28%  Similarity=0.523  Sum_probs=55.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHh---hhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996         10 TKRQRTSYTRYQTLELEKEF---HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH   69 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f---~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~   69 (222)
                      .+|+|..|+..-..+|..+|   -.++||+.+.+++||.+.|++..||..||.|+|-+.+|..
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~  250 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM  250 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence            46888999999999999999   4588999999999999999999999999999999988753

>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=1.1e-08  Score=59.41  Aligned_cols=34  Identities=32%  Similarity=0.589  Sum_probs=28.9

Q ss_pred             hcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhh
Q psy11996        155 FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK  188 (222)
Q Consensus       155 ~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k  188 (222)
                      .++||+.+++..||.++||+..||.+||-|.|.+
T Consensus         7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR   40 (40)
T PF05920_consen    7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR   40 (40)
T ss_dssp             TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence            4799999999999999999999999999999864

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

>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=98.67  E-value=2.3e-08  Score=57.99  Aligned_cols=34  Identities=32%  Similarity=0.589  Sum_probs=28.5

Q ss_pred             hCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhH
Q psy11996         31 FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK   64 (222)
Q Consensus        31 ~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k   64 (222)
                      .+|||+.++++.||..+||+..||..||-|.|.+
T Consensus         7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR   40 (40)
T PF05920_consen    7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR   40 (40)
T ss_dssp             TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence            4799999999999999999999999999998853

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

>KOG0774|consensus

Probab=98.51  E-value=6.2e-08  Score=77.35  Aligned_cols=61  Identities=28%  Similarity=0.527  Sum_probs=56.5

Q ss_pred             CCCCCCCcCCHHHHHHHHHhhh---hcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996        133 ETKRQRTSYTRYQTLELEKEFH---FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH  193 (222)
Q Consensus       133 ~~~~~r~~~~~~q~~~L~~~F~---~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~  193 (222)
                      ..+|+|..|++.-.++|..+|.   .++||+.+.+++||.+++++..||.+||.|+|-+.+|..
T Consensus       187 darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~  250 (334)
T KOG0774|consen  187 DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM  250 (334)
T ss_pred             HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence            3578899999999999999996   699999999999999999999999999999999998873

>KOG1146|consensus

Probab=98.51  E-value=2e-06  Score=82.24  Aligned_cols=187  Identities=18%  Similarity=0.176  Sum_probs=119.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhccCCCC-----------
Q psy11996         10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNNPN-----------   78 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~~~~~-----------   78 (222)
                      .++.++.+-.+++..|-.+|-.+..|+...+..|....+.+.+++.+||.+-+.+.++....+..-...           
T Consensus       705 ~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~v~g~~~~c~l~~y~t~~kan  784 (1406)
T KOG1146|consen  705 DKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQVPGDVPSCKLKPYATNTKAN  784 (1406)
T ss_pred             cccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhcccCCCCcceecccccccchh
Confidence            356678888899999999999999999999999999999999999999999998888765111111000           


Q ss_pred             ---------------cc---------------------cccccCCCCCCCCcccCCC--CCCCCCCCCCc--cc------
Q psy11996         79 ---------------LY---------------------TQYQTQGKSCTGRYQVRPI--TSPHGAYHGDL--RY------  112 (222)
Q Consensus        79 ---------------~~---------------------~~~~~~~~~~~~~~~~~p~--~sp~~~~~~~~--~~------  112 (222)
                                     ..                     .+...-+..|.-.......  .......+...  .+      
T Consensus       785 fqlh~Ktdkh~qk~~~~~hikegg~a~~~~t~~la~~~~P~~l~cn~cd~~Tns~~~L~lh~~~~~he~~~~~~ks~~~l  864 (1406)
T KOG1146|consen  785 FQLHNKTDKHVQKYQLRAHIKEGGPANEYPTKTLASGPNPVHLKCNACDTPTNSPEPLLLHTPPSEHEGPEEIYKSLLSL  864 (1406)
T ss_pred             hhhhcccchhhhccchhhhhhccCCccCCcchhhhcCCCccccccccccCCCCCccccccCCCCCccccccccchhHHHH
Confidence                           00                     0011111111111000000  00000111100  00      


Q ss_pred             ----ccccCC------------Cc-cccccccccCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCh
Q psy11996        113 ----HWTNRA------------PL-KYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTE  175 (222)
Q Consensus       113 ----p~~~~~------------~~-~~~~~~~~~~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~  175 (222)
                          ..++-+            +. ........-..--.+..|+.++..|+..|...|....+|...+.+.|...+++..
T Consensus       865 ~~~ls~~~~s~~~as~~~s~~~~~~~~s~~s~~~~~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~  944 (1406)
T KOG1146|consen  865 ACSLSAGDLSDSSASSLASPESPGGGPSGGSGVPDGMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPK  944 (1406)
T ss_pred             HHHhhccccccccccccccccCCCCCCCCCcccchhhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCc
Confidence                000000            00 0000001111113456789999999999999999999999999999999999999


Q ss_pred             hhHHHHHhhhhhhHHHhhhcc
Q psy11996        176 RQIKIWFQNRRMKWKKEHKMA  196 (222)
Q Consensus       176 ~~V~~WF~nrR~k~kk~~~~~  196 (222)
                      +.|.+||+|-|.+.++..-.+
T Consensus       945 ~~i~vw~qna~~~s~k~~~n~  965 (1406)
T KOG1146|consen  945 RVIQVWFQNARAKSKKAKLNG  965 (1406)
T ss_pred             chhHHhhhhhhhhhhhhhhcc
Confidence            999999999999999986644

>KOG2252|consensus

Probab=98.45  E-value=6.7e-07  Score=78.61  Aligned_cols=60  Identities=25%  Similarity=0.264  Sum_probs=54.9

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhH
Q psy11996        130 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW  189 (222)
Q Consensus       130 ~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~  189 (222)
                      .....|+.|.+||..|...|...|+.+++|+.+..+.|+.+|+|...-|.+||-|-|.|.
T Consensus       416 ~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  416 KMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             ccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            344667889999999999999999999999999999999999999999999999977663

>KOG2252|consensus

Probab=98.33  E-value=1.5e-06  Score=76.41  Aligned_cols=60  Identities=25%  Similarity=0.264  Sum_probs=54.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHH
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW   65 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~   65 (222)
                      ..-..||.|.+||..|...|...|..+++|+.+..+.|+..|||....|.+||-|-|.+.
T Consensus       416 ~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  416 KMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             ccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            344568889999999999999999999999999999999999999999999999987653

>KOG0773|consensus

Probab=98.04  E-value=2e-05  Score=67.59  Aligned_cols=165  Identities=19%  Similarity=0.172  Sum_probs=94.2

Q ss_pred             hhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhccCCCCcccccccCCCCC----CCCccc---------
Q psy11996         30 HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNNPNLYTQYQTQGKSC----TGRYQV---------   96 (222)
Q Consensus        30 ~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~---------   96 (222)
                      ..++||...+..-|+...+++..+|..||-|-|.......+......+.............    +...+.         
T Consensus       117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~  196 (342)
T KOG0773|consen  117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSEELLGE  196 (342)
T ss_pred             hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhccccccccccccccccc
Confidence            5588999999999999999999999999999887766654443333222111100000000    000000         


Q ss_pred             CCCCCCCCCCCCCcccccccCC----Cccc-cccccccCCCCCCCCCCcCCHHHHHHHHHhhh---hcCCCCHHHHHHHH
Q psy11996         97 RPITSPHGAYHGDLRYHWTNRA----PLKY-VKRGTVNANGETKRQRTSYTRYQTLELEKEFH---FNRYLTRRRRIEIA  168 (222)
Q Consensus        97 ~p~~sp~~~~~~~~~~p~~~~~----~~~~-~~~~~~~~~~~~~~~r~~~~~~q~~~L~~~F~---~~~~p~~~~~~~la  168 (222)
                      .+..............+.....    .... .............+....+......+|+.+..   ..+||+..++..||
T Consensus       197 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La  276 (342)
T KOG0773|consen  197 SEQDDSEDESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLA  276 (342)
T ss_pred             ccccccccccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccc
Confidence            0000000000000000000000    0000 00111111223455567899999999998843   36799999999999


Q ss_pred             HHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996        169 HALCLTERQIKIWFQNRRMKWKKEHK  194 (222)
Q Consensus       169 ~~l~l~~~~V~~WF~nrR~k~kk~~~  194 (222)
                      .++||+..||.+||-|.|.+..+-..
T Consensus       277 ~~TGLs~~Qv~NWFINaR~R~w~p~~  302 (342)
T KOG0773|consen  277 KQTGLSRPQVSNWFINARVRLWKPMI  302 (342)
T ss_pred             hhcCCCcccCCchhhhcccccCCchH
Confidence            99999999999999999988776544

>KOG1146|consensus

Probab=98.00  E-value=1.5e-05  Score=76.51  Aligned_cols=64  Identities=25%  Similarity=0.306  Sum_probs=59.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996          9 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA   72 (222)
Q Consensus         9 ~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~   72 (222)
                      .++++|+.++..||..|...|....+|...+.+.|-..+++..+.|++||+|-|.+.++.....
T Consensus       902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~  965 (1406)
T KOG1146|consen  902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG  965 (1406)
T ss_pred             hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence            4678899999999999999999999999999999999999999999999999999998875533

>KOG3623|consensus

Probab=97.69  E-value=8.6e-05  Score=67.53  Aligned_cols=117  Identities=16%  Similarity=0.223  Sum_probs=79.3

Q ss_pred             HHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhccCCCCcccccccCCCCCCCCcccCCCCC
Q psy11996         22 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNNPNLYTQYQTQGKSCTGRYQVRPITS  101 (222)
Q Consensus        22 ~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~s  101 (222)
                      +..|+.+|..|..|+.++...+|...||+.+.|+.||.++++..........+                           
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps~---------------------------  620 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPSQ---------------------------  620 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCccC---------------------------
Confidence            78899999999999999999999999999999999999998886653221100                           


Q ss_pred             CCCCCCCCcccccccCCCccccccccccCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHH
Q psy11996        102 PHGAYHGDLRYHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIW  181 (222)
Q Consensus       102 p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~W  181 (222)
                      |.+.                           ...+.++-+..++-.-|...++.+..++-.+...++..|-.....|.+|
T Consensus       621 psg~---------------------------~p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~  673 (1007)
T KOG3623|consen  621 PSGE---------------------------RPVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVW  673 (1007)
T ss_pred             CCCC---------------------------CCccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhc
Confidence            0000                           0011112222233334455555555555555556666677778889999


Q ss_pred             HhhhhhhHHHh
Q psy11996        182 FQNRRMKWKKE  192 (222)
Q Consensus       182 F~nrR~k~kk~  192 (222)
                      |.+|+..-+..
T Consensus       674 dhsrsstpsp~  684 (1007)
T KOG3623|consen  674 DHSRSSTPSPM  684 (1007)
T ss_pred             ccCCCCCCCCC
Confidence            99998766553

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

Probab=97.61  E-value=6.8e-05  Score=46.26  Aligned_cols=42  Identities=19%  Similarity=0.300  Sum_probs=31.4

Q ss_pred             HHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchh
Q psy11996         22 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM   63 (222)
Q Consensus        22 ~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~   63 (222)
                      +..|+++|....++...+...|+.+.+|+..||+.||..+..
T Consensus        10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~   51 (56)
T PF11569_consen   10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ   51 (56)
T ss_dssp             -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred             hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence            466999999999999999999999999999999999976643

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

Probab=97.53  E-value=0.00011  Score=45.40  Aligned_cols=42  Identities=19%  Similarity=0.300  Sum_probs=31.5

Q ss_pred             HHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhh
Q psy11996        146 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM  187 (222)
Q Consensus       146 ~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~  187 (222)
                      ...|+..|....++...+...|..+.+|+..||+.||..+..
T Consensus        10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~   51 (56)
T PF11569_consen   10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ   51 (56)
T ss_dssp             -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred             hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence            456999999999999999999999999999999999987653

>KOG0773|consensus

Probab=96.32  E-value=0.0029  Score=54.33  Aligned_cols=58  Identities=19%  Similarity=0.306  Sum_probs=49.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHhh---hCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996         10 TKRQRTSYTRYQTLELEKEFH---FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~---~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      ..|.+..+......+|+.++.   ..+||+..++..|+.++||+..||.+||.|.|.+.-+
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~  299 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWK  299 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCC
Confidence            445566899999999998843   3579999999999999999999999999998876554

>KOG3623|consensus

Probab=96.13  E-value=0.012  Score=54.02  Aligned_cols=52  Identities=19%  Similarity=0.260  Sum_probs=48.0

Q ss_pred             HHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhccc
Q psy11996        146 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS  197 (222)
Q Consensus       146 ~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~  197 (222)
                      +.+|+..|..|..|+.++...+|...||..+.|+.||.++++.....++..+
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps  619 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPS  619 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCcc
Confidence            8899999999999999999999999999999999999999999888765544

>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=95.39  E-value=0.041  Score=33.80  Aligned_cols=47  Identities=23%  Similarity=0.357  Sum_probs=36.7

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcch
Q psy11996         11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR   62 (222)
Q Consensus        11 ~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR   62 (222)
                      ||+|..+|-++...+-..++...     ....||..+|++..+|..|..|+.
T Consensus         1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~   47 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD   47 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred             CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence            57889999999998888888886     477899999999999999998753

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.

>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=94.41  E-value=0.11  Score=31.84  Aligned_cols=47  Identities=23%  Similarity=0.357  Sum_probs=35.4

Q ss_pred             CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhh
Q psy11996        135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR  186 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR  186 (222)
                      +++|..+|-++-..+-..++...     ....||.++|++..+|..|..|+.
T Consensus         1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~   47 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD   47 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred             CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence            46788999998888888887775     577889999999999999998854

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.

>KOG3755|consensus

Probab=92.12  E-value=0.3  Score=44.31  Aligned_cols=59  Identities=22%  Similarity=0.250  Sum_probs=47.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHh-hhCCCCCHHH---HHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996          9 ETKRQRTSYTRYQTLELEKEF-HFNRYLTRRR---RIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus         9 ~~~r~R~~~t~~q~~~L~~~f-~~~~~p~~~~---~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      ...++|+.++.+-+..|...- ...=||+.+.   ..-|...++++.+.+...|+|.|...+.
T Consensus       646 ~~p~~~~~isge~~~~~qs~i~~~gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~~  708 (769)
T KOG3755|consen  646 HKPRKRTKISGEALGILQSFITDVGLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVKH  708 (769)
T ss_pred             cCccccceecccchHHHHHHHHHhccCchhhcccccchhhhhhcccHHHHHHhhhcceeecch
Confidence            356778889999999888775 3455888777   7789999999999999999999977553

>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=87.79  E-value=1.8  Score=25.72  Aligned_cols=46  Identities=11%  Similarity=0.095  Sum_probs=34.4

Q ss_pred             cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHH
Q psy11996        140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK  190 (222)
Q Consensus       140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k  190 (222)
                      .+++.+..+|...|...     ....++|..+|++...|+.+...-..+-|
T Consensus         4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~kLR   49 (50)
T PF04545_consen    4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKKLR   49 (50)
T ss_dssp             TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence            47888999999998333     35778899999999999998865544433

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

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

Probab=85.78  E-value=1.4  Score=27.03  Aligned_cols=41  Identities=17%  Similarity=0.149  Sum_probs=33.1

Q ss_pred             CCHHHHHHHHHhhhhcC--CCCHHHHHHHHHHcCCChhhHHHH
Q psy11996        141 YTRYQTLELEKEFHFNR--YLTRRRRIEIAHALCLTERQIKIW  181 (222)
Q Consensus       141 ~~~~q~~~L~~~F~~~~--~p~~~~~~~la~~l~l~~~~V~~W  181 (222)
                      +|+.|+.+|...|...-  +|-.....+||+++|++..-|..=
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~   43 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEH   43 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHH
Confidence            57899999999998654  477788899999999998765443

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

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

Probab=84.03  E-value=1  Score=29.29  Aligned_cols=43  Identities=19%  Similarity=0.341  Sum_probs=28.4

Q ss_pred             CCCCCCCHHHHHHHHHHh-hhCCCCCHHHHHHHHHHhCCChHHHHHHhh
Q psy11996         12 RQRTSYTRYQTLELEKEF-HFNRYLTRRRRIEIAHALCLTERQIKIWFQ   59 (222)
Q Consensus        12 r~R~~~t~~q~~~L~~~f-~~~~~p~~~~~~~la~~~~l~~~~v~~WF~   59 (222)
                      ++|..||+++...+-..+ ...     .....+|..+||+...|..|-.
T Consensus         2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l~~W~~   45 (76)
T PF01527_consen    2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTLYNWRK   45 (76)
T ss_dssp             -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccccHHHH
Confidence            457789999777666665 332     4678899999999999999964

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.

>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=83.86  E-value=3.6  Score=24.40  Aligned_cols=44  Identities=11%  Similarity=0.084  Sum_probs=32.7

Q ss_pred             CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhH
Q psy11996         16 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK   64 (222)
Q Consensus        16 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k   64 (222)
                      .+++.+..+|...|..+     ....++|..+|++...|..+...-..+
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            47888999999998433     246788999999999999886544433

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

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

Probab=80.99  E-value=4.3  Score=24.84  Aligned_cols=42  Identities=17%  Similarity=0.161  Sum_probs=34.6

Q ss_pred             CCHHHHHHHHHHhhhCC--CCCHHHHHHHHHHhCCChHHHHHHh
Q psy11996         17 YTRYQTLELEKEFHFNR--YLTRRRRIEIAHALCLTERQIKIWF   58 (222)
Q Consensus        17 ~t~~q~~~L~~~f~~~~--~p~~~~~~~la~~~~l~~~~v~~WF   58 (222)
                      +|+.|..+|...|+..-  +|-.....+||..+|++..-+..-.
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            57899999999988765  4767788999999999998776543

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	222
2r5y_A	88	Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO		3e-33
2r5y_A	88	Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO		5e-33
1hom_A	68	Determination Of The Three-Dimensional Structure Of		4e-26
1hom_A	68	Determination Of The Three-Dimensional Structure Of		4e-26
1ahd_P	68	Determination Of The Nmr Solution Structure Of An A		4e-25
1ahd_P	68	Determination Of The Nmr Solution Structure Of An A		4e-25
9ant_A	62	Antennapedia Homeodomain-Dna Complex Length = 62		5e-25
9ant_A	62	Antennapedia Homeodomain-Dna Complex Length = 62		5e-25
1san_A	62	The Des(1-6)antennapedia Homeodomain: Comparison Of		5e-24
1san_A	62	The Des(1-6)antennapedia Homeodomain: Comparison Of		5e-24
1b8i_A	81	Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX		6e-23
1b8i_A	81	Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX		3e-22
1ftz_A	70	Nuclear Magnetic Resonance Solution Structure Of Th		6e-23
1ftz_A	70	Nuclear Magnetic Resonance Solution Structure Of Th		6e-23
2h1k_A	63	Crystal Structure Of The Pdx1 Homeodomain In Comple		6e-19
2h1k_A	63	Crystal Structure Of The Pdx1 Homeodomain In Comple		6e-19
2lp0_A	60	The Solution Structure Of Homeodomain-Protein Compl		3e-17
2lp0_A	60	The Solution Structure Of Homeodomain-Protein Compl		3e-17
1puf_A	77	Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo		1e-16
1puf_A	77	Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo		1e-16
2m34_A	71	Nmr Structure Of The Homeodomain Transcription Fact		3e-15
2m34_A	71	Nmr Structure Of The Homeodomain Transcription Fact		3e-15
1b72_A	97	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		5e-15
1b72_A	97	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		5e-15
3a01_A	93	Crystal Structure Of Aristaless And Clawless Homeod		7e-11
3a01_A	93	Crystal Structure Of Aristaless And Clawless Homeod		7e-11
2dmt_A	80	Solution Structure Of The Homeobox Domain Of Homeob		8e-11
2cra_A	70	Solution Structure Of The Homeobox Domain Of Human		2e-10
1hdd_C	61	Crystal Structure Of An Engrailed Homeodomain-Dna C		3e-10
1hdd_C	61	Crystal Structure Of An Engrailed Homeodomain-Dna C		3e-10
3hdd_A	60	Engrailed Homeodomain Dna Complex Length = 60		5e-10
3hdd_A	60	Engrailed Homeodomain Dna Complex Length = 60		5e-10
1ztr_A	61	Solution Structure Of Engrailed Homeodomain L16a Mu		8e-10
1ztr_A	61	Solution Structure Of Engrailed Homeodomain L16a Mu		8e-10
1p7j_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		9e-10
1p7j_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		9e-10
1p7i_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		1e-09
1p7i_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		1e-09
2hdd_A	61	Engrailed Homeodomain Q50k Variant Dna Complex Leng		1e-09
2hdd_A	61	Engrailed Homeodomain Q50k Variant Dna Complex Leng		1e-09
1jgg_A	60	Even-Skipped Homeodomain Complexed To At-Rich Dna L		2e-09
1jgg_A	60	Even-Skipped Homeodomain Complexed To At-Rich Dna L		2e-09
3a03_A	56	Crystal Structure Of Hox11l1 Homeodomain Length = 5		5e-09
3a03_A	56	Crystal Structure Of Hox11l1 Homeodomain Length = 5		5e-09
2l7z_A	73	Nmr Structure Of A13 Homedomain Length = 73		6e-09
2l7z_A	73	Nmr Structure Of A13 Homedomain Length = 73		6e-09
1du0_A	57	Engrailed Homeodomain Q50a Variant Dna Complex Leng		6e-09
1du0_A	57	Engrailed Homeodomain Q50a Variant Dna Complex Leng		6e-09
1enh_A	54	Structural Studies Of The Engrailed Homeodomain Len		9e-09
1enh_A	54	Structural Studies Of The Engrailed Homeodomain Len		9e-09
2ld5_A	67	Solution Nmr-Derived Complex Structure Of Hoxa13 Dn		1e-08
2ld5_A	67	Solution Nmr-Derived Complex Structure Of Hoxa13 Dn		1e-08
2djn_A	70	The Solution Structure Of The Homeobox Domain Of Hu		1e-08
2e1o_A	70	Solution Structure Of Rsgi Ruh-028, A Homeobox Doma		2e-08
2e1o_A	70	Solution Structure Of Rsgi Ruh-028, A Homeobox Doma		2e-08
2hos_A	63	Phage-selected Homeodomain Bound To Unmodified Dna		2e-08
2hos_A	63	Phage-selected Homeodomain Bound To Unmodified Dna		2e-08
2m0c_A	75	Solution Nmr Structure Of Homeobox Domain Of Human		3e-08
2m0c_A	75	Solution Nmr Structure Of Homeobox Domain Of Human		4e-08
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		6e-08
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		6e-08
1ig7_A	58	Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58		6e-08
1ig7_A	58	Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58		6e-08
2l7f_P	68	Solution Structure Of The Pitx2 Homeodomain Length		8e-08
2l7f_P	68	Solution Structure Of The Pitx2 Homeodomain Length		8e-08
2cue_A	80	Solution Structure Of The Homeobox Domain Of The Hu		1e-07
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		3e-07
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		3e-07
2p81_A	44	Engrailed Homeodomain Helix-Turn-Helix Motif Length		4e-07
2p81_A	44	Engrailed Homeodomain Helix-Turn-Helix Motif Length		4e-07
2l7m_P	68	Solution Structure Of The Pitx2 Homeodomain R24h Mu		4e-07
2l7m_P	68	Solution Structure Of The Pitx2 Homeodomain R24h Mu		4e-07
3a02_A	60	Crystal Structure Of Aristaless Homeodomain Length		7e-07
3a02_A	60	Crystal Structure Of Aristaless Homeodomain Length		7e-07
1zq3_P	68	Nmr Solution Structure Of The Bicoid Homeodomain Bo		2e-06
1zq3_P	68	Nmr Solution Structure Of The Bicoid Homeodomain Bo		2e-06
2l9r_A	69	Solution Nmr Structure Of Homeobox Domain Of Homeob		3e-06
2l9r_A	69	Solution Nmr Structure Of Homeobox Domain Of Homeob		3e-06
3rkq_A	58	Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Lengt		3e-06
3rkq_A	58	Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Lengt		3e-06
1nk2_P	77	VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES		7e-06
1nk2_P	77	VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES		7e-06
1fjl_A	81	Homeodomain From The Drosophila Paired Protein Boun		1e-05
1fjl_A	81	Homeodomain From The Drosophila Paired Protein Boun		1e-05
1qry_A	80	Homeobox Protein Vnd (Ventral Nervous System Defect		1e-05
1qry_A	80	Homeobox Protein Vnd (Ventral Nervous System Defect		2e-05
3cmy_A	61	Structure Of A Homeodomain In Complex With Dna Leng		6e-05
3cmy_A	61	Structure Of A Homeodomain In Complex With Dna Leng		6e-05
2vi6_A	62	Crystal Structure Of The Nanog Homeodomain Length =		6e-05
2vi6_A	62	Crystal Structure Of The Nanog Homeodomain Length =		6e-05
1ftt_A	68	Thyroid Transcription Factor 1 Homeodomain (Rattus		8e-05
1ftt_A	68	Thyroid Transcription Factor 1 Homeodomain (Rattus		8e-05
2dms_A	80	Solution Structure Of The Homeobox Domain Of Homeob		9e-05
2dmu_A	70	Solution Structure Of The Homeobox Domain Of Homeob		3e-04
2k40_A	67	Nmr Structure Of Hesx-1 Homeodomain Double Mutant R		4e-04
2k40_A	67	Nmr Structure Of Hesx-1 Homeodomain Double Mutant R		4e-04
2kt0_A	84	Solution Structure Of Human Stem Cell Transcription		4e-04
2kt0_A	84	Solution Structure Of Human Stem Cell Transcription		4e-04

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

Iteration: 1
 Score =  138 bits (347), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 68/69 (98%), Positives = 68/69 (98%)
Query: 2  STVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 61
          STVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNR
Sbjct: 20 STVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNR 79
Query: 62 RMKWKKEHK 70
          RMKWKKEHK
Sbjct: 80 RMKWKKEHK 88

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

Iteration: 1
 Score =  137 bits (345), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 70/83 (84%), Positives = 72/83 (86%), Gaps = 3/83 (3%)
Query: 112 YHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 171
           Y W  R    ++   TVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL
Sbjct: 9   YPWMKRV---HLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 65
Query: 172 CLTERQIKIWFQNRRMKWKKEHK 194
            LTERQIKIWFQNRRMKWKKEHK
Sbjct: 66  SLTERQIKIWFQNRRMKWKKEHK 88

>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 =  114 bits (285), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 56/60 (93%), Positives = 58/60 (96%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          KR R +YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE+K
Sbjct: 3  KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 62

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

Iteration: 1
 Score =  114 bits (285), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 56/60 (93%), Positives = 58/60 (96%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           KR R +YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE+K
Sbjct: 3   KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 62

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

Iteration: 1
 Score =  111 bits (277), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 55/60 (91%), Positives = 57/60 (95%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          KR R +YTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKE+K
Sbjct: 3  KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 62

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

Iteration: 1
 Score =  111 bits (277), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 55/60 (91%), Positives = 57/60 (95%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           KR R +YTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKE+K
Sbjct: 3   KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 62

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

Iteration: 1
 Score =  110 bits (276), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 55/61 (90%), Positives = 57/61 (93%)
Query: 9  ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68
          E KR R +YTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKE
Sbjct: 2  ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61
Query: 69 H 69
          +
Sbjct: 62 N 62

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

Iteration: 1
 Score =  110 bits (276), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 55/61 (90%), Positives = 57/61 (93%)
Query: 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
           E KR R +YTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKE
Sbjct: 2   ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61
Query: 193 H 193
           +
Sbjct: 62  N 62

>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 =  107 bits (267), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 52/55 (94%), Positives = 54/55 (98%)
Query: 16 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          +YTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKE+K
Sbjct: 2  TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 56

>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 =  107 bits (267), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 52/55 (94%), Positives = 54/55 (98%)
Query: 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           +YTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKE+K
Sbjct: 2   TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 56

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

Iteration: 1
 Score =  103 bits (258), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 52/68 (76%), Positives = 56/68 (82%)
Query: 1  MSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQN 60
          M+    NG  +R R +YTRYQTLELEKEFH N YLTRRRRIE+AHAL LTERQIKIWFQN
Sbjct: 11 MAIAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQN 70
Query: 61 RRMKWKKE 68
          RRMK KKE
Sbjct: 71 RRMKLKKE 78

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

Iteration: 1
 Score =  101 bits (251), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 51/67 (76%), Positives = 54/67 (80%)
Query: 126 GTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 185
                NG  +R R +YTRYQTLELEKEFH N YLTRRRRIE+AHAL LTERQIKIWFQNR
Sbjct: 12  AIAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNR 71
Query: 186 RMKWKKE 192
           RMK KKE
Sbjct: 72  RMKLKKE 78

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

Iteration: 1
 Score =  103 bits (258), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 49/65 (75%), Positives = 58/65 (89%)
Query: 9  ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68
          ++KR R +YTRYQTLELEKEFHFNRY+TRRRRI+IA+AL L+ERQIKIWFQNRRMK KK+
Sbjct: 2  DSKRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKD 61
Query: 69 HKMAS 73
            + S
Sbjct: 62 RTLDS 66

>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 =  103 bits (258), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 49/65 (75%), Positives = 58/65 (89%)
Query: 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
           ++KR R +YTRYQTLELEKEFHFNRY+TRRRRI+IA+AL L+ERQIKIWFQNRRMK KK+
Sbjct: 2   DSKRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKD 61
Query: 193 HKMAS 197
             + S
Sbjct: 62  RTLDS 66

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

Iteration: 1
 Score = 90.5 bits (223), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 44/62 (70%), Positives = 50/62 (80%)
Query: 8  GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          G  KR RT+YTR Q LELEKEF FN+Y++R RR+E+A  L LTER IKIWFQNRRMKWKK
Sbjct: 1  GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60
Query: 68 EH 69
          E 
Sbjct: 61 EE 62

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

Iteration: 1
 Score = 90.5 bits (223), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 44/62 (70%), Positives = 50/62 (80%)
Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           G  KR RT+YTR Q LELEKEF FN+Y++R RR+E+A  L LTER IKIWFQNRRMKWKK
Sbjct: 1   GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60
Query: 192 EH 193
           E 
Sbjct: 61  EE 62

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

Iteration: 1
 Score = 85.1 bits (209), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 42/58 (72%), Positives = 48/58 (82%)
Query: 10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          T+++R  YT+YQTLELEKEF FN YLTR RR E+A  L LTERQ+KIWFQNRRMK KK
Sbjct: 1  TRKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58

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

Iteration: 1
 Score = 85.1 bits (209), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 42/58 (72%), Positives = 48/58 (82%)
Query: 134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           T+++R  YT+YQTLELEKEF FN YLTR RR E+A  L LTERQ+KIWFQNRRMK KK
Sbjct: 1   TRKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58

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

Iteration: 1
 Score = 82.8 bits (203), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 42/61 (68%), Positives = 50/61 (81%)
Query: 10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69
          T+++R  YT++QTLELEKEF FN YLTR RR E+A  L LTERQ+KIWFQNRRMK KK +
Sbjct: 13 TRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKIN 72
Query: 70 K 70
          K
Sbjct: 73 K 73

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

Iteration: 1
 Score = 82.8 bits (203), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 42/61 (68%), Positives = 50/61 (81%)
Query: 134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193
           T+++R  YT++QTLELEKEF FN YLTR RR E+A  L LTERQ+KIWFQNRRMK KK +
Sbjct: 13  TRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKIN 72
Query: 194 K 194
           K
Sbjct: 73  K 73

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

Iteration: 1
 Score = 78.6 bits (192), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 36/61 (59%), Positives = 48/61 (78%)
Query: 7  NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 66
           G+++R+RT++T  Q LELEKEFH  +YL+   R +IAHAL L+E Q+KIWFQNRR KWK
Sbjct: 4  GGKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 63
Query: 67 K 67
          +
Sbjct: 64 R 64

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

Iteration: 1
 Score = 78.6 bits (192), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 36/61 (59%), Positives = 48/61 (78%)
Query: 131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190
            G+++R+RT++T  Q LELEKEFH  +YL+   R +IAHAL L+E Q+KIWFQNRR KWK
Sbjct: 4   GGKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 63
Query: 191 K 191
           +
Sbjct: 64  R 64

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

Iteration: 1
 Score = 77.4 bits (189), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 38/60 (63%), Positives = 44/60 (73%)
Query: 8  GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          G     RT++T  Q  ELEKEFHFN+YL+R RR+EIA  L L E Q+KIWFQNRRMK KK
Sbjct: 32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91

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

Iteration: 1
 Score = 77.4 bits (189), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 38/60 (63%), Positives = 44/60 (73%)
Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           G     RT++T  Q  ELEKEFHFN+YL+R RR+EIA  L L E Q+KIWFQNRRMK KK
Sbjct: 32  GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91

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

Iteration: 1
 Score = 63.9 bits (154), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 29/58 (50%), Positives = 39/58 (67%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68
          K+ RTS+TR Q  ELEK FH  +YL    R  +A  L +T+ Q+K WFQNRR KW+++
Sbjct: 18 KKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQ 75

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

Iteration: 1
 Score = 63.9 bits (154), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 29/58 (50%), Positives = 39/58 (67%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
           K+ RTS+TR Q  ELEK FH  +YL    R  +A  L +T+ Q+K WFQNRR KW+++
Sbjct: 18  KKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQ 75

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

Iteration: 1
 Score = 63.5 bits (153), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 31/66 (46%), Positives = 43/66 (65%), Gaps = 2/66 (3%)
Query: 126 GTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 185
           GT    G  +R RT +T  Q + LEK F   +YL+   RI++A +L L++ Q+K W+QNR
Sbjct: 11  GTKAKKG--RRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNR 68
Query: 186 RMKWKK 191
           RMKWKK
Sbjct: 69  RMKWKK 74

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

Iteration: 1
 Score = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 29/66 (43%), Positives = 48/66 (72%), Gaps = 2/66 (3%)
Query: 126 GTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 185
           G+  ++G  +++R  Y++ Q  ELE+E+  N+++T+ +R +I+ A  L+ERQI IWFQNR
Sbjct: 1   GSSGSSG--RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNR 58
Query: 186 RMKWKK 191
           R+K KK
Sbjct: 59  RVKEKK 64

>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 = 62.0 bits (149), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 31/59 (52%), Positives = 42/59 (71%)
Query: 9  ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          + KR RT+++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWFQN+R K KK
Sbjct: 2  DEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60

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

Iteration: 1
 Score = 62.0 bits (149), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 31/59 (52%), Positives = 42/59 (71%)
Query: 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           + KR RT+++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWFQN+R K KK
Sbjct: 2   DEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60

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

Iteration: 1
 Score = 61.2 bits (147), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 31/57 (54%), Positives = 41/57 (71%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          KR RT+++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWFQN+R K KK
Sbjct: 2  KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58

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

Iteration: 1
 Score = 61.2 bits (147), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 31/57 (54%), Positives = 41/57 (71%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           KR RT+++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWFQN+R K KK
Sbjct: 2   KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58

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

Iteration: 1
 Score = 60.1 bits (144), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 29/60 (48%), Positives = 42/60 (70%)
Query: 8  GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          G+ KR RT+++  Q    ++EF+ NRYLT RRR +++  L L E QIKIWFQN+R K ++
Sbjct: 1  GDEKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60

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

Iteration: 1
 Score = 60.1 bits (144), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 29/60 (48%), Positives = 42/60 (70%)
Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           G+ KR RT+++  Q    ++EF+ NRYLT RRR +++  L L E QIKIWFQN+R K ++
Sbjct: 1   GDEKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60

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

Iteration: 1
 Score = 60.1 bits (144), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 31/57 (54%), Positives = 40/57 (70%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          KR RT+++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWFQN R K KK
Sbjct: 2  KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58

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

Iteration: 1
 Score = 60.1 bits (144), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 31/57 (54%), Positives = 40/57 (70%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           KR RT+++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWFQN R K KK
Sbjct: 2   KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58

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

Iteration: 1
 Score = 60.1 bits (144), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 31/57 (54%), Positives = 40/57 (70%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          KR RT+++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWFQN R K KK
Sbjct: 2  KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58

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

Iteration: 1
 Score = 60.1 bits (144), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 31/57 (54%), Positives = 40/57 (70%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           KR RT+++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWFQN R K KK
Sbjct: 2   KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58

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

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/57 (52%), Positives = 41/57 (71%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          KR RT+++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWF+N+R K KK
Sbjct: 4  KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

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

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/57 (52%), Positives = 41/57 (71%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           KR RT+++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWF+N+R K KK
Sbjct: 4   KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 31/59 (52%), Positives = 41/59 (69%)
Query: 10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68
           +R RT++TR Q   LEKEF+   Y++R RR E+A  L L E  IK+WFQNRRMK K++
Sbjct: 1  VRRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 31/59 (52%), Positives = 41/59 (69%)
Query: 134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
            +R RT++TR Q   LEKEF+   Y++R RR E+A  L L E  IK+WFQNRRMK K++
Sbjct: 1   VRRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 37/54 (68%)
Query: 15 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68
          TS++R Q LELE+ F   +YL    R  +A AL +T+ Q+K WFQNRR KW+++
Sbjct: 2  TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 37/54 (68%)
Query: 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
           TS++R Q LELE+ F   +YL    R  +A AL +T+ Q+K WFQNRR KW+++
Sbjct: 2   TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 27/59 (45%), Positives = 42/59 (71%)
Query: 9  ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          E +++R  YT+ Q  ELE+E+  N+++T+ +R  I+    L+ERQ+ IWFQNRR+K KK
Sbjct: 6  EGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 27/59 (45%), Positives = 42/59 (71%)
Query: 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           E +++R  YT+ Q  ELE+E+  N+++T+ +R  I+    L+ERQ+ IWFQNRR+K KK
Sbjct: 6   EGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 29/56 (51%), Positives = 39/56 (69%)
Query: 12 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          R RT+++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWF N+R K KK
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 29/56 (51%), Positives = 39/56 (69%)
Query: 136 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           R RT+++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWF N+R K KK
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 38/53 (71%)
Query: 12 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 64
          R RT+++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWFQN+R K
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 38/53 (71%)
Query: 136 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 188
           R RT+++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWFQN+R K
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 41/57 (71%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          +++R  YT+ Q  ELE+E+  N+++T+ +R  I+    L+ERQ+ IWFQNRR+K KK
Sbjct: 2  RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 41/57 (71%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           +++R  YT+ Q  ELE+E+  N+++T+ +R  I+    L+ERQ+ IWFQNRR+K KK
Sbjct: 2   RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 27/67 (40%), Positives = 42/67 (62%), Gaps = 2/67 (2%)
Query: 126 GTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 185
           G+  ++G  ++ RT Y+ +Q   L++ F   +YL    R E+A +L LT+ Q+KIWFQN+
Sbjct: 1   GSSGSSG--RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNK 58
Query: 186 RMKWKKE 192
           R K KK 
Sbjct: 59  RSKIKKS 65

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/51 (49%), Positives = 36/51 (70%)
Query: 17 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          ++  QT+ELEK+F   +YL+   R  +A  L L+ERQ+K WFQNRR KW++
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/51 (49%), Positives = 36/51 (70%)
Query: 141 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           ++  QT+ELEK+F   +YL+   R  +A  L L+ERQ+K WFQNRR KW++
Sbjct: 14  FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/59 (47%), Positives = 40/59 (67%)
Query: 9  ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          + KR RT+++  Q   L++EF+ NRYLT RRR +++  L L E Q+K WF+N R K KK
Sbjct: 3  DEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/59 (47%), Positives = 40/59 (67%)
Query: 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           + KR RT+++  Q   L++EF+ NRYLT RRR +++  L L E Q+K WF+N R K KK
Sbjct: 3   DEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61

>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 = 55.1 bits (131), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 29/73 (39%), Positives = 43/73 (58%)
Query: 2  STVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 61
          S ++  G+ +R RT++T YQ  ELEK F    Y     R ++A    LTE ++++WFQNR
Sbjct: 1  SHMSNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNR 60
Query: 62 RMKWKKEHKMASM 74
          R KW+K  +   M
Sbjct: 61 RAKWRKRERFGQM 73

>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 = 54.7 bits (130), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 28/67 (41%), Positives = 40/67 (59%)
Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           G+ +R RT++T YQ  ELEK F    Y     R ++A    LTE ++++WFQNRR KW+K
Sbjct: 7   GKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRK 66
Query: 192 EHKMASM 198
             +   M
Sbjct: 67  RERFGQM 73

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 28/61 (45%), Positives = 40/61 (65%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          +R RT++T +Q  ELEK F    Y     R E+A  + LTE +I++WFQNRR KW+K+ K
Sbjct: 7  RRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 66
Query: 71 M 71
          +
Sbjct: 67 V 67

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 28/61 (45%), Positives = 40/61 (65%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           +R RT++T +Q  ELEK F    Y     R E+A  + LTE +I++WFQNRR KW+K+ K
Sbjct: 7   RRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 66
Query: 195 M 195
           +
Sbjct: 67  V 67

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 27/57 (47%), Positives = 38/57 (66%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          ++ RT +T  Q L LE++F   +YL+   R E + +L LTE Q+KIWFQNRR K K+
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 27/57 (47%), Positives = 38/57 (66%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           ++ RT +T  Q L LE++F   +YL+   R E + +L LTE Q+KIWFQNRR K K+
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 29/60 (48%), Positives = 37/60 (61%)
Query: 8  GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          G  +RQRT +T  Q  ELE  F  NRY     R EIA    LTE ++++WF+NRR KW+K
Sbjct: 1  GSQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 29/60 (48%), Positives = 37/60 (61%)
Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           G  +RQRT +T  Q  ELE  F  NRY     R EIA    LTE ++++WF+NRR KW+K
Sbjct: 1   GSQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 42/70 (60%), Gaps = 2/70 (2%)
Query: 126 GTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 185
           G+  ++G+  R RTS+T+ Q   LEKEF    Y     R  +A  + L E +I++WF NR
Sbjct: 1   GSSGSSGQ--RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNR 58
Query: 186 RMKWKKEHKM 195
           R KW++E K+
Sbjct: 59  RAKWRREEKL 68

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 27/58 (46%), Positives = 37/58 (63%)
Query: 12 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69
          R RT++T +Q  ELEK F    Y     R E+A  + LTE +I++WFQNRR KW+K+ 
Sbjct: 1  RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 27/58 (46%), Positives = 37/58 (63%)
Query: 136 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193
           R RT++T +Q  ELEK F    Y     R E+A  + LTE +I++WFQNRR KW+K+ 
Sbjct: 1   RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 31/41 (75%)
Query: 27 KEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          +EF+ NRYLT RRR +++  L L E QIKIWFQN+R K KK
Sbjct: 3  REFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 31/41 (75%)
Query: 151 KEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           +EF+ NRYLT RRR +++  L L E QIKIWFQN+R K KK
Sbjct: 3   REFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 28/60 (46%), Positives = 36/60 (60%)
Query: 8  GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          G  +RQRT +T  Q  ELE  F  N Y     R EIA    LTE ++++WF+NRR KW+K
Sbjct: 1  GSQRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 28/60 (46%), Positives = 36/60 (60%)
Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           G  +RQRT +T  Q  ELE  F  N Y     R EIA    LTE ++++WF+NRR KW+K
Sbjct: 1   GSQRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 25/56 (44%), Positives = 36/56 (64%)
Query: 16 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 71
          ++T +Q  ELEK F    Y     R E+A  + LTE +I++WFQNRR KW+K+ K+
Sbjct: 5  TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEKV 60

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 25/56 (44%), Positives = 36/56 (64%)
Query: 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 195
           ++T +Q  ELEK F    Y     R E+A  + LTE +I++WFQNRR KW+K+ K+
Sbjct: 5   TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEKV 60

>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 = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/63 (42%), Positives = 38/63 (60%), Gaps = 4/63 (6%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          +R RT++T  Q  ELE+ F   RYLT  R  +++  L L   Q+KIWF+NRR    + HK
Sbjct: 3  RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRR----RRHK 58
Query: 71 MAS 73
          + S
Sbjct: 59 IQS 61

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/63 (42%), Positives = 38/63 (60%), Gaps = 4/63 (6%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           +R RT++T  Q  ELE+ F   RYLT  R  +++  L L   Q+KIWF+NRR    + HK
Sbjct: 3   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRR----RRHK 58
Query: 195 MAS 197
           + S
Sbjct: 59  IQS 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 = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/49 (48%), Positives = 33/49 (67%)
Query: 21 QTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69
          Q +ELE++F   +YL+   R  +A  L LTE Q+KIWFQNRR K K++ 
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 63

>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 = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/49 (48%), Positives = 33/49 (67%)
Query: 145 QTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193
           Q +ELE++F   +YL+   R  +A  L LTE Q+KIWFQNRR K K++ 
Sbjct: 15  QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 63

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/53 (47%), Positives = 33/53 (62%)
Query: 14 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 66
          R  +++ Q  ELE+ F   RYL+   R ++A  L LT  Q+KIWFQNRR K K
Sbjct: 6  RVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/53 (47%), Positives = 33/53 (62%)
Query: 138 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190
           R  +++ Q  ELE+ F   RYL+   R ++A  L LT  Q+KIWFQNRR K K
Sbjct: 6   RVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 36/57 (63%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          +++R  +T+ QT ELE+ F   RYL+   R  +A  + LT  Q+KIWFQN R K K+
Sbjct: 10 RKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 36/57 (63%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           +++R  +T+ QT ELE+ F   RYL+   R  +A  + LT  Q+KIWFQN R K K+
Sbjct: 10  RKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/63 (39%), Positives = 38/63 (60%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          +R RT+++  Q  ELE+ F   +Y     R E+A    LTE +I++WFQNRR + +K+H 
Sbjct: 19 RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT 78
Query: 71 MAS 73
            S
Sbjct: 79 SVS 81

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/63 (39%), Positives = 38/63 (60%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           +R RT+++  Q  ELE+ F   +Y     R E+A    LTE +I++WFQNRR + +K+H 
Sbjct: 19  RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT 78
Query: 195 MAS 197
             S
Sbjct: 79  SVS 81

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 29/67 (43%), Positives = 38/67 (56%), Gaps = 1/67 (1%)
Query: 1  MSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQN 60
          MS    N + KR R  +T+ QT ELE+ F   RYL+   R  +   + LT  Q+KIWFQN
Sbjct: 4  MSDGLPNKKRKR-RVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQN 62
Query: 61 RRMKWKK 67
           R K K+
Sbjct: 63 HRYKTKR 69

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 35/57 (61%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           +++R  +T+ QT ELE+ F   RYL+   R  +   + LT  Q+KIWFQN R K K+
Sbjct: 13  RKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKR 69

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 35/58 (60%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68
          +R RT++T  Q  ELE+ F    Y     R E+A    LTE ++++WF NRR +W+K+
Sbjct: 3  RRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 35/58 (60%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
           +R RT++T  Q  ELE+ F    Y     R E+A    LTE ++++WF NRR +W+K+
Sbjct: 3   RRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 38/60 (63%)
Query: 8  GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          G  ++ RT +++ Q   L+  F   +YL+ ++  E++  L L+ +Q+K WFQN+RMK K+
Sbjct: 1  GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 38/60 (63%)
Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           G  ++ RT +++ Q   L+  F   +YL+ ++  E++  L L+ +Q+K WFQN+RMK K+
Sbjct: 1   GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 23/60 (38%), Positives = 37/60 (61%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          +++R  +++ Q  ELE+ F   +YL+   R  +A  + LT  Q+KIWFQN R K K++ K
Sbjct: 3  RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 23/60 (38%), Positives = 37/60 (61%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           +++R  +++ Q  ELE+ F   +YL+   R  +A  + LT  Q+KIWFQN R K K++ K
Sbjct: 3   RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 24/65 (36%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 126 GTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 185
           G+  ++G  +R+RT++TR Q   LE  F   RY     R E+A  + L E ++++WF+NR
Sbjct: 1   GSSGSSG--RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNR 58
Query: 186 RMKWK 190
           R K +
Sbjct: 59  RAKCR 63

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 38/66 (57%), Gaps = 2/66 (3%)
Query: 126 GTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 185
           G+  ++G  +R RT +T  Q   LE  F   +Y     R ++A  + L E ++++WF+NR
Sbjct: 1   GSSGSSG--RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNR 58
Query: 186 RMKWKK 191
           R KW++
Sbjct: 59  RAKWRR 64

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/60 (40%), Positives = 34/60 (56%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          +R RT++T+ Q   LE  F  N Y       ++A  L L   +I+IWFQNRR K K+ H+
Sbjct: 2  RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/60 (40%), Positives = 34/60 (56%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           +R RT++T+ Q   LE  F  N Y       ++A  L L   +I+IWFQNRR K K+ H+
Sbjct: 2   RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61

>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 = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 35/57 (61%)
Query: 14 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          RT ++  Q   L   F   +YL+ ++  E+++ L L+ +Q+K WFQN+RMK K+  K
Sbjct: 26 RTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK 82

>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 = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 35/57 (61%)
Query: 138 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           RT ++  Q   L   F   +YL+ ++  E+++ L L+ +Q+K WFQN+RMK K+  K
Sbjct: 26  RTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK 82

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	222
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	9e-40
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	2e-38
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	5e-39
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	6e-39
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	2e-38
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	2e-38
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	7e-36
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	7e-36
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	1e-35
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	1e-35
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	4e-35
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	4e-35
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	1e-34
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	1e-34
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	4e-34
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	4e-34
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	4e-34
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	4e-34
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	7e-34
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	7e-34
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	1e-33
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	1e-33
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	5e-33
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	5e-33
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	7e-32
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	7e-32
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	3e-31
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	3e-31
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	3e-29
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	3e-29
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	2e-28
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	2e-28
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	8e-27
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	8e-27
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	2e-26
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	2e-26
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	4e-26
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	4e-26
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	7e-26
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	7e-26
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	1e-25
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	3e-25
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	8e-24
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	8e-24
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	4e-23
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	4e-23
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	3e-22
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	3e-22
1e3o_C	160	Octamer-binding transcription factor 1; transcript	4e-22
1e3o_C	160	Octamer-binding transcription factor 1; transcript	4e-22
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	4e-19
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	4e-19
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	1e-17
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	1e-17
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	1e-16
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	1e-16
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	2e-16
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	2e-16
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	2e-16
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	2e-16
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	3e-15
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	3e-15
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	8e-15
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	8e-15
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	8e-15
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	8e-15
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	2e-14
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	2e-14
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	1e-13
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	1e-13
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	1e-13
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	3e-13
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	2e-13
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	3e-13
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	2e-13
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	2e-13
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	4e-13
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	4e-13
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	7e-13
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	7e-13
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	1e-12
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	2e-12
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	1e-12
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	1e-12
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	2e-12
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	2e-12
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	3e-12
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	3e-12
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	1e-11
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	1e-11
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	4e-11
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	7e-11
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	4e-11
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	4e-11
1uhs_A	72	HOP, homeodomain only protein; structural genomics	8e-11
1uhs_A	72	HOP, homeodomain only protein; structural genomics	8e-11
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	2e-10
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	2e-10
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	2e-10
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	2e-10
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	7e-10
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	1e-09
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	7e-08
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	7e-08
1lfb_A	99	Liver transcription factor (LFB1); transcription r	2e-06
1lfb_A	99	Liver transcription factor (LFB1); transcription r	3e-06
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	6e-06
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	6e-06
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	1e-05
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	5e-05
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	7e-05
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	7e-05
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	1e-04
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	1e-04

>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 =  130 bits (329), Expect = 9e-40
 Identities = 52/70 (74%), Positives = 57/70 (81%)

Query: 1  MSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQN 60
          M+    NG  +R R +YTRYQTLELEKEFH N YLTRRRRIE+AHAL LTERQIKIWFQN
Sbjct: 11 MAIAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQN 70

Query: 61 RRMKWKKEHK 70
          RRMK KKE +
Sbjct: 71 RRMKLKKEIQ 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 =  127 bits (321), Expect = 2e-38
 Identities = 51/68 (75%), Positives = 55/68 (80%)

Query: 127 TVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR 186
               NG  +R R +YTRYQTLELEKEFH N YLTRRRRIE+AHAL LTERQIKIWFQNRR
Sbjct: 13  IAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRR 72

Query: 187 MKWKKEHK 194
           MK KKE +
Sbjct: 73  MKLKKEIQ 80

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

 Score =  129 bits (325), Expect = 5e-39
 Identities = 68/69 (98%), Positives = 68/69 (98%)

Query: 2  STVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 61
          STVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNR
Sbjct: 20 STVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNR 79

Query: 62 RMKWKKEHK 70
          RMKWKKEHK
Sbjct: 80 RMKWKKEHK 88

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

 Score =  128 bits (324), Expect = 6e-39
 Identities = 67/69 (97%), Positives = 67/69 (97%)

Query: 126 GTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 185
            TVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNR
Sbjct: 20  STVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNR 79

Query: 186 RMKWKKEHK 194
           RMKWKKEHK
Sbjct: 80  RMKWKKEHK 88

>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 =  127 bits (321), Expect = 2e-38
 Identities = 38/69 (55%), Positives = 46/69 (66%)

Query: 2  STVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 61
           +    G     RT++T  Q  ELEKEFHFN+YL+R RR+EIA  L L E Q+KIWFQNR
Sbjct: 26 VSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNR 85

Query: 62 RMKWKKEHK 70
          RMK KK  +
Sbjct: 86 RMKQKKRER 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 =  127 bits (321), Expect = 2e-38
 Identities = 38/69 (55%), Positives = 46/69 (66%)

Query: 126 GTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 185
            +    G     RT++T  Q  ELEKEFHFN+YL+R RR+EIA  L L E Q+KIWFQNR
Sbjct: 26  VSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNR 85

Query: 186 RMKWKKEHK 194
           RMK KK  +
Sbjct: 86  RMKQKKRER 94

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

 Score =  120 bits (302), Expect = 7e-36
 Identities = 44/62 (70%), Positives = 50/62 (80%)

Query: 8  GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          G  KR RT+YTR Q LELEKEF FN+Y++R RR+E+A  L LTER IKIWFQNRRMKWKK
Sbjct: 1  GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60

Query: 68 EH 69
          E 
Sbjct: 61 EE 62

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

 Score =  120 bits (302), Expect = 7e-36
 Identities = 44/62 (70%), Positives = 50/62 (80%)

Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           G  KR RT+YTR Q LELEKEF FN+Y++R RR+E+A  L LTER IKIWFQNRRMKWKK
Sbjct: 1   GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60

Query: 192 EH 193
           E 
Sbjct: 61  EE 62

>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 =  119 bits (301), Expect = 1e-35
 Identities = 55/60 (91%), Positives = 57/60 (95%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          KR R +YTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKE+K
Sbjct: 3  KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 62

>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 =  119 bits (301), Expect = 1e-35
 Identities = 55/60 (91%), Positives = 57/60 (95%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           KR R +YTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKE+K
Sbjct: 3   KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 62

>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 =  118 bits (297), Expect = 4e-35
 Identities = 26/65 (40%), Positives = 39/65 (60%)

Query: 6  ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 65
          +    K  +  ++  QT+ELEK+F   +YL+   R  +A  L L+ERQ+K WFQNRR KW
Sbjct: 3  SGSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKW 62

Query: 66 KKEHK 70
          ++   
Sbjct: 63 RRSGP 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 =  118 bits (297), Expect = 4e-35
 Identities = 26/65 (40%), Positives = 39/65 (60%)

Query: 130 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 189
           +    K  +  ++  QT+ELEK+F   +YL+   R  +A  L L+ERQ+K WFQNRR KW
Sbjct: 3   SGSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKW 62

Query: 190 KKEHK 194
           ++   
Sbjct: 63  RRSGP 67

>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 =  117 bits (294), Expect = 1e-34
 Identities = 28/64 (43%), Positives = 41/64 (64%)

Query: 7  NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 66
            + +R RT +T  Q + LEK F   +YL+   RI++A +L L++ Q+K W+QNRRMKWK
Sbjct: 14 AKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWK 73

Query: 67 KEHK 70
          K   
Sbjct: 74 KSGP 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 =  117 bits (294), Expect = 1e-34
 Identities = 28/64 (43%), Positives = 41/64 (64%)

Query: 131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190
             + +R RT +T  Q + LEK F   +YL+   RI++A +L L++ Q+K W+QNRRMKWK
Sbjct: 14  AKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWK 73

Query: 191 KEHK 194
           K   
Sbjct: 74  KSGP 77

>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 =  115 bits (290), Expect = 4e-34
 Identities = 25/60 (41%), Positives = 36/60 (60%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          +R RT++T  Q  ELE+ F   RYLT  R  +++  L L   Q+KIWF+NRR + K +  
Sbjct: 3  RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 62

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

 Score =  115 bits (290), Expect = 4e-34
 Identities = 25/60 (41%), Positives = 36/60 (60%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           +R RT++T  Q  ELE+ F   RYLT  R  +++  L L   Q+KIWF+NRR + K +  
Sbjct: 3   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 62

>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 =  116 bits (291), Expect = 4e-34
 Identities = 42/62 (67%), Positives = 50/62 (80%)

Query: 9  ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68
           T+++R  YT++QTLELEKEF FN YLTR RR E+A  L LTERQ+KIWFQNRRMK KK 
Sbjct: 12 STRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKI 71

Query: 69 HK 70
          +K
Sbjct: 72 NK 73

>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 =  116 bits (291), Expect = 4e-34
 Identities = 42/62 (67%), Positives = 50/62 (80%)

Query: 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
            T+++R  YT++QTLELEKEF FN YLTR RR E+A  L LTERQ+KIWFQNRRMK KK 
Sbjct: 12  STRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKI 71

Query: 193 HK 194
           +K
Sbjct: 72  NK 73

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

 Score =  114 bits (288), Expect = 7e-34
 Identities = 30/59 (50%), Positives = 41/59 (69%)

Query: 9  ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
            KR RT+++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWF+N+R K KK
Sbjct: 2  AEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

>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 =  114 bits (288), Expect = 7e-34
 Identities = 30/59 (50%), Positives = 41/59 (69%)

Query: 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
             KR RT+++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWF+N+R K KK
Sbjct: 2   AEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

>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 =  114 bits (288), Expect = 1e-33
 Identities = 27/66 (40%), Positives = 45/66 (68%)

Query: 5  NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 64
          ++    +++R  Y++ Q  ELE+E+  N+++T+ +R +I+ A  L+ERQI IWFQNRR+K
Sbjct: 2  SSGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVK 61

Query: 65 WKKEHK 70
           KK   
Sbjct: 62 EKKSGP 67

>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 =  114 bits (288), Expect = 1e-33
 Identities = 27/66 (40%), Positives = 45/66 (68%)

Query: 129 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 188
           ++    +++R  Y++ Q  ELE+E+  N+++T+ +R +I+ A  L+ERQI IWFQNRR+K
Sbjct: 2   SSGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVK 61

Query: 189 WKKEHK 194
            KK   
Sbjct: 62  EKKSGP 67

>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 =  112 bits (283), Expect = 5e-33
 Identities = 31/58 (53%), Positives = 41/58 (70%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68
          +R RT++TR Q   LEKEF+   Y++R RR E+A  L L E  IK+WFQNRRMK K++
Sbjct: 2  RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59

>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 =  112 bits (283), Expect = 5e-33
 Identities = 31/58 (53%), Positives = 41/58 (70%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
           +R RT++TR Q   LEKEF+   Y++R RR E+A  L L E  IK+WFQNRRMK K++
Sbjct: 2   RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59

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

 Score =  110 bits (276), Expect = 7e-32
 Identities = 27/67 (40%), Positives = 44/67 (65%)

Query: 4  VNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 63
          ++   E +++R  YT+ Q  ELE+E+  N+++T+ +R  I+    L+ERQ+ IWFQNRR+
Sbjct: 1  MSHMLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRV 60

Query: 64 KWKKEHK 70
          K KK   
Sbjct: 61 KEKKVIN 67

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

 Score =  110 bits (276), Expect = 7e-32
 Identities = 27/67 (40%), Positives = 44/67 (65%)

Query: 128 VNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 187
           ++   E +++R  YT+ Q  ELE+E+  N+++T+ +R  I+    L+ERQ+ IWFQNRR+
Sbjct: 1   MSHMLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRV 60

Query: 188 KWKKEHK 194
           K KK   
Sbjct: 61  KEKKVIN 67

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

 Score =  109 bits (273), Expect = 3e-31
 Identities = 29/63 (46%), Positives = 40/63 (63%)

Query: 8  GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
           + K+ RTS+TR Q  ELEK FH  +YL    R  +A  L +T+ Q+K WFQNRR KW++
Sbjct: 15 PKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRR 74

Query: 68 EHK 70
          +  
Sbjct: 75 QTA 77

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

 Score =  109 bits (273), Expect = 3e-31
 Identities = 29/63 (46%), Positives = 40/63 (63%)

Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
            + K+ RTS+TR Q  ELEK FH  +YL    R  +A  L +T+ Q+K WFQNRR KW++
Sbjct: 15  PKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRR 74

Query: 192 EHK 194
           +  
Sbjct: 75  QTA 77

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

 Score =  103 bits (258), Expect = 3e-29
 Identities = 25/66 (37%), Positives = 39/66 (59%)

Query: 5  NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 64
          ++    ++ RT Y+ +Q   L++ F   +YL    R E+A +L LT+ Q+KIWFQN+R K
Sbjct: 2  SSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSK 61

Query: 65 WKKEHK 70
           KK   
Sbjct: 62 IKKSGP 67

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

 Score =  103 bits (258), Expect = 3e-29
 Identities = 25/66 (37%), Positives = 39/66 (59%)

Query: 129 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 188
           ++    ++ RT Y+ +Q   L++ F   +YL    R E+A +L LT+ Q+KIWFQN+R K
Sbjct: 2   SSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSK 61

Query: 189 WKKEHK 194
            KK   
Sbjct: 62  IKKSGP 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 =  101 bits (253), Expect = 2e-28
 Identities = 25/67 (37%), Positives = 38/67 (56%)

Query: 8  GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          G      +  +  Q +ELE++F   +YL+   R  +A  L LTE Q+KIWFQNRR K K+
Sbjct: 2  GHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61

Query: 68 EHKMASM 74
          +   + +
Sbjct: 62 KQLSSEL 68

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

 Score =  101 bits (253), Expect = 2e-28
 Identities = 25/67 (37%), Positives = 38/67 (56%)

Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           G      +  +  Q +ELE++F   +YL+   R  +A  L LTE Q+KIWFQNRR K K+
Sbjct: 2   GHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61

Query: 192 EHKMASM 198
           +   + +
Sbjct: 62  KQLSSEL 68

>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 = 96.9 bits (242), Expect = 8e-27
 Identities = 15/58 (25%), Positives = 32/58 (55%)

Query: 9  ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 66
          ++ + ++S +      LE+ F   + L  + + E+A    +T  Q+++WF N+RM+ K
Sbjct: 4  KSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 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 = 96.9 bits (242), Expect = 8e-27
 Identities = 15/58 (25%), Positives = 32/58 (55%)

Query: 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190
           ++ + ++S +      LE+ F   + L  + + E+A    +T  Q+++WF N+RM+ K
Sbjct: 4   KSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61

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

 Score = 96.4 bits (240), Expect = 2e-26
 Identities = 21/63 (33%), Positives = 38/63 (60%)

Query: 8  GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
           + ++ RT ++  Q   L   F   +YL+ ++  E+++ L L+ +Q+K WFQN+RMK K+
Sbjct: 20 VKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKR 79

Query: 68 EHK 70
            K
Sbjct: 80 WQK 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 = 96.4 bits (240), Expect = 2e-26
 Identities = 21/63 (33%), Positives = 38/63 (60%)

Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
            + ++ RT ++  Q   L   F   +YL+ ++  E+++ L L+ +Q+K WFQN+RMK K+
Sbjct: 20  VKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKR 79

Query: 192 EHK 194
             K
Sbjct: 80  WQK 82

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

 Score = 95.0 bits (237), Expect = 4e-26
 Identities = 27/57 (47%), Positives = 38/57 (66%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          ++ RT +T  Q L LE++F   +YL+   R E + +L LTE Q+KIWFQNRR 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 = 95.0 bits (237), Expect = 4e-26
 Identities = 27/57 (47%), Positives = 38/57 (66%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           ++ RT +T  Q L LE++F   +YL+   R E + +L LTE Q+KIWFQNRR K K+
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

 Score = 94.3 bits (235), Expect = 7e-26
 Identities = 21/61 (34%), Positives = 38/61 (62%)

Query: 8  GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          G  ++ RT +++ Q   L+  F   +YL+ ++  E++  L L+ +Q+K WFQN+RMK K+
Sbjct: 1  GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60

Query: 68 E 68
           
Sbjct: 61 W 61

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

 Score = 94.3 bits (235), Expect = 7e-26
 Identities = 21/61 (34%), Positives = 38/61 (62%)

Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           G  ++ RT +++ Q   L+  F   +YL+ ++  E++  L L+ +Q+K WFQN+RMK K+
Sbjct: 1   GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60

Query: 192 E 192
            
Sbjct: 61  W 61

>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 = 94.1 bits (234), Expect = 1e-25
 Identities = 25/76 (32%), Positives = 39/76 (51%)

Query: 2  STVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 61
          ++     + +++R  +T+ QT ELE+ F   RYL+   R  +A  + LT  Q+KIWFQN 
Sbjct: 1  ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNH 60

Query: 62 RMKWKKEHKMASMNNP 77
          R K K+          
Sbjct: 61 RYKTKRAQNEKGYEGH 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 = 93.3 bits (232), Expect = 3e-25
 Identities = 26/77 (33%), Positives = 39/77 (50%)

Query: 126 GTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 185
            +     + +++R  +T+ QT ELE+ F   RYL+   R  +A  + LT  Q+KIWFQN 
Sbjct: 1   ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNH 60

Query: 186 RMKWKKEHKMASMNVIP 202
           R K K+          P
Sbjct: 61  RYKTKRAQNEKGYEGHP 77

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

 Score = 88.9 bits (221), Expect = 8e-24
 Identities = 26/54 (48%), Positives = 37/54 (68%)

Query: 15 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68
          TS++R Q LELE+ F   +YL    R  +A AL +T+ Q+K WFQNRR KW+++
Sbjct: 2  TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

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

 Score = 88.9 bits (221), Expect = 8e-24
 Identities = 26/54 (48%), Positives = 37/54 (68%)

Query: 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
           TS++R Q LELE+ F   +YL    R  +A AL +T+ Q+K WFQNRR KW+++
Sbjct: 2   TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

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

 Score = 87.3 bits (217), Expect = 4e-23
 Identities = 25/56 (44%), Positives = 35/56 (62%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 66
          ++ R  +++ Q  ELE+ F   RYL+   R ++A  L LT  Q+KIWFQNRR 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 = 87.3 bits (217), Expect = 4e-23
 Identities = 25/56 (44%), Positives = 35/56 (62%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190
           ++ R  +++ Q  ELE+ F   RYL+   R ++A  L LT  Q+KIWFQNRR K K
Sbjct: 3   RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

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

 Score = 85.5 bits (212), Expect = 3e-22
 Identities = 23/64 (35%), Positives = 38/64 (59%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          +++R  +++ Q  ELE+ F   +YL+   R  +A  + LT  Q+KIWFQN R K K++ K
Sbjct: 3  RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62

Query: 71 MASM 74
            + 
Sbjct: 63 DKAA 66

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

 Score = 85.5 bits (212), Expect = 3e-22
 Identities = 23/64 (35%), Positives = 38/64 (59%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           +++R  +++ Q  ELE+ F   +YL+   R  +A  + LT  Q+KIWFQN R K K++ K
Sbjct: 3   RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62

Query: 195 MASM 198
             + 
Sbjct: 63  DKAA 66

>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 = 87.7 bits (217), Expect = 4e-22
 Identities = 20/61 (32%), Positives = 30/61 (49%)

Query: 7   NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 66
               +++RTS      + LEK F  N+  T      IA  L + +  I++WF NRR K K
Sbjct: 98  LSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEK 157

Query: 67  K 67
           +
Sbjct: 158 R 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 = 87.7 bits (217), Expect = 4e-22
 Identities = 20/61 (32%), Positives = 30/61 (49%)

Query: 131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190
               +++RTS      + LEK F  N+  T      IA  L + +  I++WF NRR K K
Sbjct: 98  LSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEK 157

Query: 191 K 191
           +
Sbjct: 158 R 158

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

 Score = 80.1 bits (197), Expect = 4e-19
 Identities = 19/69 (27%), Positives = 30/69 (43%)

Query: 6   ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 65
           A G  +++RTS        LE  F      +      +A +L L +  +++WF NRR K 
Sbjct: 95  AQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKE 154

Query: 66  KKEHKMASM 74
           K+    A  
Sbjct: 155 KRMTPAAGA 163

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

 Score = 80.1 bits (197), Expect = 4e-19
 Identities = 19/69 (27%), Positives = 30/69 (43%)

Query: 130 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 189
           A G  +++RTS        LE  F      +      +A +L L +  +++WF NRR K 
Sbjct: 95  AQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKE 154

Query: 190 KKEHKMASM 198
           K+    A  
Sbjct: 155 KRMTPAAGA 163

>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 = 75.8 bits (186), Expect = 1e-17
 Identities = 17/67 (25%), Positives = 34/67 (50%)

Query: 1   MSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQN 60
              V AN   +++RT+ +      LE+ F  +   + +  + +A  L L +  +++WF N
Sbjct: 78  NEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCN 137

Query: 61  RRMKWKK 67
           RR + K+
Sbjct: 138 RRQREKR 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 = 75.4 bits (185), Expect = 1e-17
 Identities = 17/68 (25%), Positives = 34/68 (50%)

Query: 124 KRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 183
               V AN   +++RT+ +      LE+ F  +   + +  + +A  L L +  +++WF 
Sbjct: 77  YNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFC 136

Query: 184 NRRMKWKK 191
           NRR + K+
Sbjct: 137 NRRQREKR 144

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

 Score = 70.9 bits (174), Expect = 1e-16
 Identities = 11/69 (15%), Positives = 26/69 (37%)

Query: 5  NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 64
          + +      +   +  Q   L+  F  N++  +     +     L+ R+++ WF +RR  
Sbjct: 3  SGSSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYH 62

Query: 65 WKKEHKMAS 73
           +      S
Sbjct: 63 CRNLKGSRS 71

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

 Score = 70.9 bits (174), Expect = 1e-16
 Identities = 11/69 (15%), Positives = 26/69 (37%)

Query: 129 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 188
           + +      +   +  Q   L+  F  N++  +     +     L+ R+++ WF +RR  
Sbjct: 3   SGSSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYH 62

Query: 189 WKKEHKMAS 197
            +      S
Sbjct: 63  CRNLKGSRS 71

>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 80

 Score = 70.6 bits (173), Expect = 2e-16
 Identities = 20/63 (31%), Positives = 34/63 (53%)

Query: 10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69
           KR RT+ T  Q   L +++  +   TR+    IAH + L +R +++WFQN R + +K  
Sbjct: 17 DKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSG 76

Query: 70 KMA 72
            +
Sbjct: 77 PSS 79

>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 80

 Score = 70.6 bits (173), Expect = 2e-16
 Identities = 20/63 (31%), Positives = 34/63 (53%)

Query: 134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193
            KR RT+ T  Q   L +++  +   TR+    IAH + L +R +++WFQN R + +K  
Sbjct: 17  DKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSG 76

Query: 194 KMA 196
             +
Sbjct: 77  PSS 79

>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 = 69.7 bits (171), Expect = 2e-16
 Identities = 20/60 (33%), Positives = 29/60 (48%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          +  RT +T YQ   L+  F  N Y       ++++ L L  R I +WFQN R K +K   
Sbjct: 8  RSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGP 67

>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 = 69.7 bits (171), Expect = 2e-16
 Identities = 20/60 (33%), Positives = 29/60 (48%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           +  RT +T YQ   L+  F  N Y       ++++ L L  R I +WFQN R K +K   
Sbjct: 8   RSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGP 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 = 67.0 bits (164), Expect = 3e-15
 Identities = 18/66 (27%), Positives = 29/66 (43%)

Query: 5  NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 64
          ++    KR RT  T  Q   L + F  N   +  +  E+A    L ++ IK WF+N   K
Sbjct: 2  SSGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFK 61

Query: 65 WKKEHK 70
           ++   
Sbjct: 62 ERQSGP 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 = 67.0 bits (164), Expect = 3e-15
 Identities = 18/66 (27%), Positives = 29/66 (43%)

Query: 129 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 188
           ++    KR RT  T  Q   L + F  N   +  +  E+A    L ++ IK WF+N   K
Sbjct: 2   SSGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFK 61

Query: 189 WKKEHK 194
            ++   
Sbjct: 62  ERQSGP 67

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

 Score = 65.9 bits (161), Expect = 8e-15
 Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 1/65 (1%)

Query: 10 TKRQRTSYTRYQTLELEKEFH-FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68
          + +  +  T  Q   LE  F+  N++        IA    LTE Q + WF+ R  +W++ 
Sbjct: 2  SAQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 61

Query: 69 HKMAS 73
            + S
Sbjct: 62 EGLPS 66

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

 Score = 65.9 bits (161), Expect = 8e-15
 Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 1/65 (1%)

Query: 134 TKRQRTSYTRYQTLELEKEFH-FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
           + +  +  T  Q   LE  F+  N++        IA    LTE Q + WF+ R  +W++ 
Sbjct: 2   SAQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 61

Query: 193 HKMAS 197
             + S
Sbjct: 62  EGLPS 66

>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 = 68.2 bits (166), Expect = 8e-15
 Identities = 19/63 (30%), Positives = 30/63 (47%)

Query: 5   NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 64
                 KR+RTS        LE  F  +   + ++   IA+ L L +  +++WF NRR K
Sbjct: 91  TLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQK 150

Query: 65  WKK 67
            K+
Sbjct: 151 GKR 153

>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 = 68.2 bits (166), Expect = 8e-15
 Identities = 19/63 (30%), Positives = 30/63 (47%)

Query: 129 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 188
                 KR+RTS        LE  F  +   + ++   IA+ L L +  +++WF NRR K
Sbjct: 91  TLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQK 150

Query: 189 WKK 191
            K+
Sbjct: 151 GKR 153

>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 = 67.4 bits (164), Expect = 2e-14
 Identities = 17/58 (29%), Positives = 26/58 (44%)

Query: 10  TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
            +++RTS+T      L   F  N   T +   E+A  L      +++WF NRR   K 
Sbjct: 93  KRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN 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 = 67.4 bits (164), Expect = 2e-14
 Identities = 17/58 (29%), Positives = 26/58 (44%)

Query: 134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
            +++RTS+T      L   F  N   T +   E+A  L      +++WF NRR   K 
Sbjct: 93  KRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN 150

>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 = 62.7 bits (153), Expect = 1e-13
 Identities = 24/64 (37%), Positives = 35/64 (54%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          +R RT++T+ Q   LE  F  N Y       ++A  L L   +I+IWFQNRR K K+ H+
Sbjct: 2  RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61

Query: 71 MASM 74
           +  
Sbjct: 62 ESQF 65

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

 Score = 62.7 bits (153), Expect = 1e-13
 Identities = 24/64 (37%), Positives = 35/64 (54%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           +R RT++T+ Q   LE  F  N Y       ++A  L L   +I+IWFQNRR K K+ H+
Sbjct: 2   RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61

Query: 195 MASM 198
            +  
Sbjct: 62  ESQF 65

>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 = 62.8 bits (153), Expect = 1e-13
 Identities = 22/68 (32%), Positives = 38/68 (55%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          +R+RT++TR Q   LE  F   RY     R E+A  + L E ++++WF+NRR K +++ +
Sbjct: 8  RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQ 67

Query: 71 MASMNNPN 78
                 +
Sbjct: 68 QQQNGGQS 75

>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 = 61.7 bits (150), Expect = 3e-13
 Identities = 22/63 (34%), Positives = 37/63 (58%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           +R+RT++TR Q   LE  F   RY     R E+A  + L E ++++WF+NRR K +++ +
Sbjct: 8   RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQ 67

Query: 195 MAS 197
              
Sbjct: 68  QQQ 70

>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 62.5 bits (152), Expect = 2e-13
 Identities = 18/69 (26%), Positives = 33/69 (47%)

Query: 10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69
           KR RTS+  +Q   ++  F  N     +   ++A    LT+R +++WFQN R K+++  
Sbjct: 7  GKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNL 66

Query: 70 KMASMNNPN 78
                  +
Sbjct: 67 LRQENGGVS 75

>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 62.1 bits (151), Expect = 3e-13
 Identities = 18/62 (29%), Positives = 32/62 (51%)

Query: 134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193
            KR RTS+  +Q   ++  F  N     +   ++A    LT+R +++WFQN R K+++  
Sbjct: 7   GKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNL 66

Query: 194 KM 195
             
Sbjct: 67  LR 68

>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 = 62.4 bits (152), Expect = 2e-13
 Identities = 25/63 (39%), Positives = 38/63 (60%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          +R RT+++  Q  ELE+ F   +Y     R E+A    LTE +I++WFQNRR + +K+H 
Sbjct: 19 RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT 78

Query: 71 MAS 73
            S
Sbjct: 79 SVS 81

>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 = 62.4 bits (152), Expect = 2e-13
 Identities = 25/63 (39%), Positives = 38/63 (60%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           +R RT+++  Q  ELE+ F   +Y     R E+A    LTE +I++WFQNRR + +K+H 
Sbjct: 19  RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT 78

Query: 195 MAS 197
             S
Sbjct: 79  SVS 81

>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 = 61.2 bits (149), Expect = 4e-13
 Identities = 28/68 (41%), Positives = 39/68 (57%)

Query: 8  GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          G  +RQRT +T  Q  +LE  F  NRY     R EIA    LTE ++++WF+NRR KW+K
Sbjct: 1  GSQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60

Query: 68 EHKMASMN 75
            +    +
Sbjct: 61 REEFIVTD 68

>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 = 61.2 bits (149), Expect = 4e-13
 Identities = 28/68 (41%), Positives = 39/68 (57%)

Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           G  +RQRT +T  Q  +LE  F  NRY     R EIA    LTE ++++WF+NRR KW+K
Sbjct: 1   GSQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60

Query: 192 EHKMASMN 199
             +    +
Sbjct: 61  REEFIVTD 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 = 60.3 bits (147), Expect = 7e-13
 Identities = 25/59 (42%), Positives = 36/59 (61%)

Query: 13 QRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 71
             ++T +Q  ELEK F    Y     R E+A  + LTE +I++WFQNRR KW+K+ K+
Sbjct: 2  SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEKV 60

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

 Score = 60.3 bits (147), Expect = 7e-13
 Identities = 25/59 (42%), Positives = 36/59 (61%)

Query: 137 QRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 195
              ++T +Q  ELEK F    Y     R E+A  + LTE +I++WFQNRR KW+K+ K+
Sbjct: 2   SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEKV 60

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

 Score = 60.5 bits (147), Expect = 1e-12
 Identities = 26/68 (38%), Positives = 39/68 (57%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          +R RTS+T+ Q   LEKEF    Y     R  +A  + L E +I++WF NRR KW++E K
Sbjct: 8  QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 67

Query: 71 MASMNNPN 78
          + +    +
Sbjct: 68 LRNQRRQS 75

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

 Score = 59.7 bits (145), Expect = 2e-12
 Identities = 26/68 (38%), Positives = 38/68 (55%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           +R RTS+T+ Q   LEKEF    Y     R  +A  + L E +I++WF NRR KW++E K
Sbjct: 8   QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 67

Query: 195 MASMNVIP 202
           + +     
Sbjct: 68  LRNQRRQS 75

>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 = 59.7 bits (145), Expect = 1e-12
 Identities = 19/62 (30%), Positives = 27/62 (43%)

Query: 10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69
          T R RT     Q   L   +  N       + ++     L+ R I++WFQN+R K KK  
Sbjct: 3  TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS 62

Query: 70 KM 71
           M
Sbjct: 63 IM 64

>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 = 59.7 bits (145), Expect = 1e-12
 Identities = 19/62 (30%), Positives = 27/62 (43%)

Query: 134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193
           T R RT     Q   L   +  N       + ++     L+ R I++WFQN+R K KK  
Sbjct: 3   TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS 62

Query: 194 KM 195
            M
Sbjct: 63  IM 64

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

 Score = 59.8 bits (145), Expect = 2e-12
 Identities = 14/64 (21%), Positives = 24/64 (37%), Gaps = 1/64 (1%)

Query: 5  NANGETKRQRTSYTRYQTLELEKEFH-FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 63
          ++     R RT  +      L+   H    Y  +     ++  L L +  I  +FQN+R 
Sbjct: 2  SSGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRY 61

Query: 64 KWKK 67
            K 
Sbjct: 62 HVKH 65

>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 = 59.8 bits (145), Expect = 2e-12
 Identities = 14/64 (21%), Positives = 24/64 (37%), Gaps = 1/64 (1%)

Query: 129 NANGETKRQRTSYTRYQTLELEKEFH-FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 187
           ++     R RT  +      L+   H    Y  +     ++  L L +  I  +FQN+R 
Sbjct: 2   SSGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRY 61

Query: 188 KWKK 191
             K 
Sbjct: 62  HVKH 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 = 59.3 bits (144), Expect = 3e-12
 Identities = 20/62 (32%), Positives = 34/62 (54%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          +R RT +T  Q   LE  F   +Y     R ++A  + L E ++++WF+NRR KW++   
Sbjct: 8  RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP 67

Query: 71 MA 72
           +
Sbjct: 68 SS 69

>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 = 59.3 bits (144), Expect = 3e-12
 Identities = 20/62 (32%), Positives = 34/62 (54%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           +R RT +T  Q   LE  F   +Y     R ++A  + L E ++++WF+NRR KW++   
Sbjct: 8   RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP 67

Query: 195 MA 196
            +
Sbjct: 68  SS 69

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

 Score = 58.1 bits (140), Expect = 1e-11
 Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 15/83 (18%)

Query: 12 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC---------------LTERQIKI 56
            R ++ +     +E  F+ N+Y    +R EIA+A                 +T  ++  
Sbjct: 9  GSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYN 68

Query: 57 WFQNRRMKWKKEHKMASMNNPNL 79
          WF NRR + K+   +A++   + 
Sbjct: 69 WFANRRKEIKRRANIAAILESSG 91

>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 = 58.1 bits (140), Expect = 1e-11
 Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 15/78 (19%)

Query: 136 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC---------------LTERQIKI 180
             R ++ +     +E  F+ N+Y    +R EIA+A                 +T  ++  
Sbjct: 9   GSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYN 68

Query: 181 WFQNRRMKWKKEHKMASM 198
           WF NRR + K+   +A++
Sbjct: 69  WFANRRKEIKRRANIAAI 86

>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 = 56.5 bits (136), Expect = 4e-11
 Identities = 14/69 (20%), Positives = 26/69 (37%)

Query: 10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69
          T ++    T  Q   L+  F  +  LT      +     LT R+I  WF  ++     + 
Sbjct: 11 TPQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE 70

Query: 70 KMASMNNPN 78
          +   ++  N
Sbjct: 71 EKMEIDESN 79

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

 Score = 56.2 bits (135), Expect = 7e-11
 Identities = 13/66 (19%), Positives = 25/66 (37%)

Query: 134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193
           T ++    T  Q   L+  F  +  LT      +     LT R+I  WF  ++     + 
Sbjct: 11  TPQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE 70

Query: 194 KMASMN 199
           +   ++
Sbjct: 71  EKMEID 76

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

 Score = 56.5 bits (136), Expect = 4e-11
 Identities = 13/67 (19%), Positives = 24/67 (35%)

Query: 10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69
            ++    T+ Q   LE  F  + + T+     +     L+ R+I  WF  RR       
Sbjct: 13 APQKFKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSME 72

Query: 70 KMASMNN 76
          +    + 
Sbjct: 73 QAVLDSM 79

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

 Score = 56.5 bits (136), Expect = 4e-11
 Identities = 13/64 (20%), Positives = 23/64 (35%)

Query: 134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193
             ++    T+ Q   LE  F  + + T+     +     L+ R+I  WF  RR       
Sbjct: 13  APQKFKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSME 72

Query: 194 KMAS 197
           +   
Sbjct: 73  QAVL 76

>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 = 55.1 bits (133), Expect = 8e-11
 Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 1/63 (1%)

Query: 12 RQRTSYTRYQTLELEKEFH-FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
              + T  Q   LE  F+  N++        IA    LTE Q + WF+ R  +W++   
Sbjct: 3  EGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG 62

Query: 71 MAS 73
          + S
Sbjct: 63 LPS 65

>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 = 55.1 bits (133), Expect = 8e-11
 Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 1/63 (1%)

Query: 136 RQRTSYTRYQTLELEKEFH-FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
               + T  Q   LE  F+  N++        IA    LTE Q + WF+ R  +W++   
Sbjct: 3   EGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG 62

Query: 195 MAS 197
           + S
Sbjct: 63  LPS 65

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

 Score = 54.5 bits (131), Expect = 2e-10
 Identities = 15/69 (21%), Positives = 21/69 (30%)

Query: 5  NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 64
          ++      +       Q   LE  F  N          +     +T R+I  WF  RR K
Sbjct: 2  SSGSSGPTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKK 61

Query: 65 WKKEHKMAS 73
             E    S
Sbjct: 62 VNAEETKKS 70

>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 = 54.5 bits (131), Expect = 2e-10
 Identities = 15/69 (21%), Positives = 21/69 (30%)

Query: 129 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 188
           ++      +       Q   LE  F  N          +     +T R+I  WF  RR K
Sbjct: 2   SSGSSGPTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKK 61

Query: 189 WKKEHKMAS 197
              E    S
Sbjct: 62  VNAEETKKS 70

>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 = 54.0 bits (130), Expect = 2e-10
 Identities = 10/63 (15%), Positives = 21/63 (33%)

Query: 8  GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
                    T+ Q   L+  F  +++        +     L   +IK WF + R + ++
Sbjct: 2  AHHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR 61

Query: 68 EHK 70
             
Sbjct: 62 GIV 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 = 54.0 bits (130), Expect = 2e-10
 Identities = 10/63 (15%), Positives = 21/63 (33%)

Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
                     T+ Q   L+  F  +++        +     L   +IK WF + R + ++
Sbjct: 2   AHHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR 61

Query: 192 EHK 194
              
Sbjct: 62  GIV 64

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

 Score = 55.3 bits (132), Expect = 7e-10
 Identities = 15/82 (18%), Positives = 29/82 (35%)

Query: 113 HWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC 172
                A  +  +    +     K+ R  +T  Q   L   F  N+  ++  +I I+  L 
Sbjct: 76  ALRLAACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLG 135

Query: 173 LTERQIKIWFQNRRMKWKKEHK 194
           L    +  +F N R +   +  
Sbjct: 136 LELSTVSNFFMNARRRSLDKWL 157

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

 Score = 54.5 bits (130), Expect = 1e-09
 Identities = 14/70 (20%), Positives = 26/70 (37%)

Query: 1   MSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQN 60
               +     K+ R  +T  Q   L   F  N+  ++  +I I+  L L    +  +F N
Sbjct: 88  EHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMN 147

Query: 61  RRMKWKKEHK 70
            R +   +  
Sbjct: 148 ARRRSLDKWL 157

>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 = 47.1 bits (112), Expect = 7e-08
 Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 1/58 (1%)

Query: 12 RQRTSYTRYQTLELEKEF-HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68
          +            LEK F    +Y   +R   ++  L  + R+I+ WF++RR + K  
Sbjct: 10 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPS 67

>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 = 47.1 bits (112), Expect = 7e-08
 Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 1/58 (1%)

Query: 136 RQRTSYTRYQTLELEKEF-HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
           +            LEK F    +Y   +R   ++  L  + R+I+ WF++RR + K  
Sbjct: 10  KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPS 67

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

 Score = 44.0 bits (103), Expect = 2e-06
 Identities = 14/93 (15%), Positives = 30/93 (32%), Gaps = 21/93 (22%)

Query: 126 GTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC------------- 172
             ++   + +R R  +       L + +   +  ++  R  +                  
Sbjct: 1   ARIDPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQ 60

Query: 173 --------LTERQIKIWFQNRRMKWKKEHKMAS 197
                   +TE ++  WF NRR +    HK+A 
Sbjct: 61  AQGLGSNLVTEVRVYNWFANRRKEEAFRHKLAM 93

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

 Score = 43.7 bits (102), Expect = 3e-06
 Identities = 14/93 (15%), Positives = 31/93 (33%), Gaps = 21/93 (22%)

Query: 2  STVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC------------- 48
          + ++   + +R R  +       L + +   +  ++  R  +                  
Sbjct: 1  ARIDPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQ 60

Query: 49 --------LTERQIKIWFQNRRMKWKKEHKMAS 73
                  +TE ++  WF NRR +    HK+A 
Sbjct: 61 AQGLGSNLVTEVRVYNWFANRRKEEAFRHKLAM 93

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

 Score = 41.7 bits (98), Expect = 6e-06
 Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 25 LEKEF-HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          LEK F    ++   +R   ++  L    R I+ WF+ RR + K 
Sbjct: 15 LEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 58

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

 Score = 41.7 bits (98), Expect = 6e-06
 Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 149 LEKEF-HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           LEK F    ++   +R   ++  L    R I+ WF+ RR + K 
Sbjct: 15  LEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 58

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

 Score = 43.5 bits (101), Expect = 1e-05
 Identities = 18/149 (12%), Positives = 39/149 (26%), Gaps = 29/149 (19%)

Query: 71  MASMNNPNLYTQYQTQGKSCTGRYQVRPITSPHGAYHGDLRYHWTNRAPLKYVKRGTVNA 130
           M +     LYT Y  + +    ++     +S +                      G   +
Sbjct: 71  MKTQKRAALYTWYVRKQREILRQFNQTVQSSGNMTDKSSQDQLLFLFPEFSQQSHGPGQS 130

Query: 131 NGET--------KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC---------- 172
           +           +R R  +       L + +   +  ++  R  +               
Sbjct: 131 DDACSEPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVS 190

Query: 173 -----------LTERQIKIWFQNRRMKWK 190
                      +TE ++  WF NRR +  
Sbjct: 191 PSKAHGLGSNLVTEVRVYNWFANRRKEEA 219

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

 Score = 41.9 bits (97), Expect = 5e-05
 Identities = 12/81 (14%), Positives = 25/81 (30%), Gaps = 21/81 (25%)

Query: 7   NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC------------------ 48
           N + +R R  +       L + +   +  ++  R  +                       
Sbjct: 139 NKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLG 198

Query: 49  ---LTERQIKIWFQNRRMKWK 66
              +TE ++  WF NRR +  
Sbjct: 199 SNLVTEVRVYNWFANRRKEEA 219

>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 = 39.8 bits (92), Expect = 7e-05
 Identities = 12/58 (20%), Positives = 21/58 (36%)

Query: 10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          +  +    T  Q   L+  F   ++ +     ++A    L    I  WF + R  WK 
Sbjct: 25 STGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKN 82

>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 = 39.8 bits (92), Expect = 7e-05
 Identities = 12/58 (20%), Positives = 21/58 (36%)

Query: 134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           +  +    T  Q   L+  F   ++ +     ++A    L    I  WF + R  WK 
Sbjct: 25  STGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKN 82

>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 = 41.0 bits (95), Expect = 1e-04
 Identities = 11/78 (14%), Positives = 23/78 (29%), Gaps = 21/78 (26%)

Query: 10  TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC--------------------- 48
            +R R  +       L + +   +  ++  R  +                          
Sbjct: 115 GRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNL 174

Query: 49  LTERQIKIWFQNRRMKWK 66
           +TE ++  WF NRR +  
Sbjct: 175 VTEVRVYNWFANRRKEEA 192

>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 = 41.0 bits (95), Expect = 1e-04
 Identities = 11/78 (14%), Positives = 23/78 (29%), Gaps = 21/78 (26%)

Query: 134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC--------------------- 172
            +R R  +       L + +   +  ++  R  +                          
Sbjct: 115 GRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNL 174

Query: 173 LTERQIKIWFQNRRMKWK 190
           +TE ++  WF NRR +  
Sbjct: 175 VTEVRVYNWFANRRKEEA 192

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	222
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.81
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.81
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.81
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.8
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.8
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.8
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.8
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.8
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.8
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.8
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.8
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.79
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.79
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.79
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.79
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.79
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.79
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.79
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.79
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.79
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.79
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.78
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.78
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.78
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.78
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.78
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.78
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.78
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.78
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.78
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.78
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.78
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.78
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.78
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.78
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.78
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.78
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.78
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.78
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.77
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.77
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.77
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.77
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.77
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.77
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.77
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.77
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.77
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.77
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.77
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.77
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.77
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.76
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.76
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.76
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.76
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.76
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.76
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.76
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.76
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.76
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.76
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.76
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.76
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.76
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.75
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.75
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.75
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.75
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.75
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.75
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.75
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.75
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.75
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.75
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.75
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.75
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.75
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.75
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.75
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.75
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.75
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.74
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.74
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.74
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.74
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.74
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.74
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.74
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.74
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.74
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.74
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.73
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.73
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.73
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.73
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.72
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.72
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.72
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.72
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.72
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.71
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.71
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.71
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.71
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.71
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.71
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.7
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.7
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.7
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.7
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.69
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.69
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.69
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.68
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.68
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.68
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.68
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.68
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.67
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.67
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.67
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.67
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.67
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.65
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.65
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.65
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.65
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.65
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.65
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.65
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.64
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.64
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.63
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.63
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.63
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.63
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.62
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.61
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.61
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.6
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.58
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.56
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.56
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.5
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.49
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.47
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.47
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.45
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.41
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.4
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.32
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.15
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.14
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.5
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.36
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	96.82
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	96.73
1u78_A	141	TC3 transposase, transposable element TC3 transpos	91.06
2k27_A	159	Paired box protein PAX-8; paired domain, solution	90.08
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	87.82
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	85.87
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	85.54
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	84.68
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	84.04

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

Probab=99.81  E-value=5.6e-20  Score=120.64  Aligned_cols=65  Identities=31%  Similarity=0.596  Sum_probs=61.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      .+...+|.|+.||.+|+.+|+..|..++||+..+++.||..+||++.+|++||+|||+++++...
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2dmu_A            3 SGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP   67 (70)
T ss_dssp             STTSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTST
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccCC
Confidence            45678899999999999999999999999999999999999999999999999999999998654

>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=99.81  E-value=1.4e-19  Score=120.85  Aligned_cols=71  Identities=35%  Similarity=0.575  Sum_probs=64.6

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhc
Q psy11996          3 TVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS   73 (222)
Q Consensus         3 ~~~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~   73 (222)
                      +.....+.++.|+.||..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++......
T Consensus         2 s~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~~~   72 (77)
T 1nk2_P            2 SDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKG   72 (77)
T ss_dssp             CSCCSCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhcccc
Confidence            34556678889999999999999999999999999999999999999999999999999999998766544

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

Probab=99.81  E-value=1e-19  Score=122.55  Aligned_cols=67  Identities=33%  Similarity=0.530  Sum_probs=62.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA   72 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~   72 (222)
                      .+.+.+|.|+.||.+|+.+|+..|..++||+..+++.||..+||++.+|++||+|||+++++.....
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~~   69 (80)
T 2dms_A            3 SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQ   69 (80)
T ss_dssp             CCCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCSC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHcc
Confidence            4567899999999999999999999999999999999999999999999999999999999976543

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

Probab=99.80  E-value=1.2e-19  Score=124.38  Aligned_cols=84  Identities=85%  Similarity=1.242  Sum_probs=63.3

Q ss_pred             CCcccccccCCCccccccccccCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhh
Q psy11996        108 GDLRYHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM  187 (222)
Q Consensus       108 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~  187 (222)
                      .+.++||+.......   +.....+..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+
T Consensus         5 p~~~~pwm~~~~~~~---~~~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~   81 (88)
T 2r5y_A            5 PPQIYPWMKRVHLGT---STVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRM   81 (88)
T ss_dssp             CSSCCGGGSCC------------------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             CCCCCchhhccCCCC---CCCCCCCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHH
Confidence            356677776654432   22334556788999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHhhh
Q psy11996        188 KWKKEHK  194 (222)
Q Consensus       188 k~kk~~~  194 (222)
                      ++|+..+
T Consensus        82 k~kk~~k   88 (88)
T 2r5y_A           82 KWKKEHK   88 (88)
T ss_dssp             HHHTTCC
T ss_pred             HhHhhcC
Confidence            9998653

>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=99.80  E-value=4e-20  Score=121.30  Aligned_cols=65  Identities=42%  Similarity=0.702  Sum_probs=60.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      .+...+++|+.||.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++...
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (70)
T 2cra_A            3 SGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGP   67 (70)
T ss_dssp             SSCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSCT
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccCC
Confidence            45678899999999999999999999999999999999999999999999999999999988543

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

Probab=99.80  E-value=1.4e-19  Score=121.74  Aligned_cols=68  Identities=38%  Similarity=0.650  Sum_probs=63.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhc
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS   73 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~   73 (222)
                      ++...+|.|+.||.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++..+...
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~~   70 (80)
T 2cue_A            3 SGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRN   70 (80)
T ss_dssp             SCCSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhhh
Confidence            45678899999999999999999999999999999999999999999999999999999999876553

>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=99.80  E-value=2.3e-19  Score=120.79  Aligned_cols=67  Identities=27%  Similarity=0.438  Sum_probs=62.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA   72 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~   72 (222)
                      .+...+|.|+.||.+|+.+|+..|..++||+..+++.||..+||++.+|++||+|||+++++.....
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~   69 (80)
T 2dmq_A            3 SGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQ   69 (80)
T ss_dssp             CCCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHHH
Confidence            4567889999999999999999999999999999999999999999999999999999999976543

>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=99.80  E-value=3.9e-20  Score=129.05  Aligned_cols=65  Identities=58%  Similarity=0.895  Sum_probs=57.3

Q ss_pred             CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcc
Q psy11996        132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA  196 (222)
Q Consensus       132 ~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~  196 (222)
                      +..++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+..+.+
T Consensus        32 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~g   96 (97)
T 1b72_A           32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKREREG   96 (97)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHTC-
T ss_pred             CCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhccC
Confidence            35677899999999999999999999999999999999999999999999999999999987653

>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=99.80  E-value=1.6e-19  Score=118.45  Aligned_cols=65  Identities=40%  Similarity=0.723  Sum_probs=60.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      .+...++.|+.||.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++...
T Consensus         3 ~~~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2e1o_A            3 SGSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGP   67 (70)
T ss_dssp             CCCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCCC
Confidence            45567888999999999999999999999999999999999999999999999999999998654

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

Probab=99.80  E-value=1.2e-19  Score=116.58  Aligned_cols=61  Identities=70%  Similarity=1.118  Sum_probs=56.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996          9 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH   69 (222)
Q Consensus         9 ~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~   69 (222)
                      ..+|.|+.||..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++.+
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   62 (63)
T 2h1k_A            2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE   62 (63)
T ss_dssp             ---CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhhc
Confidence            4688999999999999999999999999999999999999999999999999999999853

>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=99.80  E-value=3.3e-19  Score=119.09  Aligned_cols=71  Identities=35%  Similarity=0.563  Sum_probs=64.6

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccCCCC
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNVI  201 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~~~~  201 (222)
                      ....++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..........
T Consensus         6 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~~~~~~~   76 (77)
T 1nk2_P            6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGYEGH   76 (77)
T ss_dssp             SCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTTCCCC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhccccCCCC
Confidence            44667889999999999999999999999999999999999999999999999999999998877665543

>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=99.79  E-value=6.3e-20  Score=120.42  Aligned_cols=65  Identities=28%  Similarity=0.339  Sum_probs=60.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      .....++.|+.||.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++..+
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2da1_A            3 SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGP   67 (70)
T ss_dssp             SSCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhcc
Confidence            45678899999999999999999999999999999999999999999999999999999998654

>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=99.79  E-value=3.7e-19  Score=118.85  Aligned_cols=68  Identities=62%  Similarity=0.859  Sum_probs=62.8

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996          5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA   72 (222)
Q Consensus         5 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~   72 (222)
                      ...+..++.|+.||..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++..+..
T Consensus         8 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k~~   75 (77)
T 1puf_A            8 LHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDR   75 (77)
T ss_dssp             CCCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhhhc
Confidence            34566788999999999999999999999999999999999999999999999999999999987653

>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=99.79  E-value=7.8e-20  Score=119.98  Aligned_cols=65  Identities=31%  Similarity=0.460  Sum_probs=60.7

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996          5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH   69 (222)
Q Consensus         5 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~   69 (222)
                      ....+.++.|+.||.+|+.+|+..|..++||+..+++.||..+||++.+|++||+|||+++++..
T Consensus         2 ~~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2da2_A            2 SSGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSG   66 (70)
T ss_dssp             CCSCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCS
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhcc
Confidence            34567889999999999999999999999999999999999999999999999999999998754

>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=99.79  E-value=9.9e-20  Score=122.53  Aligned_cols=65  Identities=43%  Similarity=0.765  Sum_probs=60.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      ...+.++.|+.||.+|+.+|+..|..++||+..+++.||..+||++.+|++||+|||+++++..+
T Consensus        13 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~~   77 (80)
T 2dmt_A           13 KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGP   77 (80)
T ss_dssp             CCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCCS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcccC
Confidence            44567889999999999999999999999999999999999999999999999999999988543

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

Probab=99.79  E-value=1.2e-19  Score=120.64  Aligned_cols=70  Identities=40%  Similarity=0.710  Sum_probs=64.6

Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhh
Q psy11996          2 STVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM   71 (222)
Q Consensus         2 ~~~~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~   71 (222)
                      |..+..++.++.|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++..+.
T Consensus         1 S~~~~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r~   70 (75)
T 2m0c_A            1 SHMSNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRERF   70 (75)
T ss_dssp             CCSCCCSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCCC
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHhh
Confidence            4556777889999999999999999999999999999999999999999999999999999999986554

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

Probab=99.79  E-value=7.7e-20  Score=119.97  Aligned_cols=65  Identities=38%  Similarity=0.660  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996          5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH   69 (222)
Q Consensus         5 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~   69 (222)
                      ..+...++.|+.||.+|+.+|+..|..++||+..+++.||..+||++.+|++||+|||+++++..
T Consensus         2 s~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2djn_A            2 SSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSG   66 (70)
T ss_dssp             CSCCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSS
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccC
Confidence            34567889999999999999999999999999999999999999999999999999999988753

>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=99.79  E-value=1.9e-19  Score=114.94  Aligned_cols=58  Identities=52%  Similarity=0.811  Sum_probs=53.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996         10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      .+|.|+.||.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++
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            5788999999999999999999999999999999999999999999999999999886

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

Probab=99.79  E-value=3.2e-19  Score=112.71  Aligned_cols=57  Identities=47%  Similarity=0.774  Sum_probs=55.3

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996         11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus        11 ~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      +++|+.||.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++
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            578999999999999999999999999999999999999999999999999999886

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

Probab=99.79  E-value=3.9e-19  Score=116.59  Aligned_cols=65  Identities=31%  Similarity=0.583  Sum_probs=60.7

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      .+..++.|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..+.
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~~   68 (70)
T 2dmu_A            4 GSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGPS   68 (70)
T ss_dssp             TTSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTSTT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccCCC
Confidence            34567889999999999999999999999999999999999999999999999999999997654

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

Probab=99.79  E-value=4.6e-19  Score=115.55  Aligned_cols=63  Identities=40%  Similarity=0.637  Sum_probs=59.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996         10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA   72 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~   72 (222)
                      .++.|+.||..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++.....
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~~   64 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQH   64 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhccc
Confidence            678999999999999999999999999999999999999999999999999999999976543

>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=99.78  E-value=3.9e-19  Score=119.63  Aligned_cols=65  Identities=43%  Similarity=0.759  Sum_probs=60.6

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      ....++.|+.|+.+|+.+|+..|..++||+..++..||..|||++.+|++||+|||+|+|+..+.
T Consensus        14 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~~s   78 (80)
T 2dmt_A           14 AKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGPS   78 (80)
T ss_dssp             CCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCCSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcccCC
Confidence            44667889999999999999999999999999999999999999999999999999999997653

>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=99.78  E-value=1.9e-19  Score=121.31  Aligned_cols=65  Identities=78%  Similarity=1.151  Sum_probs=54.5

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996          5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH   69 (222)
Q Consensus         5 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~   69 (222)
                      ...+..+|.|+.||.+|+.+|+..|..++||+..+++.||..+||++.+|++||+|||+++++..
T Consensus        15 ~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   79 (81)
T 1b8i_A           15 GTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEI   79 (81)
T ss_dssp             ---------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhc
Confidence            44567789999999999999999999999999999999999999999999999999999999854

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

Probab=99.78  E-value=1.4e-19  Score=115.88  Aligned_cols=60  Identities=33%  Similarity=0.582  Sum_probs=52.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996          9 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE   68 (222)
Q Consensus         9 ~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~   68 (222)
                      +.++.|+.||..|+.+||..|..++||+..++..||..+||++.+|++||+|||+++++.
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            568899999999999999999999999999999999999999999999999999998873

>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=99.78  E-value=3.4e-19  Score=116.88  Aligned_cols=65  Identities=42%  Similarity=0.689  Sum_probs=60.4

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      .+..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+....
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~~   68 (70)
T 2cra_A            4 GSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGPS   68 (70)
T ss_dssp             SCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSCTT
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccCCC
Confidence            34667889999999999999999999999999999999999999999999999999999987643

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

Probab=99.78  E-value=8.2e-19  Score=118.03  Aligned_cols=70  Identities=31%  Similarity=0.468  Sum_probs=64.0

Q ss_pred             CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccCCCC
Q psy11996        132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNVI  201 (222)
Q Consensus       132 ~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~~~~  201 (222)
                      ...++.|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..+....+..
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~~~~~~~   74 (80)
T 2dms_A            5 SSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQQNGGQ   74 (80)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCSCCCCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHccCCCCC
Confidence            4678889999999999999999999999999999999999999999999999999999998876554443

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

Probab=99.78  E-value=4.2e-19  Score=114.02  Aligned_cols=61  Identities=70%  Similarity=1.118  Sum_probs=56.3

Q ss_pred             CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996        133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH  193 (222)
Q Consensus       133 ~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~  193 (222)
                      ..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+.+
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   62 (63)
T 2h1k_A            2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE   62 (63)
T ss_dssp             ---CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhhc
Confidence            4578899999999999999999999999999999999999999999999999999999864

>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=99.78  E-value=1.5e-19  Score=121.71  Aligned_cols=65  Identities=31%  Similarity=0.420  Sum_probs=60.6

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996          5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH   69 (222)
Q Consensus         5 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~   69 (222)
                      ....+.+|.|+.||.+|+.+|+..|..++||+..+++.||..|||++.+|++||+|||+++++..
T Consensus        12 ~~~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   76 (80)
T 2da3_A           12 EEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSG   76 (80)
T ss_dssp             CCCCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhc
Confidence            34566788999999999999999999999999999999999999999999999999999999854

>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=99.78  E-value=2.7e-19  Score=120.07  Aligned_cols=62  Identities=16%  Similarity=0.196  Sum_probs=57.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhh----CCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~----~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      ...+.||.||.||.+|+..|+..|..    ++||+..++++||..|||++.+|++||||||+|.++
T Consensus        13 ~~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           13 GGGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            34567899999999999999999999    999999999999999999999999999999998754

>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=99.78  E-value=1.1e-18  Score=117.50  Aligned_cols=70  Identities=26%  Similarity=0.404  Sum_probs=64.1

Q ss_pred             CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccCCCC
Q psy11996        132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNVI  201 (222)
Q Consensus       132 ~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~~~~  201 (222)
                      ...++.|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+.......+..
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~~~~~   74 (80)
T 2dmq_A            5 SSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQENGGV   74 (80)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHSSCCCSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHHHhcCCC
Confidence            4568889999999999999999999999999999999999999999999999999999998776655543

>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=116.60  Aligned_cols=65  Identities=31%  Similarity=0.440  Sum_probs=60.7

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      .+..++.|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..+.
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (70)
T 2da2_A            4 GSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGPS   68 (70)
T ss_dssp             SCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCSSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhcccc
Confidence            44677889999999999999999999999999999999999999999999999999999987654

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

Probab=99.78  E-value=5.6e-19  Score=120.03  Aligned_cols=65  Identities=32%  Similarity=0.528  Sum_probs=60.7

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996        130 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK  194 (222)
Q Consensus       130 ~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~  194 (222)
                      .....++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+..+
T Consensus        18 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k   82 (84)
T 2kt0_A           18 VPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK   82 (84)
T ss_dssp             CCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhh
Confidence            34567888999999999999999999999999999999999999999999999999999998765

>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=99.78  E-value=8.1e-19  Score=115.06  Aligned_cols=64  Identities=41%  Similarity=0.719  Sum_probs=60.0

Q ss_pred             CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       132 ~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      ...++.|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+....
T Consensus         5 ~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~~~   68 (70)
T 2e1o_A            5 SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGPS   68 (70)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHSCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCCCC
Confidence            3567789999999999999999999999999999999999999999999999999999998764

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

Probab=99.78  E-value=4.6e-19  Score=115.53  Aligned_cols=63  Identities=37%  Similarity=0.643  Sum_probs=59.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996         10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA   72 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~   72 (222)
                      .++.|+.||..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++..+..
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~~~   64 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDK   64 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhhHh
Confidence            578899999999999999999999999999999999999999999999999999999976543

>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=99.78  E-value=3e-19  Score=116.39  Aligned_cols=62  Identities=89%  Similarity=1.354  Sum_probs=58.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhh
Q psy11996         10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM   71 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~   71 (222)
                      .+|.|+.||.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++..+.
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~~   63 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKT   63 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSCC
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhccc
Confidence            47889999999999999999999999999999999999999999999999999999997643

>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=99.78  E-value=1.8e-19  Score=117.46  Aligned_cols=63  Identities=43%  Similarity=0.708  Sum_probs=60.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhh
Q psy11996          9 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM   71 (222)
Q Consensus         9 ~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~   71 (222)
                      +.++.|+.||..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++..+.
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~~   64 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEF   64 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhhc
Confidence            578999999999999999999999999999999999999999999999999999999997654

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

Probab=99.78  E-value=4.6e-19  Score=112.70  Aligned_cols=58  Identities=53%  Similarity=0.782  Sum_probs=55.4

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996         11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE   68 (222)
Q Consensus        11 ~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~   68 (222)
                      +|.|+.||.+|+.+|+..|..++||+..++..||..+||++.+|++||+|+|+++++.
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            6789999999999999999999999999999999999999999999999999999874

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

Probab=99.78  E-value=2.5e-19  Score=121.78  Aligned_cols=66  Identities=32%  Similarity=0.525  Sum_probs=60.9

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996          5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus         5 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      ....+.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++..+
T Consensus        17 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k   82 (84)
T 2kt0_A           17 KVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK   82 (84)
T ss_dssp             CCCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhh
Confidence            345677889999999999999999999999999999999999999999999999999999987543

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

Probab=99.78  E-value=5.4e-19  Score=117.54  Aligned_cols=69  Identities=41%  Similarity=0.723  Sum_probs=63.8

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccC
Q psy11996        130 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASM  198 (222)
Q Consensus       130 ~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~  198 (222)
                      ..+..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..+.+.+
T Consensus         5 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r~~q~   73 (75)
T 2m0c_A            5 NKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRERFGQM   73 (75)
T ss_dssp             CCSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCCCCSS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHhhhhc
Confidence            345678889999999999999999999999999999999999999999999999999999998877654

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

Probab=99.77  E-value=2.7e-19  Score=122.60  Aligned_cols=65  Identities=98%  Similarity=1.456  Sum_probs=55.3

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996          5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH   69 (222)
Q Consensus         5 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~   69 (222)
                      +..+..+|.|+.||.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++..
T Consensus        23 ~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   87 (88)
T 2r5y_A           23 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH   87 (88)
T ss_dssp             --------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhhc
Confidence            45567889999999999999999999999999999999999999999999999999999998753

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

Probab=99.77  E-value=8.7e-19  Score=117.90  Aligned_cols=67  Identities=39%  Similarity=0.655  Sum_probs=62.6

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhccc
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS  197 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~  197 (222)
                      ++..++.|+.|+.+|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+..+...
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~~   70 (80)
T 2cue_A            4 GSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRN   70 (80)
T ss_dssp             CCSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhhh
Confidence            3466788999999999999999999999999999999999999999999999999999999987654

>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=3.3e-19  Score=114.16  Aligned_cols=60  Identities=33%  Similarity=0.582  Sum_probs=53.1

Q ss_pred             CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996        133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  192 (222)
Q Consensus       133 ~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~  192 (222)
                      ..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+.
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            457889999999999999999999999999999999999999999999999999999985

>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=116.15  Aligned_cols=65  Identities=38%  Similarity=0.639  Sum_probs=60.4

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      .+..++.|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+....
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~s   68 (70)
T 2djn_A            4 GSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGPS   68 (70)
T ss_dssp             CCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccCCC
Confidence            44667889999999999999999999999999999999999999999999999999999986543

>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=99.77  E-value=8.3e-19  Score=118.30  Aligned_cols=65  Identities=37%  Similarity=0.610  Sum_probs=59.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      ...+.++.|+.||..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++...
T Consensus        14 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~   78 (81)
T 1fjl_A           14 LKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   78 (81)
T ss_dssp             ---CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhcc
Confidence            34567889999999999999999999999999999999999999999999999999999998764

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

Probab=99.77  E-value=4.6e-19  Score=117.12  Aligned_cols=63  Identities=43%  Similarity=0.682  Sum_probs=59.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996          7 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH   69 (222)
Q Consensus         7 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~   69 (222)
                      ...+++.|+.||..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++..
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   66 (73)
T 2l7z_A            4 MLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVI   66 (73)
T ss_dssp             SSCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHh
Confidence            456788999999999999999999999999999999999999999999999999999998854

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

Probab=99.77  E-value=5e-19  Score=119.11  Aligned_cols=65  Identities=18%  Similarity=0.315  Sum_probs=60.6

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhC----CCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996          5 NANGETKRQRTSYTRYQTLELEKEFHFN----RYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH   69 (222)
Q Consensus         5 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~----~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~   69 (222)
                      ....+.+|.|+.||.+|+.+|+..|..+    +||+..++++||..+||++.+|++||+|||+++++..
T Consensus         3 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~~   71 (80)
T 2da4_A            3 SGSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMG   71 (80)
T ss_dssp             CCCCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhcc
Confidence            4456788999999999999999999999    9999999999999999999999999999999998853

>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=5e-19  Score=116.11  Aligned_cols=65  Identities=28%  Similarity=0.327  Sum_probs=60.6

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      ....++.|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..+.
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (70)
T 2da1_A            4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGPS   68 (70)
T ss_dssp             SCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhccc
Confidence            34667889999999999999999999999999999999999999999999999999999997654

>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=99.77  E-value=4.1e-19  Score=115.80  Aligned_cols=65  Identities=42%  Similarity=0.677  Sum_probs=61.2

Q ss_pred             CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhccc
Q psy11996        133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS  197 (222)
Q Consensus       133 ~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~  197 (222)
                      ..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..+...
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~~~~   66 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEFIV   66 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTTTSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhhccC
Confidence            56788999999999999999999999999999999999999999999999999999999887653

>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=99.77  E-value=7.2e-19  Score=118.40  Aligned_cols=65  Identities=31%  Similarity=0.405  Sum_probs=60.5

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      ....++.|+.|+.+|+.+|+..|..++||+..++..||.+|||++.+|++||+|||+++|+....
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~   78 (80)
T 2da3_A           14 PQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSGPS   78 (80)
T ss_dssp             CCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhccC
Confidence            34667889999999999999999999999999999999999999999999999999999997653

>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=99.77  E-value=1.3e-18  Score=114.50  Aligned_cols=57  Identities=19%  Similarity=0.231  Sum_probs=54.1

Q ss_pred             CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996        136 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  192 (222)
Q Consensus       136 ~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~  192 (222)
                      ..+..||.+|+.+|+..|..++||+..++++||..+||++.||++||+|+|+++|+.
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            356789999999999999999999999999999999999999999999999999985

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

Probab=99.77  E-value=1.3e-18  Score=109.95  Aligned_cols=57  Identities=47%  Similarity=0.774  Sum_probs=55.0

Q ss_pred             CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996        135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  191 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk  191 (222)
                      ++.|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+
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            467899999999999999999999999999999999999999999999999999987

>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=99.77  E-value=4.5e-19  Score=114.95  Aligned_cols=60  Identities=30%  Similarity=0.375  Sum_probs=57.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996          9 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE   68 (222)
Q Consensus         9 ~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~   68 (222)
                      +.+|.|+.||.+|+.+|+..|..++||+..+++.||..+||++.+|++||+|||+++++.
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            468899999999999999999999999999999999999999999999999999998774

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

Probab=99.76  E-value=1.3e-18  Score=113.35  Aligned_cols=65  Identities=35%  Similarity=0.625  Sum_probs=60.7

Q ss_pred             CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccC
Q psy11996        134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASM  198 (222)
Q Consensus       134 ~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~  198 (222)
                      .++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..+...+
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~~~~~   66 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDKAA   66 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSCCSS
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhhHhhh
Confidence            46789999999999999999999999999999999999999999999999999999998776543

>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=99.76  E-value=8.7e-19  Score=111.79  Aligned_cols=58  Identities=52%  Similarity=0.811  Sum_probs=53.2

Q ss_pred             CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996        134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  191 (222)
Q Consensus       134 ~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk  191 (222)
                      .++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            4678999999999999999999999999999999999999999999999999999987

>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=99.76  E-value=2e-18  Score=115.29  Aligned_cols=65  Identities=65%  Similarity=0.921  Sum_probs=60.9

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      ....++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..+.
T Consensus        10 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k~   74 (77)
T 1puf_A           10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhhh
Confidence            34567889999999999999999999999999999999999999999999999999999998764

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

Probab=99.76  E-value=1.7e-18  Score=119.65  Aligned_cols=67  Identities=43%  Similarity=0.760  Sum_probs=61.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA   72 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~   72 (222)
                      ...+.++.|+.||.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++.....
T Consensus        13 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~   79 (93)
T 3a01_A           13 TPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEE   79 (93)
T ss_dssp             CCCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHH
Confidence            4456788999999999999999999999999999999999999999999999999999999976533

>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=99.76  E-value=1.6e-18  Score=114.24  Aligned_cols=60  Identities=27%  Similarity=0.356  Sum_probs=57.0

Q ss_pred             CCCCCCCCHHHHHHHHHHhhh-CCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996         11 KRQRTSYTRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus        11 ~r~R~~~t~~q~~~L~~~f~~-~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      .++|+.||.+|+.+|+..|.. ++||+..++..||..+||++.+|++||+|||+++++...
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            567899999999999999996 999999999999999999999999999999999999764

>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=99.76  E-value=1.1e-18  Score=113.70  Aligned_cols=64  Identities=86%  Similarity=1.312  Sum_probs=60.0

Q ss_pred             CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhccc
Q psy11996        134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS  197 (222)
Q Consensus       134 ~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~  197 (222)
                      .++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..+...
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~~~~   65 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTKG   65 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSCCCS
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhccccC
Confidence            4678999999999999999999999999999999999999999999999999999999876544

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

Probab=99.76  E-value=1.1e-18  Score=110.13  Aligned_cols=57  Identities=44%  Similarity=0.711  Sum_probs=54.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHH
Q psy11996         10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK   66 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~   66 (222)
                      .++.|+.|+.+|+..|+..|..++||+..++..||..+||++.+|++||+|||++++
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            578899999999999999999999999999999999999999999999999999864

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

Probab=99.76  E-value=8.5e-19  Score=113.98  Aligned_cols=61  Identities=39%  Similarity=0.580  Sum_probs=57.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996         10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      +|+.|+.||.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++...
T Consensus         1 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~   61 (67)
T 2k40_A            1 GRRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR   61 (67)
T ss_dssp             CCCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCC
T ss_pred             CcCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhch
Confidence            4788999999999999999999999999999999999999999999999999999988543

>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=99.76  E-value=6.5e-19  Score=118.04  Aligned_cols=62  Identities=21%  Similarity=0.256  Sum_probs=56.9

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhh-----CCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996          5 NANGETKRQRTSYTRYQTLELEKEFHF-----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus         5 ~~~~~~~r~R~~~t~~q~~~L~~~f~~-----~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      ....+.||.||.||.+|+..|+ .|..     ++||+..++++||..|||++.+|++||||||+|.++
T Consensus        12 ~~~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           12 SSGGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            3455678999999999999999 7999     999999999999999999999999999999998754

>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=99.76  E-value=2.3e-18  Score=113.26  Aligned_cols=57  Identities=19%  Similarity=0.231  Sum_probs=54.0

Q ss_pred             CCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996         12 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE   68 (222)
Q Consensus        12 r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~   68 (222)
                      .+|..||.+|+.+|+..|..++||+..++++||..+||++.||++||+|+|+++|+.
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            446789999999999999999999999999999999999999999999999999884

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

Probab=99.76  E-value=1.7e-18  Score=110.11  Aligned_cols=58  Identities=53%  Similarity=0.782  Sum_probs=55.4

Q ss_pred             CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996        135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  192 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~  192 (222)
                      ++.|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+.
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            5789999999999999999999999999999999999999999999999999999985

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

Probab=99.76  E-value=9.9e-19  Score=111.16  Aligned_cols=58  Identities=43%  Similarity=0.727  Sum_probs=50.7

Q ss_pred             CCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996        137 QRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK  194 (222)
Q Consensus       137 ~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~  194 (222)
                      +|+.||.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..+
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            5789999999999999999999999999999999999999999999999999999765

>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=99.76  E-value=9e-19  Score=111.75  Aligned_cols=59  Identities=25%  Similarity=0.445  Sum_probs=48.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHH
Q psy11996          8 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK   66 (222)
Q Consensus         8 ~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~   66 (222)
                      .+.++.|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||++++
T Consensus         3 ~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            3 EKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             ---------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            46788899999999999999999999999999999999999999999999999999864

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

Probab=99.75  E-value=2.9e-18  Score=113.28  Aligned_cols=61  Identities=26%  Similarity=0.343  Sum_probs=57.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhh-CCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996         10 TKRQRTSYTRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~~-~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      .++.|+.||.+|+.+|+..|.. ++||+..++..||..+||++.+|++||+|||+++++...
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            3567899999999999999995 999999999999999999999999999999999999764

>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=99.75  E-value=1.5e-18  Score=120.92  Aligned_cols=64  Identities=59%  Similarity=0.906  Sum_probs=57.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhh
Q psy11996          8 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM   71 (222)
Q Consensus         8 ~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~   71 (222)
                      +..++.|+.||.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++..+.
T Consensus        32 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~   95 (97)
T 1b72_A           32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE   95 (97)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhcc
Confidence            4678889999999999999999999999999999999999999999999999999999997654

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

Probab=99.75  E-value=1e-18  Score=111.09  Aligned_cols=58  Identities=43%  Similarity=0.727  Sum_probs=50.6

Q ss_pred             CCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996         13 QRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus        13 ~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      .|+.||.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++..+
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            5899999999999999999999999999999999999999999999999999988653

>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=3.3e-18  Score=111.43  Aligned_cols=63  Identities=40%  Similarity=0.637  Sum_probs=59.3

Q ss_pred             CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcc
Q psy11996        134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA  196 (222)
Q Consensus       134 ~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~  196 (222)
                      .++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+.....
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~~   64 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQH   64 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhccc
Confidence            467899999999999999999999999999999999999999999999999999999987654

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

Probab=99.75  E-value=3.1e-18  Score=118.92  Aligned_cols=67  Identities=27%  Similarity=0.415  Sum_probs=62.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhC---------------CChHHHHHHhhcchhHHHHHhh
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC---------------LTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~---------------l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      ...+.+|.|+.|+.+|+.+||..|..++||+..+++.||..+|               |++.+|++||+|||+++++...
T Consensus         3 ~~~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~   82 (95)
T 2cuf_A            3 SGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRAN   82 (95)
T ss_dssp             SSSCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhh
Confidence            4567889999999999999999999999999999999999999               9999999999999999999876


Q ss_pred             hh
Q psy11996         71 MA   72 (222)
Q Consensus        71 ~~   72 (222)
                      ..
T Consensus        83 ~~   84 (95)
T 2cuf_A           83 IA   84 (95)
T ss_dssp             CC
T ss_pred             cc
Confidence            53

>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=99.75  E-value=3.3e-18  Score=113.59  Aligned_cols=61  Identities=23%  Similarity=0.255  Sum_probs=57.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996         10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      ..++|+.||.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++..+
T Consensus         7 ~~~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (75)
T 2da5_A            7 GPTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEET   67 (75)
T ss_dssp             SSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSC
T ss_pred             CCCCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhh
Confidence            4456788999999999999999999999999999999999999999999999999999654

>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=99.75  E-value=2.6e-18  Score=115.86  Aligned_cols=65  Identities=37%  Similarity=0.609  Sum_probs=60.0

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      ..+.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+....
T Consensus        15 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~~   79 (81)
T 1fjl_A           15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHTS   79 (81)
T ss_dssp             --CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhccc
Confidence            44677889999999999999999999999999999999999999999999999999999998753

>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=99.75  E-value=1.9e-18  Score=116.43  Aligned_cols=64  Identities=80%  Similarity=1.171  Sum_probs=54.8

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK  194 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~  194 (222)
                      .+..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+|+|+..+
T Consensus        17 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   80 (81)
T 1b8i_A           17 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEIQ   80 (81)
T ss_dssp             -------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC-
T ss_pred             CCCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhcc
Confidence            3456788999999999999999999999999999999999999999999999999999998653

>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=99.75  E-value=4.5e-18  Score=112.10  Aligned_cols=63  Identities=27%  Similarity=0.367  Sum_probs=58.4

Q ss_pred             CCCCCcCCHHHHHHHHHhhhh-cCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhccc
Q psy11996        135 KRQRTSYTRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS  197 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F~~-~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~  197 (222)
                      .+.|+.|+.+|+.+|+..|.. ++||+..++..||..+||++.+|++||+|||+++|+..+...
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~~~~~   65 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLPS   65 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHCCCC
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhccCCC
Confidence            457899999999999999996 999999999999999999999999999999999999885543

>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=99.75  E-value=2.6e-18  Score=108.66  Aligned_cols=60  Identities=22%  Similarity=0.197  Sum_probs=56.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhh-CCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHH
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW   65 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~-~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~   65 (222)
                      .+...+|.||.|+.+||.+|+..|+. ++||+...++.||..+||++++|++||||+|.-.
T Consensus         3 ~~~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~~   63 (71)
T 1wi3_A            3 SGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHV   63 (71)
T ss_dssp             CCCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceeee
Confidence            45678999999999999999999999 9999999999999999999999999999999753

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

Probab=99.75  E-value=4.3e-18  Score=117.62  Aligned_cols=67  Identities=43%  Similarity=0.756  Sum_probs=61.6

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhccc
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS  197 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~  197 (222)
                      ....++.|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+|+|+......
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~   80 (93)
T 3a01_A           14 PPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEER   80 (93)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC-
T ss_pred             CCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHHH
Confidence            3466788999999999999999999999999999999999999999999999999999999876544

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

Probab=99.75  E-value=1.1e-18  Score=116.21  Aligned_cols=65  Identities=15%  Similarity=0.287  Sum_probs=59.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhh
Q psy11996          7 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM   71 (222)
Q Consensus         7 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~   71 (222)
                      .....+.|+.||.+|+.+|+..|..++||+..++++||..+||++.+|++||+|||+++++....
T Consensus         5 ~~~~~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~~   69 (76)
T 2dn0_A            5 SSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGS   69 (76)
T ss_dssp             CSCCCCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCSS
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhccc
Confidence            33456678999999999999999999999999999999999999999999999999999886543

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

Probab=99.75  E-value=2.3e-18  Score=111.93  Aligned_cols=62  Identities=39%  Similarity=0.572  Sum_probs=58.5

Q ss_pred             CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcc
Q psy11996        135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA  196 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~  196 (222)
                      ++.|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+.....
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~~~   63 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRES   63 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCCTT
T ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhchhc
Confidence            67899999999999999999999999999999999999999999999999999999876543

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

Probab=99.75  E-value=5.6e-18  Score=111.93  Aligned_cols=63  Identities=27%  Similarity=0.352  Sum_probs=58.5

Q ss_pred             CCCCCcCCHHHHHHHHHhhhh-cCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhccc
Q psy11996        135 KRQRTSYTRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS  197 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F~~-~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~  197 (222)
                      .+.|+.|+.+|+.+|+..|.. ++||+..++..||..+||++.+|++||+|||+++|+..+...
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~~~~~   66 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLPS   66 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHTCCS
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhccCCC
Confidence            467899999999999999995 999999999999999999999999999999999999886543

>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=99.75  E-value=2.7e-18  Score=115.19  Aligned_cols=61  Identities=16%  Similarity=0.197  Sum_probs=57.4

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhh----cCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  191 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~----~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk  191 (222)
                      ....++.|+.|+.+|+.+|+..|+.    ++||+..++++||..|||++.+|++||||||+|.|+
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           14 GGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            3467888999999999999999999    999999999999999999999999999999999875

>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=99.75  E-value=1.5e-18  Score=112.46  Aligned_cols=60  Identities=30%  Similarity=0.367  Sum_probs=57.4

Q ss_pred             CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996        134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH  193 (222)
Q Consensus       134 ~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~  193 (222)
                      .++.|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
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            567899999999999999999999999999999999999999999999999999998865

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

Probab=99.75  E-value=3.6e-18  Score=112.83  Aligned_cols=64  Identities=42%  Similarity=0.679  Sum_probs=59.7

Q ss_pred             CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       132 ~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      ...++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+....
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~   68 (73)
T 2l7z_A            5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINK   68 (73)
T ss_dssp             SCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSSSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHhcc
Confidence            3567889999999999999999999999999999999999999999999999999999986543

>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=99.74  E-value=4.6e-18  Score=112.38  Aligned_cols=65  Identities=22%  Similarity=0.246  Sum_probs=60.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~---~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      ...+.++.|+.|+.+|+.+|+.+|..   ++||+..+++.||..+||++.+|++||+|+|++.++...
T Consensus         3 ~~~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~   70 (73)
T 1x2n_A            3 SGSSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSGP   70 (73)
T ss_dssp             CCSSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhcccccc
Confidence            45678889999999999999999977   999999999999999999999999999999999998643

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

Probab=99.74  E-value=3.1e-18  Score=107.29  Aligned_cols=54  Identities=48%  Similarity=0.883  Sum_probs=50.9

Q ss_pred             CCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996         15 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE   68 (222)
Q Consensus        15 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~   68 (222)
                      |.||.+|+.+|+..|..++||+..++.+||..+||++.+|++||+|||+++++.
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~   55 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ   55 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhhccc
Confidence            679999999999999999999999999999999999999999999999999985

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

Probab=99.74  E-value=1.1e-17  Score=113.85  Aligned_cols=64  Identities=19%  Similarity=0.196  Sum_probs=59.0

Q ss_pred             cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccCCCCCC
Q psy11996        140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNVIPY  203 (222)
Q Consensus       140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~~~~~~  203 (222)
                      .||.+|+.+|+..|..++||+..++.+||..|||++.||++||+|||+|+++..+...+.....
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~~~~~~~~~~   80 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEIDESNA   80 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCCCCCCCCC
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHHHhhcccCCC
Confidence            7999999999999999999999999999999999999999999999999999877766655543

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

Probab=99.74  E-value=6e-18  Score=115.14  Aligned_cols=59  Identities=20%  Similarity=0.224  Sum_probs=54.9

Q ss_pred             CCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhc
Q psy11996         15 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS   73 (222)
Q Consensus        15 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~   73 (222)
                      ..||.+||.+||..|..++||+..++.+||..|||++.||++||+|||+++++.+....
T Consensus        16 k~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~~~~   74 (89)
T 2ecb_A           16 KEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKME   74 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCCC
T ss_pred             ccCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHHHhh
Confidence            38999999999999999999999999999999999999999999999999998665444

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

Probab=99.74  E-value=3.7e-18  Score=106.94  Aligned_cols=54  Identities=48%  Similarity=0.883  Sum_probs=51.0

Q ss_pred             CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996        139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  192 (222)
Q Consensus       139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~  192 (222)
                      +.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+|+|+.
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            579999999999999999999999999999999999999999999999999985

>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=99.74  E-value=1.1e-17  Score=113.19  Aligned_cols=68  Identities=15%  Similarity=0.168  Sum_probs=61.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhc
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS   73 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~---~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~   73 (222)
                      ++.+.++.|+.|+.+|+.+|+.+|..   ++||+..+++.||..+||++.||++||+|+|++.++......
T Consensus         3 ~~~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~~~~   73 (83)
T 2dmn_A            3 SGSSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQR   73 (83)
T ss_dssp             CCCCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHTCCC
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHHHhc
Confidence            45678889999999999999999987   599999999999999999999999999999999988755443

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

Probab=99.74  E-value=2.9e-18  Score=113.68  Aligned_cols=63  Identities=22%  Similarity=0.325  Sum_probs=58.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhh
Q psy11996          9 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM   71 (222)
Q Consensus         9 ~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~   71 (222)
                      ..++.|+.||.+|+.+|+..|..++||+..++++||..+||++.+|++||+|||+++++....
T Consensus         5 ~~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~   67 (74)
T 2ly9_A            5 DSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKSN   67 (74)
T ss_dssp             CCCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTTCS
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhCcC
Confidence            457789999999999999999999999999999999999999999999999999999986543

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

Probab=99.74  E-value=4.9e-18  Score=112.53  Aligned_cols=66  Identities=21%  Similarity=0.317  Sum_probs=60.8

Q ss_pred             CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccCC
Q psy11996        134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMN  199 (222)
Q Consensus       134 ~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~~  199 (222)
                      .++.|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+......+.
T Consensus         6 ~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~~~   71 (74)
T 2ly9_A            6 SFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKSNQCLH   71 (74)
T ss_dssp             CCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTTCSCCTT
T ss_pred             CCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhCcCCCCC
Confidence            456799999999999999999999999999999999999999999999999999999987765543

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

Probab=99.74  E-value=3.8e-18  Score=114.79  Aligned_cols=63  Identities=19%  Similarity=0.318  Sum_probs=59.0

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhc----CCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFN----RYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH  193 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~----~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~  193 (222)
                      ....++.|+.|+.+|+.+|+..|..+    +||+..++++||.++||++.+|++||+|||+|+|+..
T Consensus         5 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~~   71 (80)
T 2da4_A            5 SSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMG   71 (80)
T ss_dssp             CCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhcc
Confidence            34667889999999999999999999    9999999999999999999999999999999999854

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

Probab=99.74  E-value=3.9e-18  Score=113.58  Aligned_cols=64  Identities=17%  Similarity=0.276  Sum_probs=58.8

Q ss_pred             CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccC
Q psy11996        135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASM  198 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~  198 (222)
                      ...|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..+...+
T Consensus         9 ~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~~~~~   72 (76)
T 2dn0_A            9 SIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGSRSG   72 (76)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCSSSCC
T ss_pred             CCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhcccCCC
Confidence            3458999999999999999999999999999999999999999999999999999997765443

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

Probab=99.73  E-value=6.2e-18  Score=106.74  Aligned_cols=57  Identities=44%  Similarity=0.711  Sum_probs=54.2

Q ss_pred             CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHH
Q psy11996        134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK  190 (222)
Q Consensus       134 ~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k  190 (222)
                      .++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|
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            356799999999999999999999999999999999999999999999999999875

>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=99.73  E-value=4.1e-18  Score=108.65  Aligned_cols=59  Identities=25%  Similarity=0.445  Sum_probs=48.4

Q ss_pred             CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHH
Q psy11996        132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK  190 (222)
Q Consensus       132 ~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k  190 (222)
                      ...++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|
T Consensus         3 ~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            3 EKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             ---------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            35677899999999999999999999999999999999999999999999999999875

>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=99.73  E-value=5.4e-18  Score=113.52  Aligned_cols=60  Identities=22%  Similarity=0.253  Sum_probs=56.1

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhh-----cCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHF-----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  191 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~-----~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk  191 (222)
                      ....++.|+.|+.+|+.+|+ .|..     ++||+..++++||.+|||++.+|++||||||+|+++
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           14 GGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            34678889999999999999 7999     999999999999999999999999999999999875

>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=99.73  E-value=1.5e-17  Score=110.40  Aligned_cols=60  Identities=23%  Similarity=0.261  Sum_probs=56.3

Q ss_pred             CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        136 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       136 ~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      +++..||.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..+.
T Consensus         9 ~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~~   68 (75)
T 2da5_A            9 TKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETK   68 (75)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSCS
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhhc
Confidence            356779999999999999999999999999999999999999999999999999997654

>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=99.72  E-value=9.9e-18  Score=110.75  Aligned_cols=61  Identities=28%  Similarity=0.496  Sum_probs=57.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHh---hhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996         10 TKRQRTSYTRYQTLELEKEF---HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f---~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      .||+|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.+|++||+|+|+++++...
T Consensus         1 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~   64 (73)
T 1puf_B            1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG   64 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcccccc
Confidence            36889999999999999999   89999999999999999999999999999999999998654

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

Probab=99.72  E-value=2.1e-17  Score=114.68  Aligned_cols=65  Identities=28%  Similarity=0.420  Sum_probs=61.4

Q ss_pred             CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcC---------------CChhhHHHHHhhhhhhHHHhhhcc
Q psy11996        132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC---------------LTERQIKIWFQNRRMKWKKEHKMA  196 (222)
Q Consensus       132 ~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~---------------l~~~~V~~WF~nrR~k~kk~~~~~  196 (222)
                      .+.++.|+.|+..|+.+|+..|..++||+..+++.||..++               |++.+|++||+|||+++|+..+..
T Consensus         5 ~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~~~   84 (95)
T 2cuf_A            5 SSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANIA   84 (95)
T ss_dssp             SCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhhcc
Confidence            46678899999999999999999999999999999999999               999999999999999999988763

>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=99.72  E-value=3.1e-17  Score=113.59  Aligned_cols=66  Identities=21%  Similarity=0.333  Sum_probs=61.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHh---------------------CCChHHHHHHhhcchhHH
Q psy11996          7 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL---------------------CLTERQIKIWFQNRRMKW   65 (222)
Q Consensus         7 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~---------------------~l~~~~v~~WF~nrR~k~   65 (222)
                      ..+.||.|+.|++.|+.+|+..|..++||+..++++||..+                     +|++.+|++||+|||+++
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            45688999999999999999999999999999999999999                     799999999999999999


Q ss_pred             HHHhhhh
Q psy11996         66 KKEHKMA   72 (222)
Q Consensus        66 ~~~~~~~   72 (222)
                      +++.+..
T Consensus        83 kr~~~~~   89 (102)
T 2da6_A           83 AFRQKLA   89 (102)
T ss_dssp             HHHHHHH
T ss_pred             HHhhHhh
Confidence            9876654

>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=99.72  E-value=4.8e-18  Score=116.14  Aligned_cols=63  Identities=27%  Similarity=0.461  Sum_probs=57.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHh---hhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996         10 TKRQRTSYTRYQTLELEKEF---HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA   72 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f---~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~   72 (222)
                      .||.|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.+|++||+|+|+++++.....
T Consensus         1 ~rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~   66 (87)
T 1b72_B            1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKF   66 (87)
T ss_dssp             --CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGGG
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhccccc
Confidence            36889999999999999999   8999999999999999999999999999999999999865443

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

Probab=99.72  E-value=4.4e-18  Score=109.59  Aligned_cols=59  Identities=25%  Similarity=0.399  Sum_probs=55.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHh---hhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996          9 ETKRQRTSYTRYQTLELEKEF---HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus         9 ~~~r~R~~~t~~q~~~L~~~f---~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      .+++.|+.|+.+|+.+|+.+|   ..++||+..+++.||..+||++.+|++||+|+|+++++
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   89999999999999999999999999999999998764

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

Probab=99.71  E-value=1e-17  Score=116.51  Aligned_cols=62  Identities=19%  Similarity=0.291  Sum_probs=56.0

Q ss_pred             CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996        132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH  193 (222)
Q Consensus       132 ~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~  193 (222)
                      ...++.|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+|+|+..
T Consensus        23 ~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   84 (96)
T 3nar_A           23 SGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGN   84 (96)
T ss_dssp             ----CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTC
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhc
Confidence            34567889999999999999999999999999999999999999999999999999999863

>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=99.71  E-value=2.7e-17  Score=108.68  Aligned_cols=64  Identities=22%  Similarity=0.235  Sum_probs=59.0

Q ss_pred             CCCCCCCCcCCHHHHHHHHHhhhh---cCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        132 GETKRQRTSYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       132 ~~~~~~r~~~~~~q~~~L~~~F~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      +..++.|+.|+..|+.+|+.+|..   ++||+..+++.||..+||+..||++||+|+|+++++....
T Consensus         5 ~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~   71 (73)
T 1x2n_A            5 SSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSGPS   71 (73)
T ss_dssp             SSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhccccccc
Confidence            456778999999999999999987   9999999999999999999999999999999999987543

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

Probab=99.71  E-value=1.5e-17  Score=105.56  Aligned_cols=53  Identities=19%  Similarity=0.341  Sum_probs=50.6

Q ss_pred             CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996        141 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH  193 (222)
Q Consensus       141 ~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~  193 (222)
                      -+.+|+.+|+..|..++||+..++++||..+||++.+|++||+|||+++|+..
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            47899999999999999999999999999999999999999999999999753

>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=99.71  E-value=2.7e-17  Score=108.61  Aligned_cols=62  Identities=27%  Similarity=0.465  Sum_probs=58.3

Q ss_pred             CCCCCcCCHHHHHHHHHhh---hhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcc
Q psy11996        135 KRQRTSYTRYQTLELEKEF---HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA  196 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F---~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~  196 (222)
                      ++.|+.|+..|+.+|+.+|   ..++||+..++..||..+||+..+|++||+|+|+++|+.....
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~~   66 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKF   66 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTTT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcccccccc
Confidence            5788999999999999999   8999999999999999999999999999999999999876553

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

Probab=99.71  E-value=1.2e-17  Score=116.09  Aligned_cols=63  Identities=19%  Similarity=0.286  Sum_probs=55.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE   68 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~   68 (222)
                      .....+++|+.||.+|+.+|+..|..++||+..++++||..+||++.+|++||+|||+++|+.
T Consensus        21 ~~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~   83 (96)
T 3nar_A           21 PKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNG   83 (96)
T ss_dssp             ------CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhh
Confidence            345567889999999999999999999999999999999999999999999999999999874

>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=99.71  E-value=1.9e-17  Score=105.16  Aligned_cols=55  Identities=31%  Similarity=0.377  Sum_probs=52.8

Q ss_pred             CCCCCCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996         13 QRTSYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus        13 ~R~~~t~~q~~~L~~~f~~---~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      +|+.|+.+|+.+|+..|..   ++||+..++..||..+||++.+|++||+|+|+++++
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   999999999999999999999999999999999876

>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=99.70  E-value=7.1e-17  Score=111.78  Aligned_cols=73  Identities=21%  Similarity=0.327  Sum_probs=64.1

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHc---------------------CCChhhHHHHHhhhhhhH
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL---------------------CLTERQIKIWFQNRRMKW  189 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l---------------------~l~~~~V~~WF~nrR~k~  189 (222)
                      .+..++.|+.|++.|+.+|+..|..++||+..++++||..+                     +|++.+|++||+|||+++
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            34678889999999999999999999999999999999999                     799999999999999999


Q ss_pred             HHhhhcccCCCCCCC
Q psy11996        190 KKEHKMASMNVIPYH  204 (222)
Q Consensus       190 kk~~~~~~~~~~~~~  204 (222)
                      ++..+.. +...+..
T Consensus        83 kr~~~~~-~~~~~~~   96 (102)
T 2da6_A           83 AFRQKLA-MDAYSSN   96 (102)
T ss_dssp             HHHHHHH-HSSSSSS
T ss_pred             HHhhHhh-hccccCC
Confidence            9987765 4444433

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

Probab=99.70  E-value=1.9e-17  Score=107.54  Aligned_cols=60  Identities=40%  Similarity=0.687  Sum_probs=55.7

Q ss_pred             CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccC
Q psy11996        139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASM  198 (222)
Q Consensus       139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~  198 (222)
                      ..++..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+|+|+.....++
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~~~~~~   68 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSEL   68 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSSSSCCC
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhhhhhhc
Confidence            467899999999999999999999999999999999999999999999999998766554

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

Probab=99.70  E-value=1.5e-17  Score=107.08  Aligned_cols=59  Identities=25%  Similarity=0.399  Sum_probs=55.8

Q ss_pred             CCCCCCCcCCHHHHHHHHHhh---hhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996        133 ETKRQRTSYTRYQTLELEKEF---HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  191 (222)
Q Consensus       133 ~~~~~r~~~~~~q~~~L~~~F---~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk  191 (222)
                      ..++.|+.|+.+|+.+|+.+|   ..++||+..++..||..+||+..||++||+|+|+++|+
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            356788999999999999999   89999999999999999999999999999999999876

>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=99.70  E-value=7.6e-17  Score=108.97  Aligned_cols=68  Identities=16%  Similarity=0.171  Sum_probs=61.1

Q ss_pred             CCCCCCCCcCCHHHHHHHHHhhhh---cCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccCC
Q psy11996        132 GETKRQRTSYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMN  199 (222)
Q Consensus       132 ~~~~~~r~~~~~~q~~~L~~~F~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~~  199 (222)
                      ...++.|+.|+.+|+.+|+.+|..   ++||+..++..||..+||+..||++||+|+|+|+++........
T Consensus         5 ~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~~~~~~   75 (83)
T 2dmn_A            5 SSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQRRN   75 (83)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHTCCCCC
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHHHhccC
Confidence            456778999999999999999987   69999999999999999999999999999999999876655444

>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=3.7e-17  Score=103.84  Aligned_cols=55  Identities=31%  Similarity=0.351  Sum_probs=52.8

Q ss_pred             CCcCCHHHHHHHHHhhhh---cCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996        138 RTSYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  192 (222)
Q Consensus       138 r~~~~~~q~~~L~~~F~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~  192 (222)
                      ++.|+.+|+.+|+..|..   ++||+..++..||..+||++.||++||+|+|+++|+.
T Consensus         2 r~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A            2 GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             cCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            678999999999999999   9999999999999999999999999999999999873

>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=99.69  E-value=1.3e-16  Score=109.25  Aligned_cols=65  Identities=20%  Similarity=0.185  Sum_probs=58.2

Q ss_pred             CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccCCCCC
Q psy11996        138 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNVIP  202 (222)
Q Consensus       138 r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~~~~~  202 (222)
                      +..+|.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+|+++..+........
T Consensus        17 ~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~~~~~~~~~   81 (89)
T 2dmp_A           17 FKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAVLDSMGS   81 (89)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCSCCCCCCCC
T ss_pred             cccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhHhhhccccC
Confidence            34489999999999999999999999999999999999999999999999999987776544443

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

Probab=99.69  E-value=3.4e-17  Score=103.95  Aligned_cols=52  Identities=19%  Similarity=0.362  Sum_probs=49.8

Q ss_pred             CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996         17 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE   68 (222)
Q Consensus        17 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~   68 (222)
                      -|.+|+.+|+..|..++||+..++++||..+||++.+|++||+|||+++++.
T Consensus        11 ~~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg   62 (66)
T 3nau_A           11 KTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRG   62 (66)
T ss_dssp             CCHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhcc
Confidence            4789999999999999999999999999999999999999999999999874

>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=99.68  E-value=6.7e-17  Score=110.40  Aligned_cols=62  Identities=27%  Similarity=0.465  Sum_probs=57.7

Q ss_pred             CCCCCcCCHHHHHHHHHhh---hhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcc
Q psy11996        135 KRQRTSYTRYQTLELEKEF---HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA  196 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F---~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~  196 (222)
                      ++.|+.|+..|+.+|+.+|   ..++||+..++..||..+||+..||++||+|+|+|+|+.....
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~   66 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKF   66 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGGG
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhccccc
Confidence            5788999999999999999   8999999999999999999999999999999999999986543

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

Probab=99.68  E-value=1.5e-17  Score=126.42  Aligned_cols=65  Identities=28%  Similarity=0.355  Sum_probs=52.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      ...+.||+|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..+
T Consensus        95 ~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~  159 (164)
T 2xsd_C           95 AQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTP  159 (164)
T ss_dssp             -----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC
T ss_pred             ccccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhccC
Confidence            35677889999999999999999999999999999999999999999999999999999998654

>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=99.68  E-value=8.3e-17  Score=101.80  Aligned_cols=59  Identities=24%  Similarity=0.210  Sum_probs=55.5

Q ss_pred             CCCCCCCCcCCHHHHHHHHHhhhh-cCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHH
Q psy11996        132 GETKRQRTSYTRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK  190 (222)
Q Consensus       132 ~~~~~~r~~~~~~q~~~L~~~F~~-~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k  190 (222)
                      ...+|.|+.|+.+|+.+|+..|+. ++||+.+.++.||.++||++++|++||||+|.-.+
T Consensus         5 ~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~~~   64 (71)
T 1wi3_A            5 SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVK   64 (71)
T ss_dssp             CCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCC
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceeeec
Confidence            367889999999999999999999 99999999999999999999999999999997654

>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=99.68  E-value=6.9e-17  Score=110.27  Aligned_cols=59  Identities=29%  Similarity=0.339  Sum_probs=55.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHH
Q psy11996          8 GETKRQRTSYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK   66 (222)
Q Consensus         8 ~~~~r~R~~~t~~q~~~L~~~f~~---~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~   66 (222)
                      ..+++.|+.|+.+|+.+|+.+|..   ++||+..+++.||..+||++.+|++||+|||+++|
T Consensus        25 ~~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k   86 (87)
T 1mnm_C           25 STKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK   86 (87)
T ss_dssp             ESSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcc
Confidence            456777999999999999999999   99999999999999999999999999999999875

>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=99.68  E-value=1.5e-16  Score=108.88  Aligned_cols=60  Identities=22%  Similarity=0.245  Sum_probs=54.6

Q ss_pred             CCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996         13 QRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA   72 (222)
Q Consensus        13 ~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~   72 (222)
                      ++..||.+|+.+|+..|..++||+..+++.||..+||++.+|++||+|||+++++..+..
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            344599999999999999999999999999999999999999999999999988865443

>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=99.67  E-value=4e-17  Score=110.44  Aligned_cols=59  Identities=27%  Similarity=0.301  Sum_probs=54.0

Q ss_pred             CCCCCCCCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996         11 KRQRTSYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH   69 (222)
Q Consensus        11 ~r~R~~~t~~q~~~L~~~f~~---~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~   69 (222)
                      ++.|++|+.+|+.+|+.+|..   ++||+..++..||..+||++.||++||+|||+++++..
T Consensus         3 ~krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~   64 (83)
T 1le8_B            3 PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTIT   64 (83)
T ss_dssp             --CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHccccccc
Confidence            455677999999999999999   99999999999999999999999999999999998853

>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=99.67  E-value=3.8e-17  Score=122.06  Aligned_cols=63  Identities=25%  Similarity=0.425  Sum_probs=55.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE   68 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~   68 (222)
                      ...++||.|+.||..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++++.
T Consensus        83 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           83 ANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             ------CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            445678899999999999999999999999999999999999999999999999999998863

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

Probab=99.67  E-value=2.8e-17  Score=114.30  Aligned_cols=65  Identities=20%  Similarity=0.321  Sum_probs=53.4

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHH------------------hC---CChHHHHHHhhcchh
Q psy11996          5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHA------------------LC---LTERQIKIWFQNRRM   63 (222)
Q Consensus         5 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~------------------~~---l~~~~v~~WF~nrR~   63 (222)
                      ...++.||.|+.|+.+|+.+||..|..++||+..++++||..                  +|   |++.+|++||+|||+
T Consensus         4 ~~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~   83 (99)
T 1lfb_A            4 DPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRK   83 (99)
T ss_dssp             ---------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHH
Confidence            345678899999999999999999999999999999999999                  88   999999999999999


Q ss_pred             HHHHHh
Q psy11996         64 KWKKEH   69 (222)
Q Consensus        64 k~~~~~   69 (222)
                      +.+++.
T Consensus        84 k~k~k~   89 (99)
T 1lfb_A           84 EEAFRH   89 (99)
T ss_dssp             TTSCCC
T ss_pred             HHHHhc
Confidence            876644

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

Probab=99.67  E-value=2.3e-17  Score=108.42  Aligned_cols=60  Identities=23%  Similarity=0.339  Sum_probs=55.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHh-hhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996          9 ETKRQRTSYTRYQTLELEKEF-HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE   68 (222)
Q Consensus         9 ~~~r~R~~~t~~q~~~L~~~f-~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~   68 (222)
                      -+.+.|..++.+|+.+||..| ..++||+..++++||..+||++.+|++||+|||+++++.
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            355667889999999999999 999999999999999999999999999999999998863

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

Probab=99.67  E-value=4e-17  Score=106.01  Aligned_cols=56  Identities=43%  Similarity=0.720  Sum_probs=52.8

Q ss_pred             CCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996         15 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus        15 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      ..+|..|+..||..|..++||+..++.+||..+||++.+|++||+|||+++++...
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~~   64 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQL   64 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSSS
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhhh
Confidence            46899999999999999999999999999999999999999999999999988654

>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=4.4e-17  Score=107.02  Aligned_cols=59  Identities=24%  Similarity=0.347  Sum_probs=54.1

Q ss_pred             CCCCCcCCHHHHHHHHHhh-hhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996        135 KRQRTSYTRYQTLELEKEF-HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH  193 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F-~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~  193 (222)
                      .+.+..++.+|+.+||..| ..++||+..++.+||..+||++.+|++||||||+++|+..
T Consensus         9 ~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~~   68 (72)
T 2cqx_A            9 IKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSG   68 (72)
T ss_dssp             CCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCCC
Confidence            4456678889999999999 9999999999999999999999999999999999999753

>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=99.65  E-value=2.2e-16  Score=107.79  Aligned_cols=58  Identities=29%  Similarity=0.343  Sum_probs=55.0

Q ss_pred             CCCCCCCcCCHHHHHHHHHhhhh---cCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHH
Q psy11996        133 ETKRQRTSYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK  190 (222)
Q Consensus       133 ~~~~~r~~~~~~q~~~L~~~F~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k  190 (222)
                      ..++.|+.|+.+|+.+|+.+|..   ++||+..++..||..+||+..||++||+|||+|+|
T Consensus        26 ~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k   86 (87)
T 1mnm_C           26 TKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK   86 (87)
T ss_dssp             SSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcc
Confidence            45667899999999999999999   99999999999999999999999999999999987

>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=99.65  E-value=1.5e-16  Score=119.54  Aligned_cols=62  Identities=27%  Similarity=0.441  Sum_probs=58.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      ...++||+|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+
T Consensus        89 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           89 EPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             SCCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            34567889999999999999999999999999999999999999999999999999999875

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

Probab=99.65  E-value=1.8e-16  Score=101.60  Aligned_cols=54  Identities=15%  Similarity=0.148  Sum_probs=50.3

Q ss_pred             CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996        138 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  191 (222)
Q Consensus       138 r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk  191 (222)
                      +..++.+|+.+|+..|..++||+..++..||..+||++.+|++||+|||+|.++
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            345678999999999999999999999999999999999999999999998766

>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=99.65  E-value=1.1e-16  Score=121.36  Aligned_cols=61  Identities=33%  Similarity=0.447  Sum_probs=54.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996          8 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE   68 (222)
Q Consensus         8 ~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~   68 (222)
                      .+.||.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+.
T Consensus        99 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C           99 SRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            4678899999999999999999999999999999999999999999999999999998873

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

Probab=99.65  E-value=1.1e-16  Score=121.77  Aligned_cols=67  Identities=27%  Similarity=0.343  Sum_probs=53.0

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhccc
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS  197 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~  197 (222)
                      ..+.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+..+..+
T Consensus        96 ~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~  162 (164)
T 2xsd_C           96 QGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTPAAG  162 (164)
T ss_dssp             ----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC---
T ss_pred             cccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhccCCCC
Confidence            4466788999999999999999999999999999999999999999999999999999999876543

>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=99.65  E-value=2.3e-16  Score=106.63  Aligned_cols=60  Identities=27%  Similarity=0.284  Sum_probs=55.1

Q ss_pred             CCCCcCCHHHHHHHHHhhhh---cCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        136 RQRTSYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       136 ~~r~~~~~~q~~~L~~~F~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      +.++.|+.+|+.+|+.+|..   ++||+..++..||..+||+..||++||+|||+++|+....
T Consensus         4 krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~~~   66 (83)
T 1le8_B            4 YRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITIA   66 (83)
T ss_dssp             -CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSCCC
T ss_pred             CCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHccccccccC
Confidence            44667999999999999999   9999999999999999999999999999999999987543

>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=99.64  E-value=1.7e-16  Score=118.50  Aligned_cols=62  Identities=24%  Similarity=0.419  Sum_probs=55.5

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  192 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~  192 (222)
                      ....++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+|+|+.
T Consensus        84 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           84 NERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            34667889999999999999999999999999999999999999999999999999999874

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

Probab=99.64  E-value=1.5e-16  Score=110.61  Aligned_cols=66  Identities=23%  Similarity=0.346  Sum_probs=54.3

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHH------------------cC---CChhhHHHHHhhhhhhH
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHA------------------LC---LTERQIKIWFQNRRMKW  189 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~------------------l~---l~~~~V~~WF~nrR~k~  189 (222)
                      ..+.++.|+.|+..|+.+|+..|..++||+..++++||..                  ||   |++.+|++||+|||++.
T Consensus         6 ~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k~   85 (99)
T 1lfb_A            6 TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEE   85 (99)
T ss_dssp             -------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHHH
Confidence            4466788999999999999999999999999999999999                  88   99999999999999999


Q ss_pred             HHhhhcc
Q psy11996        190 KKEHKMA  196 (222)
Q Consensus       190 kk~~~~~  196 (222)
                      +++.+.+
T Consensus        86 k~k~~~~   92 (99)
T 1lfb_A           86 AFRHKLA   92 (99)
T ss_dssp             SCCC---
T ss_pred             HHhchhh
Confidence            8776543

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

Probab=99.63  E-value=2.9e-16  Score=100.67  Aligned_cols=54  Identities=15%  Similarity=0.148  Sum_probs=50.1

Q ss_pred             CCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996         14 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus        14 R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      +..++..|+..||..|..++||+..++.+||..+||++++|++||+|||+|.++
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            356779999999999999999999999999999999999999999999998654

>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=99.63  E-value=2.5e-16  Score=119.47  Aligned_cols=61  Identities=33%  Similarity=0.447  Sum_probs=54.8

Q ss_pred             CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996        132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  192 (222)
Q Consensus       132 ~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~  192 (222)
                      ...++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+||.
T Consensus        99 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C           99 SRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            3668889999999999999999999999999999999999999999999999999999985

>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=99.63  E-value=2.1e-16  Score=100.51  Aligned_cols=50  Identities=26%  Similarity=0.349  Sum_probs=46.5

Q ss_pred             HHHHHHHHHhh-hhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996        143 RYQTLELEKEF-HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  192 (222)
Q Consensus       143 ~~q~~~L~~~F-~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~  192 (222)
                      ..|+.+||..| ..++||+..++.+||.+|||+++||++||||||+++|+.
T Consensus         9 ~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~~   59 (64)
T 1x2m_A            9 AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPS   59 (64)
T ss_dssp             SCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCCS
T ss_pred             chHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCCC
Confidence            45899999999 679999999999999999999999999999999999863

>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=99.63  E-value=5.1e-16  Score=116.70  Aligned_cols=60  Identities=28%  Similarity=0.461  Sum_probs=57.4

Q ss_pred             CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996        132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  191 (222)
Q Consensus       132 ~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk  191 (222)
                      ++.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+|+||
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            466788999999999999999999999999999999999999999999999999999986

>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=99.62  E-value=3.9e-16  Score=117.72  Aligned_cols=60  Identities=32%  Similarity=0.424  Sum_probs=57.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996          8 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus         8 ~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      +++||+|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+
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            467889999999999999999999999999999999999999999999999999999887

>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=3.3e-16  Score=99.61  Aligned_cols=49  Identities=27%  Similarity=0.354  Sum_probs=46.0

Q ss_pred             HHHHHHHHHHh-hhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996         19 RYQTLELEKEF-HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus        19 ~~q~~~L~~~f-~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      ..|+.+||..| ..+.||+..++.+||..|||+++||++||||||+++|+
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            46899999999 67999999999999999999999999999999999876

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

Probab=99.61  E-value=3.6e-16  Score=119.15  Aligned_cols=64  Identities=22%  Similarity=0.271  Sum_probs=54.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996          7 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus         7 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      ..+.||.|+.||.+|+.+|+..|..++||+..+++.||..+||++.+|++||+|||++.++...
T Consensus        94 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~  157 (164)
T 2d5v_A           94 GNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWL  157 (164)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC--
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccCC
Confidence            4467899999999999999999999999999999999999999999999999999999887543

>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=99.60  E-value=1.4e-15  Score=114.76  Aligned_cols=61  Identities=31%  Similarity=0.419  Sum_probs=57.4

Q ss_pred             CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996        132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  192 (222)
Q Consensus       132 ~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~  192 (222)
                      +..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+|+|+.
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             cCCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            4567789999999999999999999999999999999999999999999999999999973

>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=99.58  E-value=2.4e-15  Score=97.38  Aligned_cols=56  Identities=18%  Similarity=0.235  Sum_probs=50.4

Q ss_pred             cCCHHHHHHHHHhhh---hcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        140 SYTRYQTLELEKEFH---FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       140 ~~~~~q~~~L~~~F~---~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      .|+.+|+.+|+.+|.   .++||+..++..||..+||+..||++||+|+|+|+++....
T Consensus         4 ~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~   62 (67)
T 3k2a_A            4 IFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMID   62 (67)
T ss_dssp             --CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC--
T ss_pred             cCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHHH
Confidence            689999999999999   99999999999999999999999999999999999986443

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

Probab=99.56  E-value=2.2e-15  Score=114.85  Aligned_cols=66  Identities=21%  Similarity=0.249  Sum_probs=54.9

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcc
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA  196 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~  196 (222)
                      ....++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+|+|+.....
T Consensus        94 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~~~  159 (164)
T 2d5v_A           94 GNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWLEH  159 (164)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC----
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccCCCC
Confidence            345678899999999999999999999999999999999999999999999999999998865543

>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=99.56  E-value=4.5e-15  Score=96.06  Aligned_cols=54  Identities=19%  Similarity=0.275  Sum_probs=50.0

Q ss_pred             CCCHHHHHHHHHHhh---hCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996         16 SYTRYQTLELEKEFH---FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH   69 (222)
Q Consensus        16 ~~t~~q~~~L~~~f~---~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~   69 (222)
                      .|+.+|+.+|+.+|.   .++||+..+++.||..+||++.||++||+|+|++.++..
T Consensus         4 ~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~   60 (67)
T 3k2a_A            4 IFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPM   60 (67)
T ss_dssp             --CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC
T ss_pred             cCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHH
Confidence            799999999999999   999999999999999999999999999999999988753

>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=99.50  E-value=2.4e-14  Score=91.28  Aligned_cols=45  Identities=20%  Similarity=0.362  Sum_probs=43.8

Q ss_pred             HHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhh
Q psy11996        143 RYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM  187 (222)
Q Consensus       143 ~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~  187 (222)
                      ++|+.+|+.+|..+++|+.+++..||..+||+.++|++||+|||+
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa   58 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKV   58 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhccc
Confidence            579999999999999999999999999999999999999999997

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

Probab=99.49  E-value=9.8e-14  Score=93.64  Aligned_cols=63  Identities=16%  Similarity=0.201  Sum_probs=56.0

Q ss_pred             CCCCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhccCCC
Q psy11996         15 TSYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNNP   77 (222)
Q Consensus        15 ~~~t~~q~~~L~~~f~~---~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~~~~   77 (222)
                      ..|+.+++.+|+.+|..   ++||+..++.+||..+||++.||.+||+|+|.+.++........++
T Consensus        10 ~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~~~~~~~p   75 (89)
T 2lk2_A           10 HMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRKDGKDP   75 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHHHHCSSC
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHHHhcCCCc
Confidence            47999999999999987   9999999999999999999999999999999999987655544333

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

Probab=99.47  E-value=1.7e-13  Score=92.47  Aligned_cols=59  Identities=15%  Similarity=0.175  Sum_probs=54.1

Q ss_pred             CcCCHHHHHHHHHhhhh---cCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhccc
Q psy11996        139 TSYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS  197 (222)
Q Consensus       139 ~~~~~~q~~~L~~~F~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~  197 (222)
                      ..|+.+++.+|+.+|..   ++||+.+++.+||..+||+..||.+||+|+|.|.++......
T Consensus        10 ~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~~~~   71 (89)
T 2lk2_A           10 HMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRKD   71 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHHHhc
Confidence            56899999999999987   999999999999999999999999999999999998765443

>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=99.47  E-value=6.7e-14  Score=89.20  Aligned_cols=46  Identities=20%  Similarity=0.339  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhH
Q psy11996         19 RYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK   64 (222)
Q Consensus        19 ~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k   64 (222)
                      .+|+.+|+.+|..+++|+.+++..||..+||+.++|++||+|+|+.
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            5789999999999999999999999999999999999999999973

>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=99.45  E-value=1.7e-14  Score=111.93  Aligned_cols=59  Identities=19%  Similarity=0.289  Sum_probs=53.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhC---------------------CChHHHHHHhhcchhHHH
Q psy11996          8 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC---------------------LTERQIKIWFQNRRMKWK   66 (222)
Q Consensus         8 ~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~---------------------l~~~~v~~WF~nrR~k~~   66 (222)
                      ++.||.|+.|+..|+.+|+..|..++||+..+|++||..+|                     |++.+|++||+|||++.+
T Consensus       113 ~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~~k  192 (194)
T 1ic8_A          113 KKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEA  192 (194)
T ss_dssp             ----CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHHCC
T ss_pred             ccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhhhh
Confidence            46789999999999999999999999999999999999999                     999999999999998865

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

Probab=99.41  E-value=2.1e-13  Score=106.90  Aligned_cols=58  Identities=21%  Similarity=0.353  Sum_probs=52.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhC---------------------CChHHHHHHhhcchhH
Q psy11996          7 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC---------------------LTERQIKIWFQNRRMK   64 (222)
Q Consensus         7 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~---------------------l~~~~v~~WF~nrR~k   64 (222)
                      .++.||.|+.|++.|+.+|+..|..++||+..+|++||..+|                     |++.+|++||+|||+.
T Consensus       139 ~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~~  217 (221)
T 2h8r_A          139 NKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKE  217 (221)
T ss_dssp             ---CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHTT
T ss_pred             cCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhhh
Confidence            356788999999999999999999999999999999999987                     8999999999999976

>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=99.40  E-value=7.7e-14  Score=108.23  Aligned_cols=61  Identities=18%  Similarity=0.265  Sum_probs=53.5

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcC---------------------CChhhHHHHHhhhhhhH
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC---------------------LTERQIKIWFQNRRMKW  189 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~---------------------l~~~~V~~WF~nrR~k~  189 (222)
                      ..+.++.|+.|+..|+.+|+..|..++||+..++++||..++                     |++.+|++||+|||++.
T Consensus       112 ~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~~  191 (194)
T 1ic8_A          112 TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEE  191 (194)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHHC
T ss_pred             cccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhhh
Confidence            346688899999999999999999999999999999999999                     99999999999999987


Q ss_pred             HH
Q psy11996        190 KK  191 (222)
Q Consensus       190 kk  191 (222)
                      +.
T Consensus       192 k~  193 (194)
T 1ic8_A          192 AF  193 (194)
T ss_dssp             C-
T ss_pred             hc
Confidence            64

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

Probab=99.32  E-value=1.6e-12  Score=101.83  Aligned_cols=59  Identities=20%  Similarity=0.323  Sum_probs=53.0

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcC---------------------CChhhHHHHHhhhhhhH
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC---------------------LTERQIKIWFQNRRMKW  189 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~---------------------l~~~~V~~WF~nrR~k~  189 (222)
                      ..+.++.|+.|++.|+.+|+..|..++||+..++++||..+|                     |++.+|++||+|||+..
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            346788899999999999999999999999999999999987                     89999999999999864

>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=99.15  E-value=1.9e-11  Score=105.59  Aligned_cols=55  Identities=25%  Similarity=0.424  Sum_probs=51.8

Q ss_pred             CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHH
Q psy11996        136 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK  190 (222)
Q Consensus       136 ~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k  190 (222)
                      +.++.++..|+..|+..|..++||+..++.+||.++||+++||++||+|||+|+|
T Consensus       367 ~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          367 AAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            4467799999999999999999999999999999999999999999999999875

>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=99.14  E-value=2e-11  Score=105.38  Aligned_cols=56  Identities=25%  Similarity=0.417  Sum_probs=51.9

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHH
Q psy11996         11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK   66 (222)
Q Consensus        11 ~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~   66 (222)
                      ++.++.|+..|+..|+..|..++||+..+|++||..+||+++||++||+|||+|.|
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

>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=98.50  E-value=8.5e-09  Score=57.55  Aligned_cols=25  Identities=64%  Similarity=1.080  Sum_probs=20.9

Q ss_pred             hhHHHHHhhhhhhHHHhhhcccCCC
Q psy11996        176 RQIKIWFQNRRMKWKKEHKMASMNV  200 (222)
Q Consensus       176 ~~V~~WF~nrR~k~kk~~~~~~~~~  200 (222)
                      +||++||||||+|+|+.........
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~~~~~   25 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFNDARDI   25 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHHTTTS
T ss_pred             CCceeccHHHHHHHHHHhHHHHHHH
Confidence            4899999999999999988755443

>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=98.36  E-value=4.1e-08  Score=54.78  Aligned_cols=21  Identities=76%  Similarity=1.211  Sum_probs=18.1

Q ss_pred             HHHHHHhhcchhHHHHHhhhh
Q psy11996         52 RQIKIWFQNRRMKWKKEHKMA   72 (222)
Q Consensus        52 ~~v~~WF~nrR~k~~~~~~~~   72 (222)
                      +||++||||||+|+++.....
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~   21 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFND   21 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHH
T ss_pred             CCceeccHHHHHHHHHHhHHH
Confidence            479999999999999987654

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

Probab=96.82  E-value=0.0015  Score=41.26  Aligned_cols=39  Identities=21%  Similarity=0.342  Sum_probs=36.8

Q ss_pred             HHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhh
Q psy11996        146 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQN  184 (222)
Q Consensus       146 ~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~n  184 (222)
                      ..+|+.+|...+.+..+..+.|..+.+|+..||+-||..
T Consensus        18 ~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~   56 (70)
T 2ys9_A           18 IQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDS   56 (70)
T ss_dssp             CHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             chHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHh
Confidence            578999999999999999999999999999999999964

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

Probab=96.73  E-value=0.0018  Score=40.90  Aligned_cols=41  Identities=20%  Similarity=0.307  Sum_probs=37.5

Q ss_pred             HHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhc
Q psy11996         20 YQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQN   60 (222)
Q Consensus        20 ~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~n   60 (222)
                      .-...|+.+|.....+...+.+.|+.+.+|+..||+.||-.
T Consensus        16 ~~~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~   56 (70)
T 2ys9_A           16 PDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDS   56 (70)
T ss_dssp             CCCHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CcchHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHh
Confidence            34578999999999999999999999999999999999953

>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=91.06  E-value=2.9  Score=29.22  Aligned_cols=40  Identities=10%  Similarity=0.223  Sum_probs=31.3

Q ss_pred             CCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhh
Q psy11996         15 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ   59 (222)
Q Consensus        15 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~   59 (222)
                      ..++.++...+...+....     ...++|..+|++...|..|+.
T Consensus         5 ~~~s~~~r~~i~~~~~~G~-----s~~~ia~~lgis~~Tv~r~~~   44 (141)
T 1u78_A            5 SALSDTERAQLDVMKLLNV-----SLHEMSRKISRSRHCIRVYLK   44 (141)
T ss_dssp             CCCCHHHHHHHHHHHHTTC-----CHHHHHHHHTCCHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHH
Confidence            4688888877777775442     256779999999999999985

>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=90.08  E-value=4.1  Score=29.40  Aligned_cols=41  Identities=10%  Similarity=0.071  Sum_probs=31.2

Q ss_pred             CCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhc
Q psy11996         15 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQN   60 (222)
Q Consensus        15 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~n   60 (222)
                      ..++.++...+...+....     ...++|..+|++...|..|+..
T Consensus        24 ~~~s~e~r~~ii~l~~~G~-----s~~~IA~~lgis~~TV~rwl~r   64 (159)
T 2k27_A           24 RPLPEVVRQRIVDLAHQGV-----RPCDISRQLRVSHGCVSKILGR   64 (159)
T ss_dssp             CSSCHHHHHHHHHHHHHTC-----CHHHHHHHHTCCSHHHHHHHCC
T ss_pred             CCCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHH
Confidence            4688888777777775442     2456799999999999999853

>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=87.82  E-value=4.8  Score=27.29  Aligned_cols=40  Identities=8%  Similarity=0.003  Sum_probs=30.1

Q ss_pred             CCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhh
Q psy11996         15 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ   59 (222)
Q Consensus        15 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~   59 (222)
                      ..++.++...+...+... + +   ..++|..+|++...|..|+.
T Consensus        16 ~~~s~~~r~~i~~~~~~g-~-s---~~~ia~~lgis~~Tv~~w~~   55 (128)
T 1pdn_C           16 RPLPNNIRLKIVEMAADG-I-R---PCVISRQLRVSHGCVSKILN   55 (128)
T ss_dssp             SCCCHHHHHHHHHHHHTT-C-C---HHHHHHHHTCCHHHHHHHHH
T ss_pred             CcCCHHHHHHHHHHHHcC-C-C---HHHHHHHHCcCHHHHHHHHH
Confidence            358888777776666533 2 2   45689999999999999985

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

Probab=85.87  E-value=1.2  Score=26.54  Aligned_cols=46  Identities=20%  Similarity=0.317  Sum_probs=32.4

Q ss_pred             CCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhc
Q psy11996         14 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQN   60 (222)
Q Consensus        14 R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~n   60 (222)
                      |..|+.+....+...+.... .......++|..+|++...|..|...
T Consensus         3 r~~ys~efK~~~~~~~~~g~-s~~~~~~~vA~~~gIs~~tl~~W~~~   48 (59)
T 2glo_A            3 RRIFTPHFKLQVLESYRNDN-DCKGNQRATARKYNIHRRQIQKWLQC   48 (59)
T ss_dssp             CCCCCHHHHHHHHHHHHHCT-TTTTCHHHHHHHTTSCHHHHHHHHTT
T ss_pred             CCcCCHHHHHHHHHHHHcCC-CcchHHHHHHHHHCcCHHHHHHHHHH
Confidence            45799987766655555432 21112568899999999999999753

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

Probab=85.54  E-value=2.4  Score=27.45  Aligned_cols=45  Identities=18%  Similarity=0.285  Sum_probs=33.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhh
Q psy11996         10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ   59 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~   59 (222)
                      +++.+..|+.++...+...+... .    ...++|..+|++...|..|..
T Consensus        16 ~~~~~~~ys~e~k~~~v~~~~~g-~----s~~~iA~~~gIs~sTl~rW~k   60 (87)
T 2elh_A           16 GKRPLRSLTPRDKIHAIQRIHDG-E----SKASVARDIGVPESTLRGWCK   60 (87)
T ss_dssp             CSSCCSSCCHHHHHHHHHHHHHT-C----CHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHCC-C----CHHHHHHHHCcCHHHHHHHHH
Confidence            34567789999866555566433 2    256789999999999999974

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

Probab=84.68  E-value=1.6  Score=25.99  Aligned_cols=46  Identities=20%  Similarity=0.304  Sum_probs=31.6

Q ss_pred             CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhh
Q psy11996        138 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQN  184 (222)
Q Consensus       138 r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~n  184 (222)
                      +..|+.++...+...+... .........+|.++||+...|..|...
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            4578888776665444433 221223668899999999999999753

>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=84.04  E-value=9.2  Score=27.04  Aligned_cols=40  Identities=10%  Similarity=0.077  Sum_probs=30.5

Q ss_pred             CCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhh
Q psy11996         15 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ   59 (222)
Q Consensus        15 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~   59 (222)
                      ..++.++...+...+... .    ...++|..+|++...|..|..
T Consensus        31 ~~~s~e~r~~iv~~~~~G-~----s~~~iA~~lgis~~TV~rw~~   70 (149)
T 1k78_A           31 RPLPDVVRQRIVELAHQG-V----RPCDISRQLRVSHGCVSKILG   70 (149)
T ss_dssp             SCCCHHHHHHHHHHHHTT-C----CHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHcC-C----CHHHHHHHHCcCHHHHHHHHH
Confidence            468888777777777533 2    245689999999999999985

---

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	222
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	1e-21
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	1e-21
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	2e-21
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	2e-21
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	5e-21
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	5e-21
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	6e-19
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	6e-19
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	2e-18
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	2e-18
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	3e-18
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	3e-18
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	3e-17
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	3e-17
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	5e-17
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	5e-17
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	6e-17
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	6e-17
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	8e-17
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	8e-17
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	3e-16
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	3e-16
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	4e-16
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	4e-16
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	6e-16
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	6e-16
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	7e-16
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	2e-15
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	1e-15
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	1e-15
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	1e-15
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	1e-15
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	2e-15
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	2e-15
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	4e-15
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	4e-15
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	8e-15
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	8e-15
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	8e-15
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	8e-15
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	9e-15
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	9e-15
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	4e-14
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	4e-14
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	1e-13
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	3e-13
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	3e-13
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	4e-13
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	4e-13
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	5e-13
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	2e-12
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	7e-13
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	9e-13
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	1e-12
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	1e-12
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	3e-12
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	3e-12
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	3e-11
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	3e-11
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	1e-10
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	1e-10
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	7e-09
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	7e-09

>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 = 82.1 bits (203), Expect = 1e-21
 Identities = 52/56 (92%), Positives = 54/56 (96%)

Query: 14 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69
          R +YTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKE+
Sbjct: 1  RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 56

>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 = 82.1 bits (203), Expect = 1e-21
 Identities = 52/56 (92%), Positives = 54/56 (96%)

Query: 138 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193
           R +YTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKE+
Sbjct: 1   RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 56

>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 = 82.2 bits (203), Expect = 2e-21
 Identities = 42/62 (67%), Positives = 50/62 (80%)

Query: 9  ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68
           T+++R  YT++QTLELEKEF FN YLTR RR E+A  L LTERQ+KIWFQNRRMK KK 
Sbjct: 12 STRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKI 71

Query: 69 HK 70
          +K
Sbjct: 72 NK 73

>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 = 82.2 bits (203), Expect = 2e-21
 Identities = 42/62 (67%), Positives = 50/62 (80%)

Query: 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
            T+++R  YT++QTLELEKEF FN YLTR RR E+A  L LTERQ+KIWFQNRRMK KK 
Sbjct: 12  STRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKI 71

Query: 193 HK 194
           +K
Sbjct: 72  NK 73

>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 = 81.0 bits (200), Expect = 5e-21
 Identities = 26/61 (42%), Positives = 37/61 (60%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          +R RTS+T+ Q   LEKEF    Y     R  +A  + L E +I++WF NRR KW++E K
Sbjct: 2  QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 61

Query: 71 M 71
          +
Sbjct: 62 L 62

>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 = 81.0 bits (200), Expect = 5e-21
 Identities = 26/61 (42%), Positives = 37/61 (60%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           +R RTS+T+ Q   LEKEF    Y     R  +A  + L E +I++WF NRR KW++E K
Sbjct: 2   QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 61

Query: 195 M 195
           +
Sbjct: 62  L 62

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Length = 57

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

 Score = 75.3 bits (185), Expect = 6e-19
 Identities = 26/57 (45%), Positives = 38/57 (66%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          K  +  ++  QT+ELEK+F   +YL+   R  +A  L L+ERQ+K WFQNRR KW++
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 = 75.3 bits (185), Expect = 6e-19
 Identities = 26/57 (45%), Positives = 38/57 (66%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           K  +  ++  QT+ELEK+F   +YL+   R  +A  L L+ERQ+K WFQNRR KW++
Sbjct: 1   KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 57

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 73.8 bits (181), Expect = 2e-18
 Identities = 27/57 (47%), Positives = 43/57 (75%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          +++R  Y++ Q  ELE+E+  N+++T+ +R +I+ A  L+ERQI 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 = 73.8 bits (181), Expect = 2e-18
 Identities = 27/57 (47%), Positives = 43/57 (75%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           +++R  Y++ Q  ELE+E+  N+++T+ +R +I+ A  L+ERQI IWFQNRR+K KK
Sbjct: 2   RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 58

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

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

 Score = 74.3 bits (182), Expect = 3e-18
 Identities = 37/60 (61%), Positives = 44/60 (73%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
             RT++T  Q  ELEKEFHFN+YL+R RR+EIA  L L E Q+KIWFQNRRMK KK  +
Sbjct: 28 SGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER 87

>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 = 74.3 bits (182), Expect = 3e-18
 Identities = 37/60 (61%), Positives = 44/60 (73%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
              RT++T  Q  ELEKEFHFN+YL+R RR+EIA  L L E Q+KIWFQNRRMK KK  +
Sbjct: 28  SGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER 87

>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 = 70.7 bits (173), Expect = 3e-17
 Identities = 25/63 (39%), Positives = 38/63 (60%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          +R RT+++  Q  ELE+ F   +Y     R E+A    LTE +I++WFQNRR + +K+H 
Sbjct: 3  RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT 62

Query: 71 MAS 73
            S
Sbjct: 63 SVS 65

>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 = 70.7 bits (173), Expect = 3e-17
 Identities = 25/63 (39%), Positives = 38/63 (60%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           +R RT+++  Q  ELE+ F   +Y     R E+A    LTE +I++WFQNRR + +K+H 
Sbjct: 3   RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT 62

Query: 195 MAS 197
             S
Sbjct: 63  SVS 65

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 66

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 70.3 bits (172), Expect = 5e-17
 Identities = 19/62 (30%), Positives = 27/62 (43%)

Query: 10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69
          T R RT     Q   L   +  N       + ++     L+ R I++WFQN+R K KK  
Sbjct: 3  TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS 62

Query: 70 KM 71
           M
Sbjct: 63 IM 64

>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 = 70.3 bits (172), Expect = 5e-17
 Identities = 19/62 (30%), Positives = 27/62 (43%)

Query: 134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193
           T R RT     Q   L   +  N       + ++     L+ R I++WFQN+R K KK  
Sbjct: 3   TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS 62

Query: 194 KM 195
            M
Sbjct: 63  IM 64

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

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

 Score = 69.9 bits (171), Expect = 6e-17
 Identities = 28/53 (52%), Positives = 37/53 (69%)

Query: 12 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 64
          R RT+++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWFQN 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 = 69.9 bits (171), Expect = 6e-17
 Identities = 28/53 (52%), Positives = 37/53 (69%)

Query: 136 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 188
           R RT+++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWFQN R K
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 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 = 70.5 bits (172), Expect = 8e-17
 Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 15/78 (19%)

Query: 12 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIA---------------HALCLTERQIKI 56
            R ++ +     +E  F+ N+Y    +R EIA                   +T  ++  
Sbjct: 2  GSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYN 61

Query: 57 WFQNRRMKWKKEHKMASM 74
          WF NRR + K+   +A++
Sbjct: 62 WFANRRKEIKRRANIAAI 79

>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 = 70.5 bits (172), Expect = 8e-17
 Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 15/78 (19%)

Query: 136 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIA---------------HALCLTERQIKI 180
             R ++ +     +E  F+ N+Y    +R EIA                   +T  ++  
Sbjct: 2   GSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYN 61

Query: 181 WFQNRRMKWKKEHKMASM 198
           WF NRR + K+   +A++
Sbjct: 62  WFANRRKEIKRRANIAAI 79

>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 = 68.0 bits (166), Expect = 3e-16
 Identities = 31/57 (54%), Positives = 40/57 (70%)

Query: 12 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68
          R RT++TR Q   LEKEF+   Y++R RR E+A  L L E  IK+WFQNRRMK K++
Sbjct: 1  RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 57

>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 = 68.0 bits (166), Expect = 3e-16
 Identities = 31/57 (54%), Positives = 40/57 (70%)

Query: 136 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
           R RT++TR Q   LEKEF+   Y++R RR E+A  L L E  IK+WFQNRRMK K++
Sbjct: 1   RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 57

>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 = 68.0 bits (166), Expect = 4e-16
 Identities = 25/60 (41%), Positives = 36/60 (60%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          +R RT++T  Q  ELE+ F   RYLT  R  +++  L L   Q+KIWF+NRR + K +  
Sbjct: 2  RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 61

>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 = 68.0 bits (166), Expect = 4e-16
 Identities = 25/60 (41%), Positives = 36/60 (60%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           +R RT++T  Q  ELE+ F   RYLT  R  +++  L L   Q+KIWF+NRR + K +  
Sbjct: 2   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 61

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 67.2 bits (164), Expect = 6e-16
 Identities = 27/57 (47%), Positives = 38/57 (66%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          ++ RT +T  Q L LE++F   +YL+   R E + +L LTE Q+KIWFQNRR 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 = 67.2 bits (164), Expect = 6e-16
 Identities = 27/57 (47%), Positives = 38/57 (66%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           ++ RT +T  Q L LE++F   +YL+   R E + +L LTE Q+KIWFQNRR K K+
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>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 = 67.8 bits (165), Expect = 7e-16
 Identities = 26/68 (38%), Positives = 37/68 (54%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           +++R  +T+ QT ELE+ F   RYL+   R  +A  + LT  Q+KIWFQN R K K+   
Sbjct: 10  RKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQN 69

Query: 195 MASMNVIP 202
                  P
Sbjct: 70  EKGYEGHP 77

>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 = 66.6 bits (162), Expect = 2e-15
 Identities = 25/60 (41%), Positives = 36/60 (60%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          +++R  +T+ QT ELE+ F   RYL+   R  +A  + LT  Q+KIWFQN R K K+   
Sbjct: 10 RKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQN 69

>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 = 66.9 bits (163), Expect = 1e-15
 Identities = 23/60 (38%), Positives = 37/60 (61%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
          +++R  +++ Q  ELE+ F   +YL+   R  +A  + LT  Q+KIWFQN R K K++ K
Sbjct: 3  RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62

>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 = 66.9 bits (163), Expect = 1e-15
 Identities = 23/60 (38%), Positives = 37/60 (61%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
           +++R  +++ Q  ELE+ F   +YL+   R  +A  + LT  Q+KIWFQN R K K++ K
Sbjct: 3   RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62

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

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

 Score = 66.5 bits (162), Expect = 1e-15
 Identities = 27/58 (46%), Positives = 36/58 (62%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68
          +RQRT +T  Q  +LE  F  NRY     R EIA    LTE ++++WF+NRR KW+K 
Sbjct: 2  RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 59

>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 = 66.5 bits (162), Expect = 1e-15
 Identities = 27/58 (46%), Positives = 36/58 (62%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
           +RQRT +T  Q  +LE  F  NRY     R EIA    LTE ++++WF+NRR KW+K 
Sbjct: 2   RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 59

>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 = 65.9 bits (161), Expect = 2e-15
 Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 1/51 (1%)

Query: 18 TRYQTLELEKEF-HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          T      LEK F    ++   +R   ++  L    R I+ WF+ RR + K 
Sbjct: 1  TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 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 = 65.9 bits (161), Expect = 2e-15
 Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 1/51 (1%)

Query: 142 TRYQTLELEKEF-HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           T      LEK F    ++   +R   ++  L    R I+ WF+ RR + K 
Sbjct: 1   TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 51

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

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

 Score = 64.9 bits (158), Expect = 4e-15
 Identities = 13/49 (26%), Positives = 21/49 (42%)

Query: 14 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR 62
          R  +T  Q   L   F  N+  ++  +I I+  L L    +  +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 = 64.9 bits (158), Expect = 4e-15
 Identities = 13/49 (26%), Positives = 21/49 (42%)

Query: 138 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR 186
           R  +T  Q   L   F  N+  ++  +I I+  L L    +  +F N R
Sbjct: 2   RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>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 = 65.0 bits (158), Expect = 8e-15
 Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 1/64 (1%)

Query: 11 KRQRTSYTRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69
               + T  Q   LE  F+  N++        IA    LTE Q + WF+ R  +W++  
Sbjct: 2  SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 61

Query: 70 KMAS 73
           + S
Sbjct: 62 GLPS 65

>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 = 65.0 bits (158), Expect = 8e-15
 Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 1/64 (1%)

Query: 135 KRQRTSYTRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193
                + T  Q   LE  F+  N++        IA    LTE Q + WF+ R  +W++  
Sbjct: 2   SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 61

Query: 194 KMAS 197
            + S
Sbjct: 62  GLPS 65

>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 = 64.5 bits (157), Expect = 8e-15
 Identities = 14/56 (25%), Positives = 30/56 (53%)

Query: 12 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          ++RT+ +      LE+ F  +   + +  + +A  L L +  +++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 = 64.5 bits (157), Expect = 8e-15
 Identities = 14/56 (25%), Positives = 30/56 (53%)

Query: 136 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           ++RT+ +      LE+ F  +   + +  + +A  L L +  +++WF NRR + K+
Sbjct: 1   KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 56

>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 = 64.4 bits (157), Expect = 9e-15
 Identities = 14/60 (23%), Positives = 24/60 (40%), Gaps = 3/60 (5%)

Query: 11 KRQRTSYTRYQTLELEKEF---HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          K +R    ++ T  +         + Y T   + +IA    LT  Q+  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 = 64.4 bits (157), Expect = 9e-15
 Identities = 14/60 (23%), Positives = 24/60 (40%), Gaps = 3/60 (5%)

Query: 135 KRQRTSYTRYQTLELEKEF---HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           K +R    ++ T  +         + Y T   + +IA    LT  Q+  WF N R +  +
Sbjct: 3   KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQ 62

>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 = 62.6 bits (152), Expect = 4e-14
 Identities = 15/53 (28%), Positives = 29/53 (54%)

Query: 14 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 66
          ++S +      LE+ F   + L  + + E+A    +T  Q+++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 = 62.6 bits (152), Expect = 4e-14
 Identities = 15/53 (28%), Positives = 29/53 (54%)

Query: 138 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190
           ++S +      LE+ F   + L  + + E+A    +T  Q+++WF N+RM+ K
Sbjct: 1   KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53

>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 = 61.3 bits (149), Expect = 1e-13
 Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 12 RQRTSYTRYQTLELEKEF-HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 66
          +            LEK F    +Y   +R   ++  L  + R+I+ 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 = 61.3 bits (149), Expect = 1e-13
 Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 136 RQRTSYTRYQTLELEKEF-HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190
           +            LEK F    +Y   +R   ++  L  + R+I+ WF++RR + K
Sbjct: 3   KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

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

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

 Score = 60.5 bits (146), Expect = 3e-13
 Identities = 14/64 (21%), Positives = 22/64 (34%), Gaps = 1/64 (1%)

Query: 8  GETKRQRTSYTRYQTLELEKEFH-FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 66
              R RT  +      L+   H    Y  +     ++  L L +  I  +FQN+R   K
Sbjct: 5  SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVK 64

Query: 67 KEHK 70
              
Sbjct: 65 HSGP 68

>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 = 60.5 bits (146), Expect = 3e-13
 Identities = 14/64 (21%), Positives = 22/64 (34%), Gaps = 1/64 (1%)

Query: 132 GETKRQRTSYTRYQTLELEKEFH-FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190
               R RT  +      L+   H    Y  +     ++  L L +  I  +FQN+R   K
Sbjct: 5   SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVK 64

Query: 191 KEHK 194
               
Sbjct: 65  HSGP 68

>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 = 4e-13
 Identities = 17/54 (31%), Positives = 22/54 (40%), Gaps = 3/54 (5%)

Query: 17 YTRYQTLELEKEFHFNR---YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          +T+     LE  F  N    YL  +    +     L+  QIK W  NRR K K 
Sbjct: 5  FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

>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 = 4e-13
 Identities = 17/54 (31%), Positives = 22/54 (40%), Gaps = 3/54 (5%)

Query: 141 YTRYQTLELEKEFHFNR---YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           +T+     LE  F  N    YL  +    +     L+  QIK W  NRR K K 
Sbjct: 5   FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

>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 = 60.1 bits (145), Expect = 5e-13
 Identities = 14/69 (20%), Positives = 26/69 (37%)

Query: 10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69
          T ++    T  Q   L+  F  +  LT      +     LT R+I  WF  ++     + 
Sbjct: 4  TPQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE 63

Query: 70 KMASMNNPN 78
          +   ++  N
Sbjct: 64 EKMEIDESN 72

>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 = 58.6 bits (141), Expect = 2e-12
 Identities = 13/66 (19%), Positives = 25/66 (37%)

Query: 134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193
           T ++    T  Q   L+  F  +  LT      +     LT R+I  WF  ++     + 
Sbjct: 4   TPQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE 63

Query: 194 KMASMN 199
           +   ++
Sbjct: 64  EKMEID 69

>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 = 59.6 bits (144), Expect = 7e-13
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 4/73 (5%)

Query: 11 KRQRTSYTRYQTLELEK---EFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          +R+R ++ +  T  L +       N Y +   + E+A    +T  Q+  WF N+R+++KK
Sbjct: 2  RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61

Query: 68 EHKMASMNNPNLY 80
                    N+Y
Sbjct: 62 NIG-KFQEEANIY 73

>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 = 59.6 bits (144), Expect = 9e-13
 Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 3/63 (4%)

Query: 135 KRQRTSYTRYQTLELEK---EFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           +R+R ++ +  T  L +       N Y +   + E+A    +T  Q+  WF N+R+++KK
Sbjct: 2   RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61

Query: 192 EHK 194
              
Sbjct: 62  NIG 64

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 67

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

 Score = 58.9 bits (142), Expect = 1e-12
 Identities = 19/57 (33%), Positives = 29/57 (50%)

Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          KR+RTS        LE  F      + ++   IA+ L L +  +++WF NRR K K+
Sbjct: 9  KRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR 65

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 67

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

 Score = 58.9 bits (142), Expect = 1e-12
 Identities = 19/57 (33%), Positives = 29/57 (50%)

Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           KR+RTS        LE  F      + ++   IA+ L L +  +++WF NRR K K+
Sbjct: 9   KRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR 65

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

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

 Score = 57.3 bits (138), Expect = 3e-12
 Identities = 20/57 (35%), Positives = 29/57 (50%)

Query: 13 QRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69
          +RTS      + LEK F  N+  T      IA  L + +  I++WF NRR K K+ +
Sbjct: 1  KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRIN 57

>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 = 57.3 bits (138), Expect = 3e-12
 Identities = 20/57 (35%), Positives = 29/57 (50%)

Query: 137 QRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193
           +RTS      + LEK F  N+  T      IA  L + +  I++WF NRR K K+ +
Sbjct: 1   KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRIN 57

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

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

 Score = 55.4 bits (133), Expect = 3e-11
 Identities = 12/68 (17%), Positives = 23/68 (33%), Gaps = 4/68 (5%)

Query: 5  NANGETKRQRTSYTRYQTLELEKEFH----FNRYLTRRRRIEIAHALCLTERQIKIWFQN 60
          ++ G TKR RT +T  Q  ++           +        +      +  + +KIW  N
Sbjct: 12 SSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHN 71

Query: 61 RRMKWKKE 68
           +      
Sbjct: 72 NKNSGPSS 79

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

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

 Score = 55.4 bits (133), Expect = 3e-11
 Identities = 12/68 (17%), Positives = 23/68 (33%), Gaps = 4/68 (5%)

Query: 129 NANGETKRQRTSYTRYQTLELEKEFH----FNRYLTRRRRIEIAHALCLTERQIKIWFQN 184
           ++ G TKR RT +T  Q  ++           +        +      +  + +KIW  N
Sbjct: 12  SSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHN 71

Query: 185 RRMKWKKE 192
            +      
Sbjct: 72  NKNSGPSS 79

>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 = 53.6 bits (128), Expect = 1e-10
 Identities = 12/78 (15%), Positives = 23/78 (29%), Gaps = 21/78 (26%)

Query: 14 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL---------------------CLTER 52
          R  +       L + +   +  ++  R  +                          +TE 
Sbjct: 1  RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 53 QIKIWFQNRRMKWKKEHK 70
          ++  WF NRR +    HK
Sbjct: 61 RVYNWFANRRKEEAFRHK 78

>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 = 53.6 bits (128), Expect = 1e-10
 Identities = 12/78 (15%), Positives = 23/78 (29%), Gaps = 21/78 (26%)

Query: 138 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL---------------------CLTER 176
           R  +       L + +   +  ++  R  +                          +TE 
Sbjct: 1   RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 177 QIKIWFQNRRMKWKKEHK 194
           ++  WF NRR +    HK
Sbjct: 61  RVYNWFANRRKEEAFRHK 78

>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 = 49.0 bits (116), Expect = 7e-09
 Identities = 12/63 (19%), Positives = 21/63 (33%)

Query: 8  GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
          G +       T+ Q   L+  F   ++  R    ++     L   +I  WF + R   K 
Sbjct: 1  GSSGSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH 60

Query: 68 EHK 70
             
Sbjct: 61 GQL 63

>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 = 49.0 bits (116), Expect = 7e-09
 Identities = 12/63 (19%), Positives = 21/63 (33%)

Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
           G +       T+ Q   L+  F   ++  R    ++     L   +I  WF + R   K 
Sbjct: 1   GSSGSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH 60

Query: 192 EHK 194
              
Sbjct: 61  GQL 63

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	222
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.86
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.84
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.84
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.84
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.84
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.84
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.84
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.83
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.83
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.83
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.83
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.83
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.83
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.82
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.82
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.82
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.82
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.82
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.82
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.81
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.81
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.81
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.81
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.81
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.8
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.8
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.8
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.8
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.79
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.79
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.79
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.78
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.78
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.78
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.77
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.77
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.77
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.77
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.77
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.76
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.75
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.75
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.75
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.75
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.74
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.73
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.72
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.72
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.71
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.7
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.7
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.7
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.7
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.67
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.65
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.65
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.65
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.63
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.63
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.61
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.61
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.6
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.6
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.59
d1hlva1	66	DNA-binding domain of centromere binding protein B	92.3
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	92.08
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	90.71
d1hlva1	66	DNA-binding domain of centromere binding protein B	90.37

>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=99.86  E-value=2.2e-22  Score=124.68  Aligned_cols=58  Identities=47%  Similarity=0.785  Sum_probs=55.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996         10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      +||+|+.||.+|+.+|+..|..++||+..++++||..+||++.+|++||||||++++|
T Consensus         1 Grr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           1 GRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            4788999999999999999999999999999999999999999999999999998764

>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=99.84  E-value=1.6e-21  Score=121.18  Aligned_cols=57  Identities=47%  Similarity=0.774  Sum_probs=55.4

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996         11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus        11 ~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      ||+|+.||++|+.+|+..|..++||+..++++||..+||++.+|++||+|+|++.++
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            578999999999999999999999999999999999999999999999999999987

>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=99.84  E-value=3.1e-21  Score=123.19  Aligned_cols=62  Identities=40%  Similarity=0.651  Sum_probs=58.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhh
Q psy11996         10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM   71 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~   71 (222)
                      +||+|++||.+|+.+|+..|+.++||+..++..||..|||++.+|++||+|||+++++....
T Consensus         1 Prr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~~   62 (67)
T d1zq3p1           1 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ   62 (67)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhhh
Confidence            46789999999999999999999999999999999999999999999999999999986643

>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=99.84  E-value=2.4e-21  Score=119.79  Aligned_cols=57  Identities=46%  Similarity=0.829  Sum_probs=55.0

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996         11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus        11 ~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      |+.|+.||++|+.+|+..|..++||+..+++.||..+||++.+|++||+|||++++|
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            578999999999999999999999999999999999999999999999999999875

>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=99.84  E-value=1.9e-21  Score=120.32  Aligned_cols=57  Identities=47%  Similarity=0.805  Sum_probs=55.0

Q ss_pred             CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996        135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  191 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk  191 (222)
                      ++.|+.||.+|+.+|+..|..++||+.++++.||..+||++.+|++||||||+|+||
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            677899999999999999999999999999999999999999999999999999875

>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=99.84  E-value=3e-21  Score=119.40  Aligned_cols=56  Identities=55%  Similarity=0.783  Sum_probs=54.5

Q ss_pred             CCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996         12 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus        12 r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      |.|+.||++|+.+|+..|..++||+..++++||..+||++.+|++||+|+|++.++
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk   56 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR   56 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhc
Confidence            57999999999999999999999999999999999999999999999999999986

>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=99.84  E-value=6.7e-21  Score=124.68  Aligned_cols=66  Identities=64%  Similarity=0.903  Sum_probs=61.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhh
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM   71 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~   71 (222)
                      ..+..|++|++||.+|+.+|+..|..++||+..+++.||..+||++++|++||+|||+++++..+.
T Consensus         9 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~   74 (77)
T d1pufa_           9 HARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             CCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHH
Confidence            344567889999999999999999999999999999999999999999999999999999987654

>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=99.83  E-value=3.9e-21  Score=117.78  Aligned_cols=55  Identities=95%  Similarity=1.463  Sum_probs=53.5

Q ss_pred             CCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996         14 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE   68 (222)
Q Consensus        14 R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~   68 (222)
                      ||.||.+|+.+|+..|..++||+..++.+||..|||++++|++||||||+++++.
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            7999999999999999999999999999999999999999999999999999874

>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=99.83  E-value=3.4e-21  Score=117.45  Aligned_cols=53  Identities=53%  Similarity=0.826  Sum_probs=51.5

Q ss_pred             CCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhH
Q psy11996         12 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK   64 (222)
Q Consensus        12 r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k   64 (222)
                      |+|+.||++|+.+|+..|..++||+..++.+||..+||++.+|++||||||+|
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            57999999999999999999999999999999999999999999999999986

>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=99.83  E-value=7.5e-21  Score=120.74  Aligned_cols=62  Identities=39%  Similarity=0.647  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996          9 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus         9 ~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      +.||.|+.||.+|+.+|+.+|..++||+..++..||..+||++.+|++||+|+|+++++...
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~   62 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   62 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhccc
Confidence            46789999999999999999999999999999999999999999999999999999998654

>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=99.83  E-value=8.2e-21  Score=121.56  Aligned_cols=62  Identities=42%  Similarity=0.700  Sum_probs=58.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhh
Q psy11996         10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM   71 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~   71 (222)
                      +||.||.||++|+.+|+..|..++||+..+++.||..+||++.+|++||+|+|++.++....
T Consensus         1 grR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~   62 (68)
T d2cuea1           1 GQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL   62 (68)
T ss_dssp             SCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhhh
Confidence            47789999999999999999999999999999999999999999999999999999986543

>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=8.6e-21  Score=117.30  Aligned_cols=57  Identities=46%  Similarity=0.829  Sum_probs=55.0

Q ss_pred             CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996        135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  191 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk  191 (222)
                      ++.|+.||++|+.+|+..|..++||+.++++.||..+||++.+|++||+|||+++||
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k~kk   57 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR   57 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhhccC
Confidence            467899999999999999999999999999999999999999999999999999986

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]}

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

Probab=99.83  E-value=5.7e-21  Score=117.06  Aligned_cols=55  Identities=95%  Similarity=1.463  Sum_probs=53.6

Q ss_pred             CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996        138 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  192 (222)
Q Consensus       138 r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~  192 (222)
                      |+.||.+|+.+|+..|..++||+..++.+||..|||++++|++||||||+|+|++
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk~   55 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   55 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhhc
Confidence            6899999999999999999999999999999999999999999999999999985

>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=99.82  E-value=1.1e-20  Score=117.39  Aligned_cols=57  Identities=47%  Similarity=0.774  Sum_probs=55.1

Q ss_pred             CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996        135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  191 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk  191 (222)
                      ++.|+.||++|+.+|+..|..++||+..++..||..+||++.+|++||||+|+++||
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            467899999999999999999999999999999999999999999999999999987

>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=99.82  E-value=1e-20  Score=120.97  Aligned_cols=61  Identities=38%  Similarity=0.682  Sum_probs=57.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996         10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      +||.|+.||+.|+.+|+..|..++||+..++..||..+||++.+|++||+|+|++.++...
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~~   62 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK   62 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhccc
Confidence            4788999999999999999999999999999999999999999999999999999998643

>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=1e-20  Score=116.91  Aligned_cols=57  Identities=54%  Similarity=0.779  Sum_probs=54.8

Q ss_pred             CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996        136 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  192 (222)
Q Consensus       136 ~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~  192 (222)
                      +.|+.||++|+.+|+..|..++||+..++.+||..+||++.+|++||||+|+++|++
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            468999999999999999999999999999999999999999999999999999974

>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=99.82  E-value=1.2e-20  Score=126.57  Aligned_cols=63  Identities=60%  Similarity=0.931  Sum_probs=56.2

Q ss_pred             CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996        132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK  194 (222)
Q Consensus       132 ~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~  194 (222)
                      +..++.|+.|+.+|+.+|+.+|..++||+.+++++||..|||+..+|++||||+|+++|+..+
T Consensus        25 ~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~~   87 (88)
T d1b72a_          25 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   87 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhcc
Confidence            455788999999999999999999999999999999999999999999999999999998754

>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=2.8e-21  Score=126.67  Aligned_cols=66  Identities=38%  Similarity=0.617  Sum_probs=60.4

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996          4 VNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH   69 (222)
Q Consensus         4 ~~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~   69 (222)
                      .....+.+|.|++||.+|+.+|+..|..++||+..++++||..+||++.+|++||+|+|++.++..
T Consensus         3 ~g~p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   68 (77)
T d1vnda_           3 DGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ   68 (77)
T ss_dssp             SCCSSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSC
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHh
Confidence            444566788899999999999999999999999999999999999999999999999999988643

>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=6.8e-21  Score=124.84  Aligned_cols=69  Identities=36%  Similarity=0.605  Sum_probs=62.0

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccCC
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMN  199 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~~  199 (222)
                      ..+.++.|+.||.+|+.+|+.+|..++||+..+++.||..+||++.+|++||+|+|+|.|+........
T Consensus         6 p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~~~   74 (77)
T d1vnda_           6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGYE   74 (77)
T ss_dssp             SSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSCCCSSCS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHhhccCCC
Confidence            345677899999999999999999999999999999999999999999999999999999866554443

>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=2.1e-20  Score=119.25  Aligned_cols=61  Identities=41%  Similarity=0.662  Sum_probs=57.9

Q ss_pred             CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      ++.|+.||.+|+.+|+..|..++||+..++..||..|||+..+|++||+|||+++|+....
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            5679999999999999999999999999999999999999999999999999999987654

>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=99.81  E-value=3.1e-20  Score=121.44  Aligned_cols=65  Identities=65%  Similarity=0.919  Sum_probs=60.3

Q ss_pred             CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcc
Q psy11996        132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA  196 (222)
Q Consensus       132 ~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~  196 (222)
                      ...++.|+.|+.+|+.+|+..|..++||+..+++.||..|||++.+|++||||||+|+|+..+..
T Consensus        11 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~~   75 (77)
T d1pufa_          11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDR   75 (77)
T ss_dssp             CTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHHh
Confidence            34567899999999999999999999999999999999999999999999999999999977643

>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=99.81  E-value=8.5e-21  Score=118.70  Aligned_cols=59  Identities=46%  Similarity=0.737  Sum_probs=56.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996         10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE   68 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~   68 (222)
                      .||.||+||++|+.+|+..|..++||+..++..||..+||++.+|++||+|+|++.++.
T Consensus         1 Qrr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1           1 QRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             SSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            46889999999999999999999999999999999999999999999999999999875

>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=2.1e-20  Score=125.38  Aligned_cols=64  Identities=59%  Similarity=0.901  Sum_probs=56.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996          7 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus         7 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      .+..+|.|+.||.+|+.+|+..|..++||+..++++||..|||++++|++||+|+|++.++..+
T Consensus        24 ~~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~~   87 (88)
T d1b72a_          24 LGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   87 (88)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhcc
Confidence            3456889999999999999999999999999999999999999999999999999999998653

>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=4e-20  Score=117.32  Aligned_cols=62  Identities=39%  Similarity=0.633  Sum_probs=58.7

Q ss_pred             CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       134 ~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      .++.|+.|+.+|+.+|+.+|..++||+..++..||..+||+..+|++||+|+|+++|+....
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~~   63 (65)
T d1fjla_           2 QRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHTS   63 (65)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhcccc
Confidence            56789999999999999999999999999999999999999999999999999999987653

>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=99.80  E-value=2.7e-20  Score=113.40  Aligned_cols=53  Identities=53%  Similarity=0.826  Sum_probs=51.3

Q ss_pred             CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhh
Q psy11996        136 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK  188 (222)
Q Consensus       136 ~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k  188 (222)
                      +.|+.||++|+.+|+..|..++||+..++.+||..|||++.+|++||||||+|
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            46899999999999999999999999999999999999999999999999986

>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=99.80  E-value=4.3e-20  Score=119.04  Aligned_cols=60  Identities=27%  Similarity=0.356  Sum_probs=56.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhh-CCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996         10 TKRQRTSYTRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH   69 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~~-~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~   69 (222)
                      +++.|++||.+|+.+|+..|.. ++||+..+++.||..+||++++|++||+|||+++++..
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            4678999999999999999986 67999999999999999999999999999999998864

>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=7.2e-20  Score=117.09  Aligned_cols=61  Identities=43%  Similarity=0.718  Sum_probs=58.1

Q ss_pred             CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996        135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM  195 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~  195 (222)
                      ++.|+.||++|+.+|+..|..++||+..+++.||..+||++.+|++||+|+|+++|+..+.
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~   62 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL   62 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhhh
Confidence            6789999999999999999999999999999999999999999999999999999987654

>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=7.8e-20  Score=116.85  Aligned_cols=64  Identities=36%  Similarity=0.638  Sum_probs=59.5

Q ss_pred             CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhccc
Q psy11996        134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS  197 (222)
Q Consensus       134 ~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~  197 (222)
                      .++.|+.||+.|+.+|+..|..++||+..++..||..+||++.+|++||+|+|+++|+..+..+
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~~~~~   65 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDKA   65 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSCCS
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhcccchh
Confidence            4678999999999999999999999999999999999999999999999999999998765543

>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=99.79  E-value=1.4e-19  Score=116.66  Aligned_cols=60  Identities=27%  Similarity=0.356  Sum_probs=56.4

Q ss_pred             CCCCCcCCHHHHHHHHHhhhh-cCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996        135 KRQRTSYTRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK  194 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F~~-~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~  194 (222)
                      ++.|+.||.+|+.+|+..|.. ++||+..+++.||.++||++.+|++||||||+++|+...
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~~   62 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   62 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhccC
Confidence            567899999999999999986 789999999999999999999999999999999999764

>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=4.9e-20  Score=117.20  Aligned_cols=60  Identities=30%  Similarity=0.375  Sum_probs=57.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996          9 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE   68 (222)
Q Consensus         9 ~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~   68 (222)
                      +.+|.|+.||.+|+.+|+.+|..++||+..+++.||..+||++.+|++||+|+|++.++.
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            468899999999999999999999999999999999999999999999999999998763

>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=99.79  E-value=4.9e-20  Score=117.39  Aligned_cols=59  Identities=32%  Similarity=0.407  Sum_probs=56.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996          9 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus         9 ~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      .++|+|+.|+.+|+.+|+.+|..++||+..+++.||..+||++.+|++||+|+|++.++
T Consensus         7 ~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk   65 (67)
T d1ocpa_           7 ARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR   65 (67)
T ss_dssp             CSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSS
T ss_pred             ccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhc
Confidence            45788999999999999999999999999999999999999999999999999999765

>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=99.78  E-value=5.5e-20  Score=114.97  Aligned_cols=59  Identities=46%  Similarity=0.739  Sum_probs=56.4

Q ss_pred             CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996        135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH  193 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~  193 (222)
                      ++.|+.||++|+.+|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.+
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            57799999999999999999999999999999999999999999999999999999863

>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=1e-19  Score=110.75  Aligned_cols=53  Identities=28%  Similarity=0.478  Sum_probs=51.1

Q ss_pred             CCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHH
Q psy11996         14 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK   66 (222)
Q Consensus        14 R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~   66 (222)
                      ||.||++|+.+|+..|..++||+..++.+||..+||++.+|++||+|+|++.|
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            78999999999999999999999999999999999999999999999999853

>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=99.78  E-value=1.1e-19  Score=112.71  Aligned_cols=56  Identities=25%  Similarity=0.438  Sum_probs=54.0

Q ss_pred             CCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996         12 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus        12 r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      |.||.|+.+|+.+|+..|..++||+..++..||..+||++++|++||+|+|++.++
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            57999999999999999999999999999999999999999999999999999875

>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=99.77  E-value=2.8e-19  Score=118.70  Aligned_cols=63  Identities=29%  Similarity=0.441  Sum_probs=58.3

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhC---------------CChHHHHHHhhcchhHHHHHhhhhc
Q psy11996         11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC---------------LTERQIKIWFQNRRMKWKKEHKMAS   73 (222)
Q Consensus        11 ~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~---------------l~~~~v~~WF~nrR~k~~~~~~~~~   73 (222)
                      ||.|+.|+++|+.+|+.+|..++||+..++++||..+|               |++.+|++||+|||+++++....+.
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~~a~   78 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANIAA   78 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhhHHH
Confidence            67899999999999999999999999999999999875               9999999999999999999766543

>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=99.77  E-value=9.6e-20  Score=117.81  Aligned_cols=62  Identities=23%  Similarity=0.211  Sum_probs=57.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhh-CCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996          6 ANGETKRQRTSYTRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus         6 ~~~~~~r~R~~~t~~q~~~L~~~f~~-~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      ++..++++|++||++|+.+|+.+|.. ++||+..+++.||..+||+..+|++||+|+|++.++
T Consensus         3 s~~~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk   65 (71)
T d1wi3a_           3 SGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             CCCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhcc
Confidence            44567889999999999999999974 899999999999999999999999999999999776

>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=99.77  E-value=1.9e-19  Score=114.41  Aligned_cols=61  Identities=30%  Similarity=0.367  Sum_probs=57.6

Q ss_pred             CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996        133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH  193 (222)
Q Consensus       133 ~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~  193 (222)
                      +.++.|+.|+.+|+.+|+..|..++||+..+++.||.++||+..+|++||+|+|++.|+..
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~~   62 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHHH
Confidence            3578899999999999999999999999999999999999999999999999999998754

>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=2.4e-19  Score=111.06  Aligned_cols=57  Identities=25%  Similarity=0.419  Sum_probs=54.6

Q ss_pred             CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996        136 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  192 (222)
Q Consensus       136 ~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~  192 (222)
                      +.|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.
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            468999999999999999999999999999999999999999999999999998873

>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=99.77  E-value=2.5e-19  Score=108.93  Aligned_cols=53  Identities=28%  Similarity=0.478  Sum_probs=51.1

Q ss_pred             CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHH
Q psy11996        138 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK  190 (222)
Q Consensus       138 r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k  190 (222)
                      |+.||++|+.+|+..|..++||+..++..||..+||+..+|++||+|+|++.|
T Consensus         1 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~K   53 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   53 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTTC
T ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhccC
Confidence            68899999999999999999999999999999999999999999999999865

>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=99.76  E-value=2.7e-19  Score=113.92  Aligned_cols=60  Identities=32%  Similarity=0.402  Sum_probs=56.8

Q ss_pred             CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996        133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  192 (222)
Q Consensus       133 ~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~  192 (222)
                      ..++.|+.|+.+|+.+|+.+|..++||+.++++.||..+||+..+|++||+|+|+++|+.
T Consensus         7 ~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_           7 ARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             CSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             ccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            457789999999999999999999999999999999999999999999999999998863

>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=99.75  E-value=5.7e-19  Score=108.90  Aligned_cols=55  Identities=36%  Similarity=0.475  Sum_probs=53.3

Q ss_pred             CCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996         13 QRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus        13 ~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      +||.|+.+|+.+|+..|..++||+..+++.||..+||++.+|++||+|+|++.++
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            5899999999999999999999999999999999999999999999999999876

>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=99.75  E-value=7.3e-19  Score=108.40  Aligned_cols=56  Identities=36%  Similarity=0.451  Sum_probs=54.0

Q ss_pred             CCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996        137 QRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  192 (222)
Q Consensus       137 ~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~  192 (222)
                      +|+.|+.+|+.+|+..|..++||+..++..||.++||++.+|++||+|+|+++|+.
T Consensus         1 kRT~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk~   56 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI   56 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHcc
Confidence            48999999999999999999999999999999999999999999999999999874

>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=99.75  E-value=1.2e-18  Score=115.62  Aligned_cols=64  Identities=28%  Similarity=0.447  Sum_probs=59.0

Q ss_pred             CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcC---------------CChhhHHHHHhhhhhhHHHhhhcccC
Q psy11996        135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC---------------LTERQIKIWFQNRRMKWKKEHKMASM  198 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~---------------l~~~~V~~WF~nrR~k~kk~~~~~~~  198 (222)
                      ++.|+.|+++|+.+|+.+|..++||+..++++||..+|               |++.+|++||+|||+++|+....+..
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~~a~~   79 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANIAAI   79 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHCCCC
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhhHHHh
Confidence            46799999999999999999999999999999999875               99999999999999999998776543

>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=99.75  E-value=8.3e-19  Score=113.32  Aligned_cols=60  Identities=23%  Similarity=0.208  Sum_probs=55.8

Q ss_pred             CCCCCCCcCCHHHHHHHHHhhhh-cCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996        133 ETKRQRTSYTRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  192 (222)
Q Consensus       133 ~~~~~r~~~~~~q~~~L~~~F~~-~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~  192 (222)
                      ..++.|+.|+++|+.+|+.+|.. ++||+.++++.||.++||+..+|++||+|+|++.|+.
T Consensus         6 ~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk~   66 (71)
T d1wi3a_           6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS   66 (71)
T ss_dssp             CCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCSS
T ss_pred             CCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhccc
Confidence            45678999999999999999974 8999999999999999999999999999999998873

>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=99.74  E-value=7.2e-19  Score=105.83  Aligned_cols=50  Identities=26%  Similarity=0.339  Sum_probs=49.0

Q ss_pred             CCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcch
Q psy11996         13 QRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR   62 (222)
Q Consensus        13 ~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR   62 (222)
                      +|+.||++|+.+|+..|..++||+..++.+||..+||++++|++||+|+|
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            58999999999999999999999999999999999999999999999998

>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=99.73  E-value=2.4e-18  Score=113.53  Aligned_cols=63  Identities=19%  Similarity=0.184  Sum_probs=56.3

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHhhh----CCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHH
Q psy11996          4 VNANGETKRQRTSYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK   66 (222)
Q Consensus         4 ~~~~~~~~r~R~~~t~~q~~~L~~~f~~----~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~   66 (222)
                      .....+.||.||.||.+|+..|+.+|+.    ++||+..++++||..|||++.+|++||+|+|.+.+
T Consensus        11 ~~~~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k   77 (80)
T d1wh7a_          11 SSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGP   77 (80)
T ss_dssp             CCCCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSC
T ss_pred             CCCccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCC
Confidence            3445567889999999999999999886    89999999999999999999999999999997654

>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=99.72  E-value=1.1e-17  Score=109.25  Aligned_cols=65  Identities=18%  Similarity=0.188  Sum_probs=57.5

Q ss_pred             CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccCCCCC
Q psy11996        138 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNVIP  202 (222)
Q Consensus       138 r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~~~~~  202 (222)
                      +..+|.+|+.+|+..|..++||+..+++.||..+||+..+|++||+|+|++.++..+........
T Consensus         8 ~k~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~~~~~~~~~   72 (76)
T d2ecba1           8 FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEIDESN   72 (76)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCCCCCCCC
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhHhhhcccCC
Confidence            33469999999999999999999999999999999999999999999999988877666555443

>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=99.72  E-value=3.3e-18  Score=102.89  Aligned_cols=50  Identities=26%  Similarity=0.339  Sum_probs=48.8

Q ss_pred             CCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhh
Q psy11996        137 QRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR  186 (222)
Q Consensus       137 ~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR  186 (222)
                      +|+.||++|+.+|+..|..++||+..++..||.++||+..+|++||+|+|
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            48999999999999999999999999999999999999999999999997

>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=99.71  E-value=6.9e-18  Score=110.33  Aligned_cols=57  Identities=21%  Similarity=0.225  Sum_probs=51.8

Q ss_pred             CCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996         14 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK   70 (222)
Q Consensus        14 R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~   70 (222)
                      +..+|.+|+.+|+..|..++||+..+++.||..+||++.+|++||+|||++.++...
T Consensus         8 ~k~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~   64 (76)
T d2ecba1           8 FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEE   64 (76)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCS
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhH
Confidence            345699999999999999999999999999999999999999999999988766543

>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=99.70  E-value=9.9e-18  Score=110.51  Aligned_cols=61  Identities=20%  Similarity=0.185  Sum_probs=55.4

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhh----cCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996        131 NGETKRQRTSYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  191 (222)
Q Consensus       131 ~~~~~~~r~~~~~~q~~~L~~~F~~----~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk  191 (222)
                      .+..++.|+.||.+|+.+|+.+|+.    ++||+.++++.||.+|||+..+|++||+|+|++.++
T Consensus        14 ~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          14 GGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             ccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            3466788999999999999998886    789999999999999999999999999999987654

>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=99.70  E-value=2.1e-17  Score=108.08  Aligned_cols=57  Identities=19%  Similarity=0.239  Sum_probs=53.5

Q ss_pred             CCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996        137 QRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH  193 (222)
Q Consensus       137 ~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~  193 (222)
                      .+..+|.+|+.+|+.+|..++||+..++..||..+||+..+|++||+|+|+++|+..
T Consensus         6 ~~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~~   62 (76)
T d2ecca1           6 SGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ   62 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhch
Confidence            455789999999999999999999999999999999999999999999999999853

>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=99.70  E-value=1.8e-17  Score=107.47  Aligned_cols=59  Identities=29%  Similarity=0.530  Sum_probs=55.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHhh---hCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996         10 TKRQRTSYTRYQTLELEKEFH---FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE   68 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~---~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~   68 (222)
                      +||+|+.|+.+|+.+|+.+|.   .++||+..+++.||..+||+..||++||+|+|++.++.
T Consensus         1 ~rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~   62 (73)
T d1pufb_           1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN   62 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhccc
Confidence            367899999999999999997   48899999999999999999999999999999998874

>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=99.70  E-value=2.6e-17  Score=107.61  Aligned_cols=57  Identities=19%  Similarity=0.231  Sum_probs=53.4

Q ss_pred             CCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996         12 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE   68 (222)
Q Consensus        12 r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~   68 (222)
                      ..+..||.+|+.+|+.+|..++||+..+++.||..+||++.+|++||+|+|++.|+.
T Consensus         5 s~~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~   61 (76)
T d2ecca1           5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhc
Confidence            345578999999999999999999999999999999999999999999999999874

>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=99.67  E-value=5.4e-17  Score=105.22  Aligned_cols=59  Identities=29%  Similarity=0.514  Sum_probs=55.2

Q ss_pred             CCCCCcCCHHHHHHHHHhhh---hcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996        135 KRQRTSYTRYQTLELEKEFH---FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH  193 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F~---~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~  193 (222)
                      ++.|+.|+++|+.+|+.+|.   .++||+..+++.||..+||+..||.+||+|+|++.++..
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            56789999999999999997   488999999999999999999999999999999998754

>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=99.65  E-value=2.6e-17  Score=107.50  Aligned_cols=55  Identities=18%  Similarity=0.250  Sum_probs=51.9

Q ss_pred             CCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhC---------------------CChHHHHHHhhcchhHHHHH
Q psy11996         14 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC---------------------LTERQIKIWFQNRRMKWKKE   68 (222)
Q Consensus        14 R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~---------------------l~~~~v~~WF~nrR~k~~~~   68 (222)
                      |++||++|+.+|+..|+.++||+..+++.||.+++                     |++.+|++||+|||++.+++
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr~   76 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFR   76 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCC
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHHh
Confidence            68999999999999999999999999999999994                     99999999999999998764

>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=99.65  E-value=2.7e-17  Score=99.18  Aligned_cols=50  Identities=28%  Similarity=0.345  Sum_probs=46.5

Q ss_pred             CHHHHHHHHHhhhh-cCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996        142 TRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  191 (222)
Q Consensus       142 ~~~q~~~L~~~F~~-~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk  191 (222)
                      |.+|..+|+.+|.. ++||+..+++.||..+||+.++|++||+|||+++|+
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            45799999999976 789999999999999999999999999999999875

>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=99.65  E-value=4.4e-17  Score=106.37  Aligned_cols=56  Identities=20%  Similarity=0.281  Sum_probs=52.5

Q ss_pred             CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcC---------------------CChhhHHHHHhhhhhhHHHhh
Q psy11996        138 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC---------------------LTERQIKIWFQNRRMKWKKEH  193 (222)
Q Consensus       138 r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~---------------------l~~~~V~~WF~nrR~k~kk~~  193 (222)
                      |+.|+++|+.+|+..|+.++||+..+++.||.+++                     |++.+|++||+|||++.|+..
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            57899999999999999999999999999999994                     899999999999999998764

>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=99.63  E-value=4.2e-17  Score=98.34  Aligned_cols=50  Identities=28%  Similarity=0.345  Sum_probs=46.2

Q ss_pred             CHHHHHHHHHHhhh-CCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996         18 TRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus        18 t~~q~~~L~~~f~~-~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      |.+|..+||..|.. ++||+..+++.||..+||++++|++||+|||+++|+
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            46799999999987 789999999999999999999999999999998764

>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=99.63  E-value=5.4e-16  Score=96.99  Aligned_cols=57  Identities=25%  Similarity=0.270  Sum_probs=52.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHH
Q psy11996         10 TKRQRTSYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK   66 (222)
Q Consensus        10 ~~r~R~~~t~~q~~~L~~~f~~---~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~   66 (222)
                      +|++|+.|+.+++.+|+.+|..   +|||+..++..||..+||+..||.+||+|+|.+..
T Consensus         2 ~krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R~l   61 (62)
T d1x2na1           2 GKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRIL   61 (62)
T ss_dssp             SCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhc
Confidence            4567889999999999999985   78999999999999999999999999999998754

>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=99.61  E-value=6.4e-16  Score=96.11  Aligned_cols=53  Identities=32%  Similarity=0.387  Sum_probs=48.9

Q ss_pred             CcCCHHHHHHHHHhhhh---cCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996        139 TSYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  191 (222)
Q Consensus       139 ~~~~~~q~~~L~~~F~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk  191 (222)
                      ..|+.+|+.+|+.+|..   ++||+.++++.||..+||+..||++||+|+|++.|.
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            34999999999999976   479999999999999999999999999999998775

>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=99.61  E-value=1.4e-16  Score=98.53  Aligned_cols=55  Identities=25%  Similarity=0.367  Sum_probs=51.0

Q ss_pred             CCCCCCCHHHHHHHHHHhhh-CCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHH
Q psy11996         12 RQRTSYTRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK   66 (222)
Q Consensus        12 r~R~~~t~~q~~~L~~~f~~-~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~   66 (222)
                      +.+++++.++..+||.+|.. ++||+..+++.||..+||++++|++||+|||+++|
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 68999999999999999999999999999999865

>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=9.2e-16  Score=95.37  Aligned_cols=52  Identities=33%  Similarity=0.397  Sum_probs=48.1

Q ss_pred             CCCHHHHHHHHHHhhhC---CCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996         16 SYTRYQTLELEKEFHFN---RYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK   67 (222)
Q Consensus        16 ~~t~~q~~~L~~~f~~~---~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~   67 (222)
                      +|+.+|+.+|+.+|..+   +||+..+++.||..+||+..+|++||+|+|++.+.
T Consensus         4 Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           4 RFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             SCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            49999999999999764   79999999999999999999999999999987654

>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=1.5e-15  Score=94.90  Aligned_cols=56  Identities=25%  Similarity=0.281  Sum_probs=51.7

Q ss_pred             CCCCCcCCHHHHHHHHHhhhh---cCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHH
Q psy11996        135 KRQRTSYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK  190 (222)
Q Consensus       135 ~~~r~~~~~~q~~~L~~~F~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k  190 (222)
                      +++|+.|+++++.+|+.+|..   ++||+..++..||..+||+..||.+||+|+|.+..
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            556789999999999999985   89999999999999999999999999999998764

>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=99.59  E-value=3.3e-16  Score=96.88  Aligned_cols=55  Identities=25%  Similarity=0.367  Sum_probs=49.8

Q ss_pred             CCCCcCCHHHHHHHHHhhhh-cCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHH
Q psy11996        136 RQRTSYTRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK  190 (222)
Q Consensus       136 ~~r~~~~~~q~~~L~~~F~~-~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k  190 (222)
                      +.+..+..++..+|+.+|.. ++||+..+++.||..+||+..+|++||+|||+++|
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            34567778888999999986 68999999999999999999999999999999976

>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=92.30  E-value=0.45  Score=28.16  Aligned_cols=50  Identities=20%  Similarity=0.201  Sum_probs=40.7

Q ss_pred             CCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHH
Q psy11996         14 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK   66 (222)
Q Consensus        14 R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~   66 (222)
                      |..+|-.+...+-..|+.++..+   ..++|..+|+....|..|..|+..-..
T Consensus         5 Rk~LT~~eK~~ii~~~e~g~k~s---q~eIA~~fGv~~STvs~IlKnK~kil~   54 (66)
T d1hlva1           5 RRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNKRAILA   54 (66)
T ss_dssp             SCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTHHHHHH
T ss_pred             cccCCHHHHHHHHHHHHcCCcch---HHHHHHHhCCChhHHHHHHHHHHHHHH
Confidence            55799999888889999987554   567899999999999999988654433

>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=92.08  E-value=0.16  Score=28.07  Aligned_cols=41  Identities=7%  Similarity=0.152  Sum_probs=35.5

Q ss_pred             CCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhh
Q psy11996         14 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ   59 (222)
Q Consensus        14 R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~   59 (222)
                      +..+|++|+..+...+....     ...++|..+|++...|..||.
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            35799999999999998764     277899999999999999984

>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=90.71  E-value=0.16  Score=28.11  Aligned_cols=41  Identities=7%  Similarity=0.152  Sum_probs=34.9

Q ss_pred             CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHh
Q psy11996        138 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ  183 (222)
Q Consensus       138 r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~  183 (222)
                      +..+|++|+..+...+....     .+..||..+|++..-|..||-
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            46799999999999997652     377889999999999999983

>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=90.37  E-value=0.46  Score=28.15  Aligned_cols=50  Identities=20%  Similarity=0.214  Sum_probs=39.8

Q ss_pred             CCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhH
Q psy11996        137 QRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW  189 (222)
Q Consensus       137 ~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~  189 (222)
                      +|..+|..+...+...|+.++..+   ..+||..+||....|..|..|+..=.
T Consensus         4 kRk~LT~~eK~~ii~~~e~g~k~s---q~eIA~~fGv~~STvs~IlKnK~kil   53 (66)
T d1hlva1           4 KRRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNKRAIL   53 (66)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTHHHHH
T ss_pred             ccccCCHHHHHHHHHHHHcCCcch---HHHHHHHhCCChhHHHHHHHHHHHHH
Confidence            355789988888888888886554   45679999999999999999875443