Psyllid ID: psy9869

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-
Protein Sequence
MYATFSSDLMTNLEDEGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELNEQEKQAQAQKAAAAALAAAAVDH
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHcccHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
ccccHHEEEEccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHccHHccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MYATFSSDLMTNLEDeganglrrrgrqtyTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELNEQEKQAQAQKAAAAALAAAAVDH
Flexible Loop (DISEMBL)
myatfssdlMTNLedeganglrrrgrqtytryqtlelekefhtnhyltrrRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELNEQEKQAQAQKAAAAALAAAAVDH
Low Complexity Region (SEG)
MYATFSSDLMTNLEDEGANglrrrgrqtytryqtlELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELNeqekqaqaqkaaaaalaaaaVDH
Disordered region (IsUnstruct)
*******************************YQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK*********************************
Disordered Region (DISOPRED)
MYAT************************YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRR*************************************
Disordered Region (DISEMBL)
MYATFSSDLMTNLEDEGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN***********************
Disordered Region (DISPRO)
MYATFSSDLMTNL************RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI******************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MYATFSSDLMTNLEDEGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxAVDH
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	111	2.2.26 [Sep-21-2011]
Q8T940	253	Homeotic protein ultrabit	N/A	N/A	0.837	0.367	0.978	4e-47
P83950	389	Homeotic protein ultrabit	N/A	N/A	0.648	0.185	0.986	1e-37
P83949	389	Homeotic protein ultrabit	yes	N/A	0.648	0.185	0.986	1e-37
P20822	385	Homeotic protein ultrabit	yes	N/A	0.648	0.187	0.986	2e-37
O76762	308	Homeobox protein abdomina	no	N/A	0.765	0.275	0.752	9e-35
B0W1V2	216	Homeobox protein abdomina	N/A	N/A	0.801	0.412	0.744	2e-33
P29552	239	Homeobox protein abdomina	N/A	N/A	0.666	0.309	0.866	6e-33
Q05007	139	Homeobox protein abdomina	N/A	N/A	0.657	0.525	0.878	1e-32
P29555	590	Homeobox protein abdomina	no	N/A	0.783	0.147	0.75	3e-32
P29556	157	Homeobox protein abdomina	N/A	N/A	0.657	0.464	0.864	1e-31

>sp|Q8T940|UBX_JUNCO Homeotic protein ultrabithorax OS=Junonia coenia GN=Ubx PE=2 SV=1

 Score =  186 bits (471), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 91/93 (97%), Positives = 91/93 (97%)

Query: 17  GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76
           GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct: 154 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 213

Query: 77  LKKEIQAIKELNEQEKQAQAQKAAAAALAAAAV 109
           LKKEIQAIKELNEQEKQAQAQKAAAAA AAAA 
Sbjct: 214 LKKEIQAIKELNEQEKQAQAQKAAAAAAAAAAA 246

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 the consensus region 5'-TTAAT[GT][GA]-3'. This homeotic protein controls development of the cells in the posterior thoracic and first abdominal segments.
Junonia coenia (taxid: 39708)

>sp|P83950|UBX_DROSI Homeotic protein ultrabithorax OS=Drosophila simulans GN=Ubx PE=3 SV=1

 Score =  154 bits (389), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 71/72 (98%), Positives = 71/72 (98%)

Query: 17  GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76
           G NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct: 290 GTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 349

Query: 77  LKKEIQAIKELN 88
           LKKEIQAIKELN
Sbjct: 350 LKKEIQAIKELN 361

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 the consensus region 5'-TTAAT[GT][GA]-3'. This homeotic protein controls development of the cells in the posterior thoracic and first abdominal segments. It activates the synthesis of the decapentaplegic (DPP) growth factor.

Drosophila simulans (taxid: 7240)

>sp|P83949|UBX_DROME Homeotic protein ultrabithorax OS=Drosophila melanogaster GN=Ubx PE=1 SV=1

 Score =  154 bits (389), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 71/72 (98%), Positives = 71/72 (98%)

Query: 17  GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76
           G NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct: 290 GTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 349

Query: 77  LKKEIQAIKELN 88
           LKKEIQAIKELN
Sbjct: 350 LKKEIQAIKELN 361

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 the consensus region 5'-TTAAT[GT][GA]-3'. This homeotic protein controls development of the cells in the posterior thoracic and first abdominal segments. It activates the synthesis of the decapentaplegic (DPP) growth factor.

Drosophila melanogaster (taxid: 7227)

>sp|P20822|UBX_DROPS Homeotic protein ultrabithorax OS=Drosophila pseudoobscura pseudoobscura GN=Ubx PE=2 SV=3

 Score =  154 bits (388), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 71/72 (98%), Positives = 71/72 (98%)

Query: 17  GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76
           G NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct: 285 GTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 344

Query: 77  LKKEIQAIKELN 88
           LKKEIQAIKELN
Sbjct: 345 LKKEIQAIKELN 356

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 the consensus region 5'-TTAAT[GT][GA]-3'. This homeotic protein controls development of the cells in the posterior thoracic and first abdominal segments. It activates the synthesis of the decapentaplegic (DPP) growth factor.

Drosophila pseudoobscura pseudoobscura (taxid: 46245)

>sp|O76762|ABDA_ANOGA Homeobox protein abdominal-A homolog OS=Anopheles gambiae GN=abd-A PE=2 SV=1

 Score =  145 bits (365), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 70/93 (75%), Positives = 78/93 (83%), Gaps = 8/93 (8%)

Query: 6   SSDLMTNLEDE-------GANGL-RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAH 57
           S+D M+N  D        G NG  RRRGRQTYTR+QTLELEKEFH NHYLTRRRRIE+AH
Sbjct: 114 STDWMSNPFDRVVCGDFAGPNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAH 173

Query: 58  ALCLTERQIKIWFQNRRMKLKKEIQAIKELNEQ 90
           ALCLTERQIKIWFQNRRMKLKKE++A+KE+NEQ
Sbjct: 174 ALCLTERQIKIWFQNRRMKLKKELRAVKEINEQ 206

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

Anopheles gambiae (taxid: 7165)

>sp|B0W1V2|ABDA_CULQU Homeobox protein abdominal-A homolog OS=Culex quinquefasciatus GN=abd-A PE=3 SV=1

 Score =  140 bits (354), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 67/90 (74%), Positives = 77/90 (85%), Gaps = 1/90 (1%)

Query: 5   FSSDLMTNLEDEGANGL-RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTE 63
            +S L+  L     NG  RRRGRQTYTR+QTLELEKEFH NHYLTRRRRIE+AHALCLTE
Sbjct: 25  IASPLLGRLRPRRPNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTE 84

Query: 64  RQIKIWFQNRRMKLKKEIQAIKELNEQEKQ 93
           RQIKIWFQNRRMKLKKE++A+KE+NEQ ++
Sbjct: 85  RQIKIWFQNRRMKLKKELRAVKEINEQARR 114

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

Culex quinquefasciatus (taxid: 7176)

>sp|P29552|ABDA_AEDAE Homeobox protein abdominal-A homolog OS=Aedes aegypti GN=abd-A PE=3 SV=2

 Score =  139 bits (349), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 65/75 (86%), Positives = 71/75 (94%), Gaps = 1/75 (1%)

Query: 17 GANGL-RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 75
          G NG  RRRGRQTYTR+QTLELEKEFH NHYLTRRRRIE+AHALCLTERQIKIWFQNRRM
Sbjct: 15 GPNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRM 74

Query: 76 KLKKEIQAIKELNEQ 90
          KLKKE++A+KE+NEQ
Sbjct: 75 KLKKELRAVKEINEQ 89

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

Aedes aegypti (taxid: 7159)

>sp|Q05007|ABDA_ARTSF Homeobox protein abdominal-A homolog (Fragment) OS=Artemia franciscana GN=ABDA PE=3 SV=1

 Score =  137 bits (346), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 65/74 (87%), Positives = 70/74 (94%), Gaps = 1/74 (1%)

Query: 18 ANGL-RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76
           NG  RRRGRQTYTRYQTLELEKEFH NHYLTRRRRIE+AHALCLTERQIKIWFQNRRMK
Sbjct: 1  PNGCPRRRGRQTYTRYQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 60

Query: 77 LKKEIQAIKELNEQ 90
          LKKE++A+KE+NEQ
Sbjct: 61 LKKELRAVKEINEQ 74

Required for segmental identity of the second through eighth abdominal segments. Once a pattern of abdA expression is turned on in a given parasegment, it remains on the more posterior parasegment, so that the complex pattern of expression is built up in the successive parasegments. The abdA product appears to repress expression of Ubx whenever they appear in the same cell, but abdA is repressed by AbdB only in the eight and ninth abdominal segments.

Artemia franciscana (taxid: 6661)

>sp|P29555|ABDA_DROME Homeobox protein abdominal-A OS=Drosophila melanogaster GN=abd-A PE=2 SV=2

 Score =  137 bits (344), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 66/88 (75%), Positives = 77/88 (87%), Gaps = 1/88 (1%)

Query: 17  GANGL-RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 75
           G NG  RRRGRQTYTR+QTLELEKEFH NHYLTRRRRIE+AHALCLTERQIKIWFQNRRM
Sbjct: 392 GPNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRM 451

Query: 76  KLKKEIQAIKELNEQEKQAQAQKAAAAA 103
           KLKKE++A+KE+NEQ ++ + ++    A
Sbjct: 452 KLKKELRAVKEINEQARRDREEQEKMKA 479

Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Required for segmental identity of the second through eighth abdominal segments. Once a pattern of abd-A expression is turned on in a given parasegment, it remains on the more posterior parasegment, so that the complex pattern of expression is built up in the successive parasegments. Appears to repress expression of Ubx whenever they appear in the same cell, but abd-A is repressed by Abd-B only in the eight and ninth abdominal segments.

Drosophila melanogaster (taxid: 7227)

>sp|P29556|ABDA_SCHGR Homeobox protein abdominal-A homolog (Fragment) OS=Schistocerca gregaria GN=ABD-A PE=3 SV=1

 Score =  135 bits (339), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 64/74 (86%), Positives = 70/74 (94%), Gaps = 1/74 (1%)

Query: 18 ANGL-RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76
           NG  RRRGRQTYTR+QTLELEKEFH NHYLTRRRRIE+AHALCLTERQIKIWFQNRRMK
Sbjct: 1  PNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 60

Query: 77 LKKEIQAIKELNEQ 90
          LKKE++A+KE+NEQ
Sbjct: 61 LKKELRAVKEINEQ 74

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

Schistocerca gregaria (taxid: 7010)

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	111
345489354	345	PREDICTED: homeotic protein ultrabithora	0.828	0.266	0.989	7e-47
164682494	254	homeobox protein [Bombyx mori]	0.837	0.366	0.989	4e-46
166429526	254	ultrabithorax [Bombyx mori] gi|164682496	0.837	0.366	0.978	1e-45
426432569	254	ultrabithorax [Biston betularia]	0.837	0.366	0.978	2e-45
47115878	253	RecName: Full=Homeotic protein ultrabith	0.837	0.367	0.978	2e-45
195349282	201	GM15411 [Drosophila sechellia] gi|194122	0.819	0.452	0.989	8e-45
392301341	105	ultrabithorax, partial [Notonecta undula	0.810	0.857	1.0	7e-44
87042406	267	ultrabithorax [Strigamia maritima]	0.765	0.318	0.964	2e-42
109944946	248	Ultrabithorax [Porcellio scaber]	0.846	0.379	0.868	1e-41
391339782	178	PREDICTED: homeotic protein ultrabithora	0.828	0.516	0.891	1e-41

>gi|345489354|ref|XP_001603621.2| PREDICTED: homeotic protein ultrabithorax-like [Nasonia vitripennis]

 Score =  191 bits (484), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 91/92 (98%), Positives = 91/92 (98%)

Query: 17  GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76
           GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct: 243 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 302

Query: 77  LKKEIQAIKELNEQEKQAQAQKAAAAALAAAA 108
           LKKEIQAIKELNEQEKQAQAQKAAAAA AAAA
Sbjct: 303 LKKEIQAIKELNEQEKQAQAQKAAAAAAAAAA 334

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|164682494|gb|ABY66344.1| homeobox protein [Bombyx mori]

 Score =  188 bits (477), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 92/93 (98%), Positives = 92/93 (98%)

Query: 17  GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76
           GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct: 155 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 214

Query: 77  LKKEIQAIKELNEQEKQAQAQKAAAAALAAAAV 109
           LKKEIQAIKELNEQEKQAQAQKAAAAA AAAAV
Sbjct: 215 LKKEIQAIKELNEQEKQAQAQKAAAAAAAAAAV 247

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|166429526|ref|NP_001107632.1| ultrabithorax [Bombyx mori] gi|164682496|gb|ABY66345.1| homeobox protein [Bombyx mori] gi|284924982|dbj|BAI67747.1| Ultrabithorax [Bombyx mori]

 Score =  186 bits (473), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 91/93 (97%), Positives = 91/93 (97%)

Query: 17  GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76
           GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct: 155 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 214

Query: 77  LKKEIQAIKELNEQEKQAQAQKAAAAALAAAAV 109
           LKKEIQAIKELNEQEKQAQAQKAAAAA AAAA 
Sbjct: 215 LKKEIQAIKELNEQEKQAQAQKAAAAAAAAAAA 247

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|426432569|gb|ADO33070.2| ultrabithorax [Biston betularia]

 Score =  186 bits (472), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 91/93 (97%), Positives = 91/93 (97%)

Query: 17  GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76
           GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct: 155 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 214

Query: 77  LKKEIQAIKELNEQEKQAQAQKAAAAALAAAAV 109
           LKKEIQAIKELNEQEKQAQAQKAAAAA AAAA 
Sbjct: 215 LKKEIQAIKELNEQEKQAQAQKAAAAAAAAAAA 247

Source: Biston betularia

Species: Biston betularia

Genus: Biston

Family: Geometridae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|47115878|sp|Q8T940.1|UBX_JUNCO RecName: Full=Homeotic protein ultrabithorax; AltName: Full=JcUbx gi|18535620|gb|AAL71873.1| ultrabithorax [Junonia coenia]

 Score =  186 bits (471), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 91/93 (97%), Positives = 91/93 (97%)

Query: 17  GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76
           GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct: 154 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 213

Query: 77  LKKEIQAIKELNEQEKQAQAQKAAAAALAAAAV 109
           LKKEIQAIKELNEQEKQAQAQKAAAAA AAAA 
Sbjct: 214 LKKEIQAIKELNEQEKQAQAQKAAAAAAAAAAA 246

Source: Junonia coenia

Species: Junonia coenia

Genus: Junonia

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195349282|ref|XP_002041174.1| GM15411 [Drosophila sechellia] gi|194122779|gb|EDW44822.1| GM15411 [Drosophila sechellia]

 Score =  184 bits (466), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 90/91 (98%), Positives = 90/91 (98%)

Query: 19  NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 78
           NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK
Sbjct: 104 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 163

Query: 79  KEIQAIKELNEQEKQAQAQKAAAAALAAAAV 109
           KEIQAIKELNEQEKQAQAQKAAAAA AAAAV
Sbjct: 164 KEIQAIKELNEQEKQAQAQKAAAAAAAAAAV 194

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|392301341|gb|AFM55056.1| ultrabithorax, partial [Notonecta undulata]

 Score =  181 bits (458), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 90/90 (100%), Positives = 90/90 (100%)

Query: 17  GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76
           GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct: 9   GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 68

Query: 77  LKKEIQAIKELNEQEKQAQAQKAAAAALAA 106
           LKKEIQAIKELNEQEKQAQAQKAAAAALAA
Sbjct: 69  LKKEIQAIKELNEQEKQAQAQKAAAAALAA 98

Source: Notonecta undulata

Species: Notonecta undulata

Genus: Notonecta

Family: Notonectidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|87042406|gb|ABD16212.1| ultrabithorax [Strigamia maritima]

 Score =  175 bits (444), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 82/85 (96%), Positives = 82/85 (96%)

Query: 17  GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76
           GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct: 161 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 220

Query: 77  LKKEIQAIKELNEQEKQAQAQKAAA 101
           LKKEIQAIKELNEQEKQAQ  K AA
Sbjct: 221 LKKEIQAIKELNEQEKQAQTAKTAA 245

Source: Strigamia maritima

Species: Strigamia maritima

Genus: Strigamia

Family: Linotaeniidae

Order: Geophilomorpha

Class: Chilopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|109944946|dbj|BAE97002.1| Ultrabithorax [Porcellio scaber]

 Score =  173 bits (439), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 86/99 (86%), Positives = 88/99 (88%), Gaps = 5/99 (5%)

Query: 17  GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76
           GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct: 127 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 186

Query: 77  LKKEIQAIKELNEQEKQAQAQKAAAAA-----LAAAAVD 110
           LKKEIQAIKELNEQEKQAQ QK    A      +AAAV+
Sbjct: 187 LKKEIQAIKELNEQEKQAQNQKIQQQAQQSQQPSAAAVN 225

Source: Porcellio scaber

Species: Porcellio scaber

Genus: Porcellio

Family: Porcellionidae

Order: Isopoda

Class: Malacostraca

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|391339782|ref|XP_003744226.1| PREDICTED: homeotic protein ultrabithorax-like [Metaseiulus occidentalis]

 Score =  173 bits (438), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 82/92 (89%), Positives = 86/92 (93%)

Query: 17  GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76
           GA+GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct: 80  GASGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 139

Query: 77  LKKEIQAIKELNEQEKQAQAQKAAAAALAAAA 108
           LKKEIQAIKELNEQE+QAQA KAA+  +  A 
Sbjct: 140 LKKEIQAIKELNEQERQAQAAKAASMGINGAG 171

Source: Metaseiulus occidentalis

Species: Metaseiulus occidentalis

Genus: Metaseiulus

Family: Phytoseiidae

Order: Mesostigmata

Class: Arachnida

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	111
UNIPROTKB|Q8T940	253	Ubx "Homeotic protein ultrabit	0.648	0.284	0.777	1.6e-24
FB|FBgn0003944	389	Ubx "Ultrabithorax" [Drosophil	0.477	0.136	1.0	3.3e-24
UNIPROTKB|P20822	385	Ubx "Homeotic protein ultrabit	0.477	0.137	1.0	3.3e-24
UNIPROTKB|P83950	389	Ubx "Homeotic protein ultrabit	0.477	0.136	1.0	3.3e-24
UNIPROTKB|Q6VPU7	387	Ubx "Ultrabithorax" [Drosophil	0.477	0.136	1.0	3.3e-24
UNIPROTKB|B0W1V2	216	abd-A "Homeobox protein abdomi	0.477	0.245	0.886	4.3e-22
UNIPROTKB|O76762	308	abd-A "Homeobox protein abdomi	0.477	0.172	0.886	4.3e-22
UNIPROTKB|P29552	239	abd-A "Homeobox protein abdomi	0.477	0.221	0.886	4.3e-22
FB|FBgn0000014	590	abd-A "abdominal A" [Drosophil	0.477	0.089	0.886	3.1e-21
ZFIN|ZDB-GENE-000823-7	224	hoxb6b "homeo box B6b" [Danio	0.441	0.218	0.836	7.5e-18

UNIPROTKB|Q8T940 Ubx "Homeotic protein ultrabithorax" [Junonia coenia (taxid:39708)]

 Score = 280 (103.6 bits), Expect = 1.6e-24, P = 1.6e-24
 Identities = 56/72 (77%), Positives = 56/72 (77%)

Query:    17 GANXXXXXXXXXXXXXXXXELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76
             GAN                ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct:   154 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 213

Query:    77 LKKEIQAIKELN 88
             LKKEIQAIKELN
Sbjct:   214 LKKEIQAIKELN 225

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

GO:0005634 "nucleus" evidence=IDA

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

FB|FBgn0003944 Ubx "Ultrabithorax" [Drosophila melanogaster (taxid:7227)]

 Score = 277 (102.6 bits), Expect = 3.3e-24, P = 3.3e-24
 Identities = 53/53 (100%), Positives = 53/53 (100%)

Query:    36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN 88
             ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN
Sbjct:   309 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN 361

GO:0005634 "nucleus" evidence=ISS;NAS;IDA

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

GO:0003677 "DNA binding" evidence=IDA

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

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

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

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

GO:0019904 "protein domain specific binding" evidence=IPI

GO:0010092 "specification of organ identity" evidence=IMP

GO:0007482 "haltere development" evidence=IMP

GO:0007494 "midgut development" evidence=TAS

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

GO:0007384 "specification of segmental identity, thorax" evidence=IMP;NAS

GO:0001706 "endoderm formation" evidence=TAS

GO:0007507 "heart development" evidence=IEP;IMP

GO:0007501 "mesodermal cell fate specification" evidence=IMP

GO:0007480 "imaginal disc-derived leg morphogenesis" evidence=IMP

GO:0035052 "dorsal vessel aortic cell fate commitment" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

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

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

GO:0045570 "regulation of imaginal disc growth" evidence=IMP

GO:0048636 "positive regulation of muscle organ development" evidence=IMP

GO:0001709 "cell fate determination" evidence=IGI;IMP

GO:0042694 "muscle cell fate specification" evidence=IMP

GO:0061327 "anterior Malpighian tubule development" evidence=IMP

GO:0060969 "negative regulation of gene silencing" evidence=IDA

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

GO:0007525 "somatic muscle development" evidence=IMP

UNIPROTKB|P20822 Ubx "Homeotic protein ultrabithorax" [Drosophila pseudoobscura pseudoobscura (taxid:46245)]

 Score = 277 (102.6 bits), Expect = 3.3e-24, P = 3.3e-24
 Identities = 53/53 (100%), Positives = 53/53 (100%)

Query:    36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN 88
             ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN
Sbjct:   304 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN 356

GO:0003677 "DNA binding" evidence=TAS

UNIPROTKB|P83950 Ubx "Homeotic protein ultrabithorax" [Drosophila simulans (taxid:7240)]

 Score = 277 (102.6 bits), Expect = 3.3e-24, P = 3.3e-24
 Identities = 53/53 (100%), Positives = 53/53 (100%)

Query:    36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN 88
             ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN
Sbjct:   309 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN 361

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

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

UNIPROTKB|Q6VPU7 Ubx "Ultrabithorax" [Drosophila virilis (taxid:7244)]

 Score = 277 (102.6 bits), Expect = 3.3e-24, P = 3.3e-24
 Identities = 53/53 (100%), Positives = 53/53 (100%)

Query:    36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN 88
             ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN
Sbjct:   306 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN 358

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

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

UNIPROTKB|B0W1V2 abd-A "Homeobox protein abdominal-A homolog" [Culex quinquefasciatus (taxid:7176)]

 Score = 257 (95.5 bits), Expect = 4.3e-22, P = 4.3e-22
 Identities = 47/53 (88%), Positives = 52/53 (98%)

Query:    36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN 88
             ELEKEFH NHYLTRRRRIE+AHALCLTERQIKIWFQNRRMKLKKE++A+KE+N
Sbjct:    57 ELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELRAVKEIN 109

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

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

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

UNIPROTKB|O76762 abd-A "Homeobox protein abdominal-A homolog" [Anopheles gambiae (taxid:7165)]

 Score = 257 (95.5 bits), Expect = 4.3e-22, P = 4.3e-22
 Identities = 47/53 (88%), Positives = 52/53 (98%)

Query:    36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN 88
             ELEKEFH NHYLTRRRRIE+AHALCLTERQIKIWFQNRRMKLKKE++A+KE+N
Sbjct:   152 ELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELRAVKEIN 204

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

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

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

UNIPROTKB|P29552 abd-A "Homeobox protein abdominal-A homolog" [Aedes aegypti (taxid:7159)]

 Score = 257 (95.5 bits), Expect = 4.3e-22, P = 4.3e-22
 Identities = 47/53 (88%), Positives = 52/53 (98%)

Query:    36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN 88
             ELEKEFH NHYLTRRRRIE+AHALCLTERQIKIWFQNRRMKLKKE++A+KE+N
Sbjct:    35 ELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELRAVKEIN 87

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

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

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

FB|FBgn0000014 abd-A "abdominal A" [Drosophila melanogaster (taxid:7227)]

 Score = 257 (95.5 bits), Expect = 3.1e-21, P = 3.1e-21
 Identities = 47/53 (88%), Positives = 52/53 (98%)

Query:    36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN 88
             ELEKEFH NHYLTRRRRIE+AHALCLTERQIKIWFQNRRMKLKKE++A+KE+N
Sbjct:   412 ELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELRAVKEIN 464

GO:0005634 "nucleus" evidence=NAS;IDA

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

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

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

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

GO:0008406 "gonad development" evidence=NAS;TAS

GO:0007422 "peripheral nervous system development" evidence=TAS

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

GO:0007506 "gonadal mesoderm development" evidence=IMP

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

GO:0007280 "pole cell migration" evidence=TAS

GO:0007494 "midgut development" evidence=TAS

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

GO:0007438 "oenocyte development" evidence=IMP

GO:0035053 "dorsal vessel heart proper cell fate commitment" evidence=IEP;IMP;TAS

GO:0007507 "heart development" evidence=IMP

GO:0007501 "mesodermal cell fate specification" evidence=IMP

GO:0007399 "nervous system development" evidence=IMP

GO:0006915 "apoptotic process" evidence=IMP

GO:0009987 "cellular process" evidence=IMP

GO:0007400 "neuroblast fate determination" evidence=IMP

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

GO:0048806 "genitalia development" evidence=IMP

GO:0010002 "cardioblast differentiation" evidence=IMP

GO:0048738 "cardiac muscle tissue development" evidence=IMP

GO:0005667 "transcription factor complex" evidence=IPI

GO:0003705 "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" evidence=IDA

GO:0014019 "neuroblast development" evidence=IMP

GO:0048636 "positive regulation of muscle organ development" evidence=IMP

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

GO:0042694 "muscle cell fate specification" evidence=IMP

ZFIN|ZDB-GENE-000823-7 hoxb6b "homeo box B6b" [Danio rerio (taxid:7955)]

 Score = 217 (81.4 bits), Expect = 7.5e-18, P = 7.5e-18
 Identities = 41/49 (83%), Positives = 45/49 (91%)

Query:    36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAI 84
             ELEKEFH N YLTRRRRIE++HALCLTERQIKIWFQNRRMK KKE +A+
Sbjct:   161 ELEKEFHFNRYLTRRRRIEISHALCLTERQIKIWFQNRRMKWKKENKAV 209

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P20822	UBX_DROPS	No assigned EC number	0.9861	0.6486	0.1870	yes	N/A
P15856	ABDA_APIME	No assigned EC number	0.8513	0.6576	0.9864	no	N/A
Q24645	ANTP_DROSU	No assigned EC number	0.9152	0.5315	0.1497	N/A	N/A
A2T7F3	HXA7_PANTR	No assigned EC number	0.9152	0.5315	0.2565	no	N/A
P09023	HXB6_MOUSE	No assigned EC number	0.8142	0.6126	0.3035	yes	N/A
P02833	ANTP_DROME	No assigned EC number	0.9152	0.5315	0.1560	no	N/A
P83950	UBX_DROSI	No assigned EC number	0.9861	0.6486	0.1850	N/A	N/A
Q8T940	UBX_JUNCO	No assigned EC number	0.9784	0.8378	0.3675	N/A	N/A
P21523	HLOX2_HIRME	No assigned EC number	0.8450	0.6396	0.6016	N/A	N/A
P24061	HXA7_COTJA	No assigned EC number	0.9152	0.5315	0.2438	N/A	N/A
A1YFA5	HXB7_GORGO	No assigned EC number	0.9152	0.5315	0.2718	N/A	N/A
Q26430	ABDA_MANSE	No assigned EC number	0.8648	0.6576	0.7525	N/A	N/A
Q9TT89	HXB7_BOVIN	No assigned EC number	0.9152	0.5315	0.2718	yes	N/A
Q9YGT4	HXB6B_DANRE	No assigned EC number	0.6867	0.7117	0.3526	yes	N/A
Q90VZ9	HXA7_CHICK	No assigned EC number	0.9152	0.5315	0.2694	no	N/A
P31268	HXA7_HUMAN	No assigned EC number	0.9152	0.5315	0.2565	no	N/A
P17509	HXB6_HUMAN	No assigned EC number	0.8142	0.6126	0.3035	yes	N/A
Q1KKX1	HXB6B_TAKRU	No assigned EC number	0.9137	0.5225	0.2489	N/A	N/A
P83949	UBX_DROME	No assigned EC number	0.9861	0.6486	0.1850	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	111
pfam00046	57	pfam00046, Homeobox, Homeobox domain	3e-23
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	9e-20
smart00389	57	smart00389, HOX, Homeodomain	3e-19
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	3e-09

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

 Score = 84.1 bits (209), Expect = 3e-23
 Identities = 32/57 (56%), Positives = 38/57 (66%)

Query: 23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          RR R T+T  Q  ELEKEF  N Y +   R E+A  L LTERQ+K+WFQNRR K K+
Sbjct: 1  RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57

Length = 57

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

 Score = 75.4 bits (186), Expect = 9e-20
 Identities = 34/58 (58%), Positives = 39/58 (67%)

Query: 23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          RR R  +T  Q  ELEKEF  N Y +R  R E+A  L LTERQ+KIWFQNRR KLK+ 
Sbjct: 1  RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58

Length = 59

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 73.8 bits (182), Expect = 3e-19
 Identities = 31/57 (54%), Positives = 39/57 (68%)

Query: 22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 78
          +RR R ++T  Q  ELEKEF  N Y +R  R E+A  L L+ERQ+K+WFQNRR K K
Sbjct: 1  KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

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

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

 Score = 50.9 bits (122), Expect = 3e-09
 Identities = 21/58 (36%), Positives = 35/58 (60%)

Query: 23  RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
           +  R+  T  Q + LE+EF  N Y +   RI+++  L +  + ++IWFQN+R K KK+
Sbjct: 52  KSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKK 109

Length = 156

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	111
KOG0488|consensus	309		99.73
KOG0489|consensus	261		99.73
KOG0487|consensus	308		99.72
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.71
KOG0850|consensus	245		99.71
KOG0843|consensus	197		99.7
KOG0484|consensus	125		99.7
KOG2251|consensus	228		99.7
KOG0485|consensus	268		99.67
KOG0842|consensus	307		99.64
KOG0492|consensus	246		99.63
KOG0848|consensus	317		99.62
KOG3802|consensus	398		99.62
KOG0494|consensus	332		99.61
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.58
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.57
COG5576	156	Homeodomain-containing transcription factor [Trans	99.57
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.57
KOG0493|consensus	342		99.55
KOG0491|consensus	194		99.48
KOG0483|consensus	198		99.46
KOG0486|consensus	351		99.42
KOG0844|consensus	408		99.38
KOG4577|consensus	383		99.35
KOG0847|consensus	288		99.34
KOG0490|consensus	235		99.15
KOG1168|consensus	385		99.15
KOG0849|consensus	354		99.06
KOG0775|consensus	304		99.04
KOG0774|consensus	334		98.92
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.71
KOG2252|consensus	558		98.4
KOG0490|consensus	235		98.14
KOG1146|consensus	1406		97.69
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	97.39
KOG0773|consensus	342		96.61
KOG3623|consensus	1007		95.69
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	95.46
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	87.34
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	80.72

>KOG0488|consensus

Probab=99.73  E-value=8.8e-18  Score=124.92  Aligned_cols=69  Identities=41%  Similarity=0.677  Sum_probs=63.5

Q ss_pred             cCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869          15 DEGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA   83 (111)
Q Consensus        15 ~~~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   83 (111)
                      ..+..+++|+.|+.||..|+..||..|+...|.+..+|..||..|||+..||++||||||+|||++...
T Consensus       165 ~~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~  233 (309)
T KOG0488|consen  165 QRSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE  233 (309)
T ss_pred             ccCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence            344457777889999999999999999999999999999999999999999999999999999997765

>KOG0489|consensus

Probab=99.73  E-value=4e-18  Score=124.32  Aligned_cols=67  Identities=72%  Similarity=1.034  Sum_probs=62.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHHH
Q psy9869          19 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK   85 (111)
Q Consensus        19 ~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~   85 (111)
                      .+..+|.|+.||..|+..||..|+.|.|.+...|.+||..|.|+++||+|||||||+|+||+++...
T Consensus       156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~  222 (261)
T KOG0489|consen  156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS  222 (261)
T ss_pred             cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence            3567899999999999999999999999999999999999999999999999999999999766533

>KOG0487|consensus

Probab=99.72  E-value=7.3e-18  Score=124.44  Aligned_cols=66  Identities=55%  Similarity=0.802  Sum_probs=61.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869          18 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA   83 (111)
Q Consensus        18 ~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   83 (111)
                      ..+..||+|.-+|+.|+..||..|..|.|.+...|.+|++.|+|+++||+|||||||.|+||.++.
T Consensus       231 ~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re  296 (308)
T KOG0487|consen  231 SARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRE  296 (308)
T ss_pred             cccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhh
Confidence            346778899999999999999999999999999999999999999999999999999999998753

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.71  E-value=2.8e-17  Score=93.94  Aligned_cols=57  Identities=49%  Similarity=0.701  Sum_probs=55.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869          23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   79 (111)
Q Consensus        23 r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   79 (111)
                      ++.|+.|+..|+..|+.+|..++||+..++..||..+||+..+|.+||+|+|.++||
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            578999999999999999999999999999999999999999999999999999986

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

>KOG0850|consensus

Probab=99.71  E-value=1.5e-17  Score=117.56  Aligned_cols=66  Identities=41%  Similarity=0.645  Sum_probs=61.3

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869          17 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   82 (111)
Q Consensus        17 ~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   82 (111)
                      +...+.|+.||-++..||..|+..|+.++|.-..||.+||..|||+..||+|||||||.|.||...
T Consensus       117 gk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k  182 (245)
T KOG0850|consen  117 GKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK  182 (245)
T ss_pred             CCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence            344566788999999999999999999999999999999999999999999999999999999766

>KOG0843|consensus

Probab=99.70  E-value=2.1e-17  Score=113.19  Aligned_cols=64  Identities=41%  Similarity=0.621  Sum_probs=60.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHH
Q psy9869          21 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAI   84 (111)
Q Consensus        21 ~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~   84 (111)
                      +++|.||.|+..|+..|+..|+.++|....+|+.||..|+|++.||+|||||||.|.||.+...
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            7788999999999999999999999999999999999999999999999999999999977653

>KOG0484|consensus

Probab=99.70  E-value=1.8e-17  Score=104.53  Aligned_cols=61  Identities=43%  Similarity=0.636  Sum_probs=58.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          20 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        20 ~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      ++.++-|+.|+..|+..|+..|-+.+||++..+++||.++.|++..|++||||||+|+||+
T Consensus        15 rKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQ   75 (125)
T KOG0484|consen   15 RKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQ   75 (125)
T ss_pred             HHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHH
Confidence            4567889999999999999999999999999999999999999999999999999999993

>KOG2251|consensus

Probab=99.70  E-value=2.1e-17  Score=116.28  Aligned_cols=68  Identities=35%  Similarity=0.502  Sum_probs=63.4

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHH
Q psy9869          17 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAI   84 (111)
Q Consensus        17 ~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~   84 (111)
                      ...++.||+||.|+..|+.+|+..|.+.+||+...+++||.+|+|.+.+|+|||+|||+|+|++++..
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            55678889999999999999999999999999999999999999999999999999999999966653

>KOG0485|consensus

Probab=99.67  E-value=1.3e-16  Score=112.29  Aligned_cols=66  Identities=39%  Similarity=0.684  Sum_probs=61.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869          18 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA   83 (111)
Q Consensus        18 ~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   83 (111)
                      .+.++|+.|++|+..|+..|+..|+...|.+..+|..||.+|.|++.||+|||||||.||||+...
T Consensus       100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa  165 (268)
T KOG0485|consen  100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA  165 (268)
T ss_pred             cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence            345788899999999999999999999999999999999999999999999999999999996554

>KOG0842|consensus

Probab=99.64  E-value=2.4e-16  Score=116.35  Aligned_cols=64  Identities=39%  Similarity=0.660  Sum_probs=58.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869          20 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA   83 (111)
Q Consensus        20 ~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   83 (111)
                      .++||.|-.|+..|..+||..|....|.+..||+.||..|.|+..||+|||||||=|.||..+.
T Consensus       151 ~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~d  214 (307)
T KOG0842|consen  151 RKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKD  214 (307)
T ss_pred             ccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhh
Confidence            4566677789999999999999999999999999999999999999999999999999995544

>KOG0492|consensus

Probab=99.63  E-value=7e-16  Score=107.87  Aligned_cols=64  Identities=44%  Similarity=0.665  Sum_probs=59.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHHH
Q psy9869          22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK   85 (111)
Q Consensus        22 ~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~   85 (111)
                      -|+.|+.||..|+..|+.-|...+|.++.++.+++..|.|++.||+|||||||+|.||.+..+-
T Consensus       144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~  207 (246)
T KOG0492|consen  144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAEL  207 (246)
T ss_pred             CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHH
Confidence            4567999999999999999999999999999999999999999999999999999999665433

>KOG0848|consensus

Probab=99.62  E-value=2.2e-16  Score=113.90  Aligned_cols=62  Identities=55%  Similarity=0.827  Sum_probs=57.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHHH
Q psy9869          24 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK   85 (111)
Q Consensus        24 ~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~   85 (111)
                      +=|-++|..|.-.||+.|..++|.++..+.+||.-|||+++||+|||||||+|+||.++...
T Consensus       201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~  262 (317)
T KOG0848|consen  201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR  262 (317)
T ss_pred             ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence            34678999999999999999999999999999999999999999999999999999887654

>KOG3802|consensus

Probab=99.62  E-value=2.1e-16  Score=119.20  Aligned_cols=77  Identities=29%  Similarity=0.385  Sum_probs=70.2

Q ss_pred             CCCcccccccCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869           6 SSDLMTNLEDEGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   82 (111)
Q Consensus         6 s~~~~~~~~~~~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   82 (111)
                      +.+..++.+.....+++||+||+|.......|+.+|..|+.|+..++..||.+|+|.+.+|+|||||||.|+||.+.
T Consensus       278 ~~~~~~~~e~i~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  278 STGSPNSIEKIGAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             ccCCCCCHHHhhccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            45666667777777789999999999999999999999999999999999999999999999999999999999665

>KOG0494|consensus

Probab=99.61  E-value=1.4e-15  Score=109.49  Aligned_cols=62  Identities=42%  Similarity=0.598  Sum_probs=57.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869          21 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   82 (111)
Q Consensus        21 ~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   82 (111)
                      ++|+.||.||..|+..|+..|++..||+...++.|+.+++|.+..|+|||||||+||||..+
T Consensus       140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek  201 (332)
T KOG0494|consen  140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEK  201 (332)
T ss_pred             ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhh
Confidence            34455899999999999999999999999999999999999999999999999999999443

>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=99.58  E-value=7.5e-15  Score=83.90  Aligned_cols=57  Identities=58%  Similarity=0.832  Sum_probs=53.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          24 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        24 ~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      +.+..++..++..|+..|..++||+..++..||..+||+..+|.+||+|+|.+.++.
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            567889999999999999999999999999999999999999999999999998763

>smart00389 HOX Homeodomain

Probab=99.57  E-value=6.6e-15  Score=83.51  Aligned_cols=55  Identities=55%  Similarity=0.809  Sum_probs=51.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhh
Q psy9869          24 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK   78 (111)
Q Consensus        24 ~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k   78 (111)
                      +.|+.++..++..|+..|..++||+..++..||..+||+..+|++||+|+|.+.+
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            5677899999999999999999999999999999999999999999999998754

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

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.57  E-value=3.8e-15  Score=101.17  Aligned_cols=68  Identities=31%  Similarity=0.505  Sum_probs=62.5

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869          16 EGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA   83 (111)
Q Consensus        16 ~~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   83 (111)
                      .+..+..+++|.+.+..|+.+|+..|..++||+..++..|+..|+|+++.|++||||+|++.|+....
T Consensus        45 ~~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~  112 (156)
T COG5576          45 QDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG  112 (156)
T ss_pred             ccCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence            34446778889999999999999999999999999999999999999999999999999999997665

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.57  E-value=3.3e-15  Score=85.86  Aligned_cols=53  Identities=19%  Similarity=0.377  Sum_probs=50.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCC----CCHHHHHHHHHHhCCCccchhhhhHHHh
Q psy9869          22 RRRGRQTYTRYQTLELEKEFHTNHY----LTRRRRIEMAHALCLTERQIKIWFQNRR   74 (111)
Q Consensus        22 ~r~~r~~~s~~q~~~L~~~F~~~~~----p~~~~~~~La~~l~l~~~~V~~WFqNrR   74 (111)
                      +++.||.|+.+|+..|+.+|..++|    |+..++..||..+||++.+|++||+|.+
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            3788999999999999999999999    9999999999999999999999999964

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

>KOG0493|consensus

Probab=99.55  E-value=4.9e-15  Score=106.85  Aligned_cols=60  Identities=50%  Similarity=0.782  Sum_probs=56.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        22 ~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      -+|.|+.|+.+||..|+..|..+.|.+...|..|+..|||.+.||+|||||+|+|.||..
T Consensus       246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT  305 (342)
T KOG0493|consen  246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST  305 (342)
T ss_pred             hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence            356799999999999999999999999999999999999999999999999999999943

>KOG0491|consensus

Probab=99.48  E-value=9.6e-15  Score=98.96  Aligned_cols=65  Identities=45%  Similarity=0.690  Sum_probs=60.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHHH
Q psy9869          21 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK   85 (111)
Q Consensus        21 ~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~   85 (111)
                      .+++.|++|+..|+..|+..|+...|.+..++.+|+..|+|++.||+.||||||.|.||.+...+
T Consensus        99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~  163 (194)
T KOG0491|consen   99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ  163 (194)
T ss_pred             HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence            45677999999999999999999999999999999999999999999999999999999776654

>KOG0483|consensus

Probab=99.46  E-value=1.2e-13  Score=96.84  Aligned_cols=64  Identities=31%  Similarity=0.477  Sum_probs=58.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHHH
Q psy9869          22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK   85 (111)
Q Consensus        22 ~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~   85 (111)
                      ...++.+++.+|...|+..|+...+..+..+..||..|||.++||.+||||||++||..+....
T Consensus        50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d  113 (198)
T KOG0483|consen   50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKD  113 (198)
T ss_pred             cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhh
Confidence            4567789999999999999999999999999999999999999999999999999998655443

>KOG0486|consensus

Probab=99.42  E-value=2e-13  Score=100.53  Aligned_cols=62  Identities=39%  Similarity=0.579  Sum_probs=58.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          20 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        20 ~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      .++++.|+.|+..|+..|+..|.++.||+...+++||.-.+|++..|++||+|||+||||..
T Consensus       110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrE  171 (351)
T KOG0486|consen  110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE  171 (351)
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhh
Confidence            36678899999999999999999999999999999999999999999999999999999943

>KOG0844|consensus

Probab=99.38  E-value=2.1e-13  Score=100.37  Aligned_cols=64  Identities=52%  Similarity=0.728  Sum_probs=58.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869          20 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA   83 (111)
Q Consensus        20 ~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   83 (111)
                      ..-||=||.|+.+|+..|++.|-+..|.+...|.+||..|+|.+..|++||||||.|+||+.-.
T Consensus       179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla  242 (408)
T KOG0844|consen  179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA  242 (408)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence            3456779999999999999999999999999999999999999999999999999999996543

>KOG4577|consensus

Probab=99.35  E-value=1.2e-12  Score=95.71  Aligned_cols=69  Identities=28%  Similarity=0.394  Sum_probs=62.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHHHH
Q psy9869          18 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKE   86 (111)
Q Consensus        18 ~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~   86 (111)
                      .+..-+|+|+.+++.|+..|+..|+..+.|..-.|+.|+..+||.-++|++||||||+|+||-++....
T Consensus       163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR  231 (383)
T KOG4577|consen  163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGR  231 (383)
T ss_pred             cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcch
Confidence            345678999999999999999999999999999999999999999999999999999999996665433

>KOG0847|consensus

Probab=99.34  E-value=5.8e-13  Score=94.18  Aligned_cols=65  Identities=42%  Similarity=0.725  Sum_probs=60.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869          18 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   82 (111)
Q Consensus        18 ~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   82 (111)
                      -++.++..|..|+..|+..|+..|+...|+-..++.+||..+|+++.+|+|||||||.||||...
T Consensus       163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA  227 (288)
T KOG0847|consen  163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA  227 (288)
T ss_pred             cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence            34667888999999999999999999999999999999999999999999999999999999544

>KOG0490|consensus

Probab=99.15  E-value=2.2e-11  Score=86.37  Aligned_cols=63  Identities=35%  Similarity=0.376  Sum_probs=59.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          19 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        19 ~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      ...+++.|+.|+..|+..|+..|...+||+...++.|+..+++++..|++||||+|++++++.
T Consensus        57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~  119 (235)
T KOG0490|consen   57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE  119 (235)
T ss_pred             hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence            356788999999999999999999999999999999999999999999999999999999854

>KOG1168|consensus

Probab=99.15  E-value=1.2e-11  Score=90.68  Aligned_cols=61  Identities=25%  Similarity=0.403  Sum_probs=58.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          20 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        20 ~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      +.++|+|+++...+.+.|+.+|...+.|+.+.+..+|.+|.|.+.+|++||||+|.|.||.
T Consensus       307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm  367 (385)
T KOG1168|consen  307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM  367 (385)
T ss_pred             cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence            5688999999999999999999999999999999999999999999999999999998883

>KOG0849|consensus

Probab=99.06  E-value=2.6e-10  Score=86.52  Aligned_cols=64  Identities=30%  Similarity=0.479  Sum_probs=59.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869          19 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   82 (111)
Q Consensus        19 ~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   82 (111)
                      .+..++.|+.|+..|+..|+..|+.++||++..++.|+..+++++..|.+||+|+|++++|...
T Consensus       173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~  236 (354)
T KOG0849|consen  173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR  236 (354)
T ss_pred             cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence            3556677899999999999999999999999999999999999999999999999999999653

>KOG0775|consensus

Probab=99.04  E-value=2.6e-10  Score=82.89  Aligned_cols=51  Identities=29%  Similarity=0.446  Sum_probs=47.3

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhh
Q psy9869          28 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK   78 (111)
Q Consensus        28 ~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k   78 (111)
                      .|...-...|.++|..++||++.++.+||..+||+..||-+||+|||.++|
T Consensus       182 CFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR  232 (304)
T KOG0775|consen  182 CFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR  232 (304)
T ss_pred             ehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence            355566789999999999999999999999999999999999999999998

>KOG0774|consensus

Probab=98.92  E-value=4.1e-10  Score=81.57  Aligned_cols=75  Identities=27%  Similarity=0.420  Sum_probs=64.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHHH---hcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHHHHHHHHHHHHHH
Q psy9869          22 RRRGRQTYTRYQTLELEKEFH---TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELNEQEKQAQA   96 (111)
Q Consensus        22 ~r~~r~~~s~~q~~~L~~~F~---~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~~~~~~~~~~~   96 (111)
                      .+|+|..|+..-..+|..+|.   .+|||+...+++||.+||++..||.+||.|+|.+++|......++..-.....+
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~~ee~~l~~~kk~  265 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKNQEEANLYAAKKA  265 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhhhhhhhhHhhccc
Confidence            467889999999999999995   599999999999999999999999999999999999988777766654444433

>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=98.71  E-value=1.3e-08  Score=54.26  Aligned_cols=34  Identities=32%  Similarity=0.585  Sum_probs=28.9

Q ss_pred             hcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhH
Q psy9869          43 TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK   76 (111)
Q Consensus        43 ~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k   76 (111)
                      .+|||+..++..|+..+||+..||..||-|.|.+
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            4899999999999999999999999999999864

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

>KOG2252|consensus

Probab=98.40  E-value=6.3e-07  Score=70.66  Aligned_cols=60  Identities=20%  Similarity=0.232  Sum_probs=55.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHh
Q psy9869          18 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKL   77 (111)
Q Consensus        18 ~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~   77 (111)
                      .....++.|.+|+..|...|...|+.+++|+.++.+.|+..|+|...-|.+||.|-|.|.
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            345567889999999999999999999999999999999999999999999999988774

>KOG0490|consensus

Probab=98.14  E-value=3.2e-06  Score=59.88  Aligned_cols=67  Identities=37%  Similarity=0.502  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869          16 EGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   82 (111)
Q Consensus        16 ~~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   82 (111)
                      .......++.++.+...++..+...|..+++|+...+..|+..+|++...|++||+|++.+.++...
T Consensus       147 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  147 GPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             CCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            3444667788999999999999999999999999999999999999999999999999999998554

>KOG1146|consensus

Probab=97.69  E-value=6.5e-05  Score=64.53  Aligned_cols=62  Identities=26%  Similarity=0.304  Sum_probs=56.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869          21 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   82 (111)
Q Consensus        21 ~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   82 (111)
                      .++..|+.++..|+..|..+|....+|...+.+.|...+++..+.|.+||+|-|.+.++...
T Consensus       902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~  963 (1406)
T KOG1146|consen  902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL  963 (1406)
T ss_pred             hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence            35567999999999999999999999999999999999999999999999999999998443

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

Probab=97.39  E-value=0.00017  Score=40.93  Aligned_cols=43  Identities=19%  Similarity=0.310  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhh
Q psy9869          33 QTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM   75 (111)
Q Consensus        33 q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~   75 (111)
                      .+..|+.+|...+++.......|..+.+|+..+|+.||-.+..
T Consensus         9 d~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~   51 (56)
T PF11569_consen    9 DIQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ   51 (56)
T ss_dssp             --HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred             chHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence            3567999999999999999999999999999999999975543

>KOG0773|consensus

Probab=96.61  E-value=0.0026  Score=47.96  Aligned_cols=61  Identities=20%  Similarity=0.316  Sum_probs=49.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHHH---hcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869          22 RRRGRQTYTRYQTLELEKEFH---TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   82 (111)
Q Consensus        22 ~r~~r~~~s~~q~~~L~~~F~---~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   82 (111)
                      ..+....+......+|+.+..   ..+||+..++..|+..+||+..+|.+||-|.|-+.-+...
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~  302 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI  302 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence            344555788888888887642   3689999999999999999999999999999988776544

>KOG3623|consensus

Probab=95.69  E-value=0.02  Score=47.55  Aligned_cols=48  Identities=17%  Similarity=0.208  Sum_probs=44.3

Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          34 TLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        34 ~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      +..|..+|..|+.|...+...++...|+....|+.||.+.++......
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~  615 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE  615 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence            778899999999999999999999999999999999999998877644

>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=95.46  E-value=0.062  Score=29.95  Aligned_cols=47  Identities=17%  Similarity=0.357  Sum_probs=34.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHh
Q psy9869          23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRR   74 (111)
Q Consensus        23 r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR   74 (111)
                      +++|..+|-.+...+-..++.+.     ....+|..+|++...|..|..|+.
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            46788899988777777777666     477889999999999999998754

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

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

Probab=87.34  E-value=2.1  Score=22.91  Aligned_cols=46  Identities=11%  Similarity=0.134  Sum_probs=32.7

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhh
Q psy9869          28 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK   78 (111)
Q Consensus        28 ~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k   78 (111)
                      .+++.+..++...|.     ......++|..+|++...|+.+...-..+.|
T Consensus         4 ~L~~~er~vi~~~y~-----~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR   49 (50)
T PF04545_consen    4 QLPPREREVIRLRYF-----EGLTLEEIAERLGISRSTVRRILKRALKKLR   49 (50)
T ss_dssp             TS-HHHHHHHHHHHT-----ST-SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHhc-----CCCCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence            467788888888882     2234677899999999999988765554443

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 ....

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

Probab=80.72  E-value=1.9  Score=24.94  Aligned_cols=46  Identities=17%  Similarity=0.293  Sum_probs=28.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHH
Q psy9869          24 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNR   73 (111)
Q Consensus        24 ~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNr   73 (111)
                      +.+..|+.++...+-..+...    ......++..+||+...+..|-.--
T Consensus         2 ~~r~~ys~e~K~~~v~~~~~~----g~sv~~va~~~gi~~~~l~~W~~~~   47 (76)
T PF01527_consen    2 RKRRRYSPEFKLQAVREYLES----GESVSEVAREYGISPSTLYNWRKQY   47 (76)
T ss_dssp             -SS----HHHHHHHHHHHHHH----HCHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHC----CCceEeeecccccccccccHHHHHH
Confidence            346788888766555554222    2567788999999999999998543

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	111
1b8i_A	81	Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX		2e-21
1hom_A	68	Determination Of The Three-Dimensional Structure Of		7e-18
2r5y_A	88	Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO		4e-17
1ahd_P	68	Determination Of The Nmr Solution Structure Of An A		6e-17
1san_A	62	The Des(1-6)antennapedia Homeodomain: Comparison Of		7e-17
9ant_A	62	Antennapedia Homeodomain-Dna Complex Length = 62		9e-17
1ftz_A	70	Nuclear Magnetic Resonance Solution Structure Of Th		6e-15
1b72_A	97	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		5e-12
2lp0_A	60	The Solution Structure Of Homeodomain-Protein Compl		5e-12
1puf_A	77	Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo		1e-11
2h1k_A	63	Crystal Structure Of The Pdx1 Homeodomain In Comple		2e-11
2m34_A	71	Nmr Structure Of The Homeodomain Transcription Fact		2e-09
1hdd_C	61	Crystal Structure Of An Engrailed Homeodomain-Dna C		1e-08
3hdd_A	60	Engrailed Homeodomain Dna Complex Length = 60		1e-08
2cra_A	70	Solution Structure Of The Homeobox Domain Of Human		2e-08
1p7j_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		2e-08
1jgg_A	60	Even-Skipped Homeodomain Complexed To At-Rich Dna L		3e-08
1p7i_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		3e-08
2hdd_A	61	Engrailed Homeodomain Q50k Variant Dna Complex Leng		4e-08
2p81_A	44	Engrailed Homeodomain Helix-Turn-Helix Motif Length		4e-08
2ld5_A	67	Solution Nmr-Derived Complex Structure Of Hoxa13 Dn		6e-08
1du0_A	57	Engrailed Homeodomain Q50a Variant Dna Complex Leng		6e-08
2l7z_A	73	Nmr Structure Of A13 Homedomain Length = 73		8e-08
1ztr_A	61	Solution Structure Of Engrailed Homeodomain L16a Mu		1e-07
1enh_A	54	Structural Studies Of The Engrailed Homeodomain Len		1e-07
2djn_A	70	The Solution Structure Of The Homeobox Domain Of Hu		2e-07
2dmt_A	80	Solution Structure Of The Homeobox Domain Of Homeob		2e-07
2e1o_A	70	Solution Structure Of Rsgi Ruh-028, A Homeobox Doma		3e-07
2hos_A	63	Phage-selected Homeodomain Bound To Unmodified Dna		7e-07
1ig7_A	58	Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58		8e-07
3a01_A	93	Crystal Structure Of Aristaless And Clawless Homeod		2e-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		6e-06
3a02_A	60	Crystal Structure Of Aristaless Homeodomain Length		2e-05
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		2e-05
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		3e-05
3a03_A	56	Crystal Structure Of Hox11l1 Homeodomain Length = 5		3e-05
1ftt_A	68	Thyroid Transcription Factor 1 Homeodomain (Rattus		1e-04
1fjl_A	81	Homeodomain From The Drosophila Paired Protein Boun		2e-04
2l7m_P	68	Solution Structure Of The Pitx2 Homeodomain R24h Mu		3e-04
1nk2_P	77	VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES		3e-04
2m0c_A	75	Solution Nmr Structure Of Homeobox Domain Of Human		5e-04
2cue_A	80	Solution Structure Of The Homeobox Domain Of The Hu		6e-04
1zq3_P	68	Nmr Solution Structure Of The Bicoid Homeodomain Bo		6e-04

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

Iteration: 1
 Score = 97.4 bits (241), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 47/48 (97%), Positives = 47/48 (97%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA 83
          ELEKEFHTNHYLTRRRRIEMAHAL LTERQIKIWFQNRRMKLKKEIQA
Sbjct: 34 ELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEIQA 81

>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 = 85.5 bits (210), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 41/45 (91%), Positives = 42/45 (93%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          ELEKEFH N YLTRRRRIE+AHALCLTERQIKIWFQNRRMK KKE
Sbjct: 16 ELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 60

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

Iteration: 1
 Score = 82.8 bits (203), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 40/45 (88%), Positives = 41/45 (91%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          ELEKEFH N YLTRRRRIE+AHAL LTERQIKIWFQNRRMK KKE
Sbjct: 42 ELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 86

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

Iteration: 1
 Score = 82.4 bits (202), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 40/45 (88%), Positives = 41/45 (91%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          ELEKEFH N YLTRRRRIE+AHAL LTERQIKIWFQNRRMK KKE
Sbjct: 16 ELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 60

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

Iteration: 1
 Score = 82.0 bits (201), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 40/45 (88%), Positives = 41/45 (91%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          ELEKEFH N YLTRRRRIE+AHAL LTERQIKIWFQNRRMK KKE
Sbjct: 10 ELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 54

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

Iteration: 1
 Score = 81.6 bits (200), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 40/45 (88%), Positives = 41/45 (91%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          ELEKEFH N YLTRRRRIE+AHAL LTERQIKIWFQNRRMK KKE
Sbjct: 17 ELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61

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

Iteration: 1
 Score = 75.9 bits (185), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 35/45 (77%), Positives = 41/45 (91%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          ELEKEFH N Y+TRRRRI++A+AL L+ERQIKIWFQNRRMK KK+
Sbjct: 17 ELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKD 61

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

Iteration: 1
 Score = 65.9 bits (159), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 31/44 (70%), Positives = 35/44 (79%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          ELEKEFH N YL+R RR+E+A  L L E Q+KIWFQNRRMK KK
Sbjct: 48 ELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91

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

Iteration: 1
 Score = 65.9 bits (159), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 33/44 (75%), Positives = 36/44 (81%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          ELEKEF  N YLTR RR E+A  L LTERQ+KIWFQNRRMK+KK
Sbjct: 15 ELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58

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

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 33/44 (75%), Positives = 36/44 (81%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          ELEKEF  N YLTR RR E+A  L LTERQ+KIWFQNRRMK+KK
Sbjct: 27 ELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/45 (71%), Positives = 36/45 (80%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          ELEKEF  N Y++R RR+E+A  L LTER IKIWFQNRRMK KKE
Sbjct: 17 ELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 27/44 (61%), Positives = 33/44 (75%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          ELEKEFH   YL+   R ++AHAL L+E Q+KIWFQNRR K K+
Sbjct: 21 ELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKR 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 = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/43 (58%), Positives = 33/43 (76%)
Query: 37 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          L++EF+ N YLT RRR +++  L L E QIKIWFQN+R K+KK
Sbjct: 18 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/43 (58%), Positives = 33/43 (76%)
Query: 37 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          L++EF+ N YLT RRR +++  L L E QIKIWFQN+R K+KK
Sbjct: 16 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 23/44 (52%), Positives = 34/44 (77%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          ELE+E+  N ++T+ +R +++ A  L+ERQI IWFQNRR+K KK
Sbjct: 21 ELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/43 (58%), Positives = 32/43 (74%)
Query: 37 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          L++EF+ N YLT RRR +++  L L E QIKIWFQN R K+KK
Sbjct: 16 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 25/44 (56%), Positives = 33/44 (75%)
Query: 37 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          LEKEF+  +Y++R RR E+A  L L E  IK+WFQNRRMK K++
Sbjct: 16 LEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 25/43 (58%), Positives = 32/43 (74%)
Query: 37 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          L++EF+ N YLT RRR +++  L L E QIKIWFQN R K+KK
Sbjct: 16 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 24/43 (55%), Positives = 33/43 (76%)
Query: 37 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          L++EF+ N YLT RRR +++  L L E QIKIWF+N+R K+KK
Sbjct: 18 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 24/42 (57%), Positives = 32/42 (76%)
Query: 38 EKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          ++EF+ N YLT RRR +++  L L E QIKIWFQN+R K+KK
Sbjct: 2  KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 36/50 (72%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK 85
          ELE+E+ TN ++T+ +R  ++    L+ERQ+ IWFQNRR+K KK I  +K
Sbjct: 15 ELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINKLK 64

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 24/43 (55%), Positives = 32/43 (74%)
Query: 37 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          L++EF+ N YLT RRR +++  L L E QIKIWF N+R K+KK
Sbjct: 14 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 36/50 (72%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK 85
          ELE+E+ TN ++T+ +R  ++    L+ERQ+ IWFQNRR+K KK I  +K
Sbjct: 21 ELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINKLK 70

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 22/42 (52%), Positives = 32/42 (76%)
Query: 38 EKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          ++EF+ N YLT RRR +++  L L E QIKIWFQN+R K+++
Sbjct: 19 KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 23/41 (56%), Positives = 31/41 (75%)
Query: 37 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKL 77
          L++EF+ N YLT RRR +++  L L E QIKIWFQN+R K+
Sbjct: 14 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKI 54

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 21/44 (47%), Positives = 29/44 (65%)
Query: 37 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          L++ F    YL    R E+A +L LT+ Q+KIWFQN+R K+KK 
Sbjct: 22 LQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKS 65

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 22/43 (51%), Positives = 30/43 (69%)
Query: 37 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          LEK F    YL+   RI++A +L L++ Q+K W+QNRRMK KK
Sbjct: 32 LEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKK 74

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 23/44 (52%), Positives = 30/44 (68%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          ELEK+F T  YL+   R  +A  L L+ERQ+K WFQNRR K ++
Sbjct: 21 ELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 22/43 (51%), Positives = 31/43 (72%)
Query: 37 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          L++EF+ N YLT RRR +++  L L E Q+K WF+N R K+KK
Sbjct: 19 LKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 22/43 (51%), Positives = 29/43 (67%)
Query: 37 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          LE++F    YL+   R E + +L LTE Q+KIWFQNRR K K+
Sbjct: 15 LERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 28/46 (60%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81
          ELEK FH   YL    R  +A  L +T+ Q+K WFQNRR K +++ 
Sbjct: 31 ELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQT 76

>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 = 46.6 bits (109), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 23/45 (51%), Positives = 30/45 (66%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          ELE++F    YL+   R  +A  L LTE Q+KIWFQNRR K K++
Sbjct: 18 ELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRK 62

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 22/43 (51%), Positives = 27/43 (62%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 78
          ELE+ F    YL+   R ++A  L LT  Q+KIWFQNRR K K
Sbjct: 16 ELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/45 (48%), Positives = 29/45 (64%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          ELEK F   HY     R E+A  + LTE +I++WFQNRR K +K+
Sbjct: 13 ELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/45 (48%), Positives = 29/45 (64%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          ELEK F   HY     R E+A  + LTE +I++WFQNRR K +K+
Sbjct: 13 ELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/45 (48%), Positives = 29/45 (64%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          ELEK F   HY     R E+A  + LTE +I++WFQNRR K +K+
Sbjct: 20 ELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 64

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/45 (44%), Positives = 28/45 (62%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          ELE+ F    YL    R  +A AL +T+ Q+K WFQNRR K +++
Sbjct: 11 ELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/45 (44%), Positives = 28/45 (62%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          ELE+ F    YL+   R  +A  + LT  Q+KIWFQN R K+K++
Sbjct: 16 ELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/45 (44%), Positives = 28/45 (62%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          ELE+ F    Y     R E+A    LTE +I++WFQNRR +L+K+
Sbjct: 32 ELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 76

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/44 (45%), Positives = 27/44 (61%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          ELE  F  NHY     R E+A    LTE ++++WF+NRR K +K
Sbjct: 17 ELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/44 (45%), Positives = 26/44 (59%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          ELE+ F    YL+   R  +A  + LT  Q+KIWFQN R K K+
Sbjct: 23 ELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66

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

Iteration: 1
 Score = 39.3 bits (90), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/44 (45%), Positives = 27/44 (61%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          ELEK F   HY     R ++A    LTE ++++WFQNRR K +K
Sbjct: 23 ELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRK 66

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

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 19/44 (43%), Positives = 26/44 (59%)
Query: 37 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          LEKEF   HY     R  +A  + L E +I++WF NRR K ++E
Sbjct: 22 LEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE 65

>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 = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 19/43 (44%), Positives = 26/43 (60%)
Query: 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 78
          ELE+ F    YLT  R  +++  L L   Q+KIWF+NRR + K
Sbjct: 16 ELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	111
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.83
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.83
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.83
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.83
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.82
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.82
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.82
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.82
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.82
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.82
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.82
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.82
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.81
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.81
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.81
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.81
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.81
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.81
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.81
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.81
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.81
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.8
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.8
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.79
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.79
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.79
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.79
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.79
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.79
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.79
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.79
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.79
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.78
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.78
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.78
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.78
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.78
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.77
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.77
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.77
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.77
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.77
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.77
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.77
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.76
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.76
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.76
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.76
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.76
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.75
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.74
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.74
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.74
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.74
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.73
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.73
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.73
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.73
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.72
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.71
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.71
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.71
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.71
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.71
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.7
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.69
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.69
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.68
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.67
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.67
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.66
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.62
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.52
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.51
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.49
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.46
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.33
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.66
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	96.45
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	87.52
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	83.79

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

Probab=99.83  E-value=1.6e-20  Score=114.68  Aligned_cols=67  Identities=28%  Similarity=0.497  Sum_probs=61.6

Q ss_pred             cCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          15 DEGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        15 ~~~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      .....+..++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||||||+|+|+..
T Consensus        15 ~~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   81 (84)
T 2kt0_A           15 EDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQ   81 (84)
T ss_dssp             SCCCCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCC
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHh
Confidence            3445567888999999999999999999999999999999999999999999999999999999854

>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=99.83  E-value=1.9e-20  Score=113.47  Aligned_cols=65  Identities=42%  Similarity=0.664  Sum_probs=60.4

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          17 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        17 ~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      ......++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||||||+|+|+..
T Consensus        12 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   76 (80)
T 2dmt_A           12 TKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSG   76 (80)
T ss_dssp             CCCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhccc
Confidence            34466788899999999999999999999999999999999999999999999999999999854

>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=99.83  E-value=1.1e-20  Score=114.86  Aligned_cols=67  Identities=96%  Similarity=1.398  Sum_probs=54.7

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869          16 EGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   82 (111)
Q Consensus        16 ~~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   82 (111)
                      .+..+.+++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+|+|+..+
T Consensus        14 ~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   80 (81)
T 1b8i_A           14 AGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEIQ   80 (81)
T ss_dssp             ----------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC-
T ss_pred             CCCCCCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhcc
Confidence            3445667889999999999999999999999999999999999999999999999999999998643

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

Probab=99.83  E-value=4.6e-20  Score=111.74  Aligned_cols=66  Identities=35%  Similarity=0.563  Sum_probs=61.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869          18 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA   83 (111)
Q Consensus        18 ~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   83 (111)
                      .++..++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||+|||+|+|+....
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~   68 (80)
T 2cue_A            3 SGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL   68 (80)
T ss_dssp             SCCSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhh
Confidence            345678899999999999999999999999999999999999999999999999999999996543

>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=99.82  E-value=5.1e-20  Score=110.83  Aligned_cols=66  Identities=39%  Similarity=0.644  Sum_probs=61.0

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869          17 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   82 (111)
Q Consensus        17 ~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   82 (111)
                      +....+++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+++|+...
T Consensus         4 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~   69 (77)
T 1nk2_P            4 GLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQN   69 (77)
T ss_dssp             CCSCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhc
Confidence            445667888999999999999999999999999999999999999999999999999999998554

>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=99.82  E-value=2.3e-20  Score=112.87  Aligned_cols=65  Identities=28%  Similarity=0.339  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          17 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        17 ~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      .....+++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||+|||+++|+.+
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            34466788999999999999999999999999999999999999999999999999999999854

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

Probab=99.82  E-value=4.1e-20  Score=109.27  Aligned_cols=64  Identities=30%  Similarity=0.502  Sum_probs=60.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          18 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        18 ~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      .++..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+..
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~   66 (70)
T 2dmu_A            3 SGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSG   66 (70)
T ss_dssp             STTSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccC
Confidence            3456788999999999999999999999999999999999999999999999999999999864

>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=99.82  E-value=2.9e-20  Score=110.01  Aligned_cols=64  Identities=42%  Similarity=0.681  Sum_probs=60.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          18 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        18 ~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      ..+..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~   66 (70)
T 2cra_A            3 SGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSG   66 (70)
T ss_dssp             SSCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccC
Confidence            3456788999999999999999999999999999999999999999999999999999999854

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

Probab=99.82  E-value=3.5e-20  Score=107.57  Aligned_cols=60  Identities=65%  Similarity=0.950  Sum_probs=55.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          21 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        21 ~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      ..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+.
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   61 (63)
T 2h1k_A            2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE   61 (63)
T ss_dssp             ---CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhh
Confidence            467889999999999999999999999999999999999999999999999999999985

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

Probab=99.82  E-value=3.2e-20  Score=115.52  Aligned_cols=69  Identities=38%  Similarity=0.651  Sum_probs=62.7

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHH
Q psy9869          16 EGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAI   84 (111)
Q Consensus        16 ~~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~   84 (111)
                      ...++..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+|+|+.....
T Consensus        11 ~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~   79 (93)
T 3a01_A           11 NRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEE   79 (93)
T ss_dssp             TSCCCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHH
Confidence            344566788999999999999999999999999999999999999999999999999999999965543

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

Probab=99.82  E-value=1.9e-20  Score=108.32  Aligned_cols=60  Identities=32%  Similarity=0.572  Sum_probs=53.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          21 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        21 ~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      .+++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.
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            467889999999999999999999999999999999999999999999999999999985

>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=99.82  E-value=4.6e-20  Score=109.03  Aligned_cols=64  Identities=31%  Similarity=0.460  Sum_probs=60.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          18 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        18 ~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      ..+..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+..
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2da2_A            3 SGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSG   66 (70)
T ss_dssp             CSCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhcc
Confidence            4567788999999999999999999999999999999999999999999999999999999854

>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=99.81  E-value=9.8e-20  Score=110.16  Aligned_cols=63  Identities=25%  Similarity=0.473  Sum_probs=59.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          19 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        19 ~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      .+.+++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||+|||+++|+..
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   66 (80)
T 2dmq_A            4 GSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNL   66 (80)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHH
Confidence            456788999999999999999999999999999999999999999999999999999999954

>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=99.81  E-value=9.9e-20  Score=107.66  Aligned_cols=63  Identities=41%  Similarity=0.680  Sum_probs=59.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          19 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        19 ~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      .+..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         4 ~~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~   66 (70)
T 2e1o_A            4 GSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSG   66 (70)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCC
Confidence            456778899999999999999999999999999999999999999999999999999999854

>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=7.5e-20  Score=110.77  Aligned_cols=64  Identities=34%  Similarity=0.501  Sum_probs=60.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          18 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        18 ~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      ..+..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~   66 (80)
T 2dms_A            3 SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQ   66 (80)
T ss_dssp             CCCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTT
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHH
Confidence            3466788999999999999999999999999999999999999999999999999999999854

>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=99.81  E-value=1.7e-19  Score=108.46  Aligned_cols=65  Identities=62%  Similarity=0.833  Sum_probs=60.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869          19 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA   83 (111)
Q Consensus        19 ~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   83 (111)
                      .+..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+++|+....
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            35577899999999999999999999999999999999999999999999999999999996543

>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=99.81  E-value=7.2e-20  Score=111.06  Aligned_cols=62  Identities=15%  Similarity=0.238  Sum_probs=58.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh----cCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869          18 ANGLRRRGRQTYTRYQTLELEKEFHT----NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   79 (111)
Q Consensus        18 ~~~~~r~~r~~~s~~q~~~L~~~F~~----~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   79 (111)
                      ..+.+++.|+.|+..|+..|+..|..    ++||+..++..||..|||++.+|+|||||||+|+|+
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            34567889999999999999999999    999999999999999999999999999999999875

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

Probab=99.81  E-value=5.2e-20  Score=108.87  Aligned_cols=64  Identities=39%  Similarity=0.674  Sum_probs=60.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          18 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        18 ~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      ..+..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+..
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2djn_A            3 SGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSG   66 (70)
T ss_dssp             SCCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccC
Confidence            3466788999999999999999999999999999999999999999999999999999999854

>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=99.81  E-value=6.5e-20  Score=105.74  Aligned_cols=58  Identities=47%  Similarity=0.811  Sum_probs=53.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869          22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   79 (111)
Q Consensus        22 ~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   79 (111)
                      .++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+
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            5788999999999999999999999999999999999999999999999999999987

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

Probab=99.81  E-value=1e-19  Score=107.07  Aligned_cols=61  Identities=41%  Similarity=0.638  Sum_probs=58.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869          22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   82 (111)
Q Consensus        22 ~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   82 (111)
                      +++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+...
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~   62 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD   62 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhc
Confidence            5788999999999999999999999999999999999999999999999999999999654

>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=99.81  E-value=6.5e-20  Score=108.36  Aligned_cols=64  Identities=27%  Similarity=0.311  Sum_probs=59.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          18 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        18 ~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      ..+..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+..
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2da1_A            3 SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSG   66 (70)
T ss_dssp             SSCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhc
Confidence            3456788999999999999999999999999999999999999999999999999999999853

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

Probab=99.80  E-value=1.2e-19  Score=103.56  Aligned_cols=57  Identities=47%  Similarity=0.792  Sum_probs=55.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869          23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   79 (111)
Q Consensus        23 r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   79 (111)
                      ++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+
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            467999999999999999999999999999999999999999999999999999987

>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=99.80  E-value=2e-19  Score=109.12  Aligned_cols=64  Identities=39%  Similarity=0.615  Sum_probs=59.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869          19 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   82 (111)
Q Consensus        19 ~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   82 (111)
                      .+.+++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+...
T Consensus        15 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~   78 (81)
T 1fjl_A           15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   78 (81)
T ss_dssp             --CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhcc
Confidence            4567889999999999999999999999999999999999999999999999999999999654

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

Probab=99.79  E-value=1.8e-19  Score=103.55  Aligned_cols=58  Identities=53%  Similarity=0.794  Sum_probs=55.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        23 r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      ++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|++
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            5789999999999999999999999999999999999999999999999999999984

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

Probab=99.79  E-value=1.2e-19  Score=113.49  Aligned_cols=67  Identities=16%  Similarity=0.145  Sum_probs=56.4

Q ss_pred             cCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          15 DEGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        15 ~~~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      .++..+..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+|+|+.+
T Consensus        18 ~p~~~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   84 (96)
T 3nar_A           18 GPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGN   84 (96)
T ss_dssp             ---------CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTC
T ss_pred             CCCCCCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhc
Confidence            3444456678899999999999999999999999999999999999999999999999999999965

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

Probab=99.79  E-value=2.1e-19  Score=102.31  Aligned_cols=57  Identities=46%  Similarity=0.737  Sum_probs=54.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhh
Q psy9869          22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK   78 (111)
Q Consensus        22 ~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k   78 (111)
                      +++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|
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            577899999999999999999999999999999999999999999999999999875

>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=2.8e-19  Score=106.75  Aligned_cols=63  Identities=44%  Similarity=0.693  Sum_probs=59.3

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          19 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        19 ~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      .+.+++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+..
T Consensus         6 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   68 (75)
T 2m0c_A            6 KGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRE   68 (75)
T ss_dssp             CSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHH
Confidence            456788899999999999999999999999999999999999999999999999999999853

>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=99.79  E-value=6.1e-20  Score=108.01  Aligned_cols=63  Identities=38%  Similarity=0.602  Sum_probs=59.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869          20 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   82 (111)
Q Consensus        20 ~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   82 (111)
                      |.+++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+...
T Consensus         1 g~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~   63 (68)
T 1yz8_P            1 GSQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREE   63 (68)
T ss_dssp             CCSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhh
Confidence            357889999999999999999999999999999999999999999999999999999998643

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

Probab=99.79  E-value=3.1e-19  Score=106.39  Aligned_cols=62  Identities=45%  Similarity=0.705  Sum_probs=58.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          20 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        20 ~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      ...++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   66 (73)
T 2l7z_A            5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVI   66 (73)
T ss_dssp             SCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHh
Confidence            45688899999999999999999999999999999999999999999999999999999854

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

Probab=99.79  E-value=2.7e-19  Score=105.25  Aligned_cols=60  Identities=40%  Similarity=0.720  Sum_probs=57.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        22 ~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      +++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~   61 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA   61 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhh
Confidence            578899999999999999999999999999999999999999999999999999999854

>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=99.79  E-value=1.8e-19  Score=106.06  Aligned_cols=60  Identities=88%  Similarity=1.285  Sum_probs=57.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        22 ~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      +++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   61 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN   61 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhc
Confidence            578899999999999999999999999999999999999999999999999999999854

>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=99.79  E-value=1.9e-19  Score=105.24  Aligned_cols=60  Identities=27%  Similarity=0.345  Sum_probs=57.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        22 ~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      +++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+..
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            578899999999999999999999999999999999999999999999999999998854

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

Probab=99.78  E-value=2.3e-19  Score=103.12  Aligned_cols=57  Identities=44%  Similarity=0.670  Sum_probs=50.6

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          25 GRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        25 ~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      +|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~   58 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE   58 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC---
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhc
Confidence            588999999999999999999999999999999999999999999999999999854

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

Probab=99.78  E-value=1.8e-19  Score=109.07  Aligned_cols=62  Identities=18%  Similarity=0.273  Sum_probs=58.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhc----CCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          19 NGLRRRGRQTYTRYQTLELEKEFHTN----HYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        19 ~~~~r~~r~~~s~~q~~~L~~~F~~~----~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      .+.+++.|+.|+..|+..|+..|..+    +||+..++..||..+||++.+|++||||+|+|+|+.
T Consensus         5 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~   70 (80)
T 2da4_A            5 SSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLM   70 (80)
T ss_dssp             CCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhc
Confidence            45678899999999999999999999    999999999999999999999999999999999984

>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=99.78  E-value=2.1e-19  Score=109.02  Aligned_cols=62  Identities=16%  Similarity=0.222  Sum_probs=57.3

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHh-----cCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869          17 GANGLRRRGRQTYTRYQTLELEKEFHT-----NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   79 (111)
Q Consensus        17 ~~~~~~r~~r~~~s~~q~~~L~~~F~~-----~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   79 (111)
                      +..+.+++.|+.|+..|+..|+ .|..     ++||+..++..||..+||++.+|+|||||||+|+++
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            3346678899999999999999 7999     999999999999999999999999999999999875

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

Probab=99.78  E-value=3.2e-19  Score=109.79  Aligned_cols=64  Identities=81%  Similarity=1.176  Sum_probs=55.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          18 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        18 ~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      ..+..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+++|+..
T Consensus        24 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   87 (88)
T 2r5y_A           24 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH   87 (88)
T ss_dssp             -------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhhc
Confidence            3456788999999999999999999999999999999999999999999999999999999853

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

Probab=99.78  E-value=4.8e-19  Score=103.82  Aligned_cols=60  Identities=40%  Similarity=0.547  Sum_probs=57.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        22 ~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      +++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+..
T Consensus         1 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~   60 (67)
T 2k40_A            1 GRRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSH   60 (67)
T ss_dssp             CCCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSC
T ss_pred             CcCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhc
Confidence            367899999999999999999999999999999999999999999999999999999854

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

Probab=99.77  E-value=6.1e-19  Score=100.08  Aligned_cols=54  Identities=43%  Similarity=0.777  Sum_probs=50.9

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          27 QTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        27 ~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      +.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+|+||.
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~   55 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ   55 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhhccc
Confidence            579999999999999999999999999999999999999999999999999984

>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=99.77  E-value=3.9e-19  Score=102.36  Aligned_cols=59  Identities=25%  Similarity=0.460  Sum_probs=48.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhh
Q psy9869          20 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK   78 (111)
Q Consensus        20 ~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k   78 (111)
                      +..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|
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            34678899999999999999999999999999999999999999999999999999875

>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=99.77  E-value=8.9e-19  Score=104.06  Aligned_cols=59  Identities=27%  Similarity=0.308  Sum_probs=55.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          23 RRGRQTYTRYQTLELEKEFHT-NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        23 r~~r~~~s~~q~~~L~~~F~~-~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      .+.|+.|+..|+..|+..|.. ++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~   61 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhc
Confidence            467899999999999999996 99999999999999999999999999999999999854

>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=99.77  E-value=6.8e-19  Score=110.14  Aligned_cols=64  Identities=55%  Similarity=0.765  Sum_probs=55.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          18 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        18 ~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      ..+..++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||||||+|+|+..
T Consensus        30 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   93 (97)
T 1b72_A           30 GLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRE   93 (97)
T ss_dssp             -------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHh
Confidence            3456788899999999999999999999999999999999999999999999999999999854

>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=9.5e-19  Score=104.92  Aligned_cols=57  Identities=21%  Similarity=0.281  Sum_probs=53.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          24 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        24 ~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      ..+..|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.
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            446679999999999999999999999999999999999999999999999999985

>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=99.77  E-value=1.4e-18  Score=104.12  Aligned_cols=59  Identities=24%  Similarity=0.280  Sum_probs=55.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        23 r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      .+.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         8 ~~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~   66 (75)
T 2da5_A            8 PTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEE   66 (75)
T ss_dssp             SCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSS
T ss_pred             CCCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhh
Confidence            35577899999999999999999999999999999999999999999999999999854

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

Probab=99.77  E-value=1.6e-18  Score=103.20  Aligned_cols=59  Identities=24%  Similarity=0.227  Sum_probs=55.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          23 RRGRQTYTRYQTLELEKEFHT-NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        23 r~~r~~~s~~q~~~L~~~F~~-~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      .+.|+.|+..|+..|+..|.. ++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~   62 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   62 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhc
Confidence            567899999999999999995 99999999999999999999999999999999999854

>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=99.76  E-value=2.1e-18  Score=102.61  Aligned_cols=64  Identities=19%  Similarity=0.243  Sum_probs=59.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          18 ANGLRRRGRQTYTRYQTLELEKEFHT---NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        18 ~~~~~r~~r~~~s~~q~~~L~~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      .++..++.|+.|+..++..|+..|..   ++||+..++..||..+||++.+|++||+|+|+++++..
T Consensus         3 ~~~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~   69 (73)
T 1x2n_A            3 SGSSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSG   69 (73)
T ss_dssp             CCSSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhccccc
Confidence            34567888999999999999999987   99999999999999999999999999999999999854

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

Probab=99.76  E-value=1.5e-18  Score=108.18  Aligned_cols=65  Identities=28%  Similarity=0.439  Sum_probs=60.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhC---------------CCccchhhhhHHHhhHhhHhHH
Q psy9869          18 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALC---------------LTERQIKIWFQNRRMKLKKEIQ   82 (111)
Q Consensus        18 ~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~---------------l~~~~V~~WFqNrR~k~kk~~~   82 (111)
                      ..+.+++.|+.|+..|+.+|+..|..++||+..++..||..||               |++.+|++||||||+++|+...
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            3456788999999999999999999999999999999999999               9999999999999999998543

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

Probab=99.76  E-value=1.1e-18  Score=104.03  Aligned_cols=61  Identities=23%  Similarity=0.292  Sum_probs=57.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          21 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        21 ~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      ..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+++|+..
T Consensus         5 ~~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   65 (74)
T 2ly9_A            5 DSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSK   65 (74)
T ss_dssp             CCCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTT
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhC
Confidence            4577899999999999999999999999999999999999999999999999999999854

>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=99.76  E-value=6.5e-19  Score=108.07  Aligned_cols=62  Identities=31%  Similarity=0.525  Sum_probs=57.7

Q ss_pred             CCCCCCCCHHHHHHHHHHH---HhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHH
Q psy9869          23 RRGRQTYTRYQTLELEKEF---HTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAI   84 (111)
Q Consensus        23 r~~r~~~s~~q~~~L~~~F---~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~   84 (111)
                      ++.|+.|+..|+.+|+..|   ..++||+..++..||..+||++.+|++||+|+|+|+|+.....
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            6789999999999999999   8999999999999999999999999999999999999976553

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

Probab=99.76  E-value=1.4e-18  Score=104.19  Aligned_cols=61  Identities=16%  Similarity=0.270  Sum_probs=56.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          21 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        21 ~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      .+...|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         7 ~~~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~   67 (76)
T 2dn0_A            7 GASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLK   67 (76)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCC
T ss_pred             CCCCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhc
Confidence            3455689999999999999999999999999999999999999999999999999999854

>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=99.75  E-value=9.9e-19  Score=104.07  Aligned_cols=62  Identities=31%  Similarity=0.517  Sum_probs=58.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHH---HhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869          22 RRRGRQTYTRYQTLELEKEF---HTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA   83 (111)
Q Consensus        22 ~r~~r~~~s~~q~~~L~~~F---~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   83 (111)
                      +++.|+.|+..|+.+|+..|   ..++||+..++..||..+||++.+|++||+|+|+++|+....
T Consensus         1 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~   65 (73)
T 1puf_B            1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGK   65 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTT
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccccccc
Confidence            36789999999999999999   899999999999999999999999999999999999986554

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

Probab=99.74  E-value=1.4e-18  Score=100.90  Aligned_cols=59  Identities=25%  Similarity=0.381  Sum_probs=56.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHH---HhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869          21 LRRRGRQTYTRYQTLELEKEF---HTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   79 (111)
Q Consensus        21 ~~r~~r~~~s~~q~~~L~~~F---~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   79 (111)
                      .+++.|+.|+..|+.+|+..|   ..++||+..++..||..+||++.+|++||+|+|+++||
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            357889999999999999999   89999999999999999999999999999999999886

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

Probab=99.74  E-value=5.6e-18  Score=98.87  Aligned_cols=60  Identities=20%  Similarity=0.221  Sum_probs=55.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHh
Q psy9869          18 ANGLRRRGRQTYTRYQTLELEKEFHT-NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKL   77 (111)
Q Consensus        18 ~~~~~r~~r~~~s~~q~~~L~~~F~~-~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~   77 (111)
                      ..+.++|.|+.|+.+|+..|+..|.. ++||+...+..|+..+||++++|++||||+|--.
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            44678899999999999999999999 9999999999999999999999999999999643

>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=1e-17  Score=102.11  Aligned_cols=64  Identities=14%  Similarity=0.228  Sum_probs=58.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          18 ANGLRRRGRQTYTRYQTLELEKEFHT---NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        18 ~~~~~r~~r~~~s~~q~~~L~~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      ....+++.|+.|+..++.+|+.+|..   ++||+..++..||..+||+..+|++||+|+|.|+++..
T Consensus         3 ~~~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~   69 (83)
T 2dmn_A            3 SGSSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDM   69 (83)
T ss_dssp             CCCCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHH
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHH
Confidence            34567888999999999999999987   69999999999999999999999999999999998853

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

Probab=99.74  E-value=2.6e-18  Score=116.73  Aligned_cols=67  Identities=25%  Similarity=0.338  Sum_probs=52.3

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869          16 EGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   82 (111)
Q Consensus        16 ~~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   82 (111)
                      ....+.+++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+|+||...
T Consensus        93 ~~~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~  159 (164)
T 2xsd_C           93 IAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTP  159 (164)
T ss_dssp             -------------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC
T ss_pred             ccccccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhccC
Confidence            3345677889999999999999999999999999999999999999999999999999999999654

>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=99.73  E-value=1.4e-17  Score=104.77  Aligned_cols=65  Identities=18%  Similarity=0.281  Sum_probs=59.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHh---------------------CCCccchhhhhHHHhhH
Q psy9869          18 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHAL---------------------CLTERQIKIWFQNRRMK   76 (111)
Q Consensus        18 ~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l---------------------~l~~~~V~~WFqNrR~k   76 (111)
                      ..+..++.|+.|++.|+.+|+..|..++||+..+++.||..|                     +|++.+|++||+|||++
T Consensus         2 ~~~~~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k   81 (102)
T 2da6_A            2 SSGSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKE   81 (102)
T ss_dssp             TTCCSCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHH
Confidence            346688899999999999999999999999999999999999                     78999999999999999


Q ss_pred             hhHhHH
Q psy9869          77 LKKEIQ   82 (111)
Q Consensus        77 ~kk~~~   82 (111)
                      +++...
T Consensus        82 ~kr~~~   87 (102)
T 2da6_A           82 EAFRQK   87 (102)
T ss_dssp             HHHHHH
T ss_pred             HHHhhH
Confidence            988543

>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=99.73  E-value=8e-18  Score=96.53  Aligned_cols=55  Identities=31%  Similarity=0.389  Sum_probs=52.9

Q ss_pred             CCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          26 RQTYTRYQTLELEKEFHT---NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        26 r~~~s~~q~~~L~~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      ++.|+..|+..|+..|..   ++||+..++..||..+||++.+|++||+|+|+++|+.
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

>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=99.73  E-value=3.9e-18  Score=113.86  Aligned_cols=65  Identities=29%  Similarity=0.462  Sum_probs=55.6

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          16 EGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        16 ~~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      .+..+.+++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+|+||.
T Consensus        81 ~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           81 VGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             --------CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             cCCCCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            34456678889999999999999999999999999999999999999999999999999999984

>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=99.73  E-value=4.1e-18  Score=115.25  Aligned_cols=61  Identities=31%  Similarity=0.458  Sum_probs=54.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          20 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        20 ~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      +.+++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+|+||.
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            4678899999999999999999999999999999999999999999999999999999984

>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=99.72  E-value=1.4e-17  Score=111.70  Aligned_cols=63  Identities=30%  Similarity=0.497  Sum_probs=59.3

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869          17 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   79 (111)
Q Consensus        17 ~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   79 (111)
                      +..+.+++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+|+||
T Consensus        88 ~~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           88 GEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             SSCCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            445677889999999999999999999999999999999999999999999999999999986

>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=96.90  Aligned_cols=53  Identities=21%  Similarity=0.391  Sum_probs=50.4

Q ss_pred             CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          29 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        29 ~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      .+..|+..|+..|..++||+..++.+||..+||+..+|++||+|||.++|+.+
T Consensus        11 ~~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg~   63 (66)
T 3nau_A           11 KTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGI   63 (66)
T ss_dssp             CCHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhccC
Confidence            47899999999999999999999999999999999999999999999999754

>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=99.71  E-value=1.7e-17  Score=101.88  Aligned_cols=59  Identities=29%  Similarity=0.366  Sum_probs=55.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhh
Q psy9869          20 GLRRRGRQTYTRYQTLELEKEFHT---NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK   78 (111)
Q Consensus        20 ~~~r~~r~~~s~~q~~~L~~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k   78 (111)
                      +.+++.|+.|+..|+.+|+..|..   ++||+..++..||..+||++.+|++||+|+|+|+|
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            456677999999999999999999   99999999999999999999999999999999987

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

Probab=99.71  E-value=6e-18  Score=100.65  Aligned_cols=59  Identities=24%  Similarity=0.342  Sum_probs=54.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHH-HhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          22 RRRGRQTYTRYQTLELEKEF-HTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        22 ~r~~r~~~s~~q~~~L~~~F-~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      ..+.+.+++..|+..|+..| ..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus         8 g~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~   67 (72)
T 2cqx_A            8 GIKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPS   67 (72)
T ss_dssp             CCCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCC
Confidence            45667778889999999999 999999999999999999999999999999999999874

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

Probab=99.71  E-value=3.3e-17  Score=101.08  Aligned_cols=53  Identities=23%  Similarity=0.280  Sum_probs=51.6

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          28 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        28 ~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      .++..|+..|+..|..++||+..++..||..+||++.+|++||||||+|+++.
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~   69 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALK   69 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSC
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHH
Confidence            89999999999999999999999999999999999999999999999999884

>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=99.71  E-value=2.4e-17  Score=100.43  Aligned_cols=59  Identities=27%  Similarity=0.318  Sum_probs=54.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          23 RRGRQTYTRYQTLELEKEFHT---NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        23 r~~r~~~s~~q~~~L~~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      ++.+++|+..|+..|+..|..   ++||+..++..||..+||++.+|++||+|+|+++|+..
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            345667999999999999999   99999999999999999999999999999999999854

>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=99.70  E-value=7.3e-17  Score=99.51  Aligned_cols=56  Identities=23%  Similarity=0.253  Sum_probs=52.4

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          26 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        26 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      +..++..|+..|+..|..++||+..++..||..+||++.+|++||+|||+|+++..
T Consensus        17 ~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~   72 (89)
T 2dmp_A           17 FKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSME   72 (89)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSC
T ss_pred             cccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHh
Confidence            34489999999999999999999999999999999999999999999999998754

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

Probab=99.69  E-value=6e-17  Score=95.58  Aligned_cols=57  Identities=42%  Similarity=0.688  Sum_probs=53.0

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          25 GRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        25 ~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      .-.-.+..|+..|+..|..++||+..++..||..+||++.+|++||||||+|+|+..
T Consensus         7 ~~~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~   63 (69)
T 2l9r_A            7 HHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ   63 (69)
T ss_dssp             SCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSS
T ss_pred             CCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhh
Confidence            345678999999999999999999999999999999999999999999999999854

>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=99.69  E-value=1.6e-17  Score=111.81  Aligned_cols=61  Identities=26%  Similarity=0.412  Sum_probs=57.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          20 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        20 ~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      +.+++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+|+||.
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            5678889999999999999999999999999999999999999999999999999999984

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

Probab=99.68  E-value=6.6e-17  Score=94.10  Aligned_cols=53  Identities=15%  Similarity=0.147  Sum_probs=49.5

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869          27 QTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   79 (111)
Q Consensus        27 ~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   79 (111)
                      ...+..|+..|+..|..++||+..++..||..+||++.+|++||||||+|.++
T Consensus         8 ~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~   60 (64)
T 2e19_A            8 QPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS   60 (64)
T ss_dssp             CCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSC
T ss_pred             CCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCC
Confidence            34568999999999999999999999999999999999999999999999876

>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=99.67  E-value=3e-17  Score=95.43  Aligned_cols=50  Identities=26%  Similarity=0.334  Sum_probs=46.5

Q ss_pred             HHHHHHHHHHH-HhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          31 RYQTLELEKEF-HTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        31 ~~q~~~L~~~F-~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      +.++..|+..| ..++||+..++..||..|||++++|++||||||+++|+.
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            44799999999 579999999999999999999999999999999999874

>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=3.7e-17  Score=102.70  Aligned_cols=63  Identities=21%  Similarity=0.283  Sum_probs=53.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHH------------------hC---CCccchhhhhHHHhhHhh
Q psy9869          20 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHA------------------LC---LTERQIKIWFQNRRMKLK   78 (111)
Q Consensus        20 ~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~------------------l~---l~~~~V~~WFqNrR~k~k   78 (111)
                      ...++.|+.|+..|+..|+..|..++||+..++++||..                  ||   |++.+|++||||||++++
T Consensus         7 ~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k~k   86 (99)
T 1lfb_A            7 KKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEA   86 (99)
T ss_dssp             ------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHHHH
Confidence            456788999999999999999999999999999999999                  88   999999999999999988


Q ss_pred             HhHH
Q psy9869          79 KEIQ   82 (111)
Q Consensus        79 k~~~   82 (111)
                      +.+.
T Consensus        87 ~k~~   90 (99)
T 1lfb_A           87 FRHK   90 (99)
T ss_dssp             CCC-
T ss_pred             Hhch
Confidence            7543

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

Probab=99.66  E-value=8.5e-17  Score=108.99  Aligned_cols=64  Identities=19%  Similarity=0.258  Sum_probs=54.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869          19 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   82 (111)
Q Consensus        19 ~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   82 (111)
                      ...+++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+|.|+...
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            4567889999999999999999999999999999999999999999999999999999998543

>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=99.62  E-value=5e-16  Score=91.04  Aligned_cols=57  Identities=19%  Similarity=0.324  Sum_probs=50.4

Q ss_pred             CCCCHHHHHHHHHHHH---hcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869          27 QTYTRYQTLELEKEFH---TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA   83 (111)
Q Consensus        27 ~~~s~~q~~~L~~~F~---~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   83 (111)
                      ..|+..++.+|+..|.   .++||+..++..||..+||+..+|++||+|+|.|.++....
T Consensus         3 g~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~   62 (67)
T 3k2a_A            3 GIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMID   62 (67)
T ss_dssp             ---CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC--
T ss_pred             CcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHHH
Confidence            3689999999999999   99999999999999999999999999999999999986543

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

Probab=99.52  E-value=4.4e-15  Score=103.14  Aligned_cols=60  Identities=20%  Similarity=0.269  Sum_probs=53.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhC---------------------CCccchhhhhHHHhhHhh
Q psy9869          20 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALC---------------------LTERQIKIWFQNRRMKLK   78 (111)
Q Consensus        20 ~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~---------------------l~~~~V~~WFqNrR~k~k   78 (111)
                      ...++.|+.|+..|+..|+..|..++||+..+++.||..|+                     |++.+|++||+|||++.+
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            56678899999999999999999999999999999999999                     999999999999999876


Q ss_pred             H
Q psy9869          79 K   79 (111)
Q Consensus        79 k   79 (111)
                      .
T Consensus       193 ~  193 (194)
T 1ic8_A          193 F  193 (194)
T ss_dssp             -
T ss_pred             c
Confidence            4

>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=99.51  E-value=2.1e-14  Score=84.14  Aligned_cols=46  Identities=17%  Similarity=0.315  Sum_probs=43.9

Q ss_pred             HHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhH
Q psy9869          31 RYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK   76 (111)
Q Consensus        31 ~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k   76 (111)
                      .+|+..|+.+|..+++|+..++..||..+||+.++|++||||+|+.
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            4689999999999999999999999999999999999999999974

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

Probab=99.49  E-value=8.6e-14  Score=85.51  Aligned_cols=58  Identities=17%  Similarity=0.263  Sum_probs=53.1

Q ss_pred             CCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869          25 GRQTYTRYQTLELEKEFHT---NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   82 (111)
Q Consensus        25 ~r~~~s~~q~~~L~~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   82 (111)
                      ....|+..+..+|+.+|..   ++||+..++..||..+||++.||.+||+|+|.|.++...
T Consensus         8 ~~~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~   68 (89)
T 2lk2_A            8 HSHMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDML   68 (89)
T ss_dssp             CCCCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHH
Confidence            3457899999999999987   999999999999999999999999999999999988544

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

Probab=99.46  E-value=6.7e-14  Score=98.60  Aligned_cols=59  Identities=22%  Similarity=0.319  Sum_probs=52.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhC---------------------CCccchhhhhHHHhhHh
Q psy9869          19 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALC---------------------LTERQIKIWFQNRRMKL   77 (111)
Q Consensus        19 ~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~---------------------l~~~~V~~WFqNrR~k~   77 (111)
                      ..+.++.|+.|++.|+..|+..|..++||+..+++.||..||                     |++.+|++||+|||++.
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            456778899999999999999999999999999999999987                     78899999999999864

>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=99.33  E-value=8.1e-13  Score=98.84  Aligned_cols=55  Identities=25%  Similarity=0.435  Sum_probs=51.6

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhh
Q psy9869          24 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK   78 (111)
Q Consensus        24 ~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k   78 (111)
                      +.++.++..++..|+..|..++||+..++.+||..+||+++||++||+|||.|+|
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            3467789999999999999999999999999999999999999999999999875

>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=98.66  E-value=2.6e-09  Score=55.20  Aligned_cols=20  Identities=75%  Similarity=1.157  Sum_probs=17.7

Q ss_pred             cchhhhhHHHhhHhhHhHHH
Q psy9869          64 RQIKIWFQNRRMKLKKEIQA   83 (111)
Q Consensus        64 ~~V~~WFqNrR~k~kk~~~~   83 (111)
                      +||+|||||||+|+||....
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~   20 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFN   20 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHH
T ss_pred             CCceeccHHHHHHHHHHhHH
Confidence            58999999999999997664

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

Probab=96.45  E-value=0.0036  Score=36.24  Aligned_cols=44  Identities=20%  Similarity=0.335  Sum_probs=39.0

Q ss_pred             CHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHH
Q psy9869          30 TRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNR   73 (111)
Q Consensus        30 s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNr   73 (111)
                      ++.-..+|+.+|.............|+.+..|+..+|+-||-.+
T Consensus        14 ~p~~~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~k   57 (70)
T 2ys9_A           14 PPPDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSR   57 (70)
T ss_dssp             CCCCCHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             CCCcchHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHhc
Confidence            33445899999999999999999999999999999999999644

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

Probab=87.52  E-value=0.73  Score=24.79  Aligned_cols=45  Identities=20%  Similarity=0.359  Sum_probs=30.7

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhH
Q psy9869          26 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQ   71 (111)
Q Consensus        26 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFq   71 (111)
                      +..++.+........+.. ..+.......+|..+||+...|..|..
T Consensus         3 r~~ys~efK~~~~~~~~~-g~s~~~~~~~vA~~~gIs~~tl~~W~~   47 (59)
T 2glo_A            3 RRIFTPHFKLQVLESYRN-DNDCKGNQRATARKYNIHRRQIQKWLQ   47 (59)
T ss_dssp             CCCCCHHHHHHHHHHHHH-CTTTTTCHHHHHHHTTSCHHHHHHHHT
T ss_pred             CCcCCHHHHHHHHHHHHc-CCCcchHHHHHHHHHCcCHHHHHHHHH
Confidence            456888876655444443 333222356889999999999999974

>1hlv_A CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} SCOP: a.4.1.7 a.4.1.7 PDB: 1bw6_A

Probab=83.79  E-value=3.5  Score=25.23  Aligned_cols=48  Identities=19%  Similarity=0.249  Sum_probs=36.9

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhh
Q psy9869          25 GRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM   75 (111)
Q Consensus        25 ~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~   75 (111)
                      .|..++.++...+-..+..++.+..   ..+|..+|++...|..|..++..
T Consensus         4 ~r~~~t~e~K~~iv~~~~~~g~~~~---~~~A~~~gvs~stl~~~~~~~~~   51 (131)
T 1hlv_A            4 KRRQLTFREKSRIIQEVEENPDLRK---GEIARRFNIPPSTLSTILKNKRA   51 (131)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSCH---HHHHHHHTCCHHHHHHHHHTHHH
T ss_pred             cceeCCHHHHHHHHHHHHHCCCCcH---HHHHHHhCCCHHHHHHHHhchhh
Confidence            5778999998777777755665543   35788999999999999977654

---

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	111
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	2e-21
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	4e-21
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	7e-20
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	1e-19
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	1e-19
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	2e-19
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	2e-17
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	3e-17
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	3e-17
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	4e-17
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	6e-17
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	8e-17
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	1e-16
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	2e-16
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	1e-15
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	2e-15
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	2e-15
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	4e-15
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	1e-14
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	3e-14
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	5e-14
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	6e-14
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	1e-13
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	2e-13
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	2e-13
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	2e-13
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	5e-13
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	1e-12
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	2e-12
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	3e-10
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	1e-09
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	2e-08

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 56

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

 Score = 77.9 bits (192), Expect = 2e-21
 Identities = 50/55 (90%), Positives = 51/55 (92%)

Query: 26 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          RQTYTRYQTLELEKEFH N YLTRRRRIE+AHAL LTERQIKIWFQNRRMK KKE
Sbjct: 1  RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 55

>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 = 77.9 bits (192), Expect = 4e-21
 Identities = 40/59 (67%), Positives = 46/59 (77%)

Query: 22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
           R+ R  YT++QTLELEKEF  N YLTR RR E+A  L LTERQ+KIWFQNRRMK+KK 
Sbjct: 13 TRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKI 71

>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 = 74.1 bits (182), Expect = 7e-20
 Identities = 26/57 (45%), Positives = 38/57 (66%)

Query: 23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          + G+  ++  QT+ELEK+F T  YL+   R  +A  L L+ERQ+K WFQNRR K ++
Sbjct: 1  KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 57

>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 = 73.7 bits (181), Expect = 1e-19
 Identities = 23/58 (39%), Positives = 34/58 (58%)

Query: 23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          +R R ++T+ Q   LEKEF   HY     R  +A  + L E +I++WF NRR K ++E
Sbjct: 2  QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE 59

>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 = 1e-19
 Identities = 34/59 (57%), Positives = 39/59 (66%)

Query: 22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
              R  +T  Q  ELEKEFH N YL+R RR+E+A  L L E Q+KIWFQNRRMK KK 
Sbjct: 27 PSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKR 85

>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 = 73.0 bits (179), Expect = 2e-19
 Identities = 27/57 (47%), Positives = 41/57 (71%)

Query: 23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          R+ R  Y++ Q  ELE+E+  N ++T+ +R +++ A  L+ERQI IWFQNRR+K KK
Sbjct: 2  RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 58

>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 = 68.0 bits (166), Expect = 2e-17
 Identities = 26/53 (49%), Positives = 34/53 (64%)

Query: 24 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76
          R R  ++  Q   L++EF+ N YLT RRR +++  L L E QIKIWFQN R K
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>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 = 67.6 bits (165), Expect = 3e-17
 Identities = 30/57 (52%), Positives = 39/57 (68%)

Query: 24 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          R R  +TR Q   LEKEF+  +Y++R RR E+A  L L E  IK+WFQNRRMK K++
Sbjct: 1  RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 57

>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 = 67.6 bits (165), Expect = 3e-17
 Identities = 25/63 (39%), Positives = 38/63 (60%)

Query: 22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81
          +RR R T++  Q  ELE+ F    Y     R E+A    LTE +I++WFQNRR +L+K+ 
Sbjct: 2  QRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH 61

Query: 82 QAI 84
           ++
Sbjct: 62 TSV 64

>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 = 67.3 bits (164), Expect = 4e-17
 Identities = 26/64 (40%), Positives = 36/64 (56%)

Query: 23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82
          RR R T+T  Q  ELE+ F    YLT  R  +++  L L   Q+KIWF+NRR + K +  
Sbjct: 2  RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 61

Query: 83 AIKE 86
            K+
Sbjct: 62 QHKD 65

>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 = 66.9 bits (163), Expect = 6e-17
 Identities = 27/57 (47%), Positives = 36/57 (63%)

Query: 23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          R+ R  +T  Q L LE++F    YL+   R E + +L LTE Q+KIWFQNRR K K+
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 66

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 66.8 bits (163), Expect = 8e-17
 Identities = 17/64 (26%), Positives = 26/64 (40%)

Query: 22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81
            R R      Q   L   +  N       + ++     L+ R I++WFQN+R K KK  
Sbjct: 3  TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS 62

Query: 82 QAIK 85
            +K
Sbjct: 63 IMMK 66

>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 = 66.2 bits (161), Expect = 1e-16
 Identities = 26/65 (40%), Positives = 37/65 (56%)

Query: 16 EGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 75
          +G    +R+ R  +T+ QT ELE+ F    YL+   R  +A  + LT  Q+KIWFQN R 
Sbjct: 3  DGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRY 62

Query: 76 KLKKE 80
          K K+ 
Sbjct: 63 KTKRA 67

>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 = 2e-16
 Identities = 12/49 (24%), Positives = 20/49 (40%)

Query: 26 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRR 74
          R  +T  Q   L   F  N   ++  +I ++  L L    +  +F N R
Sbjct: 2  RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

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

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

 Score = 63.6 bits (155), Expect = 1e-15
 Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 3/60 (5%)

Query: 23 RRGRQTYTRYQTLELEKEF---HTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          +  R    ++ T  +         + Y T   + ++A    LT  Q+  WF N R ++ +
Sbjct: 3  KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQ 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 = 63.4 bits (154), Expect = 2e-15
 Identities = 24/60 (40%), Positives = 37/60 (61%)

Query: 21 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          +RR+ R  +++ Q  ELE+ F    YL+   R  +A  + LT  Q+KIWFQN R K+K++
Sbjct: 1  MRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60

>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 = 62.7 bits (152), Expect = 2e-15
 Identities = 23/58 (39%), Positives = 32/58 (55%)

Query: 23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
          RR R  +T  Q  +LE  F  N Y     R E+A    LTE ++++WF+NRR K +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 = 62.0 bits (151), Expect = 4e-15
 Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 1/51 (1%)

Query: 30 TRYQTLELEKEF-HTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          T      LEK F     +   +R   ++  L    R I+ WF+ RR + K 
Sbjct: 1  TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 51

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 53

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

 Score = 61.1 bits (148), Expect = 1e-14
 Identities = 14/53 (26%), Positives = 27/53 (50%)

Query: 26 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 78
          + + +      LE+ F     L  + + E+A    +T  Q+++WF N+RM+ K
Sbjct: 1  KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 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 = 60.5 bits (146), Expect = 3e-14
 Identities = 17/73 (23%), Positives = 29/73 (39%), Gaps = 15/73 (20%)

Query: 23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMA---------------HALCLTERQIK 67
          R  R T+ +     +E  F+ N Y    +R E+A                   +T  ++ 
Sbjct: 1  RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVY 60

Query: 68 IWFQNRRMKLKKE 80
           WF NRR ++K+ 
Sbjct: 61 NWFANRRKEIKRR 73

>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 = 59.7 bits (144), Expect = 5e-14
 Identities = 13/60 (21%), Positives = 22/60 (36%), Gaps = 1/60 (1%)

Query: 22 RRRGRQTYTRYQTLELEKEFH-TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
            R R   +      L+   H    Y  +     ++  L L +  I  +FQN+R  +K  
Sbjct: 7  GPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS 66

>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 = 59.0 bits (143), Expect = 6e-14
 Identities = 19/60 (31%), Positives = 24/60 (40%), Gaps = 5/60 (8%)

Query: 23 RRGRQTYTRYQTLELEKEFH---TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          R  R  +T+     LE  F     N YL  +    +     L+  QIK W  NRR K K 
Sbjct: 1  RGHR--FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} Length = 72

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

 Score = 58.8 bits (142), Expect = 1e-13
 Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 1/59 (1%)

Query: 23 RRGRQTYTRYQTLELEKEFH-TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80
            G  T T  Q   LE  F+  N +        +A    LTE Q + WF+ R  + ++ 
Sbjct: 2  SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60

>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 = 58.0 bits (140), Expect = 2e-13
 Identities = 15/56 (26%), Positives = 28/56 (50%)

Query: 24 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          + R T +      LE+ F  +   + +  + MA  L L +  +++WF NRR + K+
Sbjct: 1  KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 56

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 59

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

 Score = 57.9 bits (140), Expect = 2e-13
 Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 3/60 (5%)

Query: 20 GLRRRGRQTYTRYQTLELEKEF-HTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 78
          G++              LEK F     Y   +R   ++  L  + R+I+ WF++RR + K
Sbjct: 1  GIKDSPVNKVE--PNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

>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 = 58.5 bits (141), Expect = 2e-13
 Identities = 9/70 (12%), Positives = 19/70 (27%), Gaps = 4/70 (5%)

Query: 15 DEGANGLRRRGRQTYTRYQTLELEKEFH----TNHYLTRRRRIEMAHALCLTERQIKIWF 70
             + G  +R R  +T  Q  ++                    +      +  + +KIW 
Sbjct: 10 PSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWM 69

Query: 71 QNRRMKLKKE 80
           N +      
Sbjct: 70 HNNKNSGPSS 79

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Length = 73

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.3 bits (138), Expect = 5e-13
 Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 3/67 (4%)

Query: 23 RRGRQTYTRYQTLELEK---EFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          RR R+ + +  T  L +      +N Y +   + E+A    +T  Q+  WF N+R++ KK
Sbjct: 2  RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61

Query: 80 EIQAIKE 86
           I   +E
Sbjct: 62 NIGKFQE 68

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 67

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

 Score = 55.8 bits (134), Expect = 1e-12
 Identities = 16/58 (27%), Positives = 28/58 (48%)

Query: 22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          R+R R +        LE  F      + ++   +A+ L L +  +++WF NRR K K+
Sbjct: 8  RKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR 65

>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 = 55.9 bits (134), Expect = 2e-12
 Identities = 12/63 (19%), Positives = 24/63 (38%)

Query: 23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82
           +  +  T  Q   L+  F  +  LT      +     LT R+I  WF  ++     + +
Sbjct: 5  PQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEE 64

Query: 83 AIK 85
           ++
Sbjct: 65 KME 67

>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 = 49.6 bits (118), Expect = 3e-10
 Identities = 17/54 (31%), Positives = 25/54 (46%)

Query: 26 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          R +      + LEK F  N   T      +A  L + +  I++WF NRR K K+
Sbjct: 2  RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 55

>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 = 48.6 bits (115), Expect = 1e-09
 Identities = 13/60 (21%), Positives = 21/60 (35%)

Query: 20 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79
          G      +  T+ Q   L+  F    +  R    ++     L   +I  WF + R  LK 
Sbjct: 1  GSSGSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH 60

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Length = 78

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Rat (Rattus rattus) [TaxId: 10117]

 Score = 45.5 bits (107), Expect = 2e-08
 Identities = 10/78 (12%), Positives = 21/78 (26%), Gaps = 21/78 (26%)

Query: 26 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHAL---------------------CLTER 64
          R  +       L + +      ++  R  +                          +TE 
Sbjct: 1  RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 65 QIKIWFQNRRMKLKKEIQ 82
          ++  WF NRR +     +
Sbjct: 61 RVYNWFANRRKEEAFRHK 78

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	111
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.86
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.85
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.85
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.85
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.85
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.85
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.85
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.84
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.83
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.83
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.83
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.83
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.82
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.81
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.81
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.8
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.8
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.8
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.79
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.79
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.78
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.78
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.75
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.73
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.72
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.72
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.71
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.69
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.68
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.65
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.63
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.61
d1hlva1	66	DNA-binding domain of centromere binding protein B	93.24

>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=3e-22  Score=113.29  Aligned_cols=57  Identities=47%  Similarity=0.797  Sum_probs=55.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869          23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   79 (111)
Q Consensus        23 r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   79 (111)
                      ++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||+|+|+||
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            677899999999999999999999999999999999999999999999999999885

>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=99.85  E-value=8e-22  Score=114.59  Aligned_cols=61  Identities=41%  Similarity=0.638  Sum_probs=57.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869          22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   82 (111)
Q Consensus        22 ~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   82 (111)
                      +++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||||||+++|+...
T Consensus         1 Prr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~   61 (67)
T d1zq3p1           1 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD   61 (67)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhh
Confidence            4678999999999999999999999999999999999999999999999999999998553

>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=99.85  E-value=8.8e-22  Score=111.43  Aligned_cols=57  Identities=47%  Similarity=0.792  Sum_probs=55.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869          23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   79 (111)
Q Consensus        23 r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   79 (111)
                      ++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||||+|+++||
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            467999999999999999999999999999999999999999999999999999987

>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=99.85  E-value=5.6e-22  Score=111.31  Aligned_cols=55  Identities=91%  Similarity=1.306  Sum_probs=53.6

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          26 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        26 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      |+.||..|+..|+..|..++||+..++..||..|||++.+|++||||||+|+||+
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk~   55 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   55 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhhc
Confidence            6899999999999999999999999999999999999999999999999999985

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

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

Probab=99.85  E-value=3.3e-21  Score=114.69  Aligned_cols=64  Identities=63%  Similarity=0.847  Sum_probs=59.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869          20 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA   83 (111)
Q Consensus        20 ~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   83 (111)
                      ...++.|+.|+..|+.+|+.+|..++||+..++..||..|||++.+|++||||+|+|+|+....
T Consensus        11 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~   74 (77)
T d1pufa_          11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             CTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHH
Confidence            4467789999999999999999999999999999999999999999999999999999986554

>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=99.85  E-value=2.1e-21  Score=112.14  Aligned_cols=62  Identities=40%  Similarity=0.653  Sum_probs=58.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869          22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA   83 (111)
Q Consensus        22 ~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   83 (111)
                      +++.|+.|+..|+.+|+.+|..++||+..++..||..+||++.+|++||||+|+++|++...
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            57889999999999999999999999999999999999999999999999999999996553

>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=99.85  E-value=1.4e-21  Score=110.26  Aligned_cols=57  Identities=46%  Similarity=0.790  Sum_probs=55.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869          23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   79 (111)
Q Consensus        23 r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   79 (111)
                      ++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||||+|+++||
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            568999999999999999999999999999999999999999999999999999986

>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=1.5e-21  Score=110.11  Aligned_cols=57  Identities=53%  Similarity=0.781  Sum_probs=54.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          24 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        24 ~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      +.|+.||..|+..|+..|..++||+..++..||..+||++.+|++||||+|+++||+
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            468999999999999999999999999999999999999999999999999999973

>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=99.83  E-value=1.3e-21  Score=116.49  Aligned_cols=66  Identities=39%  Similarity=0.654  Sum_probs=60.8

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          16 EGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        16 ~~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      ++.+..+++.|+.|+..|+.+|+.+|..++||+..++..||..|||++.+|++||||+|+|+|+..
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            355566788899999999999999999999999999999999999999999999999999998743

>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=99.83  E-value=3.9e-21  Score=117.02  Aligned_cols=65  Identities=54%  Similarity=0.745  Sum_probs=55.4

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          17 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        17 ~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      ...+.+++.|+.|+..|+.+|+.+|..++||+..+++.||..|||++.+|++||||+|+++|+..
T Consensus        22 ~~~~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~   86 (88)
T d1b72a_          22 PGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRE   86 (88)
T ss_dssp             --------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhc
Confidence            33456678899999999999999999999999999999999999999999999999999999854

>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=4.1e-21  Score=106.77  Aligned_cols=53  Identities=49%  Similarity=0.797  Sum_probs=51.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhH
Q psy9869          24 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK   76 (111)
Q Consensus        24 ~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k   76 (111)
                      ++|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||||||+|
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

>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=1.2e-20  Score=109.82  Aligned_cols=60  Identities=38%  Similarity=0.632  Sum_probs=57.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869          23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   82 (111)
Q Consensus        23 r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   82 (111)
                      ++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|+|+++|+...
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~   61 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK   61 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhh
Confidence            668999999999999999999999999999999999999999999999999999998544

>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=1.2e-20  Score=109.74  Aligned_cols=60  Identities=40%  Similarity=0.720  Sum_probs=57.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        22 ~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      +++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||+|+|+++|+..
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~   61 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA   61 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhcc
Confidence            578899999999999999999999999999999999999999999999999999999854

>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=99.81  E-value=2.8e-20  Score=109.22  Aligned_cols=58  Identities=28%  Similarity=0.329  Sum_probs=55.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          23 RRGRQTYTRYQTLELEKEFHT-NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        23 r~~r~~~s~~q~~~L~~~F~~-~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      ++.|++||..|+.+|+..|.. ++||+...++.||..+||++.+|++||||||+++|+.
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~   60 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS   60 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhc
Confidence            578999999999999999986 7899999999999999999999999999999999884

>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=6.8e-21  Score=108.39  Aligned_cols=58  Identities=40%  Similarity=0.625  Sum_probs=56.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        23 r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      ++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            5779999999999999999999999999999999999999999999999999999984

>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=99.80  E-value=3.7e-20  Score=107.11  Aligned_cols=61  Identities=26%  Similarity=0.328  Sum_probs=57.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          21 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        21 ~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      ..++.|+.|+.+|+.+|+.+|..++||+..++..||..+||++.+|++||+|+|++.|+..
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            3578899999999999999999999999999999999999999999999999999998743

>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=99.80  E-value=3.9e-20  Score=107.28  Aligned_cols=61  Identities=26%  Similarity=0.383  Sum_probs=57.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          20 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        20 ~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      ..+++.|+.|+..|+..|+.+|..++||+..++..||..+||++.+|++||+|+|.++||.
T Consensus         6 ~~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_           6 QARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             CCSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             hccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            3457889999999999999999999999999999999999999999999999999999874

>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=99.80  E-value=4.7e-20  Score=102.44  Aligned_cols=53  Identities=26%  Similarity=0.481  Sum_probs=51.3

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhh
Q psy9869          26 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK   78 (111)
Q Consensus        26 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k   78 (111)
                      |+.|+++|+.+|+..|..++||+..++..||..+||++.+|++||+|+|+++|
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            68999999999999999999999999999999999999999999999999875

>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=99.79  E-value=6.6e-20  Score=103.58  Aligned_cols=57  Identities=26%  Similarity=0.437  Sum_probs=54.6

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          24 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        24 ~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      +.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.
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            468999999999999999999999999999999999999999999999999999873

>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=99.79  E-value=9e-20  Score=106.90  Aligned_cols=62  Identities=21%  Similarity=0.230  Sum_probs=57.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHH-hcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          19 NGLRRRGRQTYTRYQTLELEKEFH-TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        19 ~~~~r~~r~~~s~~q~~~L~~~F~-~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      +...++.|+.|+.+|+.+|+.+|. .++||+..+++.||..+||+..+|++||+|+|++.|+.
T Consensus         4 ~~~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk~   66 (71)
T d1wi3a_           4 GSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS   66 (71)
T ss_dssp             CCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCSS
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhccc
Confidence            345678899999999999999997 58999999999999999999999999999999999874

>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=99.78  E-value=1.6e-19  Score=108.57  Aligned_cols=60  Identities=30%  Similarity=0.481  Sum_probs=55.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhC---------------CCccchhhhhHHHhhHhhHhHH
Q psy9869          23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALC---------------LTERQIKIWFQNRRMKLKKEIQ   82 (111)
Q Consensus        23 r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~---------------l~~~~V~~WFqNrR~k~kk~~~   82 (111)
                      |+.|+.|+..|+.+|+.+|..++||+..+++.||..||               |++.+|++||||||+++|+...
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~   75 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRAN   75 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhh
Confidence            57899999999999999999999999999999999875               8999999999999999999543

>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=99.78  E-value=1.5e-19  Score=101.71  Aligned_cols=56  Identities=30%  Similarity=0.437  Sum_probs=54.0

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          25 GRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        25 ~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      .|+.|+..++..|+..|..++||+..++..||..+||++.+|++||+|+|.++|+.
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            48999999999999999999999999999999999999999999999999999974

>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=99.75  E-value=8.3e-19  Score=104.90  Aligned_cols=63  Identities=14%  Similarity=0.152  Sum_probs=56.7

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHh----cCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869          17 GANGLRRRGRQTYTRYQTLELEKEFHT----NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   79 (111)
Q Consensus        17 ~~~~~~r~~r~~~s~~q~~~L~~~F~~----~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   79 (111)
                      +..+.+++.|+.|+..|+..|+.+|+.    ++||+..+++.||..+||++.+|++||||+|.+.++
T Consensus        12 ~~~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          12 SSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            334566789999999999999999986    799999999999999999999999999999988764

>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=99.73  E-value=9e-19  Score=96.06  Aligned_cols=50  Identities=24%  Similarity=0.336  Sum_probs=48.7

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHh
Q psy9869          25 GRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRR   74 (111)
Q Consensus        25 ~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR   74 (111)
                      +|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||+|
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            58999999999999999999999999999999999999999999999987

>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=7.8e-18  Score=99.70  Aligned_cols=56  Identities=21%  Similarity=0.239  Sum_probs=51.4

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869          26 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        26 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      +..+|.+|+.+|+..|..++||+..++..||..+||++.+|++||+|+|++.++..
T Consensus         8 ~k~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~   63 (76)
T d2ecba1           8 FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE   63 (76)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCC
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHh
Confidence            33469999999999999999999999999999999999999999999999877643

>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=99.72  E-value=8.6e-18  Score=99.50  Aligned_cols=57  Identities=21%  Similarity=0.281  Sum_probs=53.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869          24 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   80 (111)
Q Consensus        24 ~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   80 (111)
                      ..+.+++.+|+.+|+..|..++||+..++..||..+||+..+|++||+|+|.++|+.
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            345568999999999999999999999999999999999999999999999999974

>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=99.71  E-value=4.9e-18  Score=99.86  Aligned_cols=60  Identities=32%  Similarity=0.538  Sum_probs=55.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869          23 RRGRQTYTRYQTLELEKEFHT---NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   82 (111)
Q Consensus        23 r~~r~~~s~~q~~~L~~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   82 (111)
                      ++.|+.|+..++.+|+.+|..   +|||+..++..||..+||+..+|++||+|+|.+.++...
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~~   64 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG   64 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccch
Confidence            567899999999999999974   889999999999999999999999999999999987543

>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=99.69  E-value=5.7e-18  Score=93.46  Aligned_cols=50  Identities=28%  Similarity=0.361  Sum_probs=46.5

Q ss_pred             CHHHHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869          30 TRYQTLELEKEFHT-NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   79 (111)
Q Consensus        30 s~~q~~~L~~~F~~-~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   79 (111)
                      |++|..+|+.+|.. ++||+..++..||..+||+..+|++||+|||+++|+
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            45689999999986 799999999999999999999999999999999875

>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=99.68  E-value=1.3e-17  Score=99.12  Aligned_cols=56  Identities=18%  Similarity=0.244  Sum_probs=52.2

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhC---------------------CCccchhhhhHHHhhHhhHhH
Q psy9869          26 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALC---------------------LTERQIKIWFQNRRMKLKKEI   81 (111)
Q Consensus        26 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~---------------------l~~~~V~~WFqNrR~k~kk~~   81 (111)
                      |.+|++.|+.+|+.+|..++||+..+++.||..|+                     |++.+|++||+|||++.|+..
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr~~   77 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFRH   77 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCCC
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHHhc
Confidence            67899999999999999999999999999999994                     888999999999999998753

>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=99.65  E-value=4.6e-17  Score=91.92  Aligned_cols=55  Identities=25%  Similarity=0.387  Sum_probs=50.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhh
Q psy9869          24 RGRQTYTRYQTLELEKEFHT-NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK   78 (111)
Q Consensus        24 ~~r~~~s~~q~~~L~~~F~~-~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k   78 (111)
                      +.+..++.++..+|+.+|.. ++||+..++..||..+||++.+|++||+|||+++|
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            45677788888999999976 68999999999999999999999999999999976

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.63  E-value=3.2e-16  Score=88.69  Aligned_cols=53  Identities=32%  Similarity=0.426  Sum_probs=49.0

Q ss_pred             CCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869          27 QTYTRYQTLELEKEFHT---NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   79 (111)
Q Consensus        27 ~~~s~~q~~~L~~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   79 (111)
                      .+|+.+++.+|+.+|..   +|||+..+++.||..+||+..+|++||+|+|.+.|+
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            35999999999999976   479999999999999999999999999999998875

>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=99.61  E-value=9.9e-16  Score=87.17  Aligned_cols=56  Identities=21%  Similarity=0.302  Sum_probs=51.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhh
Q psy9869          23 RRGRQTYTRYQTLELEKEFHT---NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK   78 (111)
Q Consensus        23 r~~r~~~s~~q~~~L~~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k   78 (111)
                      ++.|+.|+.++..+|+.+|..   +|||+..++..||..+||+..+|.+||+|+|.+..
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            556788999999999999975   89999999999999999999999999999998754

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=93.24  E-value=0.14  Score=27.79  Aligned_cols=46  Identities=20%  Similarity=0.273  Sum_probs=37.7

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHh
Q psy9869          26 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRR   74 (111)
Q Consensus        26 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR   74 (111)
                      |..++-.+...+...|+.++...   ..++|..+|+....|..|..|+.
T Consensus         5 Rk~LT~~eK~~ii~~~e~g~k~s---q~eIA~~fGv~~STvs~IlKnK~   50 (66)
T d1hlva1           5 RRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNKR   50 (66)
T ss_dssp             SCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTHH
T ss_pred             cccCCHHHHHHHHHHHHcCCcch---HHHHHHHhCCChhHHHHHHHHHH
Confidence            55689988888888888887555   45689999999999999998743