Citrus Sinensis ID: 029785

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------19
Protein Sequence
MGFDDGCNTGLVLGLGFASAIETTPTNKANNINIVNHQQLQLPKGTCFEPSLSLGLPGEIYPEAATATTKKNSNSIDVNKGYEESAAAGVAEYQILNRQASPHSAVSNSFSSGRVVKRERDLSSEEIEVEKVISSRASDEDEDGVNARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDGFIMV
Secondary Structure (PSIPRED)
ccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccHHHHHccHHHHHHHHccccccccccccccccccHHHccccccHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccEEEEccccccccccHHccccccccccccccccHHHHccccHHHHHHHHHHHHHccccccEEEEEEEEEccEEEc
Coil and Loop (DISEMBL)
mgfddgcntGLVLGLGFAsaiettptnkanninivnhqqlqlpkgtcfepslslglpgeiypeaatattkknsnsidvnkgyeesaaaGVAEYQILnrqasphsavsnsfssgrvvkrerdlsseEIEVEKVISsrasdededgvNARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLsidgfimv
Flexible Loop (DISEMBL)
MGFDDGCNTGLVLGLGFASAIETTPTNKANNINIVNHQQLQLPKGTCFEPSLSLGLPGEIYPEAATattkknsnsidVNKGYEESAAAGVAEYQILNRqasphsavsnsfssgrvvkrerdlsseeievekvissrasdededgvnaRKKLRLTKEQSALLEESfkqhstlnpviISLSLSIDGFIMV
Low Complexity Region (SEG)
MGFDDGCNTGLVLGLGFASAIETTPTNKANNINIVNHQQLQLPKGTCFEPSLSLGLPGEIYPEAATATTKKNSNSIDVNKGYEESAAAGVAEYQILNRQASPHSAVSNSFSSGRVVKRERDLsseeievekvissRASDEDEDGVNARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDGFIMV
Disordered region (IsUnstruct)
*****GCNTGLVLGLGFASAIETTPTNKANNINIVNHQQLQLPKGTCFEPSLSLGLPGEIY************************************************************************************************************TLNPVIISLSLSIDGFI**
Disordered Region (DISOPRED)
****DGCNTGLVLGL******************************************G*********************************************************************************************RLTKEQSALLEESFKQHSTLNP**ISLSLSIDGFIMV
Disordered Region (DISEMBL)
MGFDDGCNTGLVLGLGFASAIETTPTNKANNINIVNHQQLQLPKGTCFEPSLSLGLPGEIYPEAATATTKKNSNSIDVNKGYEESAAAGVAEYQILNR************************************************ARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDGFIMV
Disordered Region (DISPRO)
**FDDGCNTGLVLGLGFAS********************************************************************************************************************************R*KLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDGFIMV
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGFDDGCNTGLVLGLGFASAIETTPTNKANNINIVNHQQLQLPKGTCFEPSLSLGLPGEIYPEAATATTKKNSNSIDVNKGYEESAAAGVAEYQILNRQASPHSAVSNSFSSGRVVKRERDLSSEEIEVEKVISSRASDEDEDGVNARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDGFIMV
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	188	2.2.26 [Sep-21-2011]
P46604	278	Homeobox-leucine zipper p	yes	no	0.734	0.496	0.437	9e-20
P46603	274	Homeobox-leucine zipper p	no	no	0.718	0.492	0.462	1e-19
Q6YPD0	354	Homeobox-leucine zipper p	no	no	0.207	0.110	0.825	1e-10
A2YW03	354	Homeobox-leucine zipper p	N/A	no	0.207	0.110	0.825	2e-10
Q67UE2	362	Homeobox-leucine zipper p	no	no	0.202	0.104	0.846	3e-10
A2Z1U1	276	Homeobox-leucine zipper p	N/A	no	0.202	0.137	0.846	3e-10
P46601	283	Homeobox-leucine zipper p	no	no	0.760	0.505	0.329	2e-09
Q05466	284	Homeobox-leucine zipper p	no	no	0.207	0.137	0.717	5e-09
P46665	336	Homeobox-leucine zipper p	no	no	0.382	0.214	0.512	7e-09
Q8GRL4	292	Homeobox-leucine zipper p	no	no	0.292	0.188	0.603	2e-08

>sp|P46604|HAT22_ARATH Homeobox-leucine zipper protein HAT22 OS=Arabidopsis thaliana GN=HAT22 PE=1 SV=1

 Score = 96.3 bits (238), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 81/185 (43%), Positives = 105/185 (56%), Gaps = 47/185 (25%)

Query: 1   MGFDDGCNTGLVLGLGFASAIETTPTNKANNI----NIVNHQQLQLPKGTCFEPSLSLGL 56
           MG DD CNTGLVLGLG +     TP N  + I    + V+H+ ++L      +PSL+L L
Sbjct: 1   MGLDDSCNTGLVLGLGLSP----TPNNYNHAIKKSSSTVDHRFIRL------DPSLTLSL 50

Query: 57  PGEIYPEAATATTKKNSNSIDVNKGYEESAAAGVAEYQILNRQASPHSAVSNSFSSGRVV 116
            GE                      Y+    AG  + QI  RQ S   +  +SFSSGRV 
Sbjct: 51  SGE---------------------SYKIKTGAGAGD-QIC-RQTS-SHSGISSFSSGRV- 85

Query: 117 KRERDLSSEE------IEVEKVISSRASDE--DEDGVNARKKLRLTKEQSALLEESFKQH 168
           KRER++S  +         E+V+ SR SD+  DE+GV+ARKKLRLTK+QSALLE++FK H
Sbjct: 86  KREREISGGDGEEEAEETTERVVCSRVSDDHDDEEGVSARKKLRLTKQQSALLEDNFKLH 145

Query: 169 STLNP 173
           STLNP
Sbjct: 146 STLNP 150

Probable transcription factor.
Arabidopsis thaliana (taxid: 3702)

>sp|P46603|HAT9_ARATH Homeobox-leucine zipper protein HAT9 OS=Arabidopsis thaliana GN=HAT9 PE=2 SV=2

 Score = 96.3 bits (238), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 81/175 (46%), Positives = 95/175 (54%), Gaps = 40/175 (22%)

Query: 1   MGFDDGCNTGLVLGLGFASAIETTPTNKANNINIVNHQQLQLPKGTCFEPSLSLGLPGEI 60
           MGFDD CNTGLVLGLG        P+   NN N    Q          EPSL+L L G+ 
Sbjct: 1   MGFDDTCNTGLVLGLG--------PSPIPNNYNSTIRQSSVYK----LEPSLTLCLSGD- 47

Query: 61  YPEAATATTKKNSNSIDVNKGYEESAAAGVAEYQILNRQASPHSAVSNSFSSGRVVKRER 120
                         S+ V  G ++           L RQ S   +  +SFSSGRVVKRER
Sbjct: 48  -------------PSVTVVTGADQ-----------LCRQTS-SHSGVSSFSSGRVVKRER 82

Query: 121 DLSSEEIEVEKVISSRASD--EDEDGVNARKKLRLTKEQSALLEESFKQHSTLNP 173
           D   E  E E++     SD  EDE+G++ARKKLRLTK+QSALLEESFK HSTLNP
Sbjct: 83  DGGEESPEEEEMTERVISDYHEDEEGISARKKLRLTKQQSALLEESFKDHSTLNP 137

Probable transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6YPD0|HOX27_ORYSJ Homeobox-leucine zipper protein HOX27 OS=Oryza sativa subsp. japonica GN=HOX27 PE=2 SV=1

 Score = 65.9 bits (159), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 33/40 (82%), Positives = 37/40 (92%), Gaps = 1/40 (2%)

Query: 134 SSRASDEDEDGVNARKKLRLTKEQSALLEESFKQHSTLNP 173
           SSRASD+DE G +ARKKLRL+KEQSA LEESFK+HSTLNP
Sbjct: 160 SSRASDDDE-GASARKKLRLSKEQSAFLEESFKEHSTLNP 198

Probable transcription factor.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|A2YW03|HOX27_ORYSI Homeobox-leucine zipper protein HOX27 OS=Oryza sativa subsp. indica GN=HOX27 PE=2 SV=2

 Score = 65.9 bits (159), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 33/40 (82%), Positives = 37/40 (92%), Gaps = 1/40 (2%)

Query: 134 SSRASDEDEDGVNARKKLRLTKEQSALLEESFKQHSTLNP 173
           SSRASD+DE G +ARKKLRL+KEQSA LEESFK+HSTLNP
Sbjct: 160 SSRASDDDE-GASARKKLRLSKEQSAFLEESFKEHSTLNP 198

Probable transcription factor.

Oryza sativa subsp. indica (taxid: 39946)

>sp|Q67UE2|HOX11_ORYSJ Homeobox-leucine zipper protein HOX11 OS=Oryza sativa subsp. japonica GN=HOX11 PE=2 SV=1

 Score = 65.1 bits (157), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 33/39 (84%), Positives = 36/39 (92%), Gaps = 1/39 (2%)

Query: 135 SRASDEDEDGVNARKKLRLTKEQSALLEESFKQHSTLNP 173
           SRASDED DG +ARKKLRL+KEQSA LEESFK+HSTLNP
Sbjct: 164 SRASDED-DGGSARKKLRLSKEQSAFLEESFKEHSTLNP 201

Probable transcription factor.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|A2Z1U1|HOX11_ORYSI Homeobox-leucine zipper protein HOX11 OS=Oryza sativa subsp. indica GN=HOX11 PE=2 SV=1

 Score = 64.7 bits (156), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 33/39 (84%), Positives = 36/39 (92%), Gaps = 1/39 (2%)

Query: 135 SRASDEDEDGVNARKKLRLTKEQSALLEESFKQHSTLNP 173
           SRASDED DG +ARKKLRL+KEQSA LEESFK+HSTLNP
Sbjct: 77  SRASDED-DGGSARKKLRLSKEQSAFLEESFKEHSTLNP 114

Probable transcription factor.

Oryza sativa subsp. indica (taxid: 39946)

>sp|P46601|HAT2_ARATH Homeobox-leucine zipper protein HAT2 OS=Arabidopsis thaliana GN=HAT2 PE=2 SV=2

 Score = 62.4 bits (150), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 60/182 (32%), Positives = 86/182 (47%), Gaps = 39/182 (21%)

Query: 1   MGFDDGCNTGLVLGLGFASAIETTPTNKANNINIVNHQQLQLPKGTCFEPSLSLGLPGEI 60
           MG +D    GL L LGF+        N   N ++ N+ Q +LP    F+P+  L      
Sbjct: 3   MGKED---LGLSLSLGFSQNHNPLQMNLNPNSSLSNNLQ-RLPWNQTFDPTSDL------ 52

Query: 61  YPEAATATTKKNSNSIDVNKGYEESAAAGVAEYQILNRQASPHSAVSNSFSSGRVVKRE- 119
                    K + NS       EE               +SP+S +S++ S G+  +RE 
Sbjct: 53  --------RKIDVNSFPSTVNCEEDTGV-----------SSPNSTISSTIS-GKRSEREG 92

Query: 120 -------RDLSSEEIEVEKVISSRASDEDEDG-VNARKKLRLTKEQSALLEESFKQHSTL 171
                       +EI  ++  S   SDE+EDG   +RKKLRL+K+QSA LEE+FK+H+TL
Sbjct: 93  ISGTGVGSGDDHDEITPDRGYSRGTSDEEEDGGETSRKKLRLSKDQSAFLEETFKEHNTL 152

Query: 172 NP 173
           NP
Sbjct: 153 NP 154

Probable transcription factor that plays a role in auxin-mediated morphogenesis. Negatively regulates lateral root elongation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q05466|HAT4_ARATH Homeobox-leucine zipper protein HAT4 OS=Arabidopsis thaliana GN=HAT4 PE=1 SV=1

 Score = 60.8 bits (146), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 28/39 (71%), Positives = 34/39 (87%)

Query: 135 SRASDEDEDGVNARKKLRLTKEQSALLEESFKQHSTLNP 173
           SR   +DEDG N+RKKLRL+K+QSA+LEE+FK HSTLNP
Sbjct: 115 SRGISDDEDGDNSRKKLRLSKDQSAILEETFKDHSTLNP 153

Probable transcription factor involved in the negative regulation of cell elongation and specific cell proliferation processes such as lateral root formation and secondary growth of the vascular system. Acts as mediator of the red/far-red light effects on leaf cell expansion in the shading response. Binds to the DNA sequence 5'-CAAT[GC]ATTG-3'. Negatively regulates its own expression.

Arabidopsis thaliana (taxid: 3702)

>sp|P46665|HAT14_ARATH Homeobox-leucine zipper protein HAT14 OS=Arabidopsis thaliana GN=HAT14 PE=2 SV=3

 Score = 60.1 bits (144), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 41/80 (51%), Positives = 54/80 (67%), Gaps = 8/80 (10%)

Query: 101 SPHSAVSNSFSSGRVVKR---ERDLSSEEI--EVEKVISSRASDEDEDGVN--ARKKLRL 153
           SP  +V++SF     +K    ER  +  +I  EVE+  +SRAS+ED D  N   RKKLRL
Sbjct: 136 SPPDSVTSSFQLDFGIKSYGYERRSNKRDIDDEVERS-ASRASNEDNDDENGSTRKKLRL 194

Query: 154 TKEQSALLEESFKQHSTLNP 173
           +K+QSA LE+SFK+HSTLNP
Sbjct: 195 SKDQSAFLEDSFKEHSTLNP 214

Probable transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8GRL4|HOX19_ORYSJ Homeobox-leucine zipper protein HOX19 OS=Oryza sativa subsp. japonica GN=HOX19 PE=2 SV=1

 Score = 59.3 bits (142), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 35/58 (60%), Positives = 45/58 (77%), Gaps = 3/58 (5%)

Query: 116 VKRERDLSSEEIEVEKVISSRASDEDEDGVNARKKLRLTKEQSALLEESFKQHSTLNP 173
           VKRER   +EE + E+V S+ A  +D+D  + RKKLRLTKEQSALLE+ F++HSTLNP
Sbjct: 97  VKRER---AEEADGERVSSTAAGRDDDDDGSTRKKLRLTKEQSALLEDRFREHSTLNP 151

Probable transcription factor.

Oryza sativa subsp. japonica (taxid: 39947)

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	188
302398823	289	HD domain class transcription factor [Ma	0.840	0.546	0.570	2e-39
296090659	266	unnamed protein product [Vitis vinifera]	0.765	0.541	0.573	4e-39
359497258	283	PREDICTED: homeobox-leucine zipper prote	0.792	0.526	0.553	4e-39
307715376	281	homeodomain-leucine zipper protein HD4 [	0.829	0.555	0.629	5e-35
255579497	289	homeobox protein, putative [Ricinus comm	0.835	0.543	0.559	2e-33
224097208	229	predicted protein [Populus trichocarpa]	0.579	0.475	0.695	1e-32
356541549	283	PREDICTED: homeobox-leucine zipper prote	0.835	0.554	0.513	2e-32
255648285	283	unknown [Glycine max]	0.835	0.554	0.508	7e-32
356497023	283	PREDICTED: homeobox-leucine zipper prote	0.819	0.544	0.516	2e-30
255647889	283	unknown [Glycine max]	0.819	0.544	0.516	2e-30

>gi|302398823|gb|ADL36706.1| HD domain class transcription factor [Malus x domestica]

 Score =  167 bits (423), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 105/184 (57%), Positives = 120/184 (65%), Gaps = 26/184 (14%)

Query: 1   MGFDD-GCNTGLVLGLGFASAIETTPTN----KANNINI-VNHQQLQLPKGTCFEPSLSL 54
           MGFDD  CNTGLVLGLG  S+      N      NNI   +N      P    FEPSL+L
Sbjct: 1   MGFDDHACNTGLVLGLGLTSSAPQESCNLTKFAKNNIKPSLN----SAPTSGAFEPSLTL 56

Query: 55  GLPGEIYPEAATATT---KKNSNSIDVNKGYEESAAAGVAEYQILNRQASPHS--AVSNS 109
           GL GE Y +   A+      NS+  +    Y ++AAA           +SPHS  AVSNS
Sbjct: 57  GLSGEPYHQQTVASNIYKVGNSSQDEAIDLYRQAAAA-----------SSPHSHSAVSNS 105

Query: 110 FSSGRVVKRERDLSSEEIEVEKVISSRASDEDEDGVNARKKLRLTKEQSALLEESFKQHS 169
           FSSGRVVKRERDLSSEE++V++ +SSR SDEDEDG NARKKLRLTKEQSALLEESFKQHS
Sbjct: 106 FSSGRVVKRERDLSSEEVDVDEKVSSRVSDEDEDGSNARKKLRLTKEQSALLEESFKQHS 165

Query: 170 TLNP 173
           TLNP
Sbjct: 166 TLNP 169

Source: Malus x domestica

Species: Malus x domestica

Genus: Malus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296090659|emb|CBI41059.3| unnamed protein product [Vitis vinifera]

 Score =  166 bits (420), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 101/176 (57%), Positives = 116/176 (65%), Gaps = 32/176 (18%)

Query: 1   MGFDDGCNTGLVLGLGF---ASAIETTPTNKANNINIVNHQQLQLPKGTCFEPSLSLGLP 57
           MGFDDGCNTGLVLGLGF   A+A++ TP          +H Q        FEPSL+L L 
Sbjct: 1   MGFDDGCNTGLVLGLGFTATAAALDQTPLKPCTT---TDHDQ-------SFEPSLTLSLS 50

Query: 58  GEIYPEAATATTKKNSNSIDVNKGYEESAAAGVAEYQILNRQASPHSAVSNSFSSGRVVK 117
           GE Y         + +  +D+NK  EE+AA        L RQ SPHS VS SFS+   VK
Sbjct: 51  GETY---------QVTGKMDMNKVCEEAAAD-------LYRQPSPHSTVS-SFSNA-SVK 92

Query: 118 RERDLSSEEIEVEKVISSRASDEDEDGVNARKKLRLTKEQSALLEESFKQHSTLNP 173
           RERDL SEE+E+E+ +SSR SDEDEDG N RKKLRLTKEQSALLEESFKQHSTLNP
Sbjct: 93  RERDLGSEEVEIER-LSSRVSDEDEDGSNGRKKLRLTKEQSALLEESFKQHSTLNP 147

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359497258|ref|XP_002271511.2| PREDICTED: homeobox-leucine zipper protein HAT22 [Vitis vinifera] gi|147778182|emb|CAN60988.1| hypothetical protein VITISV_022980 [Vitis vinifera]

 Score =  166 bits (420), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 104/188 (55%), Positives = 119/188 (63%), Gaps = 39/188 (20%)

Query: 1   MGFDDGCNTGLVLGLGF---ASAIETTPTNKANNINIVNHQQLQLPKGTC---------- 47
           MGFDDGCNTGLVLGLGF   A+A++ TP          +H Q    K TC          
Sbjct: 1   MGFDDGCNTGLVLGLGFTATAAALDQTPLKP---CTTTDHDQRS--KKTCLRFGPLAAAP 55

Query: 48  --FEPSLSLGLPGEIYPEAATATTKKNSNSIDVNKGYEESAAAGVAEYQILNRQASPHSA 105
             FEPSL+L L GE Y         + +  +D+NK  EE+AA        L RQ SPHS 
Sbjct: 56  TSFEPSLTLSLSGETY---------QVTGKMDMNKVCEEAAAD-------LYRQPSPHST 99

Query: 106 VSNSFSSGRVVKRERDLSSEEIEVEKVISSRASDEDEDGVNARKKLRLTKEQSALLEESF 165
           VS SFS+   VKRERDL SEE+E+E+ +SSR SDEDEDG N RKKLRLTKEQSALLEESF
Sbjct: 100 VS-SFSNA-SVKRERDLGSEEVEIER-LSSRVSDEDEDGSNGRKKLRLTKEQSALLEESF 156

Query: 166 KQHSTLNP 173
           KQHSTLNP
Sbjct: 157 KQHSTLNP 164

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|307715376|gb|ADN88095.1| homeodomain-leucine zipper protein HD4 [Gossypium hirsutum]

 Score =  152 bits (385), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 112/178 (62%), Positives = 124/178 (69%), Gaps = 22/178 (12%)

Query: 1   MGFDD-GCNTGLVLGLGFASAIETTPTNKANNINIVNHQQLQLPKGTCFEPSLSLGLPGE 59
           MG DD  CNTGLVLGLGF+SA+ET P+ K + +          P  T FEPSL+LGL G+
Sbjct: 1   MGLDDDACNTGLVLGLGFSSALET-PSKKPSCLKFEQPATTVAPPTT-FEPSLTLGLFGD 58

Query: 60  IYPEAATATTKKNSNSIDVNK-GY---EESAAAGVAEYQILNRQASPHSAVSNSFSSGRV 115
                    TKK+    DVNK GY    E   AG     +  RQASPHSAVS SFSSGRV
Sbjct: 59  ----QGYQVTKKS----DVNKSGYLHHHEEPGAG----DLYRRQASPHSAVS-SFSSGRV 105

Query: 116 VKRERDLSSEEIEVEKVISSRASDEDEDGVNARKKLRLTKEQSALLEESFKQHSTLNP 173
            KRER++SSEE+EVEK  SSR SDEDEDGVNARKKLRLTKEQSALLEESFKQHSTLNP
Sbjct: 106 -KREREVSSEELEVEKN-SSRVSDEDEDGVNARKKLRLTKEQSALLEESFKQHSTLNP 161

Source: Gossypium hirsutum

Species: Gossypium hirsutum

Genus: Gossypium

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255579497|ref|XP_002530591.1| homeobox protein, putative [Ricinus communis] gi|223529839|gb|EEF31771.1| homeobox protein, putative [Ricinus communis]

 Score =  147 bits (371), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 103/184 (55%), Positives = 114/184 (61%), Gaps = 27/184 (14%)

Query: 1   MG-FDDGCNTGLVLGLGFASAIETTPTNKANNINIVNHQQL---------QLPKGTCFEP 50
           MG  DDGCNTGLVLGLGF +A   T +N  + IN  N+Q+L         Q+     FEP
Sbjct: 1   MGCLDDGCNTGLVLGLGFTTA---TISNPDSTINNQNNQKLKTKPCLKFDQMVGTASFEP 57

Query: 51  SLSLGLPGEIYPEAATATTKKNSNSIDVNKGYEESAAAGVAEYQI-LNRQASPHSAVSNS 109
           SLSLGL       A    +  N   IDV K       A   E  + L RQASPHS  + S
Sbjct: 58  SLSLGL------SAHHIGSSNNKMKIDVIK------KATCHEDSVDLFRQASPHSCSAVS 105

Query: 110 FSSGRVVKRERDLSSEEIEVEKVISSRASDEDEDGVNARKKLRLTKEQSALLEESFKQHS 169
             S   VKRERD SSEEI+VE+V SSR SDEDEDG N RKKLRLTKEQSALLEESFKQHS
Sbjct: 106 SFSSGRVKRERDFSSEEIDVERV-SSRISDEDEDGTNTRKKLRLTKEQSALLEESFKQHS 164

Query: 170 TLNP 173
           TLNP
Sbjct: 165 TLNP 168

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224097208|ref|XP_002310877.1| predicted protein [Populus trichocarpa] gi|222853780|gb|EEE91327.1| predicted protein [Populus trichocarpa]

 Score =  144 bits (364), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 89/128 (69%), Positives = 94/128 (73%), Gaps = 19/128 (14%)

Query: 46  TCFEPSLSLGLPGEIYPEAATATTKKNSNSIDVNKGYEESAAAGVAEYQILNRQASPHSA 105
           T FEPSLSLGL  E Y            + +D  KG EES  A    +  L RQASPHSA
Sbjct: 2   TGFEPSLSLGLSAETY------------SLVDGKKGCEESIGA----HDQLYRQASPHSA 45

Query: 106 VSNSFSSGRVVKRERDLSSEEIEVEKVISSRASDEDEDGVNARKKLRLTKEQSALLEESF 165
           VS SFSSGRV KRERDLSSE+IEVE+V SSR SDEDEDG NARKKLRLTKEQSALLEESF
Sbjct: 46  VS-SFSSGRV-KRERDLSSEDIEVERV-SSRVSDEDEDGSNARKKLRLTKEQSALLEESF 102

Query: 166 KQHSTLNP 173
           KQHSTLNP
Sbjct: 103 KQHSTLNP 110

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356541549|ref|XP_003539237.1| PREDICTED: homeobox-leucine zipper protein HAT22-like [Glycine max]

 Score =  144 bits (363), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 92/179 (51%), Positives = 111/179 (62%), Gaps = 22/179 (12%)

Query: 1   MGFDDGCNTG---LVLGLGF-ASAIETTPTNKANNINIVNHQQLQLPKGTCFEPSLSLGL 56
           MG D   N+    LVLGL   AS  ET P+ K ++ ++   +          EPSL+LGL
Sbjct: 1   MGLDQDANSSGLHLVLGLSLTASVKETAPSTKPDDHHLCVIKPTPTKPYPSKEPSLTLGL 60

Query: 57  PGEIYPEAATATTKKNSNSIDVNKGYEESAAAGVAEYQILNRQASPHSAVSNSFSSGRVV 116
            G+ Y            N++ +NK Y E            +RQ SPHS VS SFS+GRV+
Sbjct: 61  SGKGY--------HVPRNNVAINKVYCEDPLE-------FSRQTSPHSVVS-SFSTGRVI 104

Query: 117 KRERDLSSEEIEV--EKVISSRASDEDEDGVNARKKLRLTKEQSALLEESFKQHSTLNP 173
           KRERDLS E++EV  E+ +SSR SDEDEDG NARKKLRLTKEQSALLEESFKQHSTLNP
Sbjct: 105 KRERDLSCEDMEVDAEERVSSRVSDEDEDGTNARKKLRLTKEQSALLEESFKQHSTLNP 163

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255648285|gb|ACU24595.1| unknown [Glycine max]

 Score =  142 bits (358), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 91/179 (50%), Positives = 110/179 (61%), Gaps = 22/179 (12%)

Query: 1   MGFDDGCNTG---LVLGLGF-ASAIETTPTNKANNINIVNHQQLQLPKGTCFEPSLSLGL 56
           MG D   N+    LVLGL   AS  ET P+ K ++ ++   +          EPSL+LGL
Sbjct: 1   MGLDQDANSSGLHLVLGLSLTASVKETAPSTKPDDHHLCVIKPTPTKPYPSKEPSLTLGL 60

Query: 57  PGEIYPEAATATTKKNSNSIDVNKGYEESAAAGVAEYQILNRQASPHSAVSNSFSSGRVV 116
            G+ Y            N++ +NK Y E            +RQ SPHS VS SF +GRV+
Sbjct: 61  SGKGY--------HVPRNNVAINKVYCEDPLE-------FSRQTSPHSVVS-SFPTGRVI 104

Query: 117 KRERDLSSEEIEV--EKVISSRASDEDEDGVNARKKLRLTKEQSALLEESFKQHSTLNP 173
           KRERDLS E++EV  E+ +SSR SDEDEDG NARKKLRLTKEQSALLEESFKQHSTLNP
Sbjct: 105 KRERDLSCEDMEVDAEERVSSRVSDEDEDGTNARKKLRLTKEQSALLEESFKQHSTLNP 163

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356497023|ref|XP_003517364.1| PREDICTED: homeobox-leucine zipper protein HAT22-like [Glycine max]

 Score =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 94/182 (51%), Positives = 112/182 (61%), Gaps = 28/182 (15%)

Query: 1   MGFDDGCNTG---LVLGLGFASAI-ETTPTNKANN---INIVNHQQLQLPKGTCFEPSLS 53
           MG D   N+    LVLGL   + + ETT + K ++   + ++     +       EPSL+
Sbjct: 1   MGLDQDANSSGLHLVLGLSLTATVKETTQSTKPDDDHHLCVIKPTPTKPYPPN--EPSLT 58

Query: 54  LGLPGEIYPEAATATTKKNSNSIDVNKGYEESAAAGVAEYQILNRQASPHSAVSNSFSSG 113
           LGL GE Y       TK+    +  N  Y E           L+RQ SPHS VS SFS+G
Sbjct: 59  LGLSGESY-----HVTKQ----VLRNNVYCEDPLE-------LSRQTSPHSVVS-SFSTG 101

Query: 114 RVVKRERDLSSEEIEVE--KVISSRASDEDEDGVNARKKLRLTKEQSALLEESFKQHSTL 171
           RVVKRERDLS E+IEVE  + +SSR SDEDEDG NARKKLRLTKEQSALLEESFKQHSTL
Sbjct: 102 RVVKRERDLSCEDIEVEAEERVSSRVSDEDEDGTNARKKLRLTKEQSALLEESFKQHSTL 161

Query: 172 NP 173
           NP
Sbjct: 162 NP 163

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255647889|gb|ACU24403.1| unknown [Glycine max]

 Score =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 94/182 (51%), Positives = 112/182 (61%), Gaps = 28/182 (15%)

Query: 1   MGFDDGCNTG---LVLGLGFASAI-ETTPTNKANN---INIVNHQQLQLPKGTCFEPSLS 53
           MG D   N+    LVLGL   + + ETT + K ++   + ++     +       EPSL+
Sbjct: 1   MGLDQDANSSGLHLVLGLSLTATVKETTQSTKPDDDHHLCVIKPTPTKPYPPN--EPSLT 58

Query: 54  LGLPGEIYPEAATATTKKNSNSIDVNKGYEESAAAGVAEYQILNRQASPHSAVSNSFSSG 113
           LGL GE Y       TK+    +  N  Y E           L+RQ SPHS VS SFS+G
Sbjct: 59  LGLSGESY-----HVTKQ----VLRNNVYCEDPLE-------LSRQTSPHSVVS-SFSTG 101

Query: 114 RVVKRERDLSSEEIEVE--KVISSRASDEDEDGVNARKKLRLTKEQSALLEESFKQHSTL 171
           RVVKRERDLS E+IEVE  + +SSR SDEDEDG NARKKLRLTKEQSALLEESFKQHSTL
Sbjct: 102 RVVKRERDLSCEDIEVEAEERVSSRVSDEDEDGTNARKKLRLTKEQSALLEESFKQHSTL 161

Query: 172 NP 173
           NP
Sbjct: 162 NP 163

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

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	188
TAIR|locus:2137599	278	HAT22 [Arabidopsis thaliana (t	0.478	0.323	0.509	2.7e-25
TAIR|locus:2059143	274	HAT9 [Arabidopsis thaliana (ta	0.664	0.456	0.466	3.6e-18
TAIR|locus:2171489	283	HAT2 [Arabidopsis thaliana (ta	0.191	0.127	0.702	1.5e-12
TAIR|locus:2129136	284	HB-2 "homeobox protein 2" [Ara	0.446	0.295	0.431	3.6e-11
TAIR|locus:2129061	282	HAT1 [Arabidopsis thaliana (ta	0.393	0.262	0.414	5.9e-10
TAIR|locus:2055028	318	HB4 "homeobox-leucine zipper p	0.563	0.333	0.365	1.2e-09
TAIR|locus:2170194	336	HAT14 "homeobox from Arabidops	0.436	0.244	0.409	7.8e-09
TAIR|locus:2103396	315	HAT3 "homeobox-leucine zipper	0.861	0.514	0.289	2.2e-07
TAIR|locus:2013980	206	HB18 "homeobox-leucine zipper	0.186	0.169	0.657	0.00025
TAIR|locus:2049614	275	HB17 "homeobox-leucine zipper	0.175	0.12	0.636	0.00053

TAIR|locus:2137599 HAT22 [Arabidopsis thaliana (taxid:3702)]

 Score = 197 (74.4 bits), Expect = 2.7e-25, Sum P(2) = 2.7e-25
 Identities = 52/102 (50%), Positives = 64/102 (62%)

Query:    80 KGYEESAAAGVAEYQILNRQASPHSAVSNSFSSGRVVKRERDLXXXXXXXXXXXXX---- 135
             + Y+    AG  + QI  RQ S HS +S SFSSGRV KRER++                 
Sbjct:    53 ESYKIKTGAGAGD-QIC-RQTSSHSGIS-SFSSGRV-KREREISGGDGEEEAEETTERVV 108

Query:   136 --RASDE--DEDGVNARKKLRLTKEQSALLEESFKQHSTLNP 173
               R SD+  DE+GV+ARKKLRLTK+QSALLE++FK HSTLNP
Sbjct:   109 CSRVSDDHDDEEGVSARKKLRLTKQQSALLEDNFKLHSTLNP 150

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

GO:0009735 "response to cytokinin stimulus" evidence=IEP

GO:0006473 "protein acetylation" evidence=RCA

TAIR|locus:2059143 HAT9 [Arabidopsis thaliana (taxid:3702)]

 Score = 220 (82.5 bits), Expect = 3.6e-18, P = 3.6e-18
 Identities = 63/135 (46%), Positives = 75/135 (55%)

Query:    46 TCFEPSLSLGLPGEIYPEAATATTKKNS-----NSIDVNKGYEESAAAGVAEYQILNRQA 100
             TC    L LGL     P    +T +++S      S+ +    + S        Q+  RQ 
Sbjct:     6 TC-NTGLVLGLGPSPIPNNYNSTIRQSSVYKLEPSLTLCLSGDPSVTVVTGADQLC-RQT 63

Query:   101 SPHSAVSNSFSSGRVVKRERDLXXXXXXXXXXXXXRASD--EDEDGVNARKKLRLTKEQS 158
             S HS VS SFSSGRVVKRERD                SD  EDE+G++ARKKLRLTK+QS
Sbjct:    64 SSHSGVS-SFSSGRVVKRERDGGEESPEEEEMTERVISDYHEDEEGISARKKLRLTKQQS 122

Query:   159 ALLEESFKQHSTLNP 173
             ALLEESFK HSTLNP
Sbjct:   123 ALLEESFKDHSTLNP 137

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

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

GO:0006473 "protein acetylation" evidence=RCA

TAIR|locus:2171489 HAT2 [Arabidopsis thaliana (taxid:3702)]

 Score = 132 (51.5 bits), Expect = 1.5e-12, Sum P(2) = 1.5e-12
 Identities = 26/37 (70%), Positives = 33/37 (89%)

Query:   138 SDEDEDG-VNARKKLRLTKEQSALLEESFKQHSTLNP 173
             SDE+EDG   +RKKLRL+K+QSA LEE+FK+H+TLNP
Sbjct:   118 SDEEEDGGETSRKKLRLSKDQSAFLEETFKEHNTLNP 154

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

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

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

GO:0009733 "response to auxin stimulus" evidence=RCA;IMP

GO:0009734 "auxin mediated signaling pathway" evidence=IEP

GO:0009826 "unidimensional cell growth" evidence=IMP

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IMP

GO:0009641 "shade avoidance" evidence=IEP

TAIR|locus:2129136 HB-2 "homeobox protein 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 157 (60.3 bits), Expect = 3.6e-11, P = 3.6e-11
 Identities = 41/95 (43%), Positives = 57/95 (60%)

Query:    80 KGYEESAAAGVAEYQILNRQ-ASPHSAVSNSFSSGRVVKRERDLXXXXXXXXXXXXXRAS 138
             +G + +     AEY   +   +SP+S VS+S  +G+  +RE D              R  
Sbjct:    69 RGIDVNRPPSTAEYGDEDAGVSSPNSTVSSS--TGKRSEREED--------TDPQGSRGI 118

Query:   139 DEDEDGVNARKKLRLTKEQSALLEESFKQHSTLNP 173
              +DEDG N+RKKLRL+K+QSA+LEE+FK HSTLNP
Sbjct:   119 SDDEDGDNSRKKLRLSKDQSAILEETFKDHSTLNP 153

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

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

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS;IDA

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

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

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

GO:0008283 "cell proliferation" evidence=IMP

GO:0009733 "response to auxin stimulus" evidence=IMP

GO:0009826 "unidimensional cell growth" evidence=IMP

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IDA

GO:0048364 "root development" evidence=IMP

GO:0009735 "response to cytokinin stimulus" evidence=IEP

GO:0009641 "shade avoidance" evidence=IEP

GO:0010017 "red or far-red light signaling pathway" evidence=IEP

GO:0010218 "response to far red light" evidence=IEP

GO:0042803 "protein homodimerization activity" evidence=IDA

GO:0010016 "shoot system morphogenesis" evidence=IMP

TAIR|locus:2129061 HAT1 [Arabidopsis thaliana (taxid:3702)]

 Score = 130 (50.8 bits), Expect = 5.9e-10, Sum P(2) = 5.9e-10
 Identities = 34/82 (41%), Positives = 49/82 (59%)

Query:   100 ASPHSAVSNSFSSGR-VVKRERDLXXXXXXXXXXXXXRAS-----DEDED--GVNARKKL 151
             +SP+S +S++ S  R   +RE                R+S     DE+ED  G   RKKL
Sbjct:    78 SSPNSTISSTVSGKRRSTEREGTSGGGCGDDLDITLDRSSSRGTSDEEEDYGGETCRKKL 137

Query:   152 RLTKEQSALLEESFKQHSTLNP 173
             RL+K+QSA+LE++FK+H+TLNP
Sbjct:   138 RLSKDQSAVLEDTFKEHNTLNP 159

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

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

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS;IDA

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

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

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

GO:0003006 "developmental process involved in reproduction" evidence=IGI

GO:0005515 "protein binding" evidence=IPI

GO:0010582 "floral meristem determinacy" evidence=IGI

GO:0043621 "protein self-association" evidence=IPI

GO:0048467 "gynoecium development" evidence=IGI

GO:0048507 "meristem development" evidence=IGI

GO:0080127 "fruit septum development" evidence=IGI

TAIR|locus:2055028 HB4 "homeobox-leucine zipper protein 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 145 (56.1 bits), Expect = 1.2e-09, P = 1.2e-09
 Identities = 42/115 (36%), Positives = 62/115 (53%)

Query:    68 TTKKNSNSIDVNKGYEESAA-AGVAEYQILNRQA---SPHSAVSNSFSSGR--VVKRERD 121
             T ++NS++    +G+  + A + VA   +    A   SP+SAVS+   + R   V R  D
Sbjct:    73 TAERNSDAGSFLRGFNVNRAQSSVAVVDLEEEAAVVSSPNSAVSSLSGNKRDLAVARGGD 132

Query:   122 LXXXXXXXXXXXXXRASDEDEDGVN---ARKKLRLTKEQSALLEESFKQHSTLNP 173
                               +DEDG N   +RKKLRL+K+Q+ +LEE+FK+HSTLNP
Sbjct:   133 ENEAERASCSRGGGSGGSDDEDGGNGDGSRKKLRLSKDQALVLEETFKEHSTLNP 187

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

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

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

GO:0009641 "shade avoidance" evidence=IEP

GO:0009725 "response to hormone stimulus" evidence=IMP

GO:0009506 "plasmodesma" evidence=IDA

GO:0010218 "response to far red light" evidence=IEP

TAIR|locus:2170194 HAT14 "homeobox from Arabidopsis thaliana" [Arabidopsis thaliana (taxid:3702)]

 Score = 138 (53.6 bits), Expect = 7.8e-09, P = 7.8e-09
 Identities = 36/88 (40%), Positives = 47/88 (53%)

Query:    92 EYQILNRQASPHSAVSNSFSSGRVVK----RERDLXXXXXXXXXXXXXRASDEDEDGVNA 147
             E  + +   SP  +V++SF     +K      R               RAS+ED D  N 
Sbjct:   127 EEAVPSMSVSPPDSVTSSFQLDFGIKSYGYERRSNKRDIDDEVERSASRASNEDNDDENG 186

Query:   148 --RKKLRLTKEQSALLEESFKQHSTLNP 173
               RKKLRL+K+QSA LE+SFK+HSTLNP
Sbjct:   187 STRKKLRLSKDQSAFLEDSFKEHSTLNP 214

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

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

TAIR|locus:2103396 HAT3 "homeobox-leucine zipper protein 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 127 (49.8 bits), Expect = 2.2e-07, P = 2.2e-07
 Identities = 55/190 (28%), Positives = 85/190 (44%)

Query:     4 DDGCNTGLVLGLGFASAIETTPTNKANNINIVNHQQLQ-LPKGTCFEPSLSLGLPGEIYP 62
             DDG    L L LGF     ++  N     +  +   +Q + +     P         ++ 
Sbjct:     5 DDGLGLSLSLSLGFNQKDPSSRLNPMPLASYASSSHMQHMQQSNYNHPQKIQNTWINMFQ 64

Query:    63 EAATATTKKNSNSIDVNKGYEESAAAGVAEYQILNRQA---SPHSAVSNSFSSGRVVKRE 119
                  ++++NS+     +G + + A       + +  A   SP+S VS S  SG+  K E
Sbjct:    65 -----SSERNSDMRSFLRGIDVNRAPSTVVVDVEDEGAGVSSPNSTVS-SVMSGK--KSE 116

Query:   120 RDLXXXXXXXXXXXXX-----RAS------DEDEDGV-----NARKKLRLTKEQSALLEE 163
             R+L                  RAS       +DEDG      ++RKKLRL+KEQ+ +LEE
Sbjct:   117 RELMAAAGAVGGGRVEDNEIERASCSLGGGSDDEDGSGNGDDSSRKKLRLSKEQALVLEE 176

Query:   164 SFKQHSTLNP 173
             +FK+HSTLNP
Sbjct:   177 TFKEHSTLNP 186

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

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

TAIR|locus:2013980 HB18 "homeobox-leucine zipper protein 18" [Arabidopsis thaliana (taxid:3702)]

 Score = 106 (42.4 bits), Expect = 0.00025, P = 0.00025
 Identities = 23/35 (65%), Positives = 25/35 (71%)

Query:   139 DEDEDGVNARKKLRLTKEQSALLEESFKQHSTLNP 173
             D+   G   RKKLRLTKEQS LLEESF Q+ TL P
Sbjct:    59 DDSNSGGRRRKKLRLTKEQSHLLEESFIQNHTLTP 93

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

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

TAIR|locus:2049614 HB17 "homeobox-leucine zipper protein 17" [Arabidopsis thaliana (taxid:3702)]

 Score = 106 (42.4 bits), Expect = 0.00053, P = 0.00053
 Identities = 21/33 (63%), Positives = 26/33 (78%)

Query:   141 DEDGVNARKKLRLTKEQSALLEESFKQHSTLNP 173
             D+     RKKLRLT+EQS LLE+SF+Q+ TLNP
Sbjct:   131 DDGSAPPRKKLRLTREQSRLLEDSFRQNHTLNP 163


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.311   0.128   0.350    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      188       175   0.00078  109 3  11 23  0.49    32
                                                     31  0.49    34


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  10
  No. of states in DFA:  547 (58 KB)
  Total size of DFA:  128 KB (2082 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  18.09u 0.10s 18.19t   Elapsed:  00:00:01
  Total cpu time:  18.09u 0.10s 18.19t   Elapsed:  00:00:01
  Start:  Tue May 21 00:21:05 2013   End:  Tue May 21 00:21:06 2013

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00008185001 SubName- Full=Chromosome undetermined scaffold_1278, whole genome shotgun sequence; (283 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	188
KOG0483	198	consensus Transcription factor HEX, contains HOX a	98.78
PF04618	111	HD-ZIP_N: HD-ZIP protein N terminus; InterPro: IPR	98.12
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	96.54
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	95.81
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	95.29
COG5576	156	Homeodomain-containing transcription factor [Trans	90.25

>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]

Probab=98.78  E-value=4.2e-09  Score=88.59  Aligned_cols=39  Identities=36%  Similarity=0.362  Sum_probs=36.3

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..+||+|||+||..+||.+|+.|++|+|+||..||.-=|
T Consensus        50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~Lg   88 (198)
T KOG0483|consen   50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELG   88 (198)
T ss_pred             cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhC
Confidence            689999999999999999999999999999999996544

>PF04618 HD-ZIP_N: HD-ZIP protein N terminus; InterPro: IPR006712 Homeodomain leucine zipper (HDZip) genes encode putative transcription factors that are unique to plants

Probab=98.12  E-value=6.5e-06  Score=64.56  Aligned_cols=36  Identities=33%  Similarity=0.299  Sum_probs=24.6

Q ss_pred             cccccccchhhhhhhhhhhhhcccccCCCCcccceeecCcc
Q 029785           75 SIDVNKGYEESAAAGVAEYQILNRQASPHSAVSNSFSSGRV  115 (188)
Q Consensus        75 ~~~~~~~~~~~~~~~~~d~~d~~~~sSPnS~vS~SfS~~~~  115 (188)
                      .|+||--+.-    ..+|..+..+||||||||| |+|++|.
T Consensus        72 giDVNr~p~~----~~~d~eEe~gvSSPNStiS-S~sgkr~  107 (111)
T PF04618_consen   72 GIDVNRLPST----VEADCEEEAGVSSPNSTIS-SVSGKRS  107 (111)
T ss_pred             ceeccCCCcc----ccccccccccccCCCccce-ecccccc
Confidence            4677764331    1123445678999999999 8999776

This observation suggests that homeobox-leucine zipper genes evolved after the divergence of plants and animals, perhaps to mediate specific regulatory events []. This domain is the N-terminal of plant homeobox-leucine zipper proteins. Its function is unknown.; GO: 0006351 transcription, DNA-dependent, 0005634 nucleus

>PF00046 Homeobox: Homeobox domain not present here

Probab=96.54  E-value=0.0021  Score=41.85  Aligned_cols=35  Identities=31%  Similarity=0.278  Sum_probs=32.8

Q ss_pred             ccccccChHHHHHHHHhhhhccCCChhhhhhhhcc
Q 029785          148 RKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSI  182 (188)
Q Consensus       148 RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~  182 (188)
                      |++-++|++|..+||+.|..+..++..+++.||.-
T Consensus         2 r~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~   36 (57)
T PF00046_consen    2 RKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKE   36 (57)
T ss_dssp             SSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHHHHhcccccccccccccc
Confidence            68889999999999999999999999999999864

; 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 ....

>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=95.81  E-value=0.012  Score=37.68  Aligned_cols=37  Identities=27%  Similarity=0.205  Sum_probs=33.3

Q ss_pred             ccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          148 RKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       148 RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      +++-+++++|..+||..|..|...++++++.||.-=|
T Consensus         2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~   38 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELG   38 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHC
Confidence            5677899999999999999999999999999997544

>smart00389 HOX Homeodomain

Probab=95.29  E-value=0.023  Score=36.37  Aligned_cols=37  Identities=24%  Similarity=0.178  Sum_probs=32.3

Q ss_pred             ccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          148 RKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       148 RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      +++-++|++|..+||..|..+...++.+++.||..=|
T Consensus         2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~   38 (56)
T smart00389        2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLG   38 (56)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHC
Confidence            3455799999999999999999999999999997544

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

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=90.25  E-value=0.33  Score=39.77  Aligned_cols=40  Identities=20%  Similarity=0.122  Sum_probs=36.1

Q ss_pred             cccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          145 VNARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       145 ~~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      -..+|+.|+|.+|..+||..|+.-.+-+..-|..|+..-+
T Consensus        50 ~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~ln   89 (156)
T COG5576          50 PPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLN   89 (156)
T ss_pred             cCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcC
Confidence            3679999999999999999999999999999999987544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	188
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	5e-08
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	9e-04

>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 = 46.8 bits (112), Expect = 5e-08
 Identities = 8/32 (25%), Positives = 17/32 (53%)

Query: 142 EDGVNARKKLRLTKEQSALLEESFKQHSTLNP 173
           +   + + K  ++ +  A LEE F++  +LN 
Sbjct: 1   KKEKSPKGKSSISPQARAFLEEVFRRKQSLNS 32

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 37.4 bits (86), Expect = 9e-04
 Identities = 10/52 (19%), Positives = 25/52 (48%), Gaps = 3/52 (5%)

Query: 118 RERDLSSEEIEVEKVISSRASDEDEDG-VNARKKLRLTKEQSALLEESFKQH 168
           +E D +S+ +E E     +A  + E+      +++   K  + + +++F Q 
Sbjct: 99  QELDAASKVMEQE--WREKAKKDLEEWNQRQSEQVEKNKINNRIADKAFYQQ 148

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	188
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	96.91
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	96.36
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	96.14
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	96.08
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	96.05
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	95.99
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	95.98
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	95.93
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	95.91
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	95.9
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	95.88
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	95.69
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	95.67
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	95.64
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	95.63
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	95.6
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	95.54
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	95.52
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	95.52
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	95.51
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	95.46
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	95.45
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	95.43
1uhs_A	72	HOP, homeodomain only protein; structural genomics	95.42
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	95.4
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	95.31
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	95.26
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	95.25
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	95.14
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	95.06
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	95.06
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	94.97
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	94.93
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	94.92
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	94.91
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	94.89
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	94.89
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	94.81
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	94.75
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	94.71
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	94.61
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	94.56
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	94.54
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	94.53
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	94.49
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	94.43
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	94.42
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	94.37
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	94.37
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	94.28
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	94.16
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	94.13
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	94.12
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	94.11
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	94.06
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	94.05
2e19_A	64	Transcription factor 8; homeobox domain, structura	93.88
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	93.7
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	93.37
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	93.15
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	92.89
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	92.29
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	92.26
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	89.89
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	89.84
1lfb_A	99	Liver transcription factor (LFB1); transcription r	89.17
1e3o_C	160	Octamer-binding transcription factor 1; transcript	88.71
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	88.27
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	87.4
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	86.24
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	80.84
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	80.79

>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=96.91  E-value=0.00074  Score=48.43  Aligned_cols=42  Identities=29%  Similarity=0.199  Sum_probs=37.5

Q ss_pred             CcccccccccChHHHHHHHHhhhhccCCChhhhhhhhccccc
Q 029785          144 GVNARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDGF  185 (188)
Q Consensus       144 G~~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~~  185 (188)
                      |..++|+-++|++|..+||..|..+.-+++..+.+||..-|.
T Consensus         1 ~~~g~~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgL   42 (76)
T 2ecc_A            1 GSSGSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGL   42 (76)
T ss_dssp             CCCSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCc
Confidence            345678888999999999999999999999999999987664

>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=96.36  E-value=0.0036  Score=42.08  Aligned_cols=39  Identities=18%  Similarity=0.239  Sum_probs=35.4

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|++-++|++|..+||..|..+..+++.++..||..=|
T Consensus         7 ~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~   45 (70)
T 2e1o_A            7 GKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQ   45 (70)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHC
Confidence            567888999999999999999999999999999997654

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

Probab=96.14  E-value=0.0046  Score=41.41  Aligned_cols=40  Identities=18%  Similarity=0.053  Sum_probs=35.4

Q ss_pred             cccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          145 VNARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       145 ~~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ...|+.-++|.+|...||..|..+.-+++.++..||..-|
T Consensus         6 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~   45 (70)
T 2dmu_A            6 SGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVH   45 (70)
T ss_dssp             SSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHC
Confidence            3567778899999999999999999999999999997544

>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=96.08  E-value=0.0062  Score=40.65  Aligned_cols=41  Identities=12%  Similarity=0.086  Sum_probs=36.2

Q ss_pred             CcccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          144 GVNARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       144 G~~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      +...|+.-++|.+|...||..|..+.-+++.++..||..-|
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~   45 (70)
T 2da2_A            5 SSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLN   45 (70)
T ss_dssp             CCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhC
Confidence            33567778899999999999999999999999999997655

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

Probab=96.05  E-value=0.0043  Score=40.93  Aligned_cols=40  Identities=18%  Similarity=0.065  Sum_probs=33.9

Q ss_pred             cccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          145 VNARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       145 ~~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ...|+.-++|.+|...||..|..+.-+++.++..||..=|
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~   41 (63)
T 2h1k_A            2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLN   41 (63)
T ss_dssp             ---CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhC
Confidence            3567788999999999999999999999999999997544

>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=95.99  E-value=0.0062  Score=41.37  Aligned_cols=39  Identities=18%  Similarity=0.192  Sum_probs=33.6

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|.+|..+||..|..+..+++.++..||..=|
T Consensus        17 ~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~   55 (80)
T 2da3_A           17 DKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVG   55 (80)
T ss_dssp             CTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHC
Confidence            445556799999999999999999999999999987544

>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=95.98  E-value=0.0083  Score=41.31  Aligned_cols=39  Identities=21%  Similarity=0.079  Sum_probs=33.9

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|.+|...||..|..+..+++.++..||..=|
T Consensus        17 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~   55 (80)
T 2dmt_A           17 GRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLG   55 (80)
T ss_dssp             CCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhC
Confidence            445566799999999999999999999999999997544

>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=95.93  E-value=0.0079  Score=40.36  Aligned_cols=39  Identities=13%  Similarity=0.113  Sum_probs=35.2

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|.+|..+||..|..+.-+++.++..||..-|
T Consensus         7 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~   45 (70)
T 2cra_A            7 GRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATS   45 (70)
T ss_dssp             CCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTC
T ss_pred             CCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHC
Confidence            567778999999999999999999999999999997655

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

Probab=95.91  E-value=0.0085  Score=40.21  Aligned_cols=39  Identities=15%  Similarity=0.051  Sum_probs=35.0

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|.+|...||..|..+.-+++.++..||..-|
T Consensus         7 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~   45 (70)
T 2djn_A            7 GRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLG   45 (70)
T ss_dssp             CCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSS
T ss_pred             CCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhC
Confidence            557777899999999999999999999999999997655

>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=95.90  E-value=0.007  Score=40.80  Aligned_cols=41  Identities=12%  Similarity=0.009  Sum_probs=35.0

Q ss_pred             CcccccccccChHHHHHHHHhhhh---ccCCChhhhhhhhcccc
Q 029785          144 GVNARKKLRLTKEQSALLEESFKQ---HSTLNPVIISLSLSIDG  184 (188)
Q Consensus       144 G~~~RKKLRLsKeQsa~LEesFk~---H~tLnpkqK~~la~~~~  184 (188)
                      +...|++-+||++|..+||..|.+   |.-+++.+|..||..-|
T Consensus         5 ~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~   48 (73)
T 1x2n_A            5 SSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTN   48 (73)
T ss_dssp             SSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHC
Confidence            335677888999999999999988   67899999999997655

>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=95.88  E-value=0.005  Score=39.99  Aligned_cols=39  Identities=23%  Similarity=0.301  Sum_probs=30.0

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|.+|..+||..|..|.-+++.++..||..=|
T Consensus         5 ~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~   43 (61)
T 1akh_A            5 SPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCG   43 (61)
T ss_dssp             -------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHC
Confidence            457778999999999999999999999999999997654

>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=95.69  E-value=0.0084  Score=41.98  Aligned_cols=40  Identities=13%  Similarity=0.120  Sum_probs=34.4

Q ss_pred             ccccccccChHHHHHHHHhhhhc---cCCChhhhhhhhccccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQH---STLNPVIISLSLSIDGF  185 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H---~tLnpkqK~~la~~~~~  185 (188)
                      ..|++-+||++|..+||+.|.+|   .-+++.+|..||..-|+
T Consensus         7 ~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gL   49 (83)
T 2dmn_A            7 GKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNL   49 (83)
T ss_dssp             CCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCC
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCc
Confidence            44667779999999999999996   89999999999986553

>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=95.67  E-value=0.0082  Score=40.09  Aligned_cols=40  Identities=15%  Similarity=0.136  Sum_probs=35.5

Q ss_pred             cccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          145 VNARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       145 ~~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ...|+.-++|.+|...||..|..+.-+++.++..||..-|
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~   41 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTN   41 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHC
Confidence            3467778899999999999999999999999999997655

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

Probab=95.64  E-value=0.011  Score=40.64  Aligned_cols=40  Identities=18%  Similarity=0.140  Sum_probs=35.7

Q ss_pred             cccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          145 VNARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       145 ~~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ...|+.-++|.+|...||..|....-+++.++..||..-|
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~   45 (80)
T 2cue_A            6 SGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKID   45 (80)
T ss_dssp             SSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTT
T ss_pred             CCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhC
Confidence            3567778899999999999999999999999999997655

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

Probab=95.63  E-value=0.012  Score=39.32  Aligned_cols=41  Identities=17%  Similarity=0.102  Sum_probs=35.7

Q ss_pred             CcccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          144 GVNARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       144 G~~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      +...|+.-++|.+|...||..|.....+++.++..||..-|
T Consensus         7 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~   47 (75)
T 2m0c_A            7 GKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTD   47 (75)
T ss_dssp             SCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhC
Confidence            44567778899999999999999999999999999997654

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

Probab=95.60  E-value=0.0076  Score=39.57  Aligned_cols=40  Identities=13%  Similarity=0.079  Sum_probs=34.7

Q ss_pred             ccccccccChHHHHHHHHhh---hhccCCChhhhhhhhccccc
Q 029785          146 NARKKLRLTKEQSALLEESF---KQHSTLNPVIISLSLSIDGF  185 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesF---k~H~tLnpkqK~~la~~~~~  185 (188)
                      +.|++-++|++|..+||..|   ..+.-+++.++..||..-|.
T Consensus         3 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L   45 (64)
T 1du6_A            3 GHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGI   45 (64)
T ss_dssp             CCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTS
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCc
Confidence            46788899999999999999   77888999999999976553

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

Probab=95.54  E-value=0.011  Score=37.53  Aligned_cols=38  Identities=21%  Similarity=0.172  Sum_probs=33.9

Q ss_pred             cccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          147 ARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       147 ~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      .|+.-++|.+|...||..|.....+++.++..||..=|
T Consensus         3 rr~Rt~~t~~q~~~Le~~F~~~~yp~~~~r~~La~~l~   40 (58)
T 3rkq_A            3 RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLK   40 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCCcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhC
Confidence            46678899999999999999999999999999987544

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

Probab=95.52  E-value=0.01  Score=39.38  Aligned_cols=38  Identities=18%  Similarity=0.141  Sum_probs=34.4

Q ss_pred             cccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          147 ARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       147 ~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      .|+.-++|.+|...||..|..+.-+++.++..||..-|
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~   39 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLN   39 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHT
T ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHC
Confidence            57778999999999999999999999999999997654

>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=95.52  E-value=0.0098  Score=40.71  Aligned_cols=39  Identities=23%  Similarity=0.039  Sum_probs=34.6

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..+|.-|+|.+|...||..|.....+++.++..||..=|
T Consensus         7 ~~~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~   45 (75)
T 2da5_A            7 GPTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETK   45 (75)
T ss_dssp             SSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHC
T ss_pred             CCCCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhC
Confidence            356777899999999999999999999999999997544

>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=95.51  E-value=0.014  Score=39.83  Aligned_cols=39  Identities=10%  Similarity=0.106  Sum_probs=35.2

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|.+|...||..|..+..+++.++..||..=|
T Consensus         7 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~   45 (80)
T 2dmq_A            7 GKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTG   45 (80)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhC
Confidence            567778899999999999999999999999999997654

>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=95.46  E-value=0.0097  Score=38.62  Aligned_cols=36  Identities=22%  Similarity=0.265  Sum_probs=31.9

Q ss_pred             cccccChHHHHHHHHhhhh---ccCCChhhhhhhhcccc
Q 029785          149 KKLRLTKEQSALLEESFKQ---HSTLNPVIISLSLSIDG  184 (188)
Q Consensus       149 KKLRLsKeQsa~LEesFk~---H~tLnpkqK~~la~~~~  184 (188)
                      |+-|+|++|..+||..|..   +.-+++.++..||..-|
T Consensus         1 rr~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~g   39 (60)
T 1k61_A            1 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTS   39 (60)
T ss_dssp             CCCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHC
T ss_pred             CcCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHC
Confidence            4568999999999999999   88899999999997655

>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=95.45  E-value=0.02  Score=40.05  Aligned_cols=39  Identities=15%  Similarity=0.144  Sum_probs=33.2

Q ss_pred             ccccccccChHHHHHHHHhhhh----ccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQ----HSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~----H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-.+|.+|...||..|..    +..++..++++||..=|
T Consensus        17 ~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lg   59 (80)
T 1wh5_A           17 RKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETG   59 (80)
T ss_dssp             SCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSC
T ss_pred             CCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhC
Confidence            4455566899999999999999    88999999999997654

>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=95.43  E-value=0.012  Score=39.16  Aligned_cols=39  Identities=21%  Similarity=0.279  Sum_probs=35.0

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|.+|..+||..|..+.-+++.++..||..-|
T Consensus         7 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~   45 (70)
T 2da1_A            7 GKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSG   45 (70)
T ss_dssp             CCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhC
Confidence            467778899999999999999999999999999997644

>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=95.42  E-value=0.011  Score=39.83  Aligned_cols=39  Identities=21%  Similarity=0.380  Sum_probs=34.3

Q ss_pred             ccccccccChHHHHHHHHhhhh-ccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQ-HSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~-H~tLnpkqK~~la~~~~  184 (188)
                      |.+++-++|.+|...||..|.. ...+++.++..||..=|
T Consensus         1 G~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~   40 (72)
T 1uhs_A            1 GSEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAG   40 (72)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHC
Confidence            3578889999999999999996 99999999999997544

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

Probab=95.40  E-value=0.013  Score=37.63  Aligned_cols=37  Identities=22%  Similarity=0.113  Sum_probs=33.5

Q ss_pred             ccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          148 RKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       148 RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      |+.-++|.+|...||..|..+.-+++.++..||..-|
T Consensus         2 r~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~   38 (58)
T 1ig7_A            2 KPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLS   38 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTT
T ss_pred             CCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHC
Confidence            5667899999999999999999999999999998655

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

Probab=95.31  E-value=0.025  Score=38.85  Aligned_cols=39  Identities=13%  Similarity=0.192  Sum_probs=34.8

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|.+|..+||..|..+..+++.++..||..=|
T Consensus        22 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~   60 (84)
T 2kt0_A           22 KQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILN   60 (84)
T ss_dssp             SCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcC
Confidence            556677899999999999999999999999999997655

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

Probab=95.26  E-value=0.019  Score=39.43  Aligned_cols=39  Identities=15%  Similarity=0.109  Sum_probs=35.2

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|.+|..+||..|.....+++.++..||..-|
T Consensus         7 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~   45 (80)
T 2dms_A            7 GRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKIN   45 (80)
T ss_dssp             CCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHC
Confidence            567778899999999999999999999999999997655

>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=95.25  E-value=0.022  Score=38.86  Aligned_cols=39  Identities=23%  Similarity=0.238  Sum_probs=34.0

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|.+|-..||..|..+..++..++..||..=|
T Consensus         9 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~   47 (77)
T 1nk2_P            9 KRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIR   47 (77)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTT
T ss_pred             CCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhC
Confidence            345566799999999999999999999999999997654

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

Probab=95.14  E-value=0.013  Score=38.31  Aligned_cols=39  Identities=15%  Similarity=0.180  Sum_probs=31.3

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|.+|...||..|..+.-+++.++..||..=|
T Consensus         3 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~   41 (62)
T 2vi6_A            3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILN   41 (62)
T ss_dssp             -----CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhC
Confidence            456677899999999999999999999999999997544

>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=95.06  E-value=0.017  Score=38.18  Aligned_cols=38  Identities=13%  Similarity=0.253  Sum_probs=34.2

Q ss_pred             cccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          147 ARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       147 ~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      .|+.-++|.+|...||..|..+.-+++.++..||..-|
T Consensus         4 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~   41 (66)
T 1bw5_A            4 TRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTG   41 (66)
T ss_dssp             SCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHC
Confidence            56778899999999999999999999999999997654

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

Probab=95.06  E-value=0.014  Score=41.56  Aligned_cols=39  Identities=21%  Similarity=0.164  Sum_probs=34.1

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      +.|++-++|++|..+||..|.....++..++..||..=|
T Consensus        25 ~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~   63 (96)
T 3nar_A           25 STGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESG   63 (96)
T ss_dssp             --CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHC
T ss_pred             CCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhC
Confidence            457888999999999999999999999999999997544

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

Probab=94.97  E-value=0.018  Score=39.27  Aligned_cols=39  Identities=18%  Similarity=0.146  Sum_probs=34.3

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..+.+-++|++|...||..|..+.-+++.++..||..-|
T Consensus         8 ~~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~   46 (76)
T 2dn0_A            8 ASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTG   46 (76)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHC
T ss_pred             CCCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhC
Confidence            345677899999999999999999999999999997644

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

Probab=94.93  E-value=0.018  Score=37.41  Aligned_cols=37  Identities=16%  Similarity=0.108  Sum_probs=33.3

Q ss_pred             ccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          148 RKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       148 RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      |+.-++|.+|...||..|..+.-+++.++..||..-|
T Consensus         3 r~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~   39 (60)
T 1jgg_A            3 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLN   39 (60)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHC
Confidence            5667899999999999999999999999999997644

>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=94.92  E-value=0.016  Score=40.46  Aligned_cols=40  Identities=20%  Similarity=0.249  Sum_probs=34.9

Q ss_pred             ccccccccChHHHHHHHHhhhh---ccCCChhhhhhhhccccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQ---HSTLNPVIISLSLSIDGF  185 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~---H~tLnpkqK~~la~~~~~  185 (188)
                      ..|+.-++|++|..+||..|..   |.-+++.+|..||..-|.
T Consensus        27 ~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL   69 (87)
T 1mnm_C           27 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSL   69 (87)
T ss_dssp             SCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCC
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCc
Confidence            4566778999999999999999   899999999999976553

>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=94.91  E-value=0.017  Score=37.61  Aligned_cols=38  Identities=24%  Similarity=0.183  Sum_probs=32.3

Q ss_pred             cccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          147 ARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       147 ~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      .|+.-++|.+|...||..|..+.-+++.++..||..-|
T Consensus         4 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~   41 (61)
T 2hdd_A            4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELG   41 (61)
T ss_dssp             ---CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHC
Confidence            46677899999999999999999999999999997654

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

Probab=94.89  E-value=0.02  Score=39.97  Aligned_cols=42  Identities=19%  Similarity=0.120  Sum_probs=33.3

Q ss_pred             cCcccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       143 dG~~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ++...|+.-++|.+|...||..|....-++..++..||..=|
T Consensus        25 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~   66 (88)
T 2r5y_A           25 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALS   66 (88)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhC
Confidence            344677888899999999999999999999999999997654

>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=94.89  E-value=0.019  Score=38.70  Aligned_cols=38  Identities=18%  Similarity=0.176  Sum_probs=33.3

Q ss_pred             cccccccChHHHHHHHHhh---hhccCCChhhhhhhhcccc
Q 029785          147 ARKKLRLTKEQSALLEESF---KQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       147 ~RKKLRLsKeQsa~LEesF---k~H~tLnpkqK~~la~~~~  184 (188)
                      .|+.-++|++|..+||..|   ..+.-+++.++..||..-|
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~   42 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCG   42 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHC
Confidence            4677899999999999999   7778899999999997655

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

Probab=94.81  E-value=0.021  Score=38.75  Aligned_cols=39  Identities=15%  Similarity=0.108  Sum_probs=35.1

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      +.|+.-++|.+|-..||..|..+.-+++.++..||..-|
T Consensus         7 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~   45 (73)
T 2l7z_A            7 GRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTN   45 (73)
T ss_dssp             CCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHC
Confidence            467788999999999999999999999999999997654

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

Probab=94.75  E-value=0.025  Score=41.15  Aligned_cols=40  Identities=23%  Similarity=0.151  Sum_probs=34.9

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhccccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDGF  185 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~~  185 (188)
                      ..+|..|+|.+|...||..|..+.-++...+.+||..-|+
T Consensus        11 ~p~k~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgL   50 (89)
T 2ecb_A           11 TPQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKL   50 (89)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCC
T ss_pred             CchhhccCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCc
Confidence            3456669999999999999999999999999999976553

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

Probab=94.71  E-value=0.024  Score=38.40  Aligned_cols=38  Identities=24%  Similarity=0.321  Sum_probs=33.6

Q ss_pred             cccccccChHHHHHHHHhhh-hccCCChhhhhhhhcccc
Q 029785          147 ARKKLRLTKEQSALLEESFK-QHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       147 ~RKKLRLsKeQsa~LEesFk-~H~tLnpkqK~~la~~~~  184 (188)
                      +++.-++|.+|...||..|. .+..+++.++..||..=|
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~   41 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAG   41 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHC
Confidence            56778999999999999999 599999999999997544

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

Probab=94.61  E-value=0.027  Score=37.87  Aligned_cols=39  Identities=26%  Similarity=0.192  Sum_probs=34.8

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..+++-++|++|...||..|.....+++.++..||..-|
T Consensus         6 ~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~   44 (74)
T 2ly9_A            6 SFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITG   44 (74)
T ss_dssp             CCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHC
T ss_pred             CCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhC
Confidence            457778999999999999999999999999999997644

>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=94.56  E-value=0.023  Score=39.54  Aligned_cols=39  Identities=21%  Similarity=0.249  Sum_probs=32.8

Q ss_pred             cccccccChHHHHHHHHhhhh---ccCCChhhhhhhhccccc
Q 029785          147 ARKKLRLTKEQSALLEESFKQ---HSTLNPVIISLSLSIDGF  185 (188)
Q Consensus       147 ~RKKLRLsKeQsa~LEesFk~---H~tLnpkqK~~la~~~~~  185 (188)
                      .++.-|||++|..+||..|..   |.-++..++..||..-|.
T Consensus         3 ~krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gL   44 (83)
T 1le8_B            3 PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSL   44 (83)
T ss_dssp             --CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCC
Confidence            355667999999999999999   899999999999976553

>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=94.54  E-value=0.025  Score=39.16  Aligned_cols=38  Identities=18%  Similarity=0.176  Sum_probs=32.8

Q ss_pred             cccccccChHHHHHHHHhh---hhccCCChhhhhhhhcccc
Q 029785          147 ARKKLRLTKEQSALLEESF---KQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       147 ~RKKLRLsKeQsa~LEesF---k~H~tLnpkqK~~la~~~~  184 (188)
                      .|+.-+||++|..+||..|   ..+.-+++.++..||..-|
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~   42 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCG   42 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHC
Confidence            3677889999999999999   7778899999999997655

>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=94.53  E-value=0.023  Score=38.05  Aligned_cols=38  Identities=18%  Similarity=0.042  Sum_probs=33.8

Q ss_pred             cccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          147 ARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       147 ~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      .|+.-++|.+|...||..|..+.-+++.++..||..=|
T Consensus         3 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~   40 (68)
T 1ahd_P            3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALS   40 (68)
T ss_dssp             SCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHT
T ss_pred             CCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHC
Confidence            46677899999999999999999999999999987544

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

Probab=94.49  E-value=0.031  Score=37.34  Aligned_cols=39  Identities=23%  Similarity=0.129  Sum_probs=34.5

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|.+|...||..|..+.-+++.++..||..=|
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~   40 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLA   40 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHT
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhC
Confidence            356777899999999999999999999999999987544

>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=94.43  E-value=0.05  Score=37.10  Aligned_cols=39  Identities=21%  Similarity=0.084  Sum_probs=34.8

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|.+|-..||..|..+..+++.++..||..=|
T Consensus        13 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~   51 (77)
T 1puf_A           13 TRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLN   51 (77)
T ss_dssp             TSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHC
Confidence            567778899999999999999999999999999997544

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

Probab=94.42  E-value=0.038  Score=39.17  Aligned_cols=38  Identities=13%  Similarity=0.081  Sum_probs=34.0

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSID  183 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~  183 (188)
                      ..|+..++|++|-.+||..|..+..++..++++||..=
T Consensus         7 ~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l   44 (95)
T 2cuf_A            7 GRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANAC   44 (95)
T ss_dssp             CCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHH
T ss_pred             CCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Confidence            45677789999999999999999999999999998753

>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=94.37  E-value=0.027  Score=40.11  Aligned_cols=41  Identities=17%  Similarity=0.079  Sum_probs=32.9

Q ss_pred             CcccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          144 GVNARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       144 G~~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      +...|+.-++|.+|...||..|..+..+++.++..||..=|
T Consensus        32 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~   72 (97)
T 1b72_A           32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLE   72 (97)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhC
Confidence            33556777899999999999999999999999999997544

>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=94.37  E-value=0.031  Score=38.39  Aligned_cols=39  Identities=13%  Similarity=0.081  Sum_probs=34.2

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|.+|-.+||..|..+..++..++..||..-|
T Consensus        18 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~   56 (81)
T 1fjl_A           18 QRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTN   56 (81)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHC
Confidence            456667799999999999999999999999999997644

>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=94.28  E-value=0.027  Score=38.04  Aligned_cols=34  Identities=9%  Similarity=0.005  Sum_probs=28.4

Q ss_pred             ccChHHHHHHHHhhh---hccCCChhhhhhhhccccc
Q 029785          152 RLTKEQSALLEESFK---QHSTLNPVIISLSLSIDGF  185 (188)
Q Consensus       152 RLsKeQsa~LEesFk---~H~tLnpkqK~~la~~~~~  185 (188)
                      +||++|..+||+.|.   .|.-+++.+|..||..-|.
T Consensus         4 ~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l   40 (67)
T 3k2a_A            4 IFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGL   40 (67)
T ss_dssp             --CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTC
T ss_pred             cCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCc
Confidence            799999999999999   7777999999999976553

>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=94.16  E-value=0.031  Score=38.70  Aligned_cols=39  Identities=18%  Similarity=0.067  Sum_probs=32.2

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|.+|...||..|..+..+++.++..||..=|
T Consensus        20 ~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~   58 (81)
T 1b8i_A           20 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALS   58 (81)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhC
Confidence            456777899999999999999999999999999997544

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

Probab=94.13  E-value=0.032  Score=36.19  Aligned_cols=34  Identities=18%  Similarity=0.059  Sum_probs=30.5

Q ss_pred             cccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          151 LRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       151 LRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      -++|.+|-..||..|..+..+++.++..||..-|
T Consensus         4 t~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~   37 (60)
T 3a02_A            4 MTFTSFQLEELEKAFSRTHYPDVFTREELAMKIG   37 (60)
T ss_dssp             -CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             cccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHC
Confidence            4799999999999999999999999999997544

>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=94.12  E-value=0.065  Score=37.74  Aligned_cols=37  Identities=19%  Similarity=0.232  Sum_probs=31.1

Q ss_pred             cccccccChHHHHHHHHhhhh-----ccCCChhhhhhhhcccc
Q 029785          147 ARKKLRLTKEQSALLEESFKQ-----HSTLNPVIISLSLSIDG  184 (188)
Q Consensus       147 ~RKKLRLsKeQsa~LEesFk~-----H~tLnpkqK~~la~~~~  184 (188)
                      .|+.-.+|.+|...|| .|.+     +.-++..++++||..=|
T Consensus        18 rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lg   59 (80)
T 1wh7_A           18 KRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETG   59 (80)
T ss_dssp             SCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSC
T ss_pred             CCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhC
Confidence            3455568999999999 7999     88999999999997544

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

Probab=94.11  E-value=0.018  Score=39.50  Aligned_cols=39  Identities=8%  Similarity=0.076  Sum_probs=33.1

Q ss_pred             ccccccccChHHHHHHHHhhhhc----cCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQH----STLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H----~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|.+|...||..|..+    ..++..++++||..-|
T Consensus         8 ~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lg   50 (80)
T 2da4_A            8 ALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELN   50 (80)
T ss_dssp             CCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhC
Confidence            34555668999999999999999    8999999999987544

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

Probab=94.06  E-value=0.021  Score=39.30  Aligned_cols=39  Identities=10%  Similarity=-0.066  Sum_probs=34.7

Q ss_pred             ccccccccChHHHHHHHHhh-hhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESF-KQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesF-k~H~tLnpkqK~~la~~~~  184 (188)
                      +.++|-|++.+|-..||..| .....+++.++.+||.-=|
T Consensus         8 g~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~   47 (72)
T 2cqx_A            8 GIKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLD   47 (72)
T ss_dssp             CCCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhC
Confidence            46888999999999999999 8888999999999997544

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

Probab=94.05  E-value=0.037  Score=36.95  Aligned_cols=38  Identities=21%  Similarity=0.192  Sum_probs=33.8

Q ss_pred             cccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          147 ARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       147 ~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      .|+.-++|.+|-..||..|..+.-+++.++..||..=|
T Consensus         3 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~   40 (68)
T 1ftt_A            3 RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIH   40 (68)
T ss_dssp             SSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHT
T ss_pred             CCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhC
Confidence            46667899999999999999999999999999997544

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

Probab=93.88  E-value=0.052  Score=36.61  Aligned_cols=39  Identities=10%  Similarity=-0.009  Sum_probs=33.3

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ++......+++|...||..|..+..++..++..||..=|
T Consensus         3 sg~~~~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~   41 (64)
T 2e19_A            3 SGSSGQPPLKNLLSLLKAYYALNAQPSAEELSKIADSVN   41 (64)
T ss_dssp             CSCSCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCCCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhC
Confidence            445556778999999999999999999999999997544

>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=93.70  E-value=0.048  Score=38.62  Aligned_cols=37  Identities=22%  Similarity=0.101  Sum_probs=32.4

Q ss_pred             ccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          148 RKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       148 RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      +|.-|+|.+|-.+||..|..+..+++.++..||..=|
T Consensus        15 ~k~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~   51 (89)
T 2dmp_A           15 QKFKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETK   51 (89)
T ss_dssp             SCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             cccccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhC
Confidence            4455699999999999999999999999999987544

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

Probab=93.37  E-value=0.054  Score=34.89  Aligned_cols=33  Identities=15%  Similarity=0.078  Sum_probs=29.6

Q ss_pred             ccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          152 RLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       152 RLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      .+|++|...||..|..+.-+++.++..||..=|
T Consensus         3 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~   35 (56)
T 3a03_A            3 SFSRSQVLELERRFLRQKYLASAERAALAKALR   35 (56)
T ss_dssp             -CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             ccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhC
Confidence            479999999999999999999999999997544

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

Probab=93.15  E-value=0.08  Score=37.65  Aligned_cols=40  Identities=18%  Similarity=0.115  Sum_probs=34.5

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhccccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDGF  185 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~~  185 (188)
                      ..|+.-++|.+|-..||..|..+..+++.++..||..=|.
T Consensus        17 ~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L   56 (93)
T 3a01_A           17 RKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKM   56 (93)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTC
T ss_pred             CCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCC
Confidence            3455567999999999999999999999999999976553

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

Probab=92.89  E-value=0.072  Score=40.83  Aligned_cols=39  Identities=18%  Similarity=0.136  Sum_probs=32.7

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+..++|++|...||..|..|.-+++.++..||..=|
T Consensus        97 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~  135 (164)
T 2d5v_A           97 PKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLG  135 (164)
T ss_dssp             ---CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHC
Confidence            456677899999999999999999999999999997544

>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=92.29  E-value=0.076  Score=40.67  Aligned_cols=39  Identities=15%  Similarity=0.153  Sum_probs=32.8

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|.+|...||..|..+..+++.++..||..-|
T Consensus        87 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~  125 (146)
T 1au7_A           87 KRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELN  125 (146)
T ss_dssp             --CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhC
Confidence            344556799999999999999999999999999997544

>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=92.26  E-value=0.13  Score=39.22  Aligned_cols=39  Identities=10%  Similarity=0.075  Sum_probs=33.5

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|++|...||..|..+..+++.++..||..=|
T Consensus        93 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~  131 (151)
T 3d1n_I           93 KRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELN  131 (151)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHC
Confidence            344556799999999999999999999999999997544

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

Probab=89.89  E-value=0.21  Score=35.18  Aligned_cols=36  Identities=36%  Similarity=0.390  Sum_probs=30.3

Q ss_pred             cccccccChHHHHHHHHhhhhccCCChhhhhhhhccccc
Q 029785          147 ARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDGF  185 (188)
Q Consensus       147 ~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~~  185 (188)
                      -|||   ||+|-..||..|....-+++..+.+||..-|.
T Consensus         8 ~~~~---~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgL   43 (66)
T 3nau_A            8 HRKK---TKEQIAHLKASFLQSQFPDDAEVYRLIEVTGL   43 (66)
T ss_dssp             ---C---CHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCC
T ss_pred             hhhh---hHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCc
Confidence            3665   89999999999999999999999999987653

>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=89.84  E-value=0.25  Score=38.06  Aligned_cols=40  Identities=18%  Similarity=0.115  Sum_probs=34.9

Q ss_pred             cccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          145 VNARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       145 ~~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ...|+.-++|.+|...||..|..+..+++.++..||..=|
T Consensus        95 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~  134 (155)
T 3l1p_A           95 ARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLG  134 (155)
T ss_dssp             CSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTT
T ss_pred             CCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcC
Confidence            3556677899999999999999999999999999997544

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

Probab=89.17  E-value=0.29  Score=35.80  Aligned_cols=36  Identities=6%  Similarity=0.118  Sum_probs=31.0

Q ss_pred             cccccccChHHHHHHHHhhhhccCCChhhhhhhhcc
Q 029785          147 ARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSI  182 (188)
Q Consensus       147 ~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~  182 (188)
                      .|+...+|.+|-..||..|..+..++..++.+||..
T Consensus        10 rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~   45 (99)
T 1lfb_A           10 RRNRFKWGPASQQILFQAYERQKNPSKEERETLVEE   45 (99)
T ss_dssp             ---CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHH
T ss_pred             CCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence            456667999999999999999999999999999976

>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=88.71  E-value=0.27  Score=37.94  Aligned_cols=39  Identities=18%  Similarity=0.183  Sum_probs=32.4

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|.+|...||..|..+..++..++..||..=|
T Consensus       101 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~  139 (160)
T 1e3o_C          101 RRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLN  139 (160)
T ss_dssp             ---CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             CCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHC
Confidence            345666789999999999999999999999999997544

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

Probab=88.27  E-value=0.26  Score=38.49  Aligned_cols=39  Identities=13%  Similarity=0.039  Sum_probs=29.7

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|.+|...||..|.....+++.++..||..=|
T Consensus        99 ~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~  137 (164)
T 2xsd_C           99 KRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQ  137 (164)
T ss_dssp             -------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             CCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHC
Confidence            445667899999999999999999999999999997544

>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=87.40  E-value=0.55  Score=35.27  Aligned_cols=37  Identities=5%  Similarity=0.138  Sum_probs=33.0

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSI  182 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~  182 (188)
                      ..|+..++|++|-.+||..|.....++...+.+||+.
T Consensus         6 ~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~   42 (102)
T 2da6_A            6 SGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEE   42 (102)
T ss_dssp             SCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHH
T ss_pred             CCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence            4566678899999999999999999999999999874

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

Probab=86.24  E-value=0.57  Score=32.25  Aligned_cols=33  Identities=15%  Similarity=0.060  Sum_probs=29.9

Q ss_pred             ccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          152 RLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       152 RLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      -+|.+|-..||..|....-+++.++..||..=|
T Consensus        10 ~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~   42 (69)
T 2l9r_A           10 HMSHTQVIELERKFSHQKYLSAPERAHLAKNLK   42 (69)
T ss_dssp             CCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTT
T ss_pred             cCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhC
Confidence            378999999999999999999999999997654

>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=80.84  E-value=1.5  Score=30.11  Aligned_cols=35  Identities=11%  Similarity=0.022  Sum_probs=26.9

Q ss_pred             cccccccccChHHHHHHHHhhh-hccCCChhhhhhhhccc
Q 029785          145 VNARKKLRLTKEQSALLEESFK-QHSTLNPVIISLSLSID  183 (188)
Q Consensus       145 ~~~RKKLRLsKeQsa~LEesFk-~H~tLnpkqK~~la~~~  183 (188)
                      .+++||.    +|...||..|. ....++..++.+||.-=
T Consensus         3 ~~~~~~~----~~~~~LE~~F~~~~~yp~~~~r~~LA~~l   38 (64)
T 1x2m_A            3 SGSSGTA----QPNAILEKVFTAITKHPDEKRLEGLSKQL   38 (64)
T ss_dssp             CSSCCSS----CHHHHHHHHHHTTCSSCCHHHHHHHHHHH
T ss_pred             CCCCCCc----hHHHHHHHHHHHcCCCcCHHHHHHHHHHh
Confidence            3566664    58999999995 45569999999998643

>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=80.79  E-value=1.1  Score=36.57  Aligned_cols=37  Identities=19%  Similarity=0.239  Sum_probs=31.8

Q ss_pred             ccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          148 RKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       148 RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      |.+-.|+++|...||..|+.|.-++..+|++||.-=|
T Consensus       367 ~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~  403 (421)
T 1mh3_A          367 AAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCG  403 (421)
T ss_dssp             HHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHT
T ss_pred             hhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHC
Confidence            3344589999999999999999999999999997544

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	188
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	97.15
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	97.13
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	97.05
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	96.94
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	96.74
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	96.71
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	96.52
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	96.49
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	96.48
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	96.44
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	96.28
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	96.27
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	96.27
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	96.26
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	96.26
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	96.08
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	96.03
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	95.94
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	95.93
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	95.9
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	95.83
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	95.83
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	95.81
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	95.8
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	95.41
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	94.8
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	94.66
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	94.66
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	94.48
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	94.3
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	94.03
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	94.0

>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=97.15  E-value=0.00016  Score=48.97  Aligned_cols=40  Identities=28%  Similarity=0.162  Sum_probs=34.4

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhccccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDGF  185 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~~  185 (188)
                      .+++.-|+|++|..+||..|..+...+..+++.||..=|+
T Consensus         3 ~~s~~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL   42 (76)
T d2ecca1           3 SGSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGL   42 (76)
T ss_dssp             CSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHcc
Confidence            3445558899999999999999999999999999986553

>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=97.13  E-value=0.00017  Score=48.30  Aligned_cols=41  Identities=10%  Similarity=0.069  Sum_probs=35.6

Q ss_pred             cccccccccChHHHHHHHHhhhh-ccCCChhhhhhhhccccc
Q 029785          145 VNARKKLRLTKEQSALLEESFKQ-HSTLNPVIISLSLSIDGF  185 (188)
Q Consensus       145 ~~~RKKLRLsKeQsa~LEesFk~-H~tLnpkqK~~la~~~~~  185 (188)
                      .+.|++.|||++|..+||..|.+ +..++..++++||..=|+
T Consensus         6 ~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl   47 (71)
T d1wi3a_           6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDL   47 (71)
T ss_dssp             CCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCC
T ss_pred             CCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCC
Confidence            36788899999999999999975 668999999999986653

>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=97.05  E-value=0.00019  Score=45.96  Aligned_cols=34  Identities=21%  Similarity=0.268  Sum_probs=31.6

Q ss_pred             cccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          151 LRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       151 LRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      -+||++|.++||..|+.+..++..++.+||..=|
T Consensus         2 t~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lg   35 (53)
T d1le8a_           2 SSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCG   35 (53)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHC
Confidence            4799999999999999999999999999998655

>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=96.94  E-value=0.00029  Score=45.69  Aligned_cols=37  Identities=19%  Similarity=0.252  Sum_probs=33.6

Q ss_pred             ccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          148 RKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       148 RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      |+..|+|++|..+||..|.....++..++..||.-=|
T Consensus         2 ~~R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~   38 (57)
T d2e1oa1           2 GGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQ   38 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTT
T ss_pred             CCCccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhC
Confidence            4678999999999999999999999999999997544

>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=96.74  E-value=0.00053  Score=46.43  Aligned_cols=40  Identities=23%  Similarity=0.151  Sum_probs=35.1

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhccccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDGF  185 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~~  185 (188)
                      .++|+=|+|++|.++||..|..+..++.++++.||..=|+
T Consensus         4 ~p~k~k~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l   43 (76)
T d2ecba1           4 TPQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKL   43 (76)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCC
Confidence            3566668899999999999999999999999999987553

>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=96.71  E-value=0.00061  Score=44.61  Aligned_cols=38  Identities=13%  Similarity=0.113  Sum_probs=34.5

Q ss_pred             cccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          147 ARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       147 ~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      .|+.-++|++|..+||..|..+..++++++++||.-=|
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~   39 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATS   39 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTC
T ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcC
Confidence            56677899999999999999999999999999998655

>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=96.52  E-value=0.00071  Score=44.06  Aligned_cols=36  Identities=22%  Similarity=0.261  Sum_probs=31.2

Q ss_pred             cccccChHHHHHHHHhhhhccC---CChhhhhhhhcccc
Q 029785          149 KKLRLTKEQSALLEESFKQHST---LNPVIISLSLSIDG  184 (188)
Q Consensus       149 KKLRLsKeQsa~LEesFk~H~t---LnpkqK~~la~~~~  184 (188)
                      |+=|||++|..+||+.|.+|..   .+++++..||..=|
T Consensus         1 r~~Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~g   39 (60)
T d1k61a_           1 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTS   39 (60)
T ss_dssp             CCCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHC
T ss_pred             CCCCCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHC
Confidence            3457999999999999999874   99999999997655

>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=96.49  E-value=0.00087  Score=44.56  Aligned_cols=39  Identities=13%  Similarity=0.251  Sum_probs=35.2

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|.+.++|++|..+||..|..+...++.+++.||..=|
T Consensus         3 ~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~   41 (66)
T d1bw5a_           3 TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTG   41 (66)
T ss_dssp             CSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHT
T ss_pred             CCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcC
Confidence            357788899999999999999999999999999997644

>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=96.48  E-value=0.00084  Score=45.74  Aligned_cols=39  Identities=21%  Similarity=0.380  Sum_probs=34.3

Q ss_pred             ccccccccChHHHHHHHHhhhh-ccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQ-HSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~-H~tLnpkqK~~la~~~~  184 (188)
                      |.|++-+||++|-.+||..|.. |...+..++++||.-=|
T Consensus         1 g~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lg   40 (72)
T d1uhsa_           1 GSEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAG   40 (72)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhC
Confidence            4789999999999999999975 67899999999997544

>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=96.44  E-value=0.0011  Score=42.78  Aligned_cols=38  Identities=21%  Similarity=0.128  Sum_probs=33.8

Q ss_pred             ccccccChHHHHHHHHhhhhccCCChhhhhhhhccccc
Q 029785          148 RKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDGF  185 (188)
Q Consensus       148 RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~~  185 (188)
                      |+..++|.+|...||..|..+..+++.++++||..=|.
T Consensus         2 r~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l   39 (58)
T d1ig7a_           2 KPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSL   39 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTC
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCC
Confidence            45568999999999999999999999999999986553

>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=96.28  E-value=0.0015  Score=43.47  Aligned_cols=37  Identities=24%  Similarity=0.149  Sum_probs=33.5

Q ss_pred             ccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          148 RKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       148 RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      |+..++|.+|...||..|..+..+++.++.+||.-=|
T Consensus         3 r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~   39 (67)
T d1zq3p1           3 RTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLA   39 (67)
T ss_dssp             CCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHT
T ss_pred             CCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhC
Confidence            5667899999999999999999999999999997544

>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=96.27  E-value=0.0012  Score=46.33  Aligned_cols=39  Identities=15%  Similarity=0.035  Sum_probs=32.5

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|.+|..+||..|..+..+++.++++||..=|
T Consensus        27 ~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~   65 (88)
T d1b72a_          27 PSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLE   65 (88)
T ss_dssp             ---CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcC
Confidence            345566699999999999999999999999999997544

>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=96.27  E-value=0.0016  Score=40.65  Aligned_cols=34  Identities=21%  Similarity=0.122  Sum_probs=31.5

Q ss_pred             cccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          151 LRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       151 LRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      -++|++|..+||..|..+...+.+++++||..=|
T Consensus         3 t~ft~~Q~~~Le~~F~~n~~P~~~~~~~LA~~l~   36 (50)
T d1s7ea1           3 LVFTDVQRRTLHAIFKENKRPSKELQITISQQLG   36 (50)
T ss_dssp             SCCCHHHHHHHHHHTTSSCSSTHHHHHHHHTTSC
T ss_pred             CCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHC
Confidence            4789999999999999999999999999998755

>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=96.26  E-value=0.0013  Score=42.46  Aligned_cols=37  Identities=16%  Similarity=0.108  Sum_probs=33.3

Q ss_pred             ccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          148 RKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       148 RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      |+.-.+|++|-..||..|..+..++++++++||.-=|
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lg   37 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLN   37 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhC
Confidence            5666799999999999999999999999999997544

>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=96.26  E-value=0.0014  Score=41.73  Aligned_cols=37  Identities=24%  Similarity=0.191  Sum_probs=32.8

Q ss_pred             ccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          148 RKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       148 RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      |+.-++|++|...||..|..+..+++.++++||..=|
T Consensus         1 R~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~lg   37 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELG   37 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             CCCccCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhC
Confidence            3455799999999999999999999999999997654

>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=96.08  E-value=0.0019  Score=43.21  Aligned_cols=39  Identities=21%  Similarity=0.199  Sum_probs=33.1

Q ss_pred             cccccccChHHHHHHHHhhhhcc---CCChhhhhhhhccccc
Q 029785          147 ARKKLRLTKEQSALLEESFKQHS---TLNPVIISLSLSIDGF  185 (188)
Q Consensus       147 ~RKKLRLsKeQsa~LEesFk~H~---tLnpkqK~~la~~~~~  185 (188)
                      .|+.-+||++|-.+||+.|.+|.   -.+..+|..||..=|+
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl   43 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGI   43 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTS
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCc
Confidence            45667899999999999999865   5999999999986553

>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=96.03  E-value=0.0026  Score=42.38  Aligned_cols=38  Identities=18%  Similarity=0.152  Sum_probs=34.7

Q ss_pred             cccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          147 ARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       147 ~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      -|+..++|++|..+||..|....-++..++.+||..=|
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~   39 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKID   39 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhC
Confidence            56778899999999999999999999999999998655

>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=95.94  E-value=0.0023  Score=41.33  Aligned_cols=37  Identities=16%  Similarity=0.159  Sum_probs=33.7

Q ss_pred             ccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          148 RKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       148 RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ||.-++|++|..+||..|..+...++.+++.||..=|
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~   37 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELN   37 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhC
Confidence            5777899999999999999999999999999997644

>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=95.93  E-value=0.0026  Score=41.71  Aligned_cols=39  Identities=13%  Similarity=-0.004  Sum_probs=33.3

Q ss_pred             ccccccccChHHHHHHHHhhhhcc---CCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHS---TLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~---tLnpkqK~~la~~~~  184 (188)
                      +.||+-+|+++|..+||+.|.+|.   ..+..+|..||..=|
T Consensus         2 ~krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~   43 (62)
T d1x2na1           2 GKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTN   43 (62)
T ss_dssp             SCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHC
Confidence            356778999999999999999865   599999999997655

>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=95.90  E-value=0.0016  Score=41.59  Aligned_cols=31  Identities=16%  Similarity=0.082  Sum_probs=27.4

Q ss_pred             ChHHHHHHHHhhhhcc-CCChhhhhhhhcccc
Q 029785          154 TKEQSALLEESFKQHS-TLNPVIISLSLSIDG  184 (188)
Q Consensus       154 sKeQsa~LEesFk~H~-tLnpkqK~~la~~~~  184 (188)
                      |++|.++||..|..++ ..++.+++.||..=|
T Consensus         1 T~~q~~iLE~~F~~~~~~P~~~~~~~LA~~~~   32 (52)
T d1x2ma1           1 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLD   32 (52)
T ss_dssp             SSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHC
T ss_pred             ChhHHHHHHHHHHHcCCCcCHHHHHHHHHHHC
Confidence            6899999999999876 699999999998655

>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=95.83  E-value=0.0025  Score=41.22  Aligned_cols=37  Identities=16%  Similarity=0.155  Sum_probs=33.5

Q ss_pred             ccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          148 RKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       148 RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      |+.-++|++|..+||..|..+..+++.+++.||.-=|
T Consensus         3 r~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~   39 (60)
T d1yz8p1           3 RQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTN   39 (60)
T ss_dssp             CSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTT
T ss_pred             CCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHC
Confidence            5667899999999999999999999999999997655

>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=95.83  E-value=0.0034  Score=42.76  Aligned_cols=35  Identities=26%  Similarity=0.205  Sum_probs=31.5

Q ss_pred             cccChHHHHHHHHhhhhccCCChhhhhhhhccccc
Q 029785          151 LRLTKEQSALLEESFKQHSTLNPVIISLSLSIDGF  185 (188)
Q Consensus       151 LRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~~  185 (188)
                      .++|++|..+||..|.++..++..++.+||..=|+
T Consensus        14 t~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l   48 (77)
T d1vnda_          14 VLFTKAQTYELERRFRQQRYLSAPEREHLASLIRL   48 (77)
T ss_dssp             CCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTC
T ss_pred             CCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCC
Confidence            45999999999999999999999999999986553

>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=95.81  E-value=0.0028  Score=41.76  Aligned_cols=37  Identities=14%  Similarity=0.084  Sum_probs=32.9

Q ss_pred             ccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          148 RKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       148 RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      |+..++|++|..+||..|.....+++.++..||..=|
T Consensus         4 r~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lg   40 (65)
T d1fjla_           4 RSRTTFSASQLDELERAFERTQYPDIYTREELAQRTN   40 (65)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhC
Confidence            4455699999999999999999999999999998655

>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=95.80  E-value=0.0027  Score=43.43  Aligned_cols=38  Identities=21%  Similarity=0.082  Sum_probs=34.1

Q ss_pred             cccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          147 ARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       147 ~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      .|+.-++|.+|..+||..|.++..++..++++||..=|
T Consensus        14 rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~   51 (77)
T d1pufa_          14 RKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLN   51 (77)
T ss_dssp             SCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhC
Confidence            45567899999999999999999999999999998655

>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=95.41  E-value=0.0045  Score=41.23  Aligned_cols=39  Identities=18%  Similarity=0.107  Sum_probs=35.1

Q ss_pred             ccccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          146 NARKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       146 ~~RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ..|+.-++|++|..+||..|......++.++++||..=|
T Consensus         8 ~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~   46 (67)
T d1ocpa_           8 RKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLG   46 (67)
T ss_dssp             SSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHT
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHc
Confidence            357788999999999999999999999999999997544

>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=94.80  E-value=0.0087  Score=38.86  Aligned_cols=33  Identities=18%  Similarity=0.005  Sum_probs=30.5

Q ss_pred             ccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          152 RLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       152 RLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      ++|++|..+||..|.....++..++.+||..=|
T Consensus         3 ~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~   35 (56)
T d9anta_           3 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALS   35 (56)
T ss_dssp             CCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHT
T ss_pred             cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhC
Confidence            689999999999999999999999999997644

>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=94.66  E-value=0.012  Score=40.14  Aligned_cols=34  Identities=15%  Similarity=0.132  Sum_probs=32.3

Q ss_pred             ccccccChHHHHHHHHhhhhccCCChhhhhhhhc
Q 029785          148 RKKLRLTKEQSALLEESFKQHSTLNPVIISLSLS  181 (188)
Q Consensus       148 RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~  181 (188)
                      |+..++|++|-.+||..|.++...+..++.+||.
T Consensus         2 r~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~   35 (82)
T d2cufa1           2 GSRFTWRKECLAVMESYFNENQYPDEAKREEIAN   35 (82)
T ss_dssp             CCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence            6788999999999999999999999999999986

>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=94.66  E-value=0.0059  Score=39.73  Aligned_cols=38  Identities=11%  Similarity=-0.075  Sum_probs=32.7

Q ss_pred             cccccccChHHHHHHHHhhhhcc-CCChhhhhhhhcccc
Q 029785          147 ARKKLRLTKEQSALLEESFKQHS-TLNPVIISLSLSIDG  184 (188)
Q Consensus       147 ~RKKLRLsKeQsa~LEesFk~H~-tLnpkqK~~la~~~~  184 (188)
                      -|.+.+.+.+|.++||+.|..++ ..+..++++||..=|
T Consensus         2 ~k~~~~~k~~~~~iLE~~F~~~~~yPs~~~~~~LA~~lg   40 (59)
T d2cqxa1           2 IKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLD   40 (59)
T ss_dssp             CCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTT
T ss_pred             CCCCCCCCccccHHHHHHHHHcCCCcCHHHHHHHHHHHC
Confidence            46778899999999999998765 699999999997655

>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=94.48  E-value=0.012  Score=39.08  Aligned_cols=37  Identities=22%  Similarity=0.203  Sum_probs=32.8

Q ss_pred             ccccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          148 RKKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       148 RKKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      |+.-++|.+|...||..|.....++..++.+||..=|
T Consensus         4 r~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~   40 (68)
T d1ftta_           4 KRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIH   40 (68)
T ss_dssp             SSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhC
Confidence            4455699999999999999999999999999998654

>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=94.30  E-value=0.014  Score=37.45  Aligned_cols=36  Identities=19%  Similarity=0.176  Sum_probs=32.1

Q ss_pred             cccccChHHHHHHHHhhhhccCCChhhhhhhhcccc
Q 029785          149 KKLRLTKEQSALLEESFKQHSTLNPVIISLSLSIDG  184 (188)
Q Consensus       149 KKLRLsKeQsa~LEesFk~H~tLnpkqK~~la~~~~  184 (188)
                      |.-+|+++|...||..|..+...++.+++.||..=|
T Consensus         1 kRT~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lg   36 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLN   36 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHT
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHC
Confidence            345799999999999999999999999999997544

>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=94.03  E-value=0.018  Score=39.43  Aligned_cols=32  Identities=3%  Similarity=0.053  Sum_probs=29.8

Q ss_pred             cccChHHHHHHHHhhhhccCCChhhhhhhhcc
Q 029785          151 LRLTKEQSALLEESFKQHSTLNPVIISLSLSI  182 (188)
Q Consensus       151 LRLsKeQsa~LEesFk~H~tLnpkqK~~la~~  182 (188)
                      .|+|++|..+||..|......+..++++||+-
T Consensus         2 ~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~   33 (78)
T d1lfba_           2 FKWGPASQQILFQAYERQKNPSKEERETLVEE   33 (78)
T ss_dssp             CCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence            47999999999999999999999999999863

>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=94.00  E-value=0.035  Score=37.56  Aligned_cols=39  Identities=15%  Similarity=0.121  Sum_probs=31.1

Q ss_pred             cccccccChHHHHHHHHhhhh----ccCCChhhhhhhhccccc
Q 029785          147 ARKKLRLTKEQSALLEESFKQ----HSTLNPVIISLSLSIDGF  185 (188)
Q Consensus       147 ~RKKLRLsKeQsa~LEesFk~----H~tLnpkqK~~la~~~~~  185 (188)
                      .|+.-++|.+|...||..|..    +...+..++++||+.=|+
T Consensus        18 kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl   60 (80)
T d1wh7a_          18 KRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGV   60 (80)
T ss_dssp             SCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCC
T ss_pred             CCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCC
Confidence            345566999999999877765    778899999999986553