Psyllid ID: psy1653

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90------
Protein Sequence
MGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELNEQEKQAQAQKAAAAALAAAAVDH
Secondary Structure (PSIPRED)
ccccccccccccHHHHHHHHHHHHHHcccccccHHHHHHHHHHHcccHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHccHHccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mganglrrrgrqtyTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELNEQEKQAQAQKAAAAALAAAAVDH
Flexible Loop (DISEMBL)
mganglrrrgrqtytryqtlelekefhtnhyltrrRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELNEQEKQAQAQKAAAAALAAAAVDH
Low Complexity Region (SEG)
MGANglrrrgrqtytryqtlELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELNeqekqaqaqkaaaaalaaaaVDH
Disordered region (IsUnstruct)
****************YQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK*********************************
Disordered Region (DISOPRED)
*************YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRR*************************************
Disordered Region (DISEMBL)
*********GRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN***********************
Disordered Region (DISPRO)
***********QTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE*******************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxAVDH
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	96	2.2.26 [Sep-21-2011]
Q8T940	253	Homeotic protein ultrabit	N/A	N/A	0.968	0.367	0.978	1e-46
P83950	389	Homeotic protein ultrabit	N/A	N/A	0.760	0.187	0.972	2e-37
P83949	389	Homeotic protein ultrabit	no	N/A	0.760	0.187	0.972	2e-37
P20822	385	Homeotic protein ultrabit	yes	N/A	0.760	0.189	0.972	1e-35
P29552	239	Homeobox protein abdomina	N/A	N/A	0.770	0.309	0.866	1e-32
Q05007	139	Homeobox protein abdomina	N/A	N/A	0.760	0.525	0.878	2e-32
B0W1V2	216	Homeobox protein abdomina	N/A	N/A	0.760	0.337	0.864	6e-32
P29555	590	Homeobox protein abdomina	no	N/A	0.906	0.147	0.75	6e-32
P29556	157	Homeobox protein abdomina	N/A	N/A	0.760	0.464	0.864	2e-31
Q26430	97	Homeobox protein abdomina	N/A	N/A	0.760	0.752	0.864	4e-31

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

 Score =  184 bits (468), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 91/93 (97%), Positives = 91/93 (97%)

Query: 2   GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
           GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct: 154 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 213

Query: 62  LKKEIQAIKELNEQEKQAQAQKAAAAALAAAAV 94
           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 =  153 bits (387), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 71/73 (97%), Positives = 72/73 (98%)

Query: 1   MGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60
           +G NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM
Sbjct: 289 LGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 348

Query: 61  KLKKEIQAIKELN 73
           KLKKEIQAIKELN
Sbjct: 349 KLKKEIQAIKELN 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 =  153 bits (387), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 71/73 (97%), Positives = 72/73 (98%)

Query: 1   MGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60
           +G NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM
Sbjct: 289 LGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 348

Query: 61  KLKKEIQAIKELN 73
           KLKKEIQAIKELN
Sbjct: 349 KLKKEIQAIKELN 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 =  147 bits (372), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 71/73 (97%), Positives = 72/73 (98%)

Query: 1   MGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60
           +G NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM
Sbjct: 284 LGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 343

Query: 61  KLKKEIQAIKELN 73
           KLKKEIQAIKELN
Sbjct: 344 KLKKEIQAIKELN 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|P29552|ABDA_AEDAE Homeobox protein abdominal-A homolog OS=Aedes aegypti GN=abd-A PE=3 SV=2

 Score =  138 bits (347), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 65/75 (86%), Positives = 71/75 (94%), Gaps = 1/75 (1%)

Query: 2  GANGL-RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60
          G NG  RRRGRQTYTR+QTLELEKEFH NHYLTRRRRIE+AHALCLTERQIKIWFQNRRM
Sbjct: 15 GPNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRM 74

Query: 61 KLKKEIQAIKELNEQ 75
          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 (344), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 65/74 (87%), Positives = 70/74 (94%), Gaps = 1/74 (1%)

Query: 3  ANGL-RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
           NG  RRRGRQTYTRYQTLELEKEFH NHYLTRRRRIE+AHALCLTERQIKIWFQNRRMK
Sbjct: 1  PNGCPRRRGRQTYTRYQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 60

Query: 62 LKKEIQAIKELNEQ 75
          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|B0W1V2|ABDA_CULQU Homeobox protein abdominal-A homolog OS=Culex quinquefasciatus GN=abd-A PE=3 SV=1

 Score =  135 bits (341), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 64/74 (86%), Positives = 70/74 (94%), Gaps = 1/74 (1%)

Query: 3   ANGL-RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
            NG  RRRGRQTYTR+QTLELEKEFH NHYLTRRRRIE+AHALCLTERQIKIWFQNRRMK
Sbjct: 38  PNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 97

Query: 62  LKKEIQAIKELNEQ 75
           LKKE++A+KE+NEQ
Sbjct: 98  LKKELRAVKEINEQ 111

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

 Score =  135 bits (340), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 66/88 (75%), Positives = 77/88 (87%), Gaps = 1/88 (1%)

Query: 2   GANGL-RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60
           G NG  RRRGRQTYTR+QTLELEKEFH NHYLTRRRRIE+AHALCLTERQIKIWFQNRRM
Sbjct: 392 GPNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRM 451

Query: 61  KLKKEIQAIKELNEQEKQAQAQKAAAAA 88
           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 =  134 bits (337), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 64/74 (86%), Positives = 70/74 (94%), Gaps = 1/74 (1%)

Query: 3  ANGL-RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
           NG  RRRGRQTYTR+QTLELEKEFH NHYLTRRRRIE+AHALCLTERQIKIWFQNRRMK
Sbjct: 1  PNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 60

Query: 62 LKKEIQAIKELNEQ 75
          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)

>sp|Q26430|ABDA_MANSE Homeobox protein abdominal-A homolog (Fragment) OS=Manduca sexta GN=ABD-A PE=3 SV=1

 Score =  133 bits (334), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 64/74 (86%), Positives = 71/74 (95%), Gaps = 1/74 (1%)

Query: 3  ANGL-RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
          +NG  RRRGRQTYTR+QTLELEKEFH NHYLTRRRRIE+AHALCLTERQIKIWFQNRRMK
Sbjct: 1  SNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 60

Query: 62 LKKEIQAIKELNEQ 75
          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. Required for segmental identity of the first through tenth abdominal segments.

Manduca sexta (taxid: 7130)

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	96
164682494	254	homeobox protein [Bombyx mori]	0.968	0.366	0.989	1e-45
166429526	254	ultrabithorax [Bombyx mori] gi|164682496	0.968	0.366	0.978	4e-45
426432569	254	ultrabithorax [Biston betularia]	0.968	0.366	0.978	4e-45
47115878	253	RecName: Full=Homeotic protein ultrabith	0.968	0.367	0.978	5e-45
195349282	201	GM15411 [Drosophila sechellia] gi|194122	0.947	0.452	0.989	2e-44
392301341	105	ultrabithorax, partial [Notonecta undula	0.937	0.857	1.0	2e-43
45553381	355	ultrabithorax, isoform F [Drosophila mel	0.947	0.256	0.989	2e-43
390178469	360	Ubx, isoform B [Drosophila pseudoobscura	0.947	0.252	0.989	3e-43
87042406	267	ultrabithorax [Strigamia maritima]	0.885	0.318	0.964	5e-42
391339782	178	PREDICTED: homeotic protein ultrabithora	0.968	0.522	0.881	2e-41

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

 Score =  187 bits (474), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 92/93 (98%), Positives = 92/93 (98%)

Query: 2   GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
           GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct: 155 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 214

Query: 62  LKKEIQAIKELNEQEKQAQAQKAAAAALAAAAV 94
           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 =  184 bits (468), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 91/93 (97%), Positives = 91/93 (97%)

Query: 2   GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
           GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct: 155 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 214

Query: 62  LKKEIQAIKELNEQEKQAQAQKAAAAALAAAAV 94
           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 =  184 bits (468), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 91/93 (97%), Positives = 91/93 (97%)

Query: 2   GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
           GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct: 155 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 214

Query: 62  LKKEIQAIKELNEQEKQAQAQKAAAAALAAAAV 94
           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 =  184 bits (468), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 91/93 (97%), Positives = 91/93 (97%)

Query: 2   GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
           GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct: 154 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 213

Query: 62  LKKEIQAIKELNEQEKQAQAQKAAAAALAAAAV 94
           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 =  182 bits (463), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 90/91 (98%), Positives = 90/91 (98%)

Query: 4   NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63
           NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK
Sbjct: 104 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 163

Query: 64  KEIQAIKELNEQEKQAQAQKAAAAALAAAAV 94
           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 =  179 bits (454), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 90/90 (100%), Positives = 90/90 (100%)

Query: 2  GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
          GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct: 9  GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 68

Query: 62 LKKEIQAIKELNEQEKQAQAQKAAAAALAA 91
          LKKEIQAIKELNEQEKQAQAQKAAAAALAA
Sbjct: 69 LKKEIQAIKELNEQEKQAQAQKAAAAALAA 98

Source: Notonecta undulata

Species: Notonecta undulata

Genus: Notonecta

Family: Notonectidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|45553381|ref|NP_996219.1| ultrabithorax, isoform F [Drosophila melanogaster] gi|45446510|gb|AAS65158.1| ultrabithorax, isoform F [Drosophila melanogaster]

 Score =  179 bits (454), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 90/91 (98%), Positives = 90/91 (98%)

Query: 4   NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63
           NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK
Sbjct: 258 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 317

Query: 64  KEIQAIKELNEQEKQAQAQKAAAAALAAAAV 94
           KEIQAIKELNEQEKQAQAQKAAAAA AAAAV
Sbjct: 318 KEIQAIKELNEQEKQAQAQKAAAAAAAAAAV 348

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|390178469|ref|XP_003736653.1| Ubx, isoform B [Drosophila pseudoobscura pseudoobscura] gi|388859455|gb|EIM52726.1| Ubx, isoform B [Drosophila pseudoobscura pseudoobscura]

 Score =  178 bits (452), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 90/91 (98%), Positives = 90/91 (98%)

Query: 4   NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63
           NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK
Sbjct: 262 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 321

Query: 64  KEIQAIKELNEQEKQAQAQKAAAAALAAAAV 94
           KEIQAIKELNEQEKQAQAQKAAAAA AAAAV
Sbjct: 322 KEIQAIKELNEQEKQAQAQKAAAAAAAAAAV 352

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  174 bits (442), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 82/85 (96%), Positives = 82/85 (96%)

Query: 2   GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
           GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct: 161 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 220

Query: 62  LKKEIQAIKELNEQEKQAQAQKAAA 86
           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|391339782|ref|XP_003744226.1| PREDICTED: homeotic protein ultrabithorax-like [Metaseiulus occidentalis]

 Score =  172 bits (437), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 82/93 (88%), Positives = 87/93 (93%)

Query: 1   MGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60
           +GA+GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM
Sbjct: 79  LGASGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 138

Query: 61  KLKKEIQAIKELNEQEKQAQAQKAAAAALAAAA 93
           KLKKEIQAIKELNEQE+QAQA KAA+  +  A 
Sbjct: 139 KLKKEIQAIKELNEQERQAQAAKAASMGINGAG 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	96
UNIPROTKB|Q8T940	253	Ubx "Homeotic protein ultrabit	0.75	0.284	0.777	1.6e-24
FB|FBgn0003944	389	Ubx "Ultrabithorax" [Drosophil	0.760	0.187	0.753	2.6e-24
UNIPROTKB|P20822	385	Ubx "Homeotic protein ultrabit	0.760	0.189	0.753	2.6e-24
UNIPROTKB|P83950	389	Ubx "Homeotic protein ultrabit	0.760	0.187	0.753	2.6e-24
UNIPROTKB|Q6VPU7	387	Ubx "Ultrabithorax" [Drosophil	0.760	0.188	0.753	2.6e-24
UNIPROTKB|B0W1V2	216	abd-A "Homeobox protein abdomi	0.552	0.245	0.886	4.3e-22
UNIPROTKB|O76762	308	abd-A "Homeobox protein abdomi	0.552	0.172	0.886	4.3e-22
UNIPROTKB|P29552	239	abd-A "Homeobox protein abdomi	0.552	0.221	0.886	4.3e-22
FB|FBgn0000014	590	abd-A "abdominal A" [Drosophil	0.552	0.089	0.886	3.1e-21
ZFIN|ZDB-GENE-000823-7	224	hoxb6b "homeo box B6b" [Danio	0.510	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:     2 GANXXXXXXXXXXXXXXXXELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
             GAN                ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK
Sbjct:   154 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 213

Query:    62 LKKEIQAIKELN 73
             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 = 278 (102.9 bits), Expect = 2.6e-24, P = 2.6e-24
 Identities = 55/73 (75%), Positives = 56/73 (76%)

Query:     1 MGANXXXXXXXXXXXXXXXXELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60
             +G N                ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM
Sbjct:   289 LGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 348

Query:    61 KLKKEIQAIKELN 73
             KLKKEIQAIKELN
Sbjct:   349 KLKKEIQAIKELN 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 = 278 (102.9 bits), Expect = 2.6e-24, P = 2.6e-24
 Identities = 55/73 (75%), Positives = 56/73 (76%)

Query:     1 MGANXXXXXXXXXXXXXXXXELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60
             +G N                ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM
Sbjct:   284 LGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 343

Query:    61 KLKKEIQAIKELN 73
             KLKKEIQAIKELN
Sbjct:   344 KLKKEIQAIKELN 356

GO:0003677 "DNA binding" evidence=TAS

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

 Score = 278 (102.9 bits), Expect = 2.6e-24, P = 2.6e-24
 Identities = 55/73 (75%), Positives = 56/73 (76%)

Query:     1 MGANXXXXXXXXXXXXXXXXELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60
             +G N                ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM
Sbjct:   289 LGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 348

Query:    61 KLKKEIQAIKELN 73
             KLKKEIQAIKELN
Sbjct:   349 KLKKEIQAIKELN 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 = 278 (102.9 bits), Expect = 2.6e-24, P = 2.6e-24
 Identities = 55/73 (75%), Positives = 56/73 (76%)

Query:     1 MGANXXXXXXXXXXXXXXXXELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60
             +G N                ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM
Sbjct:   286 LGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 345

Query:    61 KLKKEIQAIKELN 73
             KLKKEIQAIKELN
Sbjct:   346 KLKKEIQAIKELN 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:    21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN 73
             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:    21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN 73
             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:    21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN 73
             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:    21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN 73
             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:    21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAI 69
             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	0.9726	0.7604	0.1896	yes	N/A
P15856	ABDA_APIME	No assigned EC number	0.8630	0.75	0.9729	no	N/A
P14839	HXB6_CHICK	No assigned EC number	0.7125	0.8125	0.9285	no	N/A
Q24645	ANTP_DROSU	No assigned EC number	0.9152	0.6145	0.1497	N/A	N/A
A2T7F3	HXA7_PANTR	No assigned EC number	0.9152	0.6145	0.2565	no	N/A
P02830	HXA7_MOUSE	No assigned EC number	0.6781	0.8541	0.3580	yes	N/A
P02833	ANTP_DROME	No assigned EC number	0.9152	0.6145	0.1560	no	N/A
P83950	UBX_DROSI	No assigned EC number	0.9726	0.7604	0.1876	N/A	N/A
Q8T940	UBX_JUNCO	No assigned EC number	0.9784	0.9687	0.3675	N/A	N/A
P21523	HLOX2_HIRME	No assigned EC number	0.8450	0.7395	0.6016	N/A	N/A
P09634	HXA7_RAT	No assigned EC number	0.6129	0.8958	0.8190	no	N/A
P24061	HXA7_COTJA	No assigned EC number	0.9152	0.6145	0.2438	N/A	N/A
A1YFA5	HXB7_GORGO	No assigned EC number	0.9152	0.6145	0.2718	N/A	N/A
Q26430	ABDA_MANSE	No assigned EC number	0.8648	0.7604	0.7525	N/A	N/A
Q9TT89	HXB7_BOVIN	No assigned EC number	0.9152	0.6145	0.2718	yes	N/A
Q9YGT4	HXB6B_DANRE	No assigned EC number	0.6951	0.8125	0.3482	yes	N/A
Q90VZ9	HXA7_CHICK	No assigned EC number	0.9152	0.6145	0.2694	no	N/A
P31268	HXA7_HUMAN	No assigned EC number	0.9152	0.6145	0.2565	no	N/A
P17509	HXB6_HUMAN	No assigned EC number	0.8615	0.6562	0.2812	yes	N/A
P83949	UBX_DROME	No assigned EC number	0.9726	0.7604	0.1876	no	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	96
pfam00046	57	pfam00046, Homeobox, Homeobox domain	5e-22
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	2e-18
smart00389	57	smart00389, HOX, Homeodomain	4e-18
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	6e-09

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

 Score = 80.6 bits (200), Expect = 5e-22
 Identities = 32/57 (56%), Positives = 38/57 (66%)

Query: 8  RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          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 = 71.5 bits (176), Expect = 2e-18
 Identities = 34/58 (58%), Positives = 39/58 (67%)

Query: 8  RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          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 = 70.7 bits (174), Expect = 4e-18
 Identities = 31/57 (54%), Positives = 39/57 (68%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63
          +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 = 49.7 bits (119), Expect = 6e-09
 Identities = 21/58 (36%), Positives = 35/58 (60%)

Query: 8   RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
           +  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	96
KOG0489|consensus	261		99.78
KOG0488|consensus	309		99.77
KOG0850|consensus	245		99.76
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.75
KOG0843|consensus	197		99.75
KOG0484|consensus	125		99.74
KOG0487|consensus	308		99.73
KOG2251|consensus	228		99.73
KOG0485|consensus	268		99.71
KOG0842|consensus	307		99.7
KOG3802|consensus	398		99.7
KOG0492|consensus	246		99.68
KOG0848|consensus	317		99.65
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.64
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.63
KOG0494|consensus	332		99.63
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.62
COG5576	156	Homeodomain-containing transcription factor [Trans	99.62
KOG0493|consensus	342		99.58
KOG0491|consensus	194		99.57
KOG4577|consensus	383		99.53
KOG0483|consensus	198		99.49
KOG0844|consensus	408		99.48
KOG0847|consensus	288		99.44
KOG0486|consensus	351		99.43
KOG1168|consensus	385		99.3
KOG0490|consensus	235		99.26
KOG0849|consensus	354		99.12
KOG0775|consensus	304		99.07
KOG0774|consensus	334		98.89
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.68
KOG2252|consensus	558		98.53
KOG0490|consensus	235		98.26
KOG1146|consensus	1406		97.55
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	97.46
KOG0773|consensus	342		96.51
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	96.32
KOG3623|consensus	1007		96.01
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	88.2
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	87.9
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	87.49
PF09607	58	BrkDBD: Brinker DNA-binding domain; InterPro: IPR0	87.37
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	84.19
PF10668	60	Phage_terminase: Phage terminase small subunit; In	83.75
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	82.15

>KOG0489|consensus

Probab=99.78  E-value=1.7e-19  Score=125.36  Aligned_cols=68  Identities=71%  Similarity=1.022  Sum_probs=62.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHHHH
Q psy1653           3 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK   70 (96)
Q Consensus         3 ~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~~~   70 (96)
                      ..+..||.|+.||..|+..||..|..|.|.+...|.+||..|.|+++||+|||||||+||||+.+...
T Consensus       155 ~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~  222 (261)
T KOG0489|consen  155 TGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS  222 (261)
T ss_pred             ccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence            34567999999999999999999999999999999999999999999999999999999999765443

>KOG0488|consensus

Probab=99.77  E-value=5.3e-19  Score=125.24  Aligned_cols=64  Identities=44%  Similarity=0.723  Sum_probs=60.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHH
Q psy1653           5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA   68 (96)
Q Consensus         5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~   68 (96)
                      .++|+.||.||..|+..||..|+...|++..+|+.||..|||+..||++||||||+||||+...
T Consensus       170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~  233 (309)
T KOG0488|consen  170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE  233 (309)
T ss_pred             cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence            4556679999999999999999999999999999999999999999999999999999998766

>KOG0850|consensus

Probab=99.76  E-value=8.8e-19  Score=118.22  Aligned_cols=63  Identities=41%  Similarity=0.641  Sum_probs=59.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653           5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   67 (96)
Q Consensus         5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~   67 (96)
                      .+-|+.||.++..||..|...|++++|+...+|.+||..|||+..||+|||||||.|.||..+
T Consensus       120 KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k  182 (245)
T KOG0850|consen  120 KKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK  182 (245)
T ss_pred             ccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence            345678999999999999999999999999999999999999999999999999999999765

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.75  E-value=2.6e-18  Score=94.06  Aligned_cols=57  Identities=49%  Similarity=0.701  Sum_probs=55.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653           8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   64 (96)
Q Consensus         8 rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr   64 (96)
                      |+.|+.|+..|+..|+..|..++||+..++..||..+||+..+|.+||+|+|.++|+
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            578999999999999999999999999999999999999999999999999999886

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

>KOG0843|consensus

Probab=99.75  E-value=2.4e-18  Score=112.52  Aligned_cols=64  Identities=41%  Similarity=0.621  Sum_probs=60.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHHH
Q psy1653           6 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAI   69 (96)
Q Consensus         6 ~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~~   69 (96)
                      +.+|.||.|+.+|+..|+..|+.++|....+|+.||..|+|++.||+|||||||.|.||.+.+.
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            5788899999999999999999999999999999999999999999999999999999976553

>KOG0484|consensus

Probab=99.74  E-value=2.7e-18  Score=103.56  Aligned_cols=62  Identities=42%  Similarity=0.625  Sum_probs=58.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653           6 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   67 (96)
Q Consensus         6 ~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~   67 (96)
                      +.+|-|++|+..||..|+..|....||++-.+++||.++.|++..|++||||||+|++++.+
T Consensus        16 KQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr   77 (125)
T KOG0484|consen   16 KQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER   77 (125)
T ss_pred             HhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence            45677999999999999999999999999999999999999999999999999999999543

>KOG0487|consensus

Probab=99.73  E-value=1.8e-18  Score=121.68  Aligned_cols=66  Identities=55%  Similarity=0.797  Sum_probs=61.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHHHH
Q psy1653           5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK   70 (96)
Q Consensus         5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~~~   70 (96)
                      +.-|++|..+|..|+..||..|..|.|++...|.+|+..|+|+++||+|||||||+|+||..++.+
T Consensus       233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r  298 (308)
T KOG0487|consen  233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR  298 (308)
T ss_pred             cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence            345778999999999999999999999999999999999999999999999999999999875443

>KOG2251|consensus

Probab=99.73  E-value=5.7e-18  Score=113.72  Aligned_cols=65  Identities=37%  Similarity=0.530  Sum_probs=60.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHH
Q psy1653           4 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA   68 (96)
Q Consensus         4 ~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~   68 (96)
                      -++.+|.||+|+..|+++|+..|.+.+||+...+++||.+|+|++.+|+|||+|||+|+|+++..
T Consensus        34 pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q   98 (228)
T KOG2251|consen   34 PRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ   98 (228)
T ss_pred             chhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence            45668899999999999999999999999999999999999999999999999999999997554

>KOG0485|consensus

Probab=99.71  E-value=1e-17  Score=112.57  Aligned_cols=65  Identities=40%  Similarity=0.692  Sum_probs=60.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHH
Q psy1653           4 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA   68 (96)
Q Consensus         4 ~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~   68 (96)
                      ++.+|+.||+|+..|+--|+..|+...|.+..+|.-||.+|.|++.||+|||||||.||||+...
T Consensus       101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa  165 (268)
T KOG0485|consen  101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA  165 (268)
T ss_pred             ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence            44688899999999999999999999999999999999999999999999999999999996543

>KOG0842|consensus

Probab=99.70  E-value=1.6e-17  Score=116.98  Aligned_cols=62  Identities=40%  Similarity=0.688  Sum_probs=58.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653           6 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   67 (96)
Q Consensus         6 ~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~   67 (96)
                      ++||.|..||..|...||+.|....|++-.+|+.||..|.|++.||+|||||||-|+||...
T Consensus       152 ~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~  213 (307)
T KOG0842|consen  152 KKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQK  213 (307)
T ss_pred             cccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhh
Confidence            56777889999999999999999999999999999999999999999999999999999543

>KOG3802|consensus

Probab=99.70  E-value=1.1e-17  Score=120.30  Aligned_cols=67  Identities=30%  Similarity=0.430  Sum_probs=63.3

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653           1 MGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   67 (96)
Q Consensus         1 ~~~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~   67 (96)
                      |++.+++||+||.|.......|+.+|.+|+.|+..++..||.+|+|...+|+|||||||.|+||...
T Consensus       288 i~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  288 IGAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             hhccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            5677889999999999999999999999999999999999999999999999999999999999654

>KOG0492|consensus

Probab=99.68  E-value=7.4e-17  Score=107.72  Aligned_cols=61  Identities=44%  Similarity=0.710  Sum_probs=57.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653           7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   67 (96)
Q Consensus         7 ~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~   67 (96)
                      -|++|+.|+..||..|++-|...+|.++.++.+++..|.|++.||+|||||||+|.||.+.
T Consensus       144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe  204 (246)
T KOG0492|consen  144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE  204 (246)
T ss_pred             CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence            3667999999999999999999999999999999999999999999999999999999643

>KOG0848|consensus

Probab=99.65  E-value=8.4e-17  Score=110.85  Aligned_cols=65  Identities=52%  Similarity=0.795  Sum_probs=60.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHHHH
Q psy1653           6 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK   70 (96)
Q Consensus         6 ~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~~~   70 (96)
                      ++-+-|.+++..|...||..|.-++|+++.-+.+||.-|||+++||+|||||||+|+||.+++..
T Consensus       198 TkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~  262 (317)
T KOG0848|consen  198 TKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR  262 (317)
T ss_pred             cccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence            34445889999999999999999999999999999999999999999999999999999887775

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.64  E-value=3.7e-16  Score=85.93  Aligned_cols=53  Identities=19%  Similarity=0.377  Sum_probs=50.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCC----CCHHHHHHHHHHcCCCcchhhhhhchhh
Q psy1653           7 RRRGRQTYTRYQTLELEKEFHTNHY----LTRRRRIEMAHALCLTERQIKIWFQNRR   59 (96)
Q Consensus         7 ~rr~r~~~s~~q~~~L~~~F~~~~~----p~~~~~~~la~~l~l~~~~V~~WFqnrR   59 (96)
                      ++|.||.||..|+..|+..|+.++|    |+...+..||..+||++.+|++||+|.+
T Consensus         1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            4789999999999999999999999    9999999999999999999999999965

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

>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=99.63  E-value=1e-15  Score=83.74  Aligned_cols=56  Identities=59%  Similarity=0.846  Sum_probs=53.4

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653           9 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   64 (96)
Q Consensus         9 r~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr   64 (96)
                      +.++.++..++.+|+..|..++||+..++..||..+||+..+|..||+|+|.+.++
T Consensus         2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~   57 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR   57 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence            56789999999999999999999999999999999999999999999999999876

>KOG0494|consensus

Probab=99.63  E-value=4.3e-16  Score=107.13  Aligned_cols=61  Identities=43%  Similarity=0.620  Sum_probs=56.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653           7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   67 (96)
Q Consensus         7 ~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~   67 (96)
                      +|+.||.|+..|+..|+..|+...||+...++.|+.++.|++..|+|||||||+||||..+
T Consensus       141 RRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek  201 (332)
T KOG0494|consen  141 RRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEK  201 (332)
T ss_pred             cccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhh
Confidence            3445899999999999999999999999999999999999999999999999999999543

>smart00389 HOX Homeodomain

Probab=99.62  E-value=8.9e-16  Score=83.41  Aligned_cols=56  Identities=55%  Similarity=0.822  Sum_probs=52.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653           8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK   63 (96)
Q Consensus         8 rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~k   63 (96)
                      ++.|+.|+..++..|+..|..++||+..++..||..+||+..+|..||+|+|.+.+
T Consensus         1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~   56 (56)
T smart00389        1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK   56 (56)
T ss_pred             CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence            35678899999999999999999999999999999999999999999999998753

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

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.62  E-value=8e-16  Score=99.75  Aligned_cols=65  Identities=32%  Similarity=0.516  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHH
Q psy1653           4 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA   68 (96)
Q Consensus         4 ~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~   68 (96)
                      .+..+++|.+.+..|+.+|+..|+.++||+...+..|+..|+|+++.|++||||+|++.|+....
T Consensus        48 s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~  112 (156)
T COG5576          48 SSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG  112 (156)
T ss_pred             CCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence            45678889999999999999999999999999999999999999999999999999999986544

>KOG0493|consensus

Probab=99.58  E-value=2e-15  Score=103.93  Aligned_cols=60  Identities=50%  Similarity=0.782  Sum_probs=57.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         7 ~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      .||+||.|+.+||..|...|..|.|++..-|..|+.+|+|.+.||+|||||+|+|.||..
T Consensus       246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT  305 (342)
T KOG0493|consen  246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST  305 (342)
T ss_pred             hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence            467899999999999999999999999999999999999999999999999999999954

>KOG0491|consensus

Probab=99.57  E-value=7.8e-16  Score=99.63  Aligned_cols=64  Identities=45%  Similarity=0.712  Sum_probs=59.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHHHH
Q psy1653           7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK   70 (96)
Q Consensus         7 ~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~~~   70 (96)
                      +++.|++|+..|+..|+..|+...|.+..++.+|+..|+|++.||+.||||||+|.||..+...
T Consensus       100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~  163 (194)
T KOG0491|consen  100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ  163 (194)
T ss_pred             hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence            4567999999999999999999999999999999999999999999999999999999765544

>KOG4577|consensus

Probab=99.53  E-value=1.1e-14  Score=101.61  Aligned_cols=66  Identities=29%  Similarity=0.419  Sum_probs=62.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHH
Q psy1653           3 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA   68 (96)
Q Consensus         3 ~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~   68 (96)
                      +++.-||+||+++..||+.|...|...+.|....|+.|+.++||..+.|++||||||+|+||-++.
T Consensus       163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD  228 (383)
T KOG4577|consen  163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD  228 (383)
T ss_pred             cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence            566789999999999999999999999999999999999999999999999999999999986644

>KOG0483|consensus

Probab=99.49  E-value=6.2e-14  Score=93.87  Aligned_cols=61  Identities=33%  Similarity=0.509  Sum_probs=56.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653           7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   67 (96)
Q Consensus         7 ~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~   67 (96)
                      ...++.+|+..|...|+..|+...+..+..+..||..|||.++||.+||||||++||..+.
T Consensus        50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kql  110 (198)
T KOG0483|consen   50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQL  110 (198)
T ss_pred             cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhh
Confidence            3455678999999999999999999999999999999999999999999999999998553

>KOG0844|consensus

Probab=99.48  E-value=1.2e-14  Score=102.04  Aligned_cols=60  Identities=53%  Similarity=0.780  Sum_probs=57.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653           8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   67 (96)
Q Consensus         8 rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~   67 (96)
                      ||-||.|+.+|+..|+..|.+.-|-+...|.+||..|+|++..|++||||||+|+||+.-
T Consensus       182 RRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl  241 (408)
T KOG0844|consen  182 RRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL  241 (408)
T ss_pred             HHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence            677999999999999999999999999999999999999999999999999999999763

>KOG0847|consensus

Probab=99.44  E-value=5.7e-14  Score=94.84  Aligned_cols=63  Identities=43%  Similarity=0.755  Sum_probs=59.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           4 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         4 ~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      +|+++..|.+|+..|+..|+..|+...|+-..++.+||..+|+++.+|++||||||.||||..
T Consensus       164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh  226 (288)
T KOG0847|consen  164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH  226 (288)
T ss_pred             CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence            467888899999999999999999999999999999999999999999999999999999954

>KOG0486|consensus

Probab=99.43  E-value=8e-14  Score=97.97  Aligned_cols=60  Identities=40%  Similarity=0.611  Sum_probs=57.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           6 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         6 ~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      +++|.|+.|+..|+..|+..|.+|.||+...+++||.-.++++..|++||.|||+||+|.
T Consensus       111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkr  170 (351)
T KOG0486|consen  111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR  170 (351)
T ss_pred             hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhh
Confidence            457789999999999999999999999999999999999999999999999999999994

>KOG1168|consensus

Probab=99.30  E-value=1.1e-12  Score=91.81  Aligned_cols=62  Identities=24%  Similarity=0.399  Sum_probs=59.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           4 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         4 ~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      ++.+||+||.+...+...|+.+|...+.|+...+..||.+|+|....|++||||.|+|.||.
T Consensus       306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm  367 (385)
T KOG1168|consen  306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM  367 (385)
T ss_pred             ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence            56689999999999999999999999999999999999999999999999999999998884

>KOG0490|consensus

Probab=99.26  E-value=3.2e-12  Score=86.48  Aligned_cols=62  Identities=35%  Similarity=0.378  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      .++++.|+.|+..|++.|+..|...+||+...++.|+..+++++..|++||||+|+++++..
T Consensus        58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~  119 (235)
T KOG0490|consen   58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE  119 (235)
T ss_pred             ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence            45788999999999999999999999999999999999999999999999999999999865

>KOG0849|consensus

Probab=99.12  E-value=6.7e-11  Score=85.52  Aligned_cols=62  Identities=31%  Similarity=0.482  Sum_probs=58.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      .+.++.|++|+..|+..|+..|+.++||+...++.|+.++++++..|.+||+|+|.+++|..
T Consensus       174 ~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~  235 (354)
T KOG0849|consen  174 RGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH  235 (354)
T ss_pred             ccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence            44567789999999999999999999999999999999999999999999999999999965

>KOG0775|consensus

Probab=99.07  E-value=1.7e-10  Score=80.12  Aligned_cols=51  Identities=29%  Similarity=0.447  Sum_probs=46.4

Q ss_pred             CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653          14 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   64 (96)
Q Consensus        14 ~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr   64 (96)
                      |...-...|..+|..++||++.++.+||..+||+..||-.||+|||+++|-
T Consensus       183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa  233 (304)
T KOG0775|consen  183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA  233 (304)
T ss_pred             hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence            334457799999999999999999999999999999999999999999983

>KOG0774|consensus

Probab=98.89  E-value=1.9e-09  Score=74.64  Aligned_cols=72  Identities=26%  Similarity=0.421  Sum_probs=63.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHH---hCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHHHHHHHHHHHH
Q psy1653           7 RRRGRQTYTRYQTLELEKEFH---TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELNEQEKQ   78 (96)
Q Consensus         7 ~rr~r~~~s~~q~~~L~~~F~---~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~~~~~~~~~~~   78 (96)
                      .+|+|..|+....++|..+|.   .+|||+....++||.+++++..||-.||.|+|-+++|......+...--..
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~~ee~~l~~~  262 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKNQEEANLYAA  262 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhhhhhhhhHhh
Confidence            367788999999999999996   589999999999999999999999999999999999987776666544333

>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=98.68  E-value=1.5e-08  Score=51.81  Aligned_cols=34  Identities=32%  Similarity=0.585  Sum_probs=28.7

Q ss_pred             hCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhh
Q psy1653          28 TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK   61 (96)
Q Consensus        28 ~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k   61 (96)
                      .+|||+..++..|+..+|++..||..||-|.|.+
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            4799999999999999999999999999998864

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

>KOG2252|consensus

Probab=98.53  E-value=1.5e-07  Score=70.75  Aligned_cols=57  Identities=21%  Similarity=0.285  Sum_probs=53.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhh
Q psy1653           6 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKL   62 (96)
Q Consensus         6 ~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~   62 (96)
                      ..|++|.+|+..|+..|...|+.+++|+..+.+.|+.+|+|....|..||.|-|.|.
T Consensus       419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            357789999999999999999999999999999999999999999999999988774

>KOG0490|consensus

Probab=98.26  E-value=1.4e-06  Score=58.83  Aligned_cols=63  Identities=38%  Similarity=0.520  Sum_probs=58.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653           5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   67 (96)
Q Consensus         5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~   67 (96)
                      .+.++.++.+...++..|...|..+++|+...+..|+..+|++...|++||+|++.+.++...
T Consensus       151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  151 KKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             cccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            456777899999999999999999999999999999999999999999999999999988544

>KOG1146|consensus

Probab=97.55  E-value=8.2e-05  Score=61.03  Aligned_cols=60  Identities=27%  Similarity=0.347  Sum_probs=56.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         7 ~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      ++..|+.++..|+.+|...|....+|.....+.|...+++..+.|.+||+|-|.+.++..
T Consensus       903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~  962 (1406)
T KOG1146|consen  903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAK  962 (1406)
T ss_pred             hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhh
Confidence            566799999999999999999999999999999999999999999999999999998854

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

Probab=97.46  E-value=0.00011  Score=39.95  Aligned_cols=43  Identities=19%  Similarity=0.310  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhh
Q psy1653          18 QTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM   60 (96)
Q Consensus        18 q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~   60 (96)
                      ....|+.+|....++.......|..+.+|+..+|+.||-.+..
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            4566999999999999999999999999999999999976543

>KOG0773|consensus

Probab=96.51  E-value=0.0029  Score=45.51  Aligned_cols=60  Identities=20%  Similarity=0.335  Sum_probs=49.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHH-H--hCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           7 RRRGRQTYTRYQTLELEKEF-H--TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         7 ~rr~r~~~s~~q~~~L~~~F-~--~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      ..+.+..+......+|..+. +  ..+||+..+...|+.++||+..||-.||-|.|-+.-+..
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~  301 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPM  301 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCch
Confidence            34556678888888888773 3  357999999999999999999999999999988776643

>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=96.32  E-value=0.014  Score=31.19  Aligned_cols=47  Identities=17%  Similarity=0.357  Sum_probs=35.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhh
Q psy1653           8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRR   59 (96)
Q Consensus         8 rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR   59 (96)
                      +++|..+|-.+...+...++.+.     ....||..+|++..+|..|..|+.
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            46788999999888888888777     577889999999999999998753

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

>KOG3623|consensus

Probab=96.01  E-value=0.011  Score=46.90  Aligned_cols=48  Identities=17%  Similarity=0.208  Sum_probs=43.9

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653          19 TLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus        19 ~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      +.+|..+|..|+.|+..+...++...|++...|+.||.+++.......
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            778999999999999999999999999999999999999988776643

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

Probab=88.20  E-value=0.88  Score=24.35  Aligned_cols=40  Identities=18%  Similarity=0.180  Sum_probs=32.7

Q ss_pred             CCHHHHHHHHHHHHhCCC--CCHHHHHHHHHHcCCCcchhhh
Q psy1653          14 YTRYQTLELEKEFHTNHY--LTRRRRIEMAHALCLTERQIKI   53 (96)
Q Consensus        14 ~s~~q~~~L~~~F~~~~~--p~~~~~~~la~~l~l~~~~V~~   53 (96)
                      +|..|..+|...|...-|  |-......||..+|++...|-.
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~   42 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSE   42 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence            478899999999998765  5566788899999999877554

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

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

Probab=87.90  E-value=1.2  Score=24.61  Aligned_cols=46  Identities=17%  Similarity=0.290  Sum_probs=29.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchh
Q psy1653           9 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNR   58 (96)
Q Consensus         9 r~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnr   58 (96)
                      +.|..||.++...+...+....    .....++..+||+...+..|-.--
T Consensus         2 ~~r~~ys~e~K~~~v~~~~~~g----~sv~~va~~~gi~~~~l~~W~~~~   47 (76)
T PF01527_consen    2 RKRRRYSPEFKLQAVREYLESG----ESVSEVAREYGISPSTLYNWRKQY   47 (76)
T ss_dssp             -SS----HHHHHHHHHHHHHHH----CHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCC----CceEeeecccccccccccHHHHHH
Confidence            3567899998777766662222    367788999999999999998533

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

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

Probab=87.49  E-value=1.8  Score=22.20  Aligned_cols=41  Identities=7%  Similarity=0.113  Sum_probs=30.5

Q ss_pred             CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchh
Q psy1653          13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNR   58 (96)
Q Consensus        13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnr   58 (96)
                      .+++.+..+|...|..+.     ...++|..+|++...|+.+...-
T Consensus         4 ~L~~~er~vi~~~y~~~~-----t~~eIa~~lg~s~~~V~~~~~~a   44 (50)
T PF04545_consen    4 QLPPREREVIRLRYFEGL-----TLEEIAERLGISRSTVRRILKRA   44 (50)
T ss_dssp             TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHhcCCC-----CHHHHHHHHCCcHHHHHHHHHHH
Confidence            467888899999883332     46778999999999998876533

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 ....

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

Probab=87.37  E-value=1.7  Score=23.78  Aligned_cols=45  Identities=20%  Similarity=0.362  Sum_probs=24.6

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhc
Q psy1653          11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQ   56 (96)
Q Consensus        11 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFq   56 (96)
                      |..|+..........|.....--...|. .|.++||+..+|+-|.+
T Consensus         3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RA-aarkf~V~r~~Vr~W~k   47 (58)
T PF09607_consen    3 RRSYTAEFKLKVVEYAEKDNNCKGNQRA-AARKFNVSRRQVRKWRK   47 (58)
T ss_dssp             -----HHHHHHHHHHHHH-TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred             ccccChHHHHHHHHHHHHccchhhhHHH-HHHHhCccHHHHHHHHH
Confidence            5567777655555555544332223343 49999999999999985

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

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

Probab=84.19  E-value=2.4  Score=20.97  Aligned_cols=42  Identities=10%  Similarity=0.088  Sum_probs=29.5

Q ss_pred             CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhh
Q psy1653          13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRR   59 (96)
Q Consensus        13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR   59 (96)
                      .+++.+..++...|..+.     ....+|..+|++...|..|...-+
T Consensus        10 ~l~~~~~~~~~~~~~~~~-----~~~~ia~~~~~s~~~i~~~~~~~~   51 (55)
T cd06171          10 KLPEREREVILLRFGEGL-----SYEEIAEILGISRSTVRQRLHRAL   51 (55)
T ss_pred             hCCHHHHHHHHHHHhcCC-----CHHHHHHHHCcCHHHHHHHHHHHH
Confidence            356667777776664332     356679999999999999886443

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

>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes

Probab=83.75  E-value=0.7  Score=25.41  Aligned_cols=21  Identities=24%  Similarity=0.483  Sum_probs=17.9

Q ss_pred             HHHHHHHHcCCCcchhhhhhc
Q psy1653          36 RRIEMAHALCLTERQIKIWFQ   56 (96)
Q Consensus        36 ~~~~la~~l~l~~~~V~~WFq   56 (96)
                      ....||..||+++.+|+.|=.
T Consensus        24 ~lkdIA~~Lgvs~~tIr~WK~   44 (60)
T PF10668_consen   24 KLKDIAEKLGVSESTIRKWKS   44 (60)
T ss_pred             cHHHHHHHHCCCHHHHHHHhh
Confidence            455679999999999999975

Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].

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

Probab=82.15  E-value=3.9  Score=21.05  Aligned_cols=39  Identities=15%  Similarity=0.159  Sum_probs=25.7

Q ss_pred             CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhch
Q psy1653          14 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQN   57 (96)
Q Consensus        14 ~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqn   57 (96)
                      +++.+..++.-.|-.+.     ...++|..+|++...|+.|...
T Consensus        11 L~~~~r~i~~l~~~~g~-----s~~eIa~~l~~s~~~v~~~l~r   49 (54)
T PF08281_consen   11 LPERQREIFLLRYFQGM-----SYAEIAEILGISESTVKRRLRR   49 (54)
T ss_dssp             S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHCc-----CHHHHHHHHCcCHHHHHHHHHH
Confidence            45556666665554433     5778899999999999999863

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	96
1b8i_A	81	Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX		3e-21
1hom_A	68	Determination Of The Three-Dimensional Structure Of		2e-17
2r5y_A	88	Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO		8e-17
1ahd_P	68	Determination Of The Nmr Solution Structure Of An A		1e-16
1san_A	62	The Des(1-6)antennapedia Homeodomain: Comparison Of		1e-16
9ant_A	62	Antennapedia Homeodomain-Dna Complex Length = 62		2e-16
1ftz_A	70	Nuclear Magnetic Resonance Solution Structure Of Th		6e-15
2lp0_A	60	The Solution Structure Of Homeodomain-Protein Compl		5e-12
1b72_A	97	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		7e-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		3e-11
2m34_A	71	Nmr Structure Of The Homeodomain Transcription Fact		3e-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
1jgg_A	60	Even-Skipped Homeodomain Complexed To At-Rich Dna L		2e-08
1p7j_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		3e-08
1p7i_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		3e-08
2p81_A	44	Engrailed Homeodomain Helix-Turn-Helix Motif Length		5e-08
2hdd_A	61	Engrailed Homeodomain Q50k Variant Dna Complex Leng		5e-08
2ld5_A	67	Solution Nmr-Derived Complex Structure Of Hoxa13 Dn		6e-08
2l7z_A	73	Nmr Structure Of A13 Homedomain Length = 73		7e-08
1du0_A	57	Engrailed Homeodomain Q50a Variant Dna Complex Leng		8e-08
1enh_A	54	Structural Studies Of The Engrailed Homeodomain Len		2e-07
1ztr_A	61	Solution Structure Of Engrailed Homeodomain L16a Mu		2e-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		4e-07
1ig7_A	58	Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58		8e-07
2hos_A	63	Phage-selected Homeodomain Bound To Unmodified Dna		9e-07
3a01_A	93	Crystal Structure Of Aristaless And Clawless Homeod		2e-06
2l9r_A	69	Solution Nmr Structure Of Homeobox Domain Of Homeob		4e-06
3rkq_A	58	Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Lengt		5e-06
3a02_A	60	Crystal Structure Of Aristaless Homeodomain Length		2e-05
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		3e-05
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		3e-05
3a03_A	56	Crystal Structure Of Hox11l1 Homeodomain Length = 5		4e-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		2e-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		7e-04

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

Iteration: 1
 Score = 96.7 bits (239), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 47/48 (97%), Positives = 47/48 (97%)
Query: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA 68
          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 = 84.3 bits (207), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 41/45 (91%), Positives = 42/45 (93%)
Query: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          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 = 82.0 bits (201), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 40/45 (88%), Positives = 41/45 (91%)
Query: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          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 = 81.3 bits (199), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 40/45 (88%), Positives = 41/45 (91%)
Query: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          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 = 81.3 bits (199), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 40/45 (88%), Positives = 41/45 (91%)
Query: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          ELEKEFH N YLTRRRRIE+AHAL LTERQIKIWFQNRRMK KKE
Sbjct: 10 ELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 54

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

Iteration: 1
 Score = 80.9 bits (198), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 40/45 (88%), Positives = 41/45 (91%)
Query: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          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: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          ELEKEFH N Y+TRRRRI++A+AL L+ERQIKIWFQNRRMK KK+
Sbjct: 17 ELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKD 61

>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: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          ELEKEF  N YLTR RR E+A  L LTERQ+KIWFQNRRMK+KK
Sbjct: 15 ELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58

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

Iteration: 1
 Score = 65.5 bits (158), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 31/44 (70%), Positives = 35/44 (79%)
Query: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          ELEKEFH N YL+R RR+E+A  L L E Q+KIWFQNRRMK KK
Sbjct: 48 ELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91

>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: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          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 = 63.5 bits (153), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 32/45 (71%), Positives = 36/45 (80%)
Query: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          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 = 56.6 bits (135), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 27/44 (61%), Positives = 33/44 (75%)
Query: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          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 = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/43 (58%), Positives = 33/43 (76%)
Query: 22 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          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 = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/43 (58%), Positives = 33/43 (76%)
Query: 22 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          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 = 53.9 bits (128), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 23/44 (52%), Positives = 34/44 (77%)
Query: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          ELE+E+  N ++T+ +R +++ A  L+ERQI IWFQNRR+K KK
Sbjct: 21 ELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/44 (56%), Positives = 33/44 (75%)
Query: 22 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          LEKEF+  +Y++R RR E+A  L L E  IK+WFQNRRMK K++
Sbjct: 16 LEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59

>pdb|1P7J|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52e 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: 22 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          L++EF+ N YLT RRR +++  L L E QIKIWFQN R K+KK
Sbjct: 16 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58

>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: 22 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          L++EF+ N YLT RRR +++  L L E QIKIWFQN R K+KK
Sbjct: 16 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 24/41 (58%), Positives = 31/41 (75%)
Query: 24 KEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          +EF+ N YLT RRR +++  L L E QIKIWFQN+R K+KK
Sbjct: 3  REFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 24/43 (55%), Positives = 33/43 (76%)
Query: 22 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          L++EF+ N YLT RRR +++  L L E QIKIWF+N+R K+KK
Sbjct: 18 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 36/50 (72%)
Query: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK 70
          ELE+E+ TN ++T+ +R  ++    L+ERQ+ IWFQNRR+K KK I  +K
Sbjct: 15 ELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINKLK 64

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 36/50 (72%)
Query: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK 70
          ELE+E+ TN ++T+ +R  ++    L+ERQ+ IWFQNRR+K KK I  +K
Sbjct: 21 ELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINKLK 70

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 24/43 (55%), Positives = 32/43 (74%)
Query: 22 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          L++EF+ N YLT RRR +++  L L E QIKIWF N+R K+KK
Sbjct: 14 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 23/41 (56%), Positives = 31/41 (75%)
Query: 22 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKL 62
          L++EF+ N YLT RRR +++  L L E QIKIWFQN+R K+
Sbjct: 14 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKI 54

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 22/41 (53%), Positives = 31/41 (75%)
Query: 24 KEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          +EF+ N YLT RRR +++  L L E QIKIWFQN+R K+++
Sbjct: 20 REFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 21/44 (47%), Positives = 29/44 (65%)
Query: 22 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          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: 22 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          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 = 50.1 bits (118), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 23/44 (52%), Positives = 30/44 (68%)
Query: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          ELEK+F T  YL+   R  +A  L L+ERQ+K WFQNRR K ++
Sbjct: 21 ELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64

>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: 22 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          LE++F    YL+   R E + +L LTE Q+KIWFQNRR K K+
Sbjct: 15 LERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 22/45 (48%), Positives = 31/45 (68%)
Query: 22 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
          L++EF+ N YLT RRR +++  L L E Q+K WF+N R K+KK  
Sbjct: 19 LKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKKST 63

>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: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
          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 = 4e-06,   Method: Compositional matrix adjust.
 Identities = 23/45 (51%), Positives = 30/45 (66%)
Query: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          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 = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 22/43 (51%), Positives = 27/43 (62%)
Query: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63
          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: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          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 = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/45 (48%), Positives = 29/45 (64%)
Query: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          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: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          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 = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 20/46 (43%), Positives = 28/46 (60%)
Query: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
          ELE+ F    YL    R  +A AL +T+ Q+K WFQNRR K +++ 
Sbjct: 11 ELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQT 56

>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: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          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: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          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 = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/44 (45%), Positives = 27/44 (61%)
Query: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          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 = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/44 (45%), Positives = 26/44 (59%)
Query: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          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 = 39.7 bits (91), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/44 (45%), Positives = 27/44 (61%)
Query: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          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: 22 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          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 = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 18/39 (46%), Positives = 24/39 (61%)
Query: 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRR 59
          ELE+ F    YLT  R  +++  L L   Q+KIWF+NRR
Sbjct: 16 ELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRR 54

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	96
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	1e-37
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	1e-36
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	2e-36
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	2e-34
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	9e-33
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	1e-32
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	9e-32
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	9e-32
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	5e-31
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	2e-30
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	2e-30
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	2e-30
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	4e-30
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	3e-28
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	2e-25
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	1e-23
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	2e-23
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	3e-23
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	3e-23
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	2e-22
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	3e-22
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	3e-21
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	3e-21
1e3o_C	160	Octamer-binding transcription factor 1; transcript	1e-20
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	9e-20
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	2e-16
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	2e-16
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	6e-16
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	2e-15
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	4e-14
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	7e-14
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	6e-13
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	1e-12
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	5e-12
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	1e-11
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	1e-11
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	1e-11
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	2e-11
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	2e-11
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	2e-11
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	4e-11
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	4e-11
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	5e-11
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	5e-11
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	1e-10
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	2e-10
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	5e-10
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	8e-10
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	1e-09
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	2e-09
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	3e-08
1uhs_A	72	HOP, homeodomain only protein; structural genomics	5e-08
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	2e-06
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	2e-05
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	2e-05
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	2e-05
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	3e-05
1lfb_A	99	Liver transcription factor (LFB1); transcription r	8e-04

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

 Score =  120 bits (303), Expect = 1e-37
 Identities = 65/68 (95%), Positives = 65/68 (95%)

Query: 1  MGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60
           G NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHAL LTERQIKIWFQNRRM
Sbjct: 14 AGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRM 73

Query: 61 KLKKEIQA 68
          KLKKEIQA
Sbjct: 74 KLKKEIQA 81

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

 Score =  118 bits (296), Expect = 1e-36
 Identities = 52/64 (81%), Positives = 55/64 (85%)

Query: 2  GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
           ANG  +R R +YTRYQTLELEKEFH N YLTRRRRIE+AHAL LTERQIKIWFQNRRMK
Sbjct: 23 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMK 82

Query: 62 LKKE 65
           KKE
Sbjct: 83 WKKE 86

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

 Score =  117 bits (295), Expect = 2e-36
 Identities = 35/67 (52%), Positives = 41/67 (61%)

Query: 2  GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
             G     R  +T  Q  ELEKEFH N YL+R RR+E+A  L L E Q+KIWFQNRRMK
Sbjct: 29 PGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMK 88

Query: 62 LKKEIQA 68
           KK  + 
Sbjct: 89 QKKRERE 95

>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A 1hom_A 1ftz_A Length = 68

 Score =  111 bits (280), Expect = 2e-34
 Identities = 54/66 (81%), Positives = 58/66 (87%)

Query: 6  LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          +R+RGRQTYTRYQTLELEKEFH N YLTRRRRIE+AHAL LTERQIKIWFQNRRMK KKE
Sbjct: 1  MRKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 60

Query: 66 IQAIKE 71
           +   E
Sbjct: 61 NKTKGE 66

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

 Score =  108 bits (270), Expect = 9e-33
 Identities = 40/59 (67%), Positives = 46/59 (77%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
           R+ R  YT++QTLELEKEF  N YLTR RR E+A  L LTERQ+KIWFQNRRMK+KK 
Sbjct: 13 TRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKI 71

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

 Score =  107 bits (268), Expect = 1e-32
 Identities = 40/61 (65%), Positives = 45/61 (73%)

Query: 5  GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          G  +R R  YTR Q LELEKEF  N Y++R RR+E+A  L LTER IKIWFQNRRMK KK
Sbjct: 1  GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60

Query: 65 E 65
          E
Sbjct: 61 E 61

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

 Score =  105 bits (263), Expect = 9e-32
 Identities = 26/67 (38%), Positives = 37/67 (55%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
           RR R T+T  Q  ELE+ F    YLT  R  +++  L L   Q+KIWF+NRR + K + 
Sbjct: 2  PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQS 61

Query: 67 QAIKELN 73
             K+ +
Sbjct: 62 DQHKDQS 68

>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 70

 Score =  105 bits (263), Expect = 9e-32
 Identities = 26/62 (41%), Positives = 39/62 (62%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
           + G+  ++  QT+ELEK+F T  YL+   R  +A  L L+ERQ+K WFQNRR K ++  
Sbjct: 7  GKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSG 66

Query: 67 QA 68
           +
Sbjct: 67 PS 68

>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 70

 Score =  103 bits (258), Expect = 5e-31
 Identities = 27/59 (45%), Positives = 41/59 (69%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
           R+ R  Y++ Q  ELE+E+  N ++T+ +R +++ A  L+ERQI IWFQNRR+K KK 
Sbjct: 7  GRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKS 65

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

 Score =  102 bits (255), Expect = 2e-30
 Identities = 29/67 (43%), Positives = 44/67 (65%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
           R+ R  YT+ Q  ELE+E+ TN ++T+ +R  ++    L+ERQ+ IWFQNRR+K KK I
Sbjct: 7  GRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVI 66

Query: 67 QAIKELN 73
            +K  +
Sbjct: 67 NKLKTTS 73

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

 Score =  101 bits (253), Expect = 2e-30
 Identities = 31/58 (53%), Positives = 40/58 (68%)

Query: 8  RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          RR R  +TR Q   LEKEF+  +Y++R RR E+A  L L E  IK+WFQNRRMK K++
Sbjct: 2  RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59

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

 Score =  101 bits (254), Expect = 2e-30
 Identities = 27/67 (40%), Positives = 38/67 (56%)

Query: 2  GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
                RR R  +T  Q + LEK F    YL+   RI++A +L L++ Q+K W+QNRRMK
Sbjct: 12 TKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMK 71

Query: 62 LKKEIQA 68
           KK   +
Sbjct: 72 WKKSGPS 78

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

 Score =  100 bits (252), Expect = 4e-30
 Identities = 27/57 (47%), Positives = 39/57 (68%)

Query: 8  RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          +R R  ++  Q   L++EF+ N YLT RRR +++  L L E QIKIWF+N+R K+KK
Sbjct: 4  KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

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

 Score = 96.9 bits (241), Expect = 3e-28
 Identities = 28/72 (38%), Positives = 40/72 (55%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
          R++ R ++TR Q  ELEK FH   YL    R  +A  L +T+ Q+K WFQNRR K +++ 
Sbjct: 17 RKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQT 76

Query: 67 QAIKELNEQEKQ 78
             +E   Q   
Sbjct: 77 AEEREAERQAAN 88

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

 Score = 89.4 bits (222), Expect = 2e-25
 Identities = 25/62 (40%), Positives = 37/62 (59%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
           R+ R  Y+ +Q   L++ F    YL    R E+A +L LT+ Q+KIWFQN+R K+KK  
Sbjct: 7  GRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSG 66

Query: 67 QA 68
           +
Sbjct: 67 PS 68

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

 Score = 84.3 bits (209), Expect = 1e-23
 Identities = 25/64 (39%), Positives = 35/64 (54%)

Query: 5  GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          G         +  Q +ELE++F    YL+   R  +A  L LTE Q+KIWFQNRR K K+
Sbjct: 2  GHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61

Query: 65 EIQA 68
          +  +
Sbjct: 62 KQLS 65

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

 Score = 84.5 bits (209), Expect = 2e-23
 Identities = 19/61 (31%), Positives = 36/61 (59%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
          +++ R  ++  Q   L   F    YL+ ++  E+++ L L+ +Q+K WFQN+RMK K+  
Sbjct: 22 KQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQ 81

Query: 67 Q 67
          +
Sbjct: 82 K 82

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

 Score = 83.1 bits (206), Expect = 3e-23
 Identities = 27/57 (47%), Positives = 36/57 (63%)

Query: 8  RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          R+ R  +T  Q L LE++F    YL+   R E + +L LTE Q+KIWFQNRR K K+
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

 Score = 83.0 bits (206), Expect = 3e-23
 Identities = 15/56 (26%), Positives = 29/56 (51%)

Query: 8  RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63
           +G+ + +      LE+ F     L  + + E+A    +T  Q+++WF N+RM+ K
Sbjct: 6  PKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61

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

 Score = 81.6 bits (202), Expect = 2e-22
 Identities = 20/61 (32%), Positives = 37/61 (60%)

Query: 5  GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          G +++ R  +++ Q   L+  F    YL+ ++  E++  L L+ +Q+K WFQN+RMK K+
Sbjct: 1  GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60

Query: 65 E 65
           
Sbjct: 61 W 61

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

 Score = 81.3 bits (201), Expect = 3e-22
 Identities = 26/67 (38%), Positives = 36/67 (53%)

Query: 2  GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
          G    +R+ R  +T+ QT ELE+ F    YL+   R  +A  + LT  Q+KIWFQN R K
Sbjct: 4  GLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYK 63

Query: 62 LKKEIQA 68
           K+    
Sbjct: 64 TKRAQNE 70

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

 Score = 78.1 bits (193), Expect = 3e-21
 Identities = 23/53 (43%), Positives = 34/53 (64%)

Query: 13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          +++R Q LELE+ F    YL    R  +A AL +T+ Q+K WFQNRR K +++
Sbjct: 3  SFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

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

 Score = 78.0 bits (193), Expect = 3e-21
 Identities = 26/57 (45%), Positives = 35/57 (61%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63
          RR+ R  +++ Q  ELE+ F    YL+   R ++A  L LT  Q+KIWFQNRR K K
Sbjct: 2  RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A Length = 160

 Score = 79.2 bits (195), Expect = 1e-20
 Identities = 19/58 (32%), Positives = 28/58 (48%)

Query: 7   RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
           RR+ R +      + LEK F  N   T      +A  L + +  I++WF NRR K K+
Sbjct: 101 RRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 158

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

 Score = 74.7 bits (184), Expect = 9e-20
 Identities = 24/66 (36%), Positives = 38/66 (57%)

Query: 6  LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          +RR+ R  +++ Q  ELE+ F    YL+   R  +A  + LT  Q+KIWFQN R K+K++
Sbjct: 1  MRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60

Query: 66 IQAIKE 71
           +    
Sbjct: 61 AKDKAA 66

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

 Score = 68.9 bits (168), Expect = 2e-16
 Identities = 18/68 (26%), Positives = 30/68 (44%)

Query: 1   MGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60
           + A G +R+ R +        LE  F      +      +A +L L +  +++WF NRR 
Sbjct: 93  IAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQ 152

Query: 61  KLKKEIQA 68
           K K+   A
Sbjct: 153 KEKRMTPA 160

>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1 Length = 146

 Score = 68.1 bits (166), Expect = 2e-16
 Identities = 19/64 (29%), Positives = 34/64 (53%)

Query: 1   MGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60
           +GAN  +R+ R T +      LE+ F  +   + +  + MA  L L +  +++WF NRR 
Sbjct: 81  VGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQ 140

Query: 61  KLKK 64
           + K+
Sbjct: 141 REKR 144

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

 Score = 65.1 bits (159), Expect = 6e-16
 Identities = 10/57 (17%), Positives = 22/57 (38%)

Query: 8  RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
             +   +  Q   L+  F  N +  +     +     L+ R+++ WF +RR   + 
Sbjct: 9  SIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRN 65

>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70

 Score = 63.5 bits (155), Expect = 2e-15
 Identities = 20/59 (33%), Positives = 28/59 (47%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
           R  R  +T YQ   L+  F  N Y       ++++ L L  R I +WFQN R K +K 
Sbjct: 7  GRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKS 65

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

 Score = 61.0 bits (148), Expect = 4e-14
 Identities = 18/58 (31%), Positives = 32/58 (55%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
           +R R T T  Q   L +++  +   TR+    +AH + L +R +++WFQN R + +K
Sbjct: 17 DKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERK 74

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

 Score = 62.0 bits (150), Expect = 7e-14
 Identities = 19/63 (30%), Positives = 27/63 (42%)

Query: 2   GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
           G    +R+ R ++T      L   F  N   T +   EMA  L      +++WF NRR  
Sbjct: 88  GEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQT 147

Query: 62  LKK 64
           LK 
Sbjct: 148 LKN 150

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

 Score = 59.7 bits (144), Expect = 6e-13
 Identities = 16/64 (25%), Positives = 29/64 (45%)

Query: 1   MGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60
                 R+R R +        LE  F  +   + ++   +A+ L L +  +++WF NRR 
Sbjct: 90  ETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQ 149

Query: 61  KLKK 64
           K K+
Sbjct: 150 KGKR 153

>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70

 Score = 57.0 bits (138), Expect = 1e-12
 Identities = 17/61 (27%), Positives = 27/61 (44%)

Query: 4  NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63
              +R R   T  Q   L + F  N+  +  +  EMA    L ++ IK WF+N   K +
Sbjct: 4  GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKER 63

Query: 64 K 64
          +
Sbjct: 64 Q 64

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

 Score = 55.2 bits (133), Expect = 5e-12
 Identities = 16/59 (27%), Positives = 31/59 (52%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
           +R R ++  +Q   ++  F  NH    +   ++A    LT+R +++WFQN R K ++ 
Sbjct: 7  GKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRN 65

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

 Score = 54.2 bits (131), Expect = 1e-11
 Identities = 24/58 (41%), Positives = 31/58 (53%)

Query: 8  RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          RR R  +T+ Q   LE  F  N Y       ++A  L L   +I+IWFQNRR KLK+ 
Sbjct: 2  RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRS 59

>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription regulation; HET: DNA; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 3a01_B Length = 81

 Score = 54.7 bits (132), Expect = 1e-11
 Identities = 25/59 (42%), Positives = 36/59 (61%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          +RR R T++  Q  ELE+ F    Y     R E+A    LTE +I++WFQNRR +L+K+
Sbjct: 18 QRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 76

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

 Score = 54.3 bits (131), Expect = 1e-11
 Identities = 22/59 (37%), Positives = 33/59 (55%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
           RR R T+TR Q   LE  F    Y     R E+A  + L E ++++WF+NRR K +++
Sbjct: 7  GRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQ 65

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

 Score = 53.9 bits (130), Expect = 2e-11
 Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 10/82 (12%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
           +R R ++T+ Q   LEKEF   HY     R  +A  + L E +I++WF NRR K ++  
Sbjct: 7  GQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRR-- 64

Query: 67 QAIKELNEQEKQAQAQKAAAAA 88
                  +EK    ++ +  +
Sbjct: 65 --------EEKLRNQRRQSGPS 78

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

 Score = 53.9 bits (130), Expect = 2e-11
 Identities = 24/61 (39%), Positives = 34/61 (55%)

Query: 5  GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          G +RR R  +T  Q  +LE  F  N Y     R E+A    LTE ++++WF+NRR K +K
Sbjct: 1  GSQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60

Query: 65 E 65
           
Sbjct: 61 R 61

>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 71

 Score = 53.7 bits (129), Expect = 2e-11
 Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 1/59 (1%)

Query: 7  RRRGRQTYTRYQTLELEKEFH-TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
            R R   +      L+   H    Y  +     ++  L L +  I  +FQN+R  +K 
Sbjct: 7  GPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH 65

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

 Score = 52.7 bits (127), Expect = 4e-11
 Identities = 19/59 (32%), Positives = 30/59 (50%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
           RR R  +T  Q   LE  F    Y     R ++A  + L E ++++WF+NRR K ++ 
Sbjct: 7  GRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRS 65

>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 89

 Score = 53.4 bits (128), Expect = 4e-11
 Identities = 15/61 (24%), Positives = 25/61 (40%)

Query: 11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK 70
           +  T+ Q   LE  F  + + T+     +     L+ R+I  WF  RR       QA+ 
Sbjct: 17 FKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAVL 76

Query: 71 E 71
          +
Sbjct: 77 D 77

>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 66

 Score = 52.4 bits (126), Expect = 5e-11
 Identities = 17/64 (26%), Positives = 26/64 (40%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
            R R      Q   L   +  N       + ++     L+ R I++WFQN+R K KK  
Sbjct: 3  TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS 62

Query: 67 QAIK 70
            +K
Sbjct: 63 IMMK 66

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

 Score = 52.4 bits (126), Expect = 5e-11
 Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 1/61 (1%)

Query: 6  LRRRGRQTYTRYQTLELEKEFH-TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          +  +     T  Q   LE  F+  N +        +A    LTE Q + WF+ R  + ++
Sbjct: 1  MSAQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRR 60

Query: 65 E 65
           
Sbjct: 61 S 61

>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens} Length = 66

 Score = 51.3 bits (123), Expect = 1e-10
 Identities = 12/63 (19%), Positives = 23/63 (36%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
               +  T+ Q   L+  F  + +        +     L   +IK WF + R + ++ I
Sbjct: 4  HHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGI 63

Query: 67 QAI 69
            I
Sbjct: 64 VHI 66

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

 Score = 51.1 bits (123), Expect = 2e-10
 Identities = 25/55 (45%), Positives = 34/55 (61%)

Query: 11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
            T+T +Q  ELEK F   HY     R E+A  + LTE +I++WFQNRR K +K+
Sbjct: 3  HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 89

 Score = 50.8 bits (121), Expect = 5e-10
 Identities = 12/60 (20%), Positives = 23/60 (38%)

Query: 11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK 70
           +  T  Q   L+  F  +  LT      +     LT R+I  WF  ++     + + ++
Sbjct: 15 FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKME 74

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

 Score = 51.8 bits (123), Expect = 8e-10
 Identities = 12/58 (20%), Positives = 23/58 (39%)

Query: 7   RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
            ++ R  +T  Q   L   F  N   ++  +I ++  L L    +  +F N R +   
Sbjct: 97  PKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLD 154

>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor, structural genomics, loop insertion, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 95

 Score = 49.6 bits (118), Expect = 1e-09
 Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 15/73 (20%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALC---------------LTERQI 51
           R  R T+ +     +E  F+ N Y    +R E+A+A                 +T  ++
Sbjct: 7  GRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKV 66

Query: 52 KIWFQNRRMKLKK 64
            WF NRR ++K+
Sbjct: 67 YNWFANRRKEIKR 79

>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 75

 Score = 48.7 bits (116), Expect = 2e-09
 Identities = 14/55 (25%), Positives = 19/55 (34%)

Query: 11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
           +     Q   LE  F  N          +     +T R+I  WF  RR K+  E
Sbjct: 11 YKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAE 65

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

 Score = 45.2 bits (107), Expect = 3e-08
 Identities = 15/65 (23%), Positives = 27/65 (41%), Gaps = 3/65 (4%)

Query: 5  GLRRRGRQTYTRYQTLELEKEF-HTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63
          G++              LEK F     Y   +R   ++  L  + R+I+ WF++RR + K
Sbjct: 8  GIKDSPVNKVE--PNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 65

Query: 64 KEIQA 68
              +
Sbjct: 66 PSGPS 70

>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac development, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 72

 Score = 44.7 bits (106), Expect = 5e-08
 Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 1/59 (1%)

Query: 8  RRGRQTYTRYQTLELEKEFH-TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
            G  T T  Q   LE  F+  N +        +A    LTE Q + WF+ R  + ++ 
Sbjct: 2  SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60

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

 Score = 43.1 bits (100), Expect = 2e-06
 Identities = 13/83 (15%), Positives = 23/83 (27%), Gaps = 21/83 (25%)

Query: 2   GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALC---------------- 45
             N   RR R  +       L + +      ++  R  +                     
Sbjct: 137 PTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHG 196

Query: 46  -----LTERQIKIWFQNRRMKLK 63
                +TE ++  WF NRR +  
Sbjct: 197 LGSNLVTEVRVYNWFANRRKEEA 219

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

 Score = 38.7 bits (89), Expect = 2e-05
 Identities = 11/63 (17%), Positives = 25/63 (39%)

Query: 2  GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
          G++G                LE+ +  +  L      +++ A  L+ +Q+  WF +R  +
Sbjct: 1  GSSGSSGPLPIPPPPPDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSRLPQ 60

Query: 62 LKK 64
            +
Sbjct: 61 PAE 63

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

 Score = 38.6 bits (89), Expect = 2e-05
 Identities = 11/58 (18%), Positives = 17/58 (29%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
                  T  Q   L+  F    + +     ++A    L    I  WF + R   K 
Sbjct: 25 STGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKN 82

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

 Score = 37.9 bits (88), Expect = 2e-05
 Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 1/44 (2%)

Query: 22 LEKEF-HTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          LEK F     +   +R   ++  L    R I+ WF+ RR + K 
Sbjct: 15 LEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 58

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

 Score = 39.5 bits (91), Expect = 3e-05
 Identities = 12/78 (15%), Positives = 22/78 (28%), Gaps = 21/78 (26%)

Query: 7   RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALC--------------------- 45
            RR R  +       L + +      ++  R  +                          
Sbjct: 115 GRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNL 174

Query: 46  LTERQIKIWFQNRRMKLK 63
           +TE ++  WF NRR +  
Sbjct: 175 VTEVRVYNWFANRRKEEA 192

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

 Score = 34.8 bits (79), Expect = 8e-04
 Identities = 12/83 (14%), Positives = 23/83 (27%), Gaps = 21/83 (25%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALC--------------------- 45
           RR R  +       L + +      ++  R  +                          
Sbjct: 9  GRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNL 68

Query: 46 LTERQIKIWFQNRRMKLKKEIQA 68
          +TE ++  WF NRR +     + 
Sbjct: 69 VTEVRVYNWFANRRKEEAFRHKL 91

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	96
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.86
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.85
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.85
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.85
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.85
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.85
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.85
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.85
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.85
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.84
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.84
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.84
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.84
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.84
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.84
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.84
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.84
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.84
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.84
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.83
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.83
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.83
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.83
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.83
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.83
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.82
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.82
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.82
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.82
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.82
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.82
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.82
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.82
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.81
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.81
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.81
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.81
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.8
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.8
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.8
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.8
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.8
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.8
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.8
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.79
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.79
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.79
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.79
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.79
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.79
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.79
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.78
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.78
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.78
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.77
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.77
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.76
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.76
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.75
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.75
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.75
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.75
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.75
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.74
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.73
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.73
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.73
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.72
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.72
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.71
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.7
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.65
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.57
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.54
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.51
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.5
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.39
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.72
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	97.24
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	90.46
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	88.15
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	87.85
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	83.8
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	81.54
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	80.96

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

Probab=99.86  E-value=1.3e-21  Score=113.44  Aligned_cols=67  Identities=34%  Similarity=0.556  Sum_probs=62.1

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHH
Q psy1653           2 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA   68 (96)
Q Consensus         2 ~~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~   68 (96)
                      ++++..++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||+|||+++|+....
T Consensus         2 s~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~   68 (80)
T 2cue_A            2 SSGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL   68 (80)
T ss_dssp             CSCCSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhh
Confidence            4566788899999999999999999999999999999999999999999999999999999996543

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

Probab=99.85  E-value=1.6e-21  Score=110.42  Aligned_cols=65  Identities=29%  Similarity=0.497  Sum_probs=60.6

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           2 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         2 ~~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      ++++..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         2 s~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~   66 (70)
T 2dmu_A            2 SSGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSG   66 (70)
T ss_dssp             CSTTSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTS
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccC
Confidence            34566788999999999999999999999999999999999999999999999999999999853

>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=99.85  E-value=1.2e-21  Score=110.99  Aligned_cols=63  Identities=43%  Similarity=0.716  Sum_probs=59.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           3 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         3 ~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      +.+..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+.
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~   65 (70)
T 2cra_A            3 SGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKS   65 (70)
T ss_dssp             SSCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSS
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhccc
Confidence            456678889999999999999999999999999999999999999999999999999999985

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

Probab=99.85  E-value=1.7e-21  Score=108.29  Aligned_cols=60  Identities=65%  Similarity=0.950  Sum_probs=55.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           6 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         6 ~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      ..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+.
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            478889999999999999999999999999999999999999999999999999999985

>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=99.85  E-value=1.6e-21  Score=110.31  Aligned_cols=64  Identities=31%  Similarity=0.486  Sum_probs=60.2

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           2 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         2 ~~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      ++.+..++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||+|||+++|+.
T Consensus         2 ~~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   65 (70)
T 2da2_A            2 SSGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKS   65 (70)
T ss_dssp             CCSCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhc
Confidence            3466788899999999999999999999999999999999999999999999999999999874

>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.85  E-value=3.4e-21  Score=109.09  Aligned_cols=65  Identities=40%  Similarity=0.667  Sum_probs=60.3

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           2 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         2 ~~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      ++++..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         2 s~~~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~   66 (70)
T 2e1o_A            2 SSGSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSG   66 (70)
T ss_dssp             CCCCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCC
Confidence            34566788899999999999999999999999999999999999999999999999999999853

>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=99.85  E-value=3.8e-21  Score=111.32  Aligned_cols=65  Identities=25%  Similarity=0.466  Sum_probs=60.8

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           2 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         2 ~~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      ++.+..++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||+|||+++|+..
T Consensus         2 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   66 (80)
T 2dmq_A            2 SSGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNL   66 (80)
T ss_dssp             CCCCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHH
Confidence            34567788999999999999999999999999999999999999999999999999999999854

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

Probab=99.85  E-value=9.2e-22  Score=109.00  Aligned_cols=61  Identities=33%  Similarity=0.599  Sum_probs=52.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      |+.++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+.
T Consensus         1 g~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A            1 GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             -------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            4578899999999999999999999999999999999999999999999999999999984

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

Probab=99.85  E-value=5.8e-21  Score=109.96  Aligned_cols=65  Identities=38%  Similarity=0.620  Sum_probs=59.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653           3 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   67 (96)
Q Consensus         3 ~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~   67 (96)
                      ...++++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||+|||+++|+...
T Consensus         5 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~   69 (77)
T 1nk2_P            5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQN   69 (77)
T ss_dssp             CSCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhc
Confidence            34566778999999999999999999999999999999999999999999999999999998543

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

Probab=99.84  E-value=2e-21  Score=109.98  Aligned_cols=64  Identities=39%  Similarity=0.700  Sum_probs=60.1

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           2 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         2 ~~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      ++++..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+.
T Consensus         2 s~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   65 (70)
T 2djn_A            2 SSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKS   65 (70)
T ss_dssp             CSCCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSS
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhccc
Confidence            3466778899999999999999999999999999999999999999999999999999999874

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

Probab=99.84  E-value=5.3e-21  Score=110.82  Aligned_cols=64  Identities=34%  Similarity=0.501  Sum_probs=60.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           3 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         3 ~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      +.++.++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||+|||+++|+..
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            4566788899999999999999999999999999999999999999999999999999999853

>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=99.84  E-value=2.6e-21  Score=109.44  Aligned_cols=63  Identities=27%  Similarity=0.340  Sum_probs=59.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           3 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         3 ~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      +.+..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+.
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   65 (70)
T 2da1_A            3 SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQS   65 (70)
T ss_dssp             SSCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhh
Confidence            456678899999999999999999999999999999999999999999999999999999884

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

Probab=99.84  E-value=2.8e-21  Score=114.98  Aligned_cols=66  Identities=39%  Similarity=0.678  Sum_probs=61.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHHH
Q psy1653           4 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAI   69 (96)
Q Consensus         4 ~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~~   69 (96)
                      ..+.++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+|+|+.....
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~   79 (93)
T 3a01_A           14 PPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEE   79 (93)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHH
Confidence            456778899999999999999999999999999999999999999999999999999999965443

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

Probab=99.84  E-value=2e-21  Score=112.93  Aligned_cols=65  Identities=97%  Similarity=1.427  Sum_probs=54.5

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           2 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         2 ~~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      |+.+..++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||+|||+++|+..
T Consensus        15 ~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   79 (81)
T 1b8i_A           15 GTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEI   79 (81)
T ss_dssp             ---------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhc
Confidence            34567788999999999999999999999999999999999999999999999999999999853

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

Probab=99.84  E-value=6.6e-21  Score=108.73  Aligned_cols=66  Identities=44%  Similarity=0.671  Sum_probs=61.1

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           1 MGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         1 ~~~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      |+.....++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         1 ~s~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   66 (73)
T 2l7z_A            1 MSHMLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVI   66 (73)
T ss_dssp             CCSSSCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSS
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHh
Confidence            345567788999999999999999999999999999999999999999999999999999999853

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

Probab=99.84  E-value=3.6e-21  Score=106.25  Aligned_cols=58  Identities=47%  Similarity=0.811  Sum_probs=53.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653           7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   64 (96)
Q Consensus         7 ~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr   64 (96)
                      .++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+
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            5788999999999999999999999999999999999999999999999999999986

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

Probab=99.84  E-value=5.7e-21  Score=109.22  Aligned_cols=64  Identities=44%  Similarity=0.697  Sum_probs=60.4

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           2 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         2 ~~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      .+.+++++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+.
T Consensus         4 ~~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   67 (75)
T 2m0c_A            4 SNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKR   67 (75)
T ss_dssp             CCCSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHH
Confidence            4567788899999999999999999999999999999999999999999999999999999874

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

Probab=99.84  E-value=7.5e-21  Score=103.92  Aligned_cols=57  Identities=47%  Similarity=0.792  Sum_probs=55.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653           8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   64 (96)
Q Consensus         8 rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr   64 (96)
                      ++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+
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            578999999999999999999999999999999999999999999999999999986

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

Probab=99.84  E-value=1.4e-20  Score=108.36  Aligned_cols=64  Identities=63%  Similarity=0.847  Sum_probs=59.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653           4 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   67 (96)
Q Consensus         4 ~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~   67 (96)
                      .+..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+...
T Consensus        10 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k   73 (77)
T 1puf_A           10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINK   73 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhh
Confidence            3556788999999999999999999999999999999999999999999999999999999654

>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=6.7e-21  Score=110.39  Aligned_cols=61  Identities=44%  Similarity=0.742  Sum_probs=57.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      .+.++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||+|||+++|+.
T Consensus        15 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~   75 (80)
T 2dmt_A           15 KKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKS   75 (80)
T ss_dssp             CCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcc
Confidence            4567789999999999999999999999999999999999999999999999999999874

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

Probab=99.83  E-value=1e-20  Score=106.57  Aligned_cols=61  Identities=41%  Similarity=0.638  Sum_probs=58.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653           7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   67 (96)
Q Consensus         7 ~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~   67 (96)
                      +++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+...
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            6788999999999999999999999999999999999999999999999999999998653

>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription regulation; HET: DNA; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 3a01_B

Probab=99.83  E-value=1.6e-20  Score=108.98  Aligned_cols=64  Identities=39%  Similarity=0.615  Sum_probs=58.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653           4 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   67 (96)
Q Consensus         4 ~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~   67 (96)
                      .++.++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+...
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            3456788999999999999999999999999999999999999999999999999999999653

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

Probab=99.83  E-value=3.4e-21  Score=108.52  Aligned_cols=62  Identities=39%  Similarity=0.602  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      |..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         1 g~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~   62 (68)
T 1yz8_P            1 GSQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE   62 (68)
T ss_dssp             CCSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHh
Confidence            45788999999999999999999999999999999999999999999999999999999854

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

Probab=99.83  E-value=1e-20  Score=104.11  Aligned_cols=58  Identities=53%  Similarity=0.794  Sum_probs=55.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         8 rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      ++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|++
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            5789999999999999999999999999999999999999999999999999999884

>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=1.4e-20  Score=109.89  Aligned_cols=62  Identities=31%  Similarity=0.523  Sum_probs=58.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           4 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         4 ~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      .+..++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||+|||+++|+.
T Consensus        19 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~   80 (84)
T 2kt0_A           19 PVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRW   80 (84)
T ss_dssp             CSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence            45678889999999999999999999999999999999999999999999999999999874

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

Probab=99.82  E-value=2e-20  Score=105.40  Aligned_cols=60  Identities=40%  Similarity=0.720  Sum_probs=57.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         7 ~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      +++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
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

>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=1e-20  Score=109.46  Aligned_cols=62  Identities=29%  Similarity=0.384  Sum_probs=58.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           4 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         4 ~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      ....++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||+|||+++|+.
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   75 (80)
T 2da3_A           14 PQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKS   75 (80)
T ss_dssp             CCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhh
Confidence            34567789999999999999999999999999999999999999999999999999999985

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

Probab=99.82  E-value=8.6e-21  Score=109.90  Aligned_cols=64  Identities=17%  Similarity=0.269  Sum_probs=59.7

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhC----CCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           2 GANGLRRRGRQTYTRYQTLELEKEFHTN----HYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         2 ~~~~~~rr~r~~~s~~q~~~L~~~F~~~----~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      +..++.++.|+.|+..|+.+|+..|..+    +||+..++..||..+||++.+|++||||||+|+|+.
T Consensus         3 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~   70 (80)
T 2da4_A            3 SGSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLM   70 (80)
T ss_dssp             CCCCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhc
Confidence            3456678889999999999999999999    999999999999999999999999999999999984

>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=99.82  E-value=1e-20  Score=105.90  Aligned_cols=60  Identities=27%  Similarity=0.343  Sum_probs=57.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           6 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         6 ~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      +.++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+.
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   61 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR   61 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHH
Confidence            367889999999999999999999999999999999999999999999999999999874

>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=99.82  E-value=1.2e-20  Score=106.36  Aligned_cols=60  Identities=88%  Similarity=1.285  Sum_probs=57.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         7 ~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      +++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
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            578899999999999999999999999999999999999999999999999999999853

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

Probab=99.82  E-value=1.7e-20  Score=102.34  Aligned_cols=57  Identities=46%  Similarity=0.737  Sum_probs=54.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653           7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK   63 (96)
Q Consensus         7 ~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~k   63 (96)
                      +++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|
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            578899999999999999999999999999999999999999999999999999875

>1wh5_A ZF-HD homeobox family protein; structural genomics, zinc finger homeobox family protein, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} SCOP: a.4.1.1

Probab=99.82  E-value=1.3e-20  Score=109.27  Aligned_cols=60  Identities=15%  Similarity=0.241  Sum_probs=56.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653           5 GLRRRGRQTYTRYQTLELEKEFHT----NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   64 (96)
Q Consensus         5 ~~~rr~r~~~s~~q~~~L~~~F~~----~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr   64 (96)
                      +.+++.|+.|+..|+..|+..|..    ++||+..++..||..|||++.+|++||||||+|+++
T Consensus        15 ~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           15 GIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            357888999999999999999999    999999999999999999999999999999999875

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

Probab=99.82  E-value=1.9e-20  Score=110.27  Aligned_cols=62  Identities=82%  Similarity=1.213  Sum_probs=54.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           4 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         4 ~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      .+..++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||+|||+++|+.
T Consensus        25 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~   86 (88)
T 2r5y_A           25 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   86 (88)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhh
Confidence            45678899999999999999999999999999999999999999999999999999999984

>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=99.81  E-value=2.2e-20  Score=103.02  Aligned_cols=59  Identities=25%  Similarity=0.460  Sum_probs=48.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653           5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK   63 (96)
Q Consensus         5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~k   63 (96)
                      ++.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|
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            45678899999999999999999999999999999999999999999999999999875

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

Probab=99.81  E-value=2.4e-20  Score=102.59  Aligned_cols=57  Identities=44%  Similarity=0.670  Sum_probs=50.6

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653          10 GRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus        10 ~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      +|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
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            589999999999999999999999999999999999999999999999999999864

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

Probab=99.81  E-value=1.9e-20  Score=108.69  Aligned_cols=60  Identities=17%  Similarity=0.221  Sum_probs=56.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHh-----CCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653           4 NGLRRRGRQTYTRYQTLELEKEFHT-----NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   64 (96)
Q Consensus         4 ~~~~rr~r~~~s~~q~~~L~~~F~~-----~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr   64 (96)
                      .+.++|.|+.|+..|+..|+ .|..     ++||+..++..||..|||++.+|+|||||||+|+++
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           14 GGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            45568889999999999999 7999     999999999999999999999999999999999875

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

Probab=99.81  E-value=3.9e-20  Score=103.80  Aligned_cols=59  Identities=41%  Similarity=0.562  Sum_probs=56.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         8 rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      ++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~   60 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSH   60 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSC
T ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhc
Confidence            67899999999999999999999999999999999999999999999999999998853

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

Probab=99.80  E-value=9e-20  Score=108.73  Aligned_cols=65  Identities=28%  Similarity=0.439  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcC---------------CCcchhhhhhchhhhhhHHHHH
Q psy1653           3 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALC---------------LTERQIKIWFQNRRMKLKKEIQ   67 (96)
Q Consensus         3 ~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~---------------l~~~~V~~WFqnrR~k~kr~~~   67 (96)
                      +.++.++.|+.|+..|+.+|+..|..++||+..++..||..|+               |++.+|++||+|||+++|+...
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            4566788999999999999999999999999999999999999               9999999999999999998643

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

Probab=99.80  E-value=6.7e-20  Score=99.62  Aligned_cols=54  Identities=43%  Similarity=0.777  Sum_probs=50.9

Q ss_pred             CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653          12 QTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus        12 ~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      |.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+.
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            679999999999999999999999999999999999999999999999999984

>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=99.80  E-value=2.4e-20  Score=109.44  Aligned_cols=62  Identities=31%  Similarity=0.525  Sum_probs=57.3

Q ss_pred             CCCCCCCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHHH
Q psy1653           8 RRGRQTYTRYQTLELEKEF---HTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAI   69 (96)
Q Consensus         8 rr~r~~~s~~q~~~L~~~F---~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~~   69 (96)
                      ++.|+.|+..|+.+|+..|   ..++||+..++..||..+||++.+|++||+|+|.++|+.....
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   8999999999999999999999999999999999999965443

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

Probab=99.80  E-value=1.5e-19  Score=103.02  Aligned_cols=59  Identities=24%  Similarity=0.227  Sum_probs=55.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           8 RRGRQTYTRYQTLELEKEFHT-NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         8 rr~r~~~s~~q~~~L~~~F~~-~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      .+.|+.|+..|+..|+..|.. ++||+..++..||..+||++.+|++||+|||+++|+..
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            466899999999999999995 99999999999999999999999999999999999854

>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=99.80  E-value=1.2e-19  Score=103.13  Aligned_cols=59  Identities=27%  Similarity=0.308  Sum_probs=55.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           8 RRGRQTYTRYQTLELEKEFHT-NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         8 rr~r~~~s~~q~~~L~~~F~~-~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      .+.|+.|+..|+..|+..|.. ++||+..++..||..+||++.+|++||+|||+++|+..
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            356899999999999999996 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=99.80  E-value=2e-19  Score=102.48  Aligned_cols=63  Identities=19%  Similarity=0.271  Sum_probs=58.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           3 ANGLRRRGRQTYTRYQTLELEKEFHT---NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         3 ~~~~~rr~r~~~s~~q~~~L~~~F~~---~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      +.+..++.|+.|+..|+.+|+..|..   ++||+..++..||..+||++.+|++||+|+|+++++.
T Consensus         3 ~~~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~   68 (73)
T 1x2n_A            3 SGSSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQS   68 (73)
T ss_dssp             CCSSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhcccc
Confidence            34567888999999999999999987   9999999999999999999999999999999999885

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

Probab=99.80  E-value=9.5e-20  Score=108.99  Aligned_cols=62  Identities=56%  Similarity=0.802  Sum_probs=55.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      +..++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||||||+++|+..
T Consensus        32 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   93 (97)
T 1b72_A           32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRE   93 (97)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHh
Confidence            45678899999999999999999999999999999999999999999999999999999854

>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=99.79  E-value=2.8e-19  Score=107.60  Aligned_cols=65  Identities=20%  Similarity=0.307  Sum_probs=60.9

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHc---------------------CCCcchhhhhhchhhh
Q psy1653           2 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHAL---------------------CLTERQIKIWFQNRRM   60 (96)
Q Consensus         2 ~~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l---------------------~l~~~~V~~WFqnrR~   60 (96)
                      |+.+..++.|+.|++.|+.+|+..|..++||+..+++.||..|                     +|++.+|++||+|||+
T Consensus         1 ~~~~~~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~   80 (102)
T 2da6_A            1 GSSGSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRK   80 (102)
T ss_dssp             CTTCCSCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHH
Confidence            5677889999999999999999999999999999999999999                     7899999999999999


Q ss_pred             hhHHHH
Q psy1653          61 KLKKEI   66 (96)
Q Consensus        61 k~kr~~   66 (96)
                      ++++..
T Consensus        81 k~kr~~   86 (102)
T 2da6_A           81 EEAFRQ   86 (102)
T ss_dssp             HHHHHH
T ss_pred             HHHHhh
Confidence            998853

>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=99.79  E-value=2.4e-19  Score=102.86  Aligned_cols=57  Identities=21%  Similarity=0.281  Sum_probs=53.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           9 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         9 r~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      ..|..|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|+|.++|+.
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            346679999999999999999999999999999999999999999999999999884

>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=99.79  E-value=2.7e-19  Score=102.48  Aligned_cols=60  Identities=23%  Similarity=0.269  Sum_probs=55.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         7 ~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      ..+.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         7 ~~~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~   66 (75)
T 2da5_A            7 GPTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEE   66 (75)
T ss_dssp             SSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSS
T ss_pred             CCCCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhh
Confidence            345677899999999999999999999999999999999999999999999999999853

>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=1.1e-19  Score=108.51  Aligned_cols=63  Identities=17%  Similarity=0.152  Sum_probs=56.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           4 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         4 ~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      .+..++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||||||+|+|+.+
T Consensus        22 ~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   84 (96)
T 3nar_A           22 KSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGN   84 (96)
T ss_dssp             -----CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhc
Confidence            344567899999999999999999999999999999999999999999999999999999864

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

Probab=99.79  E-value=2e-19  Score=102.66  Aligned_cols=61  Identities=23%  Similarity=0.292  Sum_probs=57.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           6 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         6 ~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      ..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
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            3567899999999999999999999999999999999999999999999999999999853

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

Probab=99.79  E-value=1.5e-19  Score=103.77  Aligned_cols=61  Identities=16%  Similarity=0.284  Sum_probs=57.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      ......|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+.
T Consensus         6 ~~~~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~   66 (76)
T 2dn0_A            6 SGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNL   66 (76)
T ss_dssp             SCCCCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSC
T ss_pred             CCCCCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHh
Confidence            3455679999999999999999999999999999999999999999999999999999884

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

Probab=99.79  E-value=3.1e-19  Score=99.70  Aligned_cols=60  Identities=20%  Similarity=0.213  Sum_probs=56.4

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHcCCCcchhhhhhchhhhh
Q psy1653           2 GANGLRRRGRQTYTRYQTLELEKEFHT-NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK   61 (96)
Q Consensus         2 ~~~~~~rr~r~~~s~~q~~~L~~~F~~-~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k   61 (96)
                      |+.+.++|.||.|+.+|+.+|+..|.. ++||+...++.|+.++||++.+|++||||+|--
T Consensus         2 ~~~~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~   62 (71)
T 1wi3_A            2 SSGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYH   62 (71)
T ss_dssp             CCCCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceee
Confidence            456778999999999999999999999 999999999999999999999999999999853

>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=99.78  E-value=4.1e-19  Score=101.14  Aligned_cols=61  Identities=31%  Similarity=0.528  Sum_probs=57.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653           7 RRRGRQTYTRYQTLELEKEF---HTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   67 (96)
Q Consensus         7 ~rr~r~~~s~~q~~~L~~~F---~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~   67 (96)
                      .++.|+.|+..|+.+|+..|   ..++||+..++..||..+||++.+|++||+|+|.++++...
T Consensus         1 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~   64 (73)
T 1puf_B            1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG   64 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcccccc
Confidence            36789999999999999999   89999999999999999999999999999999999998543

>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=99.78  E-value=7.6e-19  Score=102.44  Aligned_cols=63  Identities=14%  Similarity=0.219  Sum_probs=58.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           3 ANGLRRRGRQTYTRYQTLELEKEFHT---NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         3 ~~~~~rr~r~~~s~~q~~~L~~~F~~---~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      ++..+++.|+.|+..++.+|+.+|..   ++||+..++..||..+||++.+|.+||+|+|.|+++.
T Consensus         3 ~~~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~   68 (83)
T 2dmn_A            3 SGSSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPD   68 (83)
T ss_dssp             CCCCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHH
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHH
Confidence            45567788999999999999999987   6999999999999999999999999999999999874

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

Probab=99.78  E-value=1.5e-19  Score=100.54  Aligned_cols=59  Identities=25%  Similarity=0.381  Sum_probs=55.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653           6 LRRRGRQTYTRYQTLELEKEF---HTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   64 (96)
Q Consensus         6 ~~rr~r~~~s~~q~~~L~~~F---~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr   64 (96)
                      ..++.|+.|+..|+.+|+..|   ..++||+..++..||..+||++.+|++||+|+|+++|+
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            357789999999999999999   89999999999999999999999999999999999876

>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=99.77  E-value=2.7e-19  Score=114.06  Aligned_cols=64  Identities=30%  Similarity=0.479  Sum_probs=55.5

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           2 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         2 ~~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      |..+++++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+|+|+.
T Consensus        82 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           82 GANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             -------CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            3445678889999999999999999999999999999999999999999999999999999874

>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain, hoogsteen base PAIR, transcription/DNA complex; HET: 5IU; 2.10A {Synthetic} SCOP: a.4.1.1

Probab=99.77  E-value=8.3e-19  Score=96.37  Aligned_cols=55  Identities=31%  Similarity=0.389  Sum_probs=52.8

Q ss_pred             CCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653          11 RQTYTRYQTLELEKEFHT---NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus        11 r~~~s~~q~~~L~~~F~~---~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      ++.|+..|+.+|+..|..   ++||+..++..||..+||++.+|++||+|+|+++|+.
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            679999999999999999   9999999999999999999999999999999999863

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

Probab=99.76  E-value=1e-18  Score=111.81  Aligned_cols=61  Identities=30%  Similarity=0.477  Sum_probs=57.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653           4 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   64 (96)
Q Consensus         4 ~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr   64 (96)
                      .+++++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+|+||
T Consensus        90 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           90 PSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            4567788999999999999999999999999999999999999999999999999999986

>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.1

Probab=99.76  E-value=8.7e-19  Score=102.89  Aligned_cols=59  Identities=29%  Similarity=0.366  Sum_probs=55.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653           5 GLRRRGRQTYTRYQTLELEKEFHT---NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK   63 (96)
Q Consensus         5 ~~~rr~r~~~s~~q~~~L~~~F~~---~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~k   63 (96)
                      +.+++.|+.|+..|+.+|+..|..   ++||+..++..||..+||++.+|++||+|||+|+|
T Consensus        25 ~~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k   86 (87)
T 1mnm_C           25 STKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK   86 (87)
T ss_dssp             ESSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcc
Confidence            456777999999999999999999   99999999999999999999999999999999987

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

Probab=99.75  E-value=6.7e-19  Score=114.17  Aligned_cols=63  Identities=25%  Similarity=0.360  Sum_probs=51.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           4 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         4 ~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      .+++++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+|+|+..
T Consensus        96 ~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~  158 (164)
T 2xsd_C           96 QGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMT  158 (164)
T ss_dssp             ----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSC
T ss_pred             cccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhcc
Confidence            456788899999999999999999999999999999999999999999999999999999854

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A

Probab=99.75  E-value=9.6e-19  Score=112.97  Aligned_cols=61  Identities=31%  Similarity=0.458  Sum_probs=54.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      +++++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+|+||.
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            4578889999999999999999999999999999999999999999999999999999874

>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration calorimetry, protein-DNA complex, transcription/DNA complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1akh_B* 1apl_C* 1yrn_B*

Probab=99.75  E-value=2e-18  Score=100.57  Aligned_cols=59  Identities=27%  Similarity=0.337  Sum_probs=53.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           7 RRRGRQTYTRYQTLELEKEFHT---NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         7 ~rr~r~~~s~~q~~~L~~~F~~---~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      +++.+++|+..|+.+|+..|..   ++||+..++..||..+||++.+|++||+|||+++|+.
T Consensus         2 K~krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~   63 (83)
T 1le8_B            2 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTI   63 (83)
T ss_dssp             ---CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHcccccc
Confidence            3455677999999999999999   9999999999999999999999999999999999985

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

Probab=99.75  E-value=7.1e-19  Score=100.11  Aligned_cols=59  Identities=24%  Similarity=0.342  Sum_probs=54.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHH-HhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           7 RRRGRQTYTRYQTLELEKEF-HTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         7 ~rr~r~~~s~~q~~~L~~~F-~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      ..+.+..++..|+..|+..| ..++||+...+..||..+||++.+|++||||||+++|+.
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            34567778889999999999 999999999999999999999999999999999999863

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

Probab=99.75  E-value=2.4e-18  Score=95.92  Aligned_cols=53  Identities=21%  Similarity=0.391  Sum_probs=50.3

Q ss_pred             CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653          14 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus        14 ~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      -+..|+..|+..|..++||+..++.+||..+||++.+|++||+|||.++|+.+
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            46899999999999999999999999999999999999999999999999854

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

Probab=99.74  E-value=1.6e-18  Score=104.09  Aligned_cols=64  Identities=20%  Similarity=0.275  Sum_probs=53.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHH------------------cC---CCcchhhhhhchhhhh
Q psy1653           3 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHA------------------LC---LTERQIKIWFQNRRMK   61 (96)
Q Consensus         3 ~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~------------------l~---l~~~~V~~WFqnrR~k   61 (96)
                      ...+.++.|+.|+..|+.+|+..|..++||+...+++||..                  ||   |++.+|++||+|||++
T Consensus         5 ~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k   84 (99)
T 1lfb_A            5 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE   84 (99)
T ss_dssp             --------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHH
Confidence            34567888999999999999999999999999999999999                  88   9999999999999999


Q ss_pred             hHHHH
Q psy1653          62 LKKEI   66 (96)
Q Consensus        62 ~kr~~   66 (96)
                      +++..
T Consensus        85 ~k~k~   89 (99)
T 1lfb_A           85 EAFRH   89 (99)
T ss_dssp             TSCCC
T ss_pred             HHHhc
Confidence            87743

>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=99.73  E-value=3.2e-18  Score=95.24  Aligned_cols=50  Identities=26%  Similarity=0.334  Sum_probs=46.1

Q ss_pred             HHHHHHHHHHH-HhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653          16 RYQTLELEKEF-HTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus        16 ~~q~~~L~~~F-~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      +.++..|+..| ..+.||+...+..||..|||++.+|++||||||+++|+.
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            34799999999 568999999999999999999999999999999999863

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

Probab=99.73  E-value=5.1e-18  Score=100.09  Aligned_cols=54  Identities=22%  Similarity=0.284  Sum_probs=51.9

Q ss_pred             CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653          12 QTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus        12 ~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      ..|+..|+..|+..|..++||+..++..||..|||++.+|++||||||+++++.
T Consensus        16 k~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~   69 (89)
T 2ecb_A           16 KEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALK   69 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSC
T ss_pred             ccCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHH
Confidence            389999999999999999999999999999999999999999999999999873

>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=99.73  E-value=2.7e-18  Score=110.38  Aligned_cols=61  Identities=26%  Similarity=0.412  Sum_probs=57.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      +.+++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+|+|+.
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            4577889999999999999999999999999999999999999999999999999999974

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

Probab=99.72  E-value=7.5e-18  Score=95.14  Aligned_cols=57  Identities=42%  Similarity=0.702  Sum_probs=53.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           9 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         9 r~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      ..-..++..|+..|+..|..++||+...+..||..+||++.+|++||||||+|+|+.
T Consensus         6 ~~~~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~   62 (69)
T 2l9r_A            6 HHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRK   62 (69)
T ss_dssp             CSCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCS
T ss_pred             CCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhh
Confidence            344578999999999999999999999999999999999999999999999999874

>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=99.72  E-value=1e-17  Score=98.79  Aligned_cols=55  Identities=24%  Similarity=0.274  Sum_probs=52.0

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653          11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus        11 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      +..|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+|+++.
T Consensus        17 ~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~   71 (89)
T 2dmp_A           17 FKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSM   71 (89)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTS
T ss_pred             cccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHH
Confidence            4459999999999999999999999999999999999999999999999999874

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

Probab=99.71  E-value=1.4e-17  Score=92.74  Aligned_cols=54  Identities=15%  Similarity=0.138  Sum_probs=50.2

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653          11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   64 (96)
Q Consensus        11 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr   64 (96)
                      +..+...|+..|+..|..++||+..++..||..+||++.+|++||+|||+|.++
T Consensus         7 ~~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~   60 (64)
T 2e19_A            7 GQPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS   60 (64)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSC
T ss_pred             CCCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCC
Confidence            445678999999999999999999999999999999999999999999998765

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

Probab=99.70  E-value=9.1e-18  Score=108.59  Aligned_cols=61  Identities=20%  Similarity=0.287  Sum_probs=54.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      .+.++.|+.|+..|+..|+..|..++||+...+..||..+||++.+|++||||||+|+|+.
T Consensus        95 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~  155 (164)
T 2d5v_A           95 NTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDK  155 (164)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhcccccc
Confidence            3568889999999999999999999999999999999999999999999999999999874

>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=99.65  E-value=1.5e-16  Score=89.22  Aligned_cols=55  Identities=20%  Similarity=0.349  Sum_probs=50.0

Q ss_pred             CCCCHHHHHHHHHHHH---hCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653          12 QTYTRYQTLELEKEFH---TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus        12 ~~~s~~q~~~L~~~F~---~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      ..|+..++.+|+..|.   .++||+..++..||..+||++.+|++||+|+|.|+++..
T Consensus         3 g~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~   60 (67)
T 3k2a_A            3 GIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPM   60 (67)
T ss_dssp             ---CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC
T ss_pred             CcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHH
Confidence            3789999999999999   999999999999999999999999999999999998853

>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=99.57  E-value=6.2e-16  Score=102.53  Aligned_cols=60  Identities=20%  Similarity=0.269  Sum_probs=53.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcC---------------------CCcchhhhhhchhhhhhH
Q psy1653           5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALC---------------------LTERQIKIWFQNRRMKLK   63 (96)
Q Consensus         5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~---------------------l~~~~V~~WFqnrR~k~k   63 (96)
                      .+.+|.|+.|+..|+..|+..|..++||+...++.||..|+                     |++.+|++||+|||++++
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            45678899999999999999999999999999999999999                     999999999999999876


Q ss_pred             H
Q psy1653          64 K   64 (96)
Q Consensus        64 r   64 (96)
                      .
T Consensus       193 ~  193 (194)
T 1ic8_A          193 F  193 (194)
T ss_dssp             -
T ss_pred             c
Confidence            3

>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=99.54  E-value=2.5e-14  Score=80.25  Aligned_cols=46  Identities=17%  Similarity=0.315  Sum_probs=43.7

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhh
Q psy1653          16 RYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK   61 (96)
Q Consensus        16 ~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k   61 (96)
                      ..|+..|+.+|..+++|+..++..||..+||+.++|++||||||+.
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            4689999999999999999999999999999999999999999963

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

Probab=99.51  E-value=4.4e-14  Score=83.01  Aligned_cols=56  Identities=18%  Similarity=0.290  Sum_probs=52.0

Q ss_pred             CCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653          11 RQTYTRYQTLELEKEFHT---NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus        11 r~~~s~~q~~~L~~~F~~---~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      -..|+..+..+|..+|..   ++||+..++..||..+||++.||.+||+|+|.|.++..
T Consensus         9 ~~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~   67 (89)
T 2lk2_A            9 SHMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDM   67 (89)
T ss_dssp             CCCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHH
Confidence            457899999999999987   99999999999999999999999999999999998753

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

Probab=99.50  E-value=1.9e-14  Score=96.74  Aligned_cols=58  Identities=21%  Similarity=0.303  Sum_probs=52.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcC---------------------CCcchhhhhhchhhhhh
Q psy1653           5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALC---------------------LTERQIKIWFQNRRMKL   62 (96)
Q Consensus         5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~---------------------l~~~~V~~WFqnrR~k~   62 (96)
                      .+.+|.|+.|++.|+.+|+..|..++||+..+++.||..||                     |++.+|++||+|||.+.
T Consensus       140 ~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~~~  218 (221)
T 2h8r_A          140 KKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEE  218 (221)
T ss_dssp             --CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhhhh
Confidence            35678899999999999999999999999999999999987                     88999999999999764

>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding cooperativity, maltose binding protein, MBP, sugar binding, DNA binding protein; 2.10A {Escherichia coli} SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A

Probab=99.39  E-value=1.9e-13  Score=97.35  Aligned_cols=54  Identities=26%  Similarity=0.447  Sum_probs=51.1

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653          10 GRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK   63 (96)
Q Consensus        10 ~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~k   63 (96)
                      -++.++..++..|+..|..++||+..++.+||..+||+++||++||+|||.|+|
T Consensus       368 ~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          368 AAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            366799999999999999999999999999999999999999999999999875

>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=98.72  E-value=1.7e-09  Score=53.53  Aligned_cols=20  Identities=75%  Similarity=1.157  Sum_probs=17.3

Q ss_pred             chhhhhhchhhhhhHHHHHH
Q psy1653          49 RQIKIWFQNRRMKLKKEIQA   68 (96)
Q Consensus        49 ~~V~~WFqnrR~k~kr~~~~   68 (96)
                      +||+|||||||+|+|+....
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~   20 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFN   20 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHH
T ss_pred             CCceeccHHHHHHHHHHhHH
Confidence            48999999999999996554

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

Probab=97.24  E-value=0.00029  Score=39.14  Aligned_cols=56  Identities=18%  Similarity=0.230  Sum_probs=46.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchh
Q psy1653           3 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNR   58 (96)
Q Consensus         3 ~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnr   58 (96)
                      +.|.....-...++.-.+.|..+|..-..+.......|+.+.+|+..+|+.||-.|
T Consensus         2 ~~~~~pp~l~~~~p~~~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~k   57 (70)
T 2ys9_A            2 SSGSSGPLPIPPPPPDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSR   57 (70)
T ss_dssp             CCCCCSSCCCCCCCCCCHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             CCCCCCCCcCCCCCCcchHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHhc
Confidence            34444555556666778999999999999999999999999999999999999644

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

Probab=90.46  E-value=0.4  Score=24.74  Aligned_cols=45  Identities=20%  Similarity=0.372  Sum_probs=31.0

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhc
Q psy1653          11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQ   56 (96)
Q Consensus        11 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFq   56 (96)
                      +..|+.++...+...+... .+.......+|..+||+...|..|..
T Consensus         3 r~~ys~efK~~~~~~~~~g-~s~~~~~~~vA~~~gIs~~tl~~W~~   47 (59)
T 2glo_A            3 RRIFTPHFKLQVLESYRND-NDCKGNQRATARKYNIHRRQIQKWLQ   47 (59)
T ss_dssp             CCCCCHHHHHHHHHHHHHC-TTTTTCHHHHHHHTTSCHHHHHHHHT
T ss_pred             CCcCCHHHHHHHHHHHHcC-CCcchHHHHHHHHHCcCHHHHHHHHH
Confidence            4578888876664444433 22112256889999999999999975

>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=88.15  E-value=1.6  Score=25.70  Aligned_cols=48  Identities=19%  Similarity=0.249  Sum_probs=36.9

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhh
Q psy1653          10 GRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM   60 (96)
Q Consensus        10 ~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~   60 (96)
                      .|..|+.++...+...+..++.+..   ..+|..+||+...|..|..++..
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            4778999998888777765655543   35788999999999999976544

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

Probab=87.85  E-value=1.5  Score=24.28  Aligned_cols=44  Identities=14%  Similarity=0.302  Sum_probs=31.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhc
Q psy1653           8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQ   56 (96)
Q Consensus         8 rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFq   56 (96)
                      ++.+..|+.++.......+.. ..    ....+|..+||+...|..|..
T Consensus        17 ~~~~~~ys~e~k~~~v~~~~~-g~----s~~~iA~~~gIs~sTl~rW~k   60 (87)
T 2elh_A           17 KRPLRSLTPRDKIHAIQRIHD-GE----SKASVARDIGVPESTLRGWCK   60 (87)
T ss_dssp             SSCCSSCCHHHHHHHHHHHHH-TC----CHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHC-CC----CHHHHHHHHCcCHHHHHHHHH
Confidence            345668898886655556643 32    255779999999999999984

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

Probab=83.80  E-value=2.9  Score=23.16  Aligned_cols=48  Identities=10%  Similarity=0.162  Sum_probs=33.0

Q ss_pred             CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653          13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus        13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      .++..+..+|.-.|..+.     ...++|..+|++...|+.+...-+.+.++.
T Consensus        37 ~L~~~~r~vl~l~~~~g~-----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~   84 (92)
T 3hug_A           37 QLSAEHRAVIQRSYYRGW-----STAQIATDLGIAEGTVKSRLHYAVRALRLT   84 (92)
T ss_dssp             TSCHHHHHHHHHHHTSCC-----CHHHHHHHHTSCHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            356666667766554332     356789999999999999887555555543

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=81.54  E-value=2.9  Score=19.54  Aligned_cols=40  Identities=13%  Similarity=0.219  Sum_probs=27.8

Q ss_pred             CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhch
Q psy1653          13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQN   57 (96)
Q Consensus        13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqn   57 (96)
                      .++..+...+...+... .    ....+|..+|++...|..|+..
T Consensus         5 ~l~~~~~~~i~~~~~~g-~----s~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C            5 ALSDTERAQLDVMKLLN-V----SLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             CCCHHHHHHHHHHHHTT-C----CHHHHHHHHTCCHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHcC-C----CHHHHHHHHCcCHHHHHHHHhh
Confidence            46676665555555433 2    2557899999999999999853

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

Probab=80.96  E-value=2.8  Score=23.43  Aligned_cols=43  Identities=14%  Similarity=0.234  Sum_probs=30.7

Q ss_pred             CCCCCHHHHHHHHHHHHhC-CCCCHHHHHHHHHHcCCCcchhhhhhch
Q psy1653          11 RQTYTRYQTLELEKEFHTN-HYLTRRRRIEMAHALCLTERQIKIWFQN   57 (96)
Q Consensus        11 r~~~s~~q~~~L~~~F~~~-~~p~~~~~~~la~~l~l~~~~V~~WFqn   57 (96)
                      |..|+..+.......+... ..    ....+|..+||+...|..|...
T Consensus         3 r~~ys~e~k~~~v~~~~~~~g~----s~~~ia~~~gIs~~tl~rW~~~   46 (97)
T 2jn6_A            3 TKTYSEEFKRDAVALYENSDGA----SLQQIANDLGINRVTLKNWIIK   46 (97)
T ss_dssp             CCCCCHHHHHHHHHHHTTGGGS----CHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHcCCC----hHHHHHHHHCcCHHHHHHHHHH
Confidence            3568888776665555432 22    3567899999999999999853

---

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	96
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	3e-20
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	2e-19
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	3e-18
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	3e-18
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	8e-18
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	1e-17
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	2e-16
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	5e-16
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	9e-16
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	1e-15
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	1e-15
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	2e-15
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	3e-15
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	4e-15
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	2e-14
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	3e-14
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	7e-14
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	7e-14
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	2e-13
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	8e-13
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	1e-12
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	2e-12
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	2e-12
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	2e-12
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	3e-12
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	4e-12
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	2e-11
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	4e-11
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	4e-11
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	5e-09
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	2e-08
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	4e-07

>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 = 74.4 bits (183), Expect = 3e-20
 Identities = 50/55 (90%), Positives = 51/55 (92%)

Query: 11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          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 = 73.3 bits (180), Expect = 2e-19
 Identities = 40/59 (67%), Positives = 46/59 (77%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
           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 = 69.5 bits (170), Expect = 3e-18
 Identities = 26/57 (45%), Positives = 38/57 (66%)

Query: 8  RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          + G+  ++  QT+ELEK+F T  YL+   R  +A  L L+ERQ+K WFQNRR K ++
Sbjct: 1  KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 57

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.4 bits (172), Expect = 3e-18
 Identities = 34/59 (57%), Positives = 39/59 (66%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
              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 = 68.4 bits (167), Expect = 8e-18
 Identities = 27/57 (47%), Positives = 41/57 (71%)

Query: 8  RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          R+ R  Y++ Q  ELE+E+  N ++T+ +R +++ A  L+ERQI IWFQNRR+K KK
Sbjct: 2  RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 58

>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 = 67.9 bits (166), Expect = 1e-17
 Identities = 23/58 (39%), Positives = 34/58 (58%)

Query: 8  RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          +R R ++T+ Q   LEKEF   HY     R  +A  + L E +I++WF NRR K ++E
Sbjct: 2  QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE 59

>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 = 64.9 bits (158), Expect = 2e-16
 Identities = 26/53 (49%), Positives = 34/53 (64%)

Query: 9  RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
          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 = 63.8 bits (155), Expect = 5e-16
 Identities = 30/57 (52%), Positives = 39/57 (68%)

Query: 9  RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          R R  +TR Q   LEKEF+  +Y++R RR E+A  L L E  IK+WFQNRRMK K++
Sbjct: 1  RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 57

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 67

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 63.4 bits (154), Expect = 9e-16
 Identities = 26/64 (40%), Positives = 36/64 (56%)

Query: 8  RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 67
          RR R T+T  Q  ELE+ F    YLT  R  +++  L L   Q+KIWF+NRR + K +  
Sbjct: 2  RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 61

Query: 68 AIKE 71
            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 = 63.0 bits (153), Expect = 1e-15
 Identities = 27/57 (47%), Positives = 36/57 (63%)

Query: 8  RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          R+ R  +T  Q L LE++F    YL+   R E + +L LTE Q+KIWFQNRR K K+
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 50

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 62.6 bits (152), Expect = 1e-15
 Identities = 12/49 (24%), Positives = 20/49 (40%)

Query: 11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRR 59
          R  +T  Q   L   F  N   ++  +I ++  L L    +  +F N R
Sbjct: 2  RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>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 = 62.6 bits (152), Expect = 2e-15
 Identities = 25/63 (39%), Positives = 38/63 (60%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
          +RR R T++  Q  ELE+ F    Y     R E+A    LTE +I++WFQNRR +L+K+ 
Sbjct: 2  QRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH 61

Query: 67 QAI 69
           ++
Sbjct: 62 TSV 64

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

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

 Score = 61.8 bits (150), Expect = 3e-15
 Identities = 17/64 (26%), Positives = 26/64 (40%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
            R R      Q   L   +  N       + ++     L+ R I++WFQN+R K KK  
Sbjct: 3  TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS 62

Query: 67 QAIK 70
            +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 = 62.0 bits (150), Expect = 4e-15
 Identities = 26/64 (40%), Positives = 36/64 (56%)

Query: 2  GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
          G    +R+ R  +T+ QT ELE+ F    YL+   R  +A  + LT  Q+KIWFQN R K
Sbjct: 4  GLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYK 63

Query: 62 LKKE 65
           K+ 
Sbjct: 64 TKRA 67

>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 = 59.7 bits (145), Expect = 2e-14
 Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 3/60 (5%)

Query: 8  RRGRQTYTRYQTLELEKEF---HTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          +  R    ++ T  +         + Y T   + ++A    LT  Q+  WF N R ++ +
Sbjct: 3  KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQ 62

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 52

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 59.0 bits (143), Expect = 3e-14
 Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 1/51 (1%)

Query: 15 TRYQTLELEKEF-HTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          T      LEK F     +   +R   ++  L    R I+ WF+ RR + K 
Sbjct: 1  TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 51

>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 = 58.4 bits (141), Expect = 7e-14
 Identities = 23/58 (39%), Positives = 32/58 (55%)

Query: 8  RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          RR R  +T  Q  +LE  F  N Y     R E+A    LTE ++++WF+NRR K +K 
Sbjct: 2  RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 59

>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 = 58.8 bits (142), Expect = 7e-14
 Identities = 24/60 (40%), Positives = 37/60 (61%)

Query: 6  LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
          +RR+ R  +++ Q  ELE+ F    YL+   R  +A  + LT  Q+KIWFQN R K+K++
Sbjct: 1  MRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60

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

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

 Score = 57.2 bits (138), Expect = 2e-13
 Identities = 14/53 (26%), Positives = 27/53 (50%)

Query: 11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63
          + + +      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 = 56.2 bits (135), Expect = 8e-13
 Identities = 17/73 (23%), Positives = 29/73 (39%), Gaps = 15/73 (20%)

Query: 8  RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMA---------------HALCLTERQIK 52
          R  R T+ +     +E  F+ N Y    +R E+A                   +T  ++ 
Sbjct: 1  RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVY 60

Query: 53 IWFQNRRMKLKKE 65
           WF NRR ++K+ 
Sbjct: 61 NWFANRRKEIKRR 73

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 60

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

 Score = 55.2 bits (133), Expect = 1e-12
 Identities = 19/60 (31%), Positives = 24/60 (40%), Gaps = 5/60 (8%)

Query: 8  RRGRQTYTRYQTLELEKEFH---TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          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 = 55.4 bits (133), Expect = 2e-12
 Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 1/59 (1%)

Query: 8  RRGRQTYTRYQTLELEKEFH-TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
            G  T T  Q   LE  F+  N +        +A    LTE Q + WF+ R  + ++ 
Sbjct: 2  SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 80

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 55.4 bits (133), Expect = 2e-12
 Identities = 9/68 (13%), Positives = 19/68 (27%), Gaps = 4/68 (5%)

Query: 2  GANGLRRRGRQTYTRYQTLELEKEFH----TNHYLTRRRRIEMAHALCLTERQIKIWFQN 57
           + G  +R R  +T  Q  ++                    +      +  + +KIW  N
Sbjct: 12 SSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHN 71

Query: 58 RRMKLKKE 65
           +      
Sbjct: 72 NKNSGPSS 79

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 2e-12
 Identities = 13/60 (21%), Positives = 22/60 (36%), Gaps = 1/60 (1%)

Query: 7  RRRGRQTYTRYQTLELEKEFH-TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
            R R   +      L+   H    Y  +     ++  L L +  I  +FQN+R  +K  
Sbjct: 7  GPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS 66

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

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

 Score = 54.0 bits (130), Expect = 3e-12
 Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 3/60 (5%)

Query: 5  GLRRRGRQTYTRYQTLELEKEF-HTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63
          G++              LEK F     Y   +R   ++  L  + R+I+ WF++RR + K
Sbjct: 1  GIKDSPVNKVE--PNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

>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 = 53.8 bits (129), Expect = 4e-12
 Identities = 15/56 (26%), Positives = 28/56 (50%)

Query: 9  RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          + R T +      LE+ F  +   + +  + MA  L L +  +++WF NRR + K+
Sbjct: 1  KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 56

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

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

 Score = 52.7 bits (126), Expect = 2e-11
 Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 3/67 (4%)

Query: 8  RRGRQTYTRYQTLELEK---EFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          RR R+ + +  T  L +      +N Y +   + E+A    +T  Q+  WF N+R++ KK
Sbjct: 2  RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61

Query: 65 EIQAIKE 71
           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 = 51.5 bits (123), Expect = 4e-11
 Identities = 16/58 (27%), Positives = 28/58 (48%)

Query: 7  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          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 = 51.7 bits (123), Expect = 4e-11
 Identities = 12/63 (19%), Positives = 24/63 (38%)

Query: 8  RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 67
           +  +  T  Q   L+  F  +  LT      +     LT R+I  WF  ++     + +
Sbjct: 5  PQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEE 64

Query: 68 AIK 70
           ++
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 = 46.1 bits (109), Expect = 5e-09
 Identities = 17/54 (31%), Positives = 25/54 (46%)

Query: 11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          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 = 45.1 bits (106), Expect = 2e-08
 Identities = 13/60 (21%), Positives = 21/60 (35%)

Query: 5  GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
          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 = 41.7 bits (97), Expect = 4e-07
 Identities = 10/78 (12%), Positives = 21/78 (26%), Gaps = 21/78 (26%)

Query: 11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHAL---------------------CLTER 49
          R  +       L + +      ++  R  +                          +TE 
Sbjct: 1  RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 50 QIKIWFQNRRMKLKKEIQ 67
          ++  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	96
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.88
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.88
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.87
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.87
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.87
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.87
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.87
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.87
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.86
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.86
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.85
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.85
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.84
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.84
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.84
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.83
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.83
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.83
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.83
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.81
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.81
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.81
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.78
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.77
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.75
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.74
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.74
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.71
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.71
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.68
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.67
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.65
d1hlva1	66	DNA-binding domain of centromere binding protein B	94.64
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	89.8
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	83.31
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	81.07
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	80.54

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=2.3e-23  Score=112.91  Aligned_cols=57  Identities=47%  Similarity=0.797  Sum_probs=54.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653           8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   64 (96)
Q Consensus         8 rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr   64 (96)
                      ++.|+.||..|+.+|+..|..++||+..++..||..|||++.+|++||||||+|+||
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            567899999999999999999999999999999999999999999999999999875

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.88  E-value=4.1e-23  Score=111.99  Aligned_cols=57  Identities=47%  Similarity=0.792  Sum_probs=55.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653           8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   64 (96)
Q Consensus         8 rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr   64 (96)
                      |+.|+.|++.|+..|+..|..++||+..++..||..|||++.+|++||||+|+++||
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            567999999999999999999999999999999999999999999999999999987

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=99.87  E-value=7.2e-23  Score=110.63  Aligned_cols=57  Identities=46%  Similarity=0.790  Sum_probs=55.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653           8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   64 (96)
Q Consensus         8 rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr   64 (96)
                      |++|+.||+.|+..|+..|..++||+..++..||..|||++.+|++||+|||+++||
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            567999999999999999999999999999999999999999999999999999986

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.87  E-value=1.2e-22  Score=112.37  Aligned_cols=62  Identities=40%  Similarity=0.636  Sum_probs=58.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653           6 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   67 (96)
Q Consensus         6 ~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~   67 (96)
                      ++++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|+|+++|+...
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~   62 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   62 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhccc
Confidence            36788999999999999999999999999999999999999999999999999999998654

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.87  E-value=8.2e-23  Score=113.68  Aligned_cols=60  Identities=42%  Similarity=0.644  Sum_probs=57.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         7 ~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      +++.|++|+..|+..|+..|..++||+..++..||..|||++.+|++||||||+++|+..
T Consensus         1 Prr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~   60 (67)
T d1zq3p1           1 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQS   60 (67)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhh
Confidence            467899999999999999999999999999999999999999999999999999999854

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.87  E-value=7.3e-23  Score=110.60  Aligned_cols=57  Identities=53%  Similarity=0.781  Sum_probs=54.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           9 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         9 r~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      |.|+.||..|+..|+..|..++||+..++..||..+||++.+|++||||+|+++|++
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            568999999999999999999999999999999999999999999999999999873

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

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

Probab=99.87  E-value=7.6e-23  Score=110.00  Aligned_cols=55  Identities=91%  Similarity=1.306  Sum_probs=53.5

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653          11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus        11 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      |+.||..|+..|+..|..++||+..++..||..|||++.+|++||||||+|+|++
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            7899999999999999999999999999999999999999999999999999984

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

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

Probab=99.87  E-value=2.4e-22  Score=114.41  Aligned_cols=63  Identities=63%  Similarity=0.862  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653           5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   67 (96)
Q Consensus         5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~   67 (96)
                      ...++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||||||+++|+...
T Consensus        11 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~   73 (77)
T d1pufa_          11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINK   73 (77)
T ss_dssp             CTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHH
Confidence            346778999999999999999999999999999999999999999999999999999998644

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]}

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

Probab=99.86  E-value=2.6e-22  Score=106.97  Aligned_cols=53  Identities=49%  Similarity=0.797  Sum_probs=51.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhh
Q psy1653           9 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK   61 (96)
Q Consensus         9 r~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k   61 (96)
                      |+|+.||..|+..|+..|..++||+..++..||..|||++.+|++||||||+|
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            56899999999999999999999999999999999999999999999999986

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.86  E-value=1.4e-22  Score=115.43  Aligned_cols=63  Identities=40%  Similarity=0.646  Sum_probs=58.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           3 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         3 ~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      ...++++.|++|+..|+.+|+..|..++||+..++..||..|||++.+|++||||+|+++|+.
T Consensus         5 ~p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   67 (77)
T d1vnda_           5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRA   67 (77)
T ss_dssp             CSSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHH
Confidence            345567789999999999999999999999999999999999999999999999999998874

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=1.1e-21  Score=109.35  Aligned_cols=60  Identities=38%  Similarity=0.632  Sum_probs=56.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653           8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ   67 (96)
Q Consensus         8 rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~   67 (96)
                      ++.|+.||..|+.+|+..|..++||+...+..||..+||++.+|++||+|+|.++|+...
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            567999999999999999999999999999999999999999999999999999998543

>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=99.85  E-value=7.5e-22  Score=109.99  Aligned_cols=59  Identities=41%  Similarity=0.737  Sum_probs=57.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         7 ~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      +++.|+.|+..|+..|+..|..++||+...+..||..|||++.+|++||+|+|.++|+.
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~   60 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ   60 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhc
Confidence            57889999999999999999999999999999999999999999999999999999885

>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=99.84  E-value=1.2e-21  Score=114.12  Aligned_cols=62  Identities=56%  Similarity=0.802  Sum_probs=55.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      +.+++.|+.|+..|+.+|+..|..++||+..+++.||..|||++.+|++||||+|+++|+..
T Consensus        25 ~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~   86 (88)
T d1b72a_          25 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRE   86 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhc
Confidence            45678899999999999999999999999999999999999999999999999999999854

>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=99.84  E-value=3.6e-22  Score=108.90  Aligned_cols=58  Identities=40%  Similarity=0.625  Sum_probs=56.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         8 rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      ++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.
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            5789999999999999999999999999999999999999999999999999999984

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

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

Probab=99.84  E-value=2.8e-21  Score=108.60  Aligned_cols=58  Identities=28%  Similarity=0.329  Sum_probs=54.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           8 RRGRQTYTRYQTLELEKEFHT-NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         8 rr~r~~~s~~q~~~L~~~F~~-~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      ++.|++||..|+.+|+..|.. ++||+...++.||..+||++.+|++||||||+++|+.
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            467999999999999999986 7899999999999999999999999999999999885

>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=99.83  E-value=2e-21  Score=107.72  Aligned_cols=60  Identities=27%  Similarity=0.343  Sum_probs=57.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           6 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         6 ~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      +.+|.|+.|+..|+.+|+..|..|+||+..++..||..+||++.+|++||+|+|++.|+.
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~   61 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR   61 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSC
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHH
Confidence            367889999999999999999999999999999999999999999999999999998874

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

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

Probab=99.83  E-value=1.5e-21  Score=108.46  Aligned_cols=59  Identities=27%  Similarity=0.400  Sum_probs=56.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653           6 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   64 (96)
Q Consensus         6 ~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr   64 (96)
                      .+++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|.++|+
T Consensus         7 ~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk   65 (67)
T d1ocpa_           7 ARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR   65 (67)
T ss_dssp             CSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSS
T ss_pred             ccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhc
Confidence            45788999999999999999999999999999999999999999999999999999886

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.83  E-value=3.5e-21  Score=104.22  Aligned_cols=57  Identities=26%  Similarity=0.437  Sum_probs=54.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           9 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         9 r~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      |.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|+|.++|+.
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            468999999999999999999999999999999999999999999999999999863

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

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

Probab=99.83  E-value=4e-21  Score=102.26  Aligned_cols=53  Identities=26%  Similarity=0.481  Sum_probs=51.3

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653          11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK   63 (96)
Q Consensus        11 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~k   63 (96)
                      |+.||+.|+.+|+..|..++||+..++..||..+||++.+|++||+|+|.++|
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

>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=99.81  E-value=1.3e-20  Score=105.69  Aligned_cols=62  Identities=21%  Similarity=0.230  Sum_probs=56.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653           4 NGLRRRGRQTYTRYQTLELEKEFH-TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus         4 ~~~~rr~r~~~s~~q~~~L~~~F~-~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      ++..++.|+.|+..|+.+|+..|. .++||+..+++.||..+||++.+|++||+|+|.++|+.
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            345677899999999999999997 48999999999999999999999999999999998863

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-containing protein 1, HMBOX1 (Flj21616)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=1.8e-20  Score=107.85  Aligned_cols=60  Identities=30%  Similarity=0.481  Sum_probs=55.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcC---------------CCcchhhhhhchhhhhhHHHHH
Q psy1653           8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALC---------------LTERQIKIWFQNRRMKLKKEIQ   67 (96)
Q Consensus         8 rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~---------------l~~~~V~~WFqnrR~k~kr~~~   67 (96)
                      ++.|+.|++.|+.+|+..|..++||+..+++.||..+|               |++.+|++||||||+++|+...
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=99.81  E-value=2.2e-20  Score=100.70  Aligned_cols=56  Identities=30%  Similarity=0.437  Sum_probs=53.8

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653          10 GRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus        10 ~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      .||.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|.++|+.
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            48999999999999999999999999999999999999999999999999999873

>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=99.78  E-value=7.5e-20  Score=96.17  Aligned_cols=50  Identities=24%  Similarity=0.336  Sum_probs=48.8

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhh
Q psy1653          10 GRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRR   59 (96)
Q Consensus        10 ~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR   59 (96)
                      +|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||+|
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            58999999999999999999999999999999999999999999999997

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.77  E-value=1.3e-19  Score=103.75  Aligned_cols=62  Identities=15%  Similarity=0.153  Sum_probs=56.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653           3 ANGLRRRGRQTYTRYQTLELEKEFHT----NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   64 (96)
Q Consensus         3 ~~~~~rr~r~~~s~~q~~~L~~~F~~----~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr   64 (96)
                      ..++++|.|+.|+..|+..|+.+|+.    ++||+..++..||..|||++.+|++||||+|.+.+.
T Consensus        13 ~~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          13 SGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            34567788999999999999999986    789999999999999999999999999999988764

>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=99.75  E-value=1.4e-18  Score=98.52  Aligned_cols=56  Identities=21%  Similarity=0.287  Sum_probs=52.7

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653          10 GRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus        10 ~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      .+..++..|+.+|+..|..++||+..++..||..+||+..+|++||+|+|.++|+.
T Consensus         6 ~~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~   61 (76)
T d2ecca1           6 SGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhc
Confidence            34568999999999999999999999999999999999999999999999999874

>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=99.74  E-value=1.8e-18  Score=97.37  Aligned_cols=59  Identities=32%  Similarity=0.553  Sum_probs=54.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHH---hCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653           8 RRGRQTYTRYQTLELEKEFH---TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI   66 (96)
Q Consensus         8 rr~r~~~s~~q~~~L~~~F~---~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~   66 (96)
                      ++.|+.|+..|+.+|+.+|.   .+|||+..++..||..+||+..+|.+||+|+|.+.++..
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~   63 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccc
Confidence            56789999999999999997   488999999999999999999999999999999988743

>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=99.74  E-value=2.1e-18  Score=97.69  Aligned_cols=55  Identities=22%  Similarity=0.260  Sum_probs=50.7

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653          11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus        11 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~   65 (96)
                      +..+|..|+.+|+..|..++||+..+++.||..+||++.+|++||+|+|.+.++.
T Consensus         8 ~k~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~   62 (76)
T d2ecba1           8 FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALK   62 (76)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHH
Confidence            3346899999999999999999999999999999999999999999999887653

>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=99.71  E-value=1.5e-18  Score=91.76  Aligned_cols=50  Identities=28%  Similarity=0.361  Sum_probs=46.4

Q ss_pred             CHHHHHHHHHHHHh-CCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653          15 TRYQTLELEKEFHT-NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   64 (96)
Q Consensus        15 s~~q~~~L~~~F~~-~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr   64 (96)
                      |..|..+|+..|.. ++||+..++..||..+||++.+|++||+|||+++|+
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            45689999999987 689999999999999999999999999999999875

>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=99.71  E-value=2.7e-18  Score=97.62  Aligned_cols=55  Identities=18%  Similarity=0.262  Sum_probs=51.7

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcC---------------------CCcchhhhhhchhhhhhHHH
Q psy1653          11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALC---------------------LTERQIKIWFQNRRMKLKKE   65 (96)
Q Consensus        11 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~---------------------l~~~~V~~WFqnrR~k~kr~   65 (96)
                      |++|++.|+.+|+..|+.++||+..+++.||..|+                     |++.+|++||+|||.+.|+.
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr~   76 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFR   76 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCC
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHHh
Confidence            67899999999999999999999999999999994                     88999999999999998864

>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=99.68  E-value=6.8e-18  Score=91.31  Aligned_cols=55  Identities=25%  Similarity=0.387  Sum_probs=50.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653           9 RGRQTYTRYQTLELEKEFHT-NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK   63 (96)
Q Consensus         9 r~r~~~s~~q~~~L~~~F~~-~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~k   63 (96)
                      +.+..++.++..+|+..|.. ++||+..++..||..+||++.+|++||+|||.++|
T Consensus         3 k~~~~~k~~~~~iLE~~F~~~~~yPs~~~~~~LA~~lgls~~qV~~WFqNrR~k~r   58 (59)
T d2cqxa1           3 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK   58 (59)
T ss_dssp             CCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCccccHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccC
Confidence            45677888889999999986 68999999999999999999999999999999876

>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=99.67  E-value=5.5e-17  Score=87.96  Aligned_cols=53  Identities=32%  Similarity=0.426  Sum_probs=48.8

Q ss_pred             CCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653          12 QTYTRYQTLELEKEFHT---NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK   64 (96)
Q Consensus        12 ~~~s~~q~~~L~~~F~~---~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr   64 (96)
                      .+|+..++.+|+.+|..   +|||+..+++.||..+||++.+|++||+|+|.+.|.
T Consensus         3 ~Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           3 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             CSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            34999999999999976   479999999999999999999999999999998764

>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=99.65  E-value=1.8e-16  Score=86.41  Aligned_cols=56  Identities=21%  Similarity=0.302  Sum_probs=51.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653           8 RRGRQTYTRYQTLELEKEFHT---NHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK   63 (96)
Q Consensus         8 rr~r~~~s~~q~~~L~~~F~~---~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~k   63 (96)
                      ++.|+.|+..++.+|+.+|..   +|||+..++..||..+||+..+|.+||+|+|.+..
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            455778999999999999985   79999999999999999999999999999997753

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

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

Probab=94.64  E-value=0.054  Score=28.28  Aligned_cols=45  Identities=18%  Similarity=0.244  Sum_probs=37.3

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchh
Q psy1653          11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNR   58 (96)
Q Consensus        11 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnr   58 (96)
                      |..++..+...+...|+.++...   ...+|..+||+...|..|..|+
T Consensus         5 Rk~LT~~eK~~ii~~~e~g~k~s---q~eIA~~fGv~~STvs~IlKnK   49 (66)
T d1hlva1           5 RRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNK   49 (66)
T ss_dssp             SCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTH
T ss_pred             cccCCHHHHHHHHHHHHcCCcch---HHHHHHHhCCChhHHHHHHHHH
Confidence            44689998888888999887554   4568999999999999999874

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=89.80  E-value=0.34  Score=23.25  Aligned_cols=41  Identities=10%  Similarity=0.222  Sum_probs=34.0

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhc
Q psy1653          11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQ   56 (96)
Q Consensus        11 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFq   56 (96)
                      +..++.+|+..+...+.... +    ...+|..+||+...|.-||-
T Consensus         3 ~~~lt~~q~~~a~~l~~~G~-s----~~~iA~~~gVSr~TiYry~p   43 (47)
T d1ijwc_           3 PRAINKHEQEQISRLLEKGH-P----RQQLAIIFGIGVSTLYRYFP   43 (47)
T ss_dssp             CCSSCHHHHHHHHHHHHTTC-C----HHHHHHHHTCCHHHHHHHSC
T ss_pred             CCcCCHHHHHHHHHHHHCCC-C----HHHHHHHHCcCHHHHHhhCC
Confidence            45789999999999887543 3    77889999999999999984

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=83.31  E-value=0.87  Score=24.21  Aligned_cols=42  Identities=14%  Similarity=0.234  Sum_probs=30.9

Q ss_pred             CCCCCHHHHHHHHHHHHhC-CCCCHHHHHHHHHHcCCCcchhhhhhc
Q psy1653          11 RQTYTRYQTLELEKEFHTN-HYLTRRRRIEMAHALCLTERQIKIWFQ   56 (96)
Q Consensus        11 r~~~s~~q~~~L~~~F~~~-~~p~~~~~~~la~~l~l~~~~V~~WFq   56 (96)
                      |..|+.+.....-..+... ..    ....+|..+||++..|..|.+
T Consensus         3 rk~Ys~EfK~~aV~l~~~~~g~----s~~~vA~~lGIs~~tl~~W~k   45 (89)
T d2jn6a1           3 TKTYSEEFKRDAVALYENSDGA----SLQQIANDLGINRVTLKNWII   45 (89)
T ss_dssp             CCCCCHHHHHHHHHHHTTGGGS----CHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHcCCC----cHHHHHHHHCCCHHHHHHHHH
Confidence            4569998777766665432 22    255689999999999999985

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=81.07  E-value=1.5  Score=21.85  Aligned_cols=45  Identities=7%  Similarity=-0.027  Sum_probs=31.2

Q ss_pred             CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653          14 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK   63 (96)
Q Consensus        14 ~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~k   63 (96)
                      +++.+..++.-.|-.+.     ...++|..+|++...|+.....-+.+.+
T Consensus        19 Lp~~~r~v~~l~~~~~~-----s~~eIA~~lgis~~tv~~~l~ra~~~Lr   63 (68)
T d1or7a1          19 LPEDLRMAITLRELDGL-----SYEEIAAIMDCPVGTVRSRIFRAREAID   63 (68)
T ss_dssp             SCHHHHHHHHHHHTTCC-----CHHHHHHHTTSCHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence            45556666666555444     3667899999999999998875554444

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=80.54  E-value=1.6  Score=21.73  Aligned_cols=46  Identities=13%  Similarity=0.096  Sum_probs=32.5

Q ss_pred             CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653          13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK   63 (96)
Q Consensus        13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~k   63 (96)
                      .+++.+..++.-.|-.+.     ...++|..+|++...|+.....-+.+.+
T Consensus        21 ~L~~~~r~v~~l~~~~~~-----s~~eIA~~lgis~~tv~~~~~ra~~~Lr   66 (71)
T d1rp3a2          21 KLPEREKLVIQLIFYEEL-----PAKEVAKILETSVSRVSQLKAKALERLR   66 (71)
T ss_dssp             TSCHHHHHHHHHHHTSCC-----CHHHHHHHTTSCHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhHhC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            466777777777665443     4677899999999999887764444443