Psyllid ID: psy8536

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180------
Protein Sequence
KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVVIKDPSKDLFLSNKVMYTYLVFQVKIWFQNRRAKERKQLKKREEVVIKDPSKDLFLSNKVMIRKISVSPPFSFRSSETTATSYILDIDTRKTRTKDKYRVVYSDQQRLELEKEFHY
Secondary Structure (PSIPRED)
cccccccccEEEccHHHHHHHHHcccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHcHHHHHHHHcHHHHHHHHHccccHHccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHcHHHHcccccccccccccccccccccccccHHHHHHHHHHHHHHccHHHHccccccccccccccccccccccccccccccccccccccEEEcccccccccEcccccEEEEccHHHHHHHHHccc
Coil and Loop (DISEMBL)
ktrtkdkyrVVYSDQQRLELEKEFHYSRYITIRRKAELAnslglserQVKIWFQNRRAKERKQLKKREEvvikdpskdlflsnkVMYTYLVFQVKIWFQNRRAKERKQLKKREEvvikdpskdlflsNKVMIRKisvsppfsfrssettatsyildidtrktrtkdkyrVVYSDQQRLELEKEFHY
Flexible Loop (DISEMBL)
ktrtkdkyrvvysdqqrlelekefhysryiTIRRKAELanslglserqvkiwfqnrrakerkqlkkreevvikdpskdlflsnKVMYTYLVFQVKIWFQNRRAKErkqlkkreevvikdpskdlflsnkVMIRKIsvsppfsfrssettatsyildidtrktrtkdkyrvvysdqqrlelekefhy
Low Complexity Region (SEG)
KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVVIKDPSKDLFLSNKVMYTYLVFQVKIWFQNRRAKERKQLKKREEVVIKDPSKDLFLSNKVMIRKISVSPPFSFRSSETTATSYILDIDTRKTRTKDKYRVVYSDQQRLELEKEFHY
Disordered region (IsUnstruct)
********RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQN**************VVIKDPSKDLFLSNKVMYTYLVFQVKIWFQNR***************I*****DLFLSNKVMIRKISVSPPFSF*****TATSYILDIDTRKTRTKDKYRVVY**************
Disordered Region (DISOPRED)
***********YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRA****************************************************************************************************************VYSDQQRLELEK**H*
Disordered Region (DISEMBL)
KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVVIKDPSKDLFLSNKVMYTYLVFQVKIWFQNRRAKERKQLKKREEVVIKDPSKDLFLSNKVMIRKISVSPPFSFRSSETTATSYILDIDTRKTRTKDKYRVVYSDQQRLELEKEFHY
Disordered Region (DISPRO)
**********VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK***********************YLVFQVKIWFQNRRAKERKQLKKREEVVIKDPSKDLFLSNKV****ISVSPPFSFRSSETTATSYILDIDTRKTRTKDKYRVVYSDQQRLELEKEFHY
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVVIKDPSKDLFLSNKVMYTYLVFQVKIWFQNRRAKERKQLKKREEVVIKDPSKDLFLSNKVMIRKISVSPPFSFRSSETTATSYILDIDTRKTRTKDKYRVVYSDQQRLELEKEFHY
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	186	2.2.26 [Sep-21-2011]
Q04649	313	Homeobox protein CDX-2 OS	N/A	N/A	0.360	0.214	0.895	1e-28
P46692	248	Homeobox protein CHOX-CAD	no	N/A	0.360	0.270	0.880	2e-28
Q9DEB6	260	Homeobox protein CDX-1 OS	no	N/A	0.360	0.257	0.880	2e-28
Q99626	313	Homeobox protein CDX-2 OS	yes	N/A	0.360	0.214	0.895	3e-28
Q90X89	262	Homeobox protein CDX-1 OS	no	N/A	0.360	0.255	0.880	2e-27
P18111	268	Homeobox protein CDX-1 OS	yes	N/A	0.360	0.25	0.865	2e-27
P47902	265	Homeobox protein CDX-1 OS	no	N/A	0.333	0.233	0.903	2e-27
A2T7H5	265	Homeobox protein CDX-1 OS	N/A	N/A	0.333	0.233	0.903	3e-27
P43241	311	Homeobox protein CDX-2 OS	no	N/A	0.354	0.212	0.878	4e-27
Q05095	123	Homeobox protein CDX-1 (F	no	N/A	0.333	0.504	0.903	5e-27

>sp|Q04649|CDX2_MESAU Homeobox protein CDX-2 OS=Mesocricetus auratus GN=CDX2 PE=2 SV=1

 Score =  126 bits (316), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 60/67 (89%), Positives = 63/67 (94%)

Query: 1   KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
           KTRTKDKYRVVY+D QRLELEKEFHYSRYITIRRKAELA +LGLSERQVKIWFQNRRAKE
Sbjct: 181 KTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELAATLGLSERQVKIWFQNRRAKE 240

Query: 61  RKQLKKR 67
           RK  KK+
Sbjct: 241 RKINKKK 247

Involved in the transcriptional regulation of multiple genes expressed in the intestinal epithelium. Important in broad range of functions from early differentiation to maintenance of the intestinal epithelial lining of both the small and large intestine.
Mesocricetus auratus (taxid: 10036)

>sp|P46692|HMD1_CHICK Homeobox protein CHOX-CAD OS=Gallus gallus GN=CHOX-CAD1 PE=2 SV=1

 Score =  125 bits (313), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 59/67 (88%), Positives = 63/67 (94%)

Query: 1   KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
           KTRTKDKYRVVY+D QRLELEKEFHYSRYITIRRKAELA +LGL+ERQVKIWFQNRRAKE
Sbjct: 133 KTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELAAALGLTERQVKIWFQNRRAKE 192

Query: 61  RKQLKKR 67
           RK  KK+
Sbjct: 193 RKVNKKK 199

May play an important role during the early steps of organogenesis.

Gallus gallus (taxid: 9031)

>sp|Q9DEB6|CDX1_CHICK Homeobox protein CDX-1 OS=Gallus gallus GN=CDX1 PE=2 SV=2

 Score =  125 bits (313), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 59/67 (88%), Positives = 63/67 (94%)

Query: 1   KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
           KTRTKDKYRVVY+D QRLELEKEFHYSRYITIRRKAELA +LGL+ERQVKIWFQNRRAKE
Sbjct: 145 KTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELAAALGLTERQVKIWFQNRRAKE 204

Query: 61  RKQLKKR 67
           RK  KK+
Sbjct: 205 RKVNKKK 211

Gallus gallus (taxid: 9031)

>sp|Q99626|CDX2_HUMAN Homeobox protein CDX-2 OS=Homo sapiens GN=CDX2 PE=1 SV=3

 Score =  124 bits (312), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 60/67 (89%), Positives = 63/67 (94%)

Query: 1   KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
           KTRTKDKYRVVY+D QRLELEKEFHYSRYITIRRKAELA +LGLSERQVKIWFQNRRAKE
Sbjct: 182 KTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELAATLGLSERQVKIWFQNRRAKE 241

Query: 61  RKQLKKR 67
           RK  KK+
Sbjct: 242 RKINKKK 248

Involved in the transcriptional regulation of multiple genes expressed in the intestinal epithelium. Important in broad range of functions from early differentiation to maintenance of the intestinal epithelial lining of both the small and large intestine.

Homo sapiens (taxid: 9606)

>sp|Q90X89|CDX1_XENTR Homeobox protein CDX-1 OS=Xenopus tropicalis GN=cdx1 PE=2 SV=1

 Score =  122 bits (305), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 59/67 (88%), Positives = 62/67 (92%)

Query: 1   KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
           KTRTKDKYRVVY+D QRLELEKEFHYSRYITIRRKAELA SL L+ERQVKIWFQNRRAKE
Sbjct: 145 KTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELAASLALTERQVKIWFQNRRAKE 204

Query: 61  RKQLKKR 67
           RK  KK+
Sbjct: 205 RKVNKKK 211

Xenopus tropicalis (taxid: 8364)

>sp|P18111|CDX1_MOUSE Homeobox protein CDX-1 OS=Mus musculus GN=Cdx1 PE=2 SV=2

 Score =  122 bits (305), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 58/67 (86%), Positives = 63/67 (94%)

Query: 1   KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
           KTRTKDKYRVVY+D QRLELEKEFHYSRYITIRRK+ELA +LGL+ERQVKIWFQNRRAKE
Sbjct: 150 KTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKSELAANLGLTERQVKIWFQNRRAKE 209

Query: 61  RKQLKKR 67
           RK  KK+
Sbjct: 210 RKVNKKK 216

Could play a role in the terminal differentiation of the intestine.

Mus musculus (taxid: 10090)

>sp|P47902|CDX1_HUMAN Homeobox protein CDX-1 OS=Homo sapiens GN=CDX1 PE=2 SV=2

 Score =  122 bits (305), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 56/62 (90%), Positives = 60/62 (96%)

Query: 1   KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
           KTRTKDKYRVVY+D QRLELEKEFHYSRYITIRRK+ELA +LGL+ERQVKIWFQNRRAKE
Sbjct: 150 KTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKSELAANLGLTERQVKIWFQNRRAKE 209

Query: 61  RK 62
           RK
Sbjct: 210 RK 211

Could play a role in the terminal differentiation of the intestine.

Homo sapiens (taxid: 9606)

>sp|A2T7H5|CDX1_PONPY Homeobox protein CDX-1 OS=Pongo pygmaeus GN=CDX1 PE=3 SV=1

 Score =  121 bits (303), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 56/62 (90%), Positives = 60/62 (96%)

Query: 1   KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
           KTRTKDKYRVVY+D QRLELEKEFHYSRYITIRRK+ELA +LGL+ERQVKIWFQNRRAKE
Sbjct: 150 KTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKSELAANLGLTERQVKIWFQNRRAKE 209

Query: 61  RK 62
           RK
Sbjct: 210 RK 211

Could play a role in the terminal differentiation of the intestine.

Pongo pygmaeus (taxid: 9600)

>sp|P43241|CDX2_MOUSE Homeobox protein CDX-2 OS=Mus musculus GN=Cdx2 PE=1 SV=1

 Score =  120 bits (302), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 58/66 (87%), Positives = 62/66 (93%)

Query: 1   KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
           KTRTKDKYRVVY+D QRLELEKEFH+SRYITIRRK+ELA +LGLSERQVKIWFQNRRAKE
Sbjct: 181 KTRTKDKYRVVYTDHQRLELEKEFHFSRYITIRRKSELAATLGLSERQVKIWFQNRRAKE 240

Query: 61  RKQLKK 66
           RK  KK
Sbjct: 241 RKIKKK 246

Involved in the transcriptional regulation of multiple genes expressed in the intestinal epithelium. Important in broad range of functions from early differentiation to maintenance of the intestinal epithelial lining of both the small and large intestine.

Mus musculus (taxid: 10090)

>sp|Q05095|CDX1_RAT Homeobox protein CDX-1 (Fragment) OS=Rattus norvegicus GN=Cdx1 PE=2 SV=1

 Score =  120 bits (301), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 56/62 (90%), Positives = 60/62 (96%)

Query: 1  KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
          KTRTKDKYRVVY+D QRLELEKEFHYSRYITIRRK+ELA +LGL+ERQVKIWFQNRRAKE
Sbjct: 1  KTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKSELAANLGLTERQVKIWFQNRRAKE 60

Query: 61 RK 62
          RK
Sbjct: 61 RK 62

Could play a role in the terminal differentiation of the intestine.

Rattus norvegicus (taxid: 10116)

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	186
112984380	244	caudal-like [Bombyx mori] gi|521229|dbj|	0.397	0.303	0.932	5e-32
321475788	564	putative para-hox caudal protein [Daphni	0.397	0.131	0.864	2e-31
452836056	290	caudal protein [Periplaneta americana]	0.397	0.255	0.891	5e-31
86515350	249	caudal [Tribolium castaneum] gi|3929892|	0.424	0.317	0.848	5e-31
270006390	112	caudal-2 [Tribolium castaneum]	0.424	0.705	0.848	2e-30
52693900	116	caudal [Gryllus bimaculatus]	0.392	0.629	0.905	4e-30
340721613	605	PREDICTED: hypothetical protein LOC10065	0.376	0.115	0.864	1e-29
405973631	329	Homeobox protein CDX-1 [Crassostrea giga	0.387	0.218	0.853	1e-29
38488502	315	homeodomain transcription factor [Artemi	0.370	0.219	0.837	2e-29
383855394	345	PREDICTED: uncharacterized protein LOC10	0.403	0.217	0.853	4e-29

>gi|112984380|ref|NP_001037514.1| caudal-like [Bombyx mori] gi|521229|dbj|BAA04086.1| cad protein [Bombyx mori]

 Score =  142 bits (359), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 69/74 (93%), Positives = 72/74 (97%)

Query: 1   KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
           KTRTKDKYRVVYSD QRLELEKEFHYSRYITIRRKAELA SLGLSERQVKIWFQNRRAKE
Sbjct: 116 KTRTKDKYRVVYSDHQRLELEKEFHYSRYITIRRKAELAVSLGLSERQVKIWFQNRRAKE 175

Query: 61  RKQLKKREEVVIKD 74
           RKQ+KKREEVV+K+
Sbjct: 176 RKQVKKREEVVMKE 189

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321475788|gb|EFX86750.1| putative para-hox caudal protein [Daphnia pulex]

 Score =  140 bits (353), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 64/74 (86%), Positives = 71/74 (95%)

Query: 1   KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
           KTRTKDKYRVVY+D QRLELEKEFHYSRYITIRRK+ELA+ LGLSERQVKIWFQNRRAKE
Sbjct: 422 KTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKSELASVLGLSERQVKIWFQNRRAKE 481

Query: 61  RKQLKKREEVVIKD 74
           RKQ+KKREE++ K+
Sbjct: 482 RKQVKKREEMLHKE 495

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|452836056|gb|AGG14204.1| caudal protein [Periplaneta americana]

 Score =  139 bits (350), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 66/74 (89%), Positives = 70/74 (94%)

Query: 1   KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
           KTRTKDKYRVVYSD QRLELEKEFHYSRYITIRRKAELA +LGLSERQVKIWFQNRRAKE
Sbjct: 189 KTRTKDKYRVVYSDHQRLELEKEFHYSRYITIRRKAELAANLGLSERQVKIWFQNRRAKE 248

Query: 61  RKQLKKREEVVIKD 74
           RKQ+KKREE++ K 
Sbjct: 249 RKQVKKREELLHKG 262

Source: Periplaneta americana

Species: Periplaneta americana

Genus: Periplaneta

Family: Blattidae

Order: Blattodea

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|86515350|ref|NP_001034498.1| caudal [Tribolium castaneum] gi|3929892|emb|CAA06527.1| caudal protein [Tribolium castaneum]

 Score =  139 bits (350), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 67/79 (84%), Positives = 73/79 (92%)

Query: 1   KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
           KTRTKDKYRVVY+D QR+ELEKEF+YSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE
Sbjct: 152 KTRTKDKYRVVYTDHQRVELEKEFYYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 211

Query: 61  RKQLKKREEVVIKDPSKDL 79
           RKQ+KKREEV  KD   ++
Sbjct: 212 RKQVKKREEVTQKDSPMNM 230

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270006390|gb|EFA02838.1| caudal-2 [Tribolium castaneum]

 Score =  137 bits (344), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 67/79 (84%), Positives = 73/79 (92%)

Query: 1  KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
          KTRTKDKYRVVY+D QR+ELEKEF+YSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE
Sbjct: 8  KTRTKDKYRVVYTDHQRVELEKEFYYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 67

Query: 61 RKQLKKREEVVIKDPSKDL 79
          RKQ+KKREEV  KD   ++
Sbjct: 68 RKQVKKREEVTQKDSPMNM 86

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|52693900|dbj|BAD51739.1| caudal [Gryllus bimaculatus]

 Score =  136 bits (343), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 67/74 (90%), Positives = 71/74 (95%)

Query: 1  KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
          KTRTKDKYRVVYSD QRLELEKEFHYSRYITIRRKAELA SLGLSERQVKIWFQNRRAKE
Sbjct: 19 KTRTKDKYRVVYSDHQRLELEKEFHYSRYITIRRKAELAASLGLSERQVKIWFQNRRAKE 78

Query: 61 RKQLKKREEVVIKD 74
          RKQ+KKREE++ K+
Sbjct: 79 RKQVKKREELLHKE 92

Source: Gryllus bimaculatus

Species: Gryllus bimaculatus

Genus: Gryllus

Family: Gryllidae

Order: Orthoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340721613|ref|XP_003399212.1| PREDICTED: hypothetical protein LOC100651931 [Bombus terrestris]

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 64/74 (86%), Positives = 69/74 (93%)

Query: 1   KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
           KTRTKDKYRVVY+D QRLELEKEFHYSRYITIRRKAELA +L LSERQVKIWFQNRRAKE
Sbjct: 487 KTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELAANLALSERQVKIWFQNRRAKE 546

Query: 61  RKQLKKREEVVIKD 74
           RKQ+KKREE+  K+
Sbjct: 547 RKQVKKREELEQKE 560

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|405973631|gb|EKC38333.1| Homeobox protein CDX-1 [Crassostrea gigas]

 Score =  134 bits (338), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 64/75 (85%), Positives = 68/75 (90%)

Query: 1   KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
           KTRTKDKYRVVYSD QRLELEKEFHYSRYITIRRKAELA +L LSERQVKIWFQNRRAKE
Sbjct: 171 KTRTKDKYRVVYSDHQRLELEKEFHYSRYITIRRKAELAQNLALSERQVKIWFQNRRAKE 230

Query: 61  RKQLKKREEVVIKDP 75
           RKQ KKR+E+   +P
Sbjct: 231 RKQNKKRDEISPSNP 245

Source: Crassostrea gigas

Species: Crassostrea gigas

Genus: Crassostrea

Family: Ostreidae

Order: Ostreoida

Class: Bivalvia

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|38488502|emb|CAD98862.1| homeodomain transcription factor [Artemia franciscana]

 Score =  134 bits (336), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 62/74 (83%), Positives = 70/74 (94%)

Query: 1   KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
           KTRTKDKYRVVY+D QRLELEKEFHY++YITIRRK+ELA  LGLSERQVKIWFQNRRAK+
Sbjct: 204 KTRTKDKYRVVYTDHQRLELEKEFHYNKYITIRRKSELATVLGLSERQVKIWFQNRRAKD 263

Query: 61  RKQLKKREEVVIKD 74
           RKQ+KKREEV +K+
Sbjct: 264 RKQMKKREEVTVKE 277

Source: Artemia franciscana

Species: Artemia franciscana

Genus: Artemia

Family: Artemiidae

Order: Anostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383855394|ref|XP_003703198.1| PREDICTED: uncharacterized protein LOC100879814 [Megachile rotundata]

 Score =  133 bits (334), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 64/75 (85%), Positives = 68/75 (90%)

Query: 1   KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
           KTRTKDKYRVVY+D QRLELEKEFH+SRYITIRRKAELA +L LSERQVKIWFQNRRAKE
Sbjct: 201 KTRTKDKYRVVYTDHQRLELEKEFHFSRYITIRRKAELAANLALSERQVKIWFQNRRAKE 260

Query: 61  RKQLKKREEVVIKDP 75
           RKQ KKREE+  K P
Sbjct: 261 RKQGKKREELDQKSP 275

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	186
UNIPROTKB|F1P2M4	274	CDX2 "Uncharacterized protein"	0.360	0.244	0.910	1.3e-27
ZFIN|ZDB-GENE-050510-1	228	cdx1a "caudal type homeo box t	0.408	0.333	0.815	4.5e-27
UNIPROTKB|F1MJX0	142	CDX2 "Uncharacterized protein"	0.360	0.471	0.895	5.7e-27
UNIPROTKB|E2RI97	314	CDX2 "Uncharacterized protein"	0.360	0.213	0.895	5.7e-27
UNIPROTKB|H0YJ33	156	CDX2 "Homeobox protein CDX-2"	0.360	0.429	0.895	5.7e-27
UNIPROTKB|Q99626	313	CDX2 "Homeobox protein CDX-2"	0.360	0.214	0.895	5.7e-27
UNIPROTKB|F1RSU9	311	CDX2 "Uncharacterized protein"	0.360	0.215	0.895	5.7e-27
UNIPROTKB|F1M7G8	239	Cdx2 "Protein Cdx2" [Rattus no	0.360	0.280	0.895	5.7e-27
RGD|621233	123	Cdx1 "caudal type homeo box 1"	0.370	0.560	0.840	7.3e-27
UNIPROTKB|Q05095	123	Cdx1 "Homeobox protein CDX-1"	0.370	0.560	0.840	7.3e-27

UNIPROTKB|F1P2M4 CDX2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 309 (113.8 bits), Expect = 1.3e-27, P = 1.3e-27
 Identities = 61/67 (91%), Positives = 64/67 (95%)

Query:     1 KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
             KTRTKDKYRVVY+D QRLELEKEFHYSRYITIRRKAELA+SLGLSERQVKIWFQNRRAKE
Sbjct:   174 KTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELASSLGLSERQVKIWFQNRRAKE 233

Query:    61 RKQLKKR 67
             RK  KK+
Sbjct:   234 RKINKKK 240

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

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

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

GO:0000794 "condensed nuclear chromosome" evidence=IEA

GO:0001568 "blood vessel development" evidence=IEA

GO:0001829 "trophectodermal cell differentiation" evidence=IEA

GO:0003714 "transcription corepressor activity" evidence=IEA

GO:0008333 "endosome to lysosome transport" evidence=IEA

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

GO:0017053 "transcriptional repressor complex" evidence=IEA

GO:0035019 "somatic stem cell maintenance" evidence=IEA

GO:0045197 "establishment or maintenance of epithelial cell apical/basal polarity" evidence=IEA

GO:0045597 "positive regulation of cell differentiation" evidence=IEA

GO:0060711 "labyrinthine layer development" evidence=IEA

ZFIN|ZDB-GENE-050510-1 cdx1a "caudal type homeo box transcription factor 1 a" [Danio rerio (taxid:7955)]

 Score = 304 (112.1 bits), Expect = 4.5e-27, P = 4.5e-27
 Identities = 62/76 (81%), Positives = 66/76 (86%)

Query:     1 KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
             KTRTKDKYRVVYSD QRLELEKEFH+SRYITIRRKAELA +L LSERQVKIWFQNRRAKE
Sbjct:   125 KTRTKDKYRVVYSDVQRLELEKEFHFSRYITIRRKAELAGTLNLSERQVKIWFQNRRAKE 184

Query:    61 RKQLKKREEVVIKDPS 76
             RK  KKR + V +  S
Sbjct:   185 RKMNKKRLQQVQQSSS 200

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

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

GO:0001756 "somitogenesis" evidence=IGI

GO:0048384 "retinoic acid receptor signaling pathway" evidence=IGI

GO:0048793 "pronephros development" evidence=IGI

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

GO:0031016 "pancreas development" evidence=IGI

GO:0021906 "hindbrain-spinal cord boundary formation" evidence=IMP

GO:0021903 "rostrocaudal neural tube patterning" evidence=IGI

GO:0009948 "anterior/posterior axis specification" evidence=IGI

GO:0030097 "hemopoiesis" evidence=IGI

UNIPROTKB|F1MJX0 CDX2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 60/67 (89%), Positives = 63/67 (94%)

Query:     1 KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
             KTRTKDKYRVVY+D QRLELEKEFHYSRYITIRRKAELA +LGLSERQVKIWFQNRRAKE
Sbjct:    18 KTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELAATLGLSERQVKIWFQNRRAKE 77

Query:    61 RKQLKKR 67
             RK  KK+
Sbjct:    78 RKINKKK 84

GO:0060711 "labyrinthine layer development" evidence=IEA

GO:0045597 "positive regulation of cell differentiation" evidence=IEA

GO:0045197 "establishment or maintenance of epithelial cell apical/basal polarity" evidence=IEA

GO:0035019 "somatic stem cell maintenance" evidence=IEA

GO:0017053 "transcriptional repressor complex" evidence=IEA

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

GO:0008333 "endosome to lysosome transport" evidence=IEA

GO:0003714 "transcription corepressor activity" evidence=IEA

GO:0001829 "trophectodermal cell differentiation" evidence=IEA

GO:0001568 "blood vessel development" evidence=IEA

GO:0000794 "condensed nuclear chromosome" evidence=IEA

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

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

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

UNIPROTKB|E2RI97 CDX2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 60/67 (89%), Positives = 63/67 (94%)

Query:     1 KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
             KTRTKDKYRVVY+D QRLELEKEFHYSRYITIRRKAELA +LGLSERQVKIWFQNRRAKE
Sbjct:   182 KTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELAATLGLSERQVKIWFQNRRAKE 241

Query:    61 RKQLKKR 67
             RK  KK+
Sbjct:   242 RKINKKK 248

GO:0060711 "labyrinthine layer development" evidence=IEA

GO:0045597 "positive regulation of cell differentiation" evidence=IEA

GO:0045197 "establishment or maintenance of epithelial cell apical/basal polarity" evidence=IEA

GO:0035019 "somatic stem cell maintenance" evidence=IEA

GO:0017053 "transcriptional repressor complex" evidence=IEA

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

GO:0008333 "endosome to lysosome transport" evidence=IEA

GO:0003714 "transcription corepressor activity" evidence=IEA

GO:0001829 "trophectodermal cell differentiation" evidence=IEA

GO:0001568 "blood vessel development" evidence=IEA

GO:0000794 "condensed nuclear chromosome" evidence=IEA

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

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

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

UNIPROTKB|H0YJ33 CDX2 "Homeobox protein CDX-2" [Homo sapiens (taxid:9606)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 60/67 (89%), Positives = 63/67 (94%)

Query:     1 KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
             KTRTKDKYRVVY+D QRLELEKEFHYSRYITIRRKAELA +LGLSERQVKIWFQNRRAKE
Sbjct:    25 KTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELAATLGLSERQVKIWFQNRRAKE 84

Query:    61 RKQLKKR 67
             RK  KK+
Sbjct:    85 RKINKKK 91

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

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

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|Q99626 CDX2 "Homeobox protein CDX-2" [Homo sapiens (taxid:9606)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 60/67 (89%), Positives = 63/67 (94%)

Query:     1 KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
             KTRTKDKYRVVY+D QRLELEKEFHYSRYITIRRKAELA +LGLSERQVKIWFQNRRAKE
Sbjct:   182 KTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELAATLGLSERQVKIWFQNRRAKE 241

Query:    61 RKQLKKR 67
             RK  KK+
Sbjct:   242 RKINKKK 248

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

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

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

GO:0000794 "condensed nuclear chromosome" evidence=IEA

GO:0001568 "blood vessel development" evidence=IEA

GO:0001829 "trophectodermal cell differentiation" evidence=IEA

GO:0003714 "transcription corepressor activity" evidence=IEA

GO:0008333 "endosome to lysosome transport" evidence=IEA

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

GO:0017053 "transcriptional repressor complex" evidence=IEA

GO:0035019 "somatic stem cell maintenance" evidence=IEA

GO:0045197 "establishment or maintenance of epithelial cell apical/basal polarity" evidence=IEA

GO:0045597 "positive regulation of cell differentiation" evidence=IEA

GO:0060711 "labyrinthine layer development" evidence=IEA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0009887 "organ morphogenesis" evidence=TAS

UNIPROTKB|F1RSU9 CDX2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 60/67 (89%), Positives = 63/67 (94%)

Query:     1 KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
             KTRTKDKYRVVY+D QRLELEKEFHYSRYITIRRKAELA +LGLSERQVKIWFQNRRAKE
Sbjct:   182 KTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELAATLGLSERQVKIWFQNRRAKE 241

Query:    61 RKQLKKR 67
             RK  KK+
Sbjct:   242 RKINKKK 248

GO:0060711 "labyrinthine layer development" evidence=IEA

GO:0045597 "positive regulation of cell differentiation" evidence=IEA

GO:0045197 "establishment or maintenance of epithelial cell apical/basal polarity" evidence=IEA

GO:0035019 "somatic stem cell maintenance" evidence=IEA

GO:0017053 "transcriptional repressor complex" evidence=IEA

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

GO:0008333 "endosome to lysosome transport" evidence=IEA

GO:0003714 "transcription corepressor activity" evidence=IEA

GO:0001829 "trophectodermal cell differentiation" evidence=IEA

GO:0001568 "blood vessel development" evidence=IEA

GO:0000794 "condensed nuclear chromosome" evidence=IEA

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

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

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

UNIPROTKB|F1M7G8 Cdx2 "Protein Cdx2" [Rattus norvegicus (taxid:10116)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 60/67 (89%), Positives = 63/67 (94%)

Query:     1 KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
             KTRTKDKYRVVY+D QRLELEKEFHYSRYITIRRKAELA +LGLSERQVKIWFQNRRAKE
Sbjct:   110 KTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELAATLGLSERQVKIWFQNRRAKE 169

Query:    61 RKQLKKR 67
             RK  KK+
Sbjct:   170 RKINKKK 176

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

RGD|621233 Cdx1 "caudal type homeo box 1" [Rattus norvegicus (taxid:10116)]

 Score = 302 (111.4 bits), Expect = 7.3e-27, P = 7.3e-27
 Identities = 58/69 (84%), Positives = 65/69 (94%)

Query:     1 KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
             KTRTKDKYRVVY+D QRLELEKEFHYSRYITIRRK+ELA +LGL+ERQVKIWFQNRRAKE
Sbjct:     1 KTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKSELAANLGLTERQVKIWFQNRRAKE 60

Query:    61 RKQLKKREE 69
             RK  KK+++
Sbjct:    61 RKVNKKKQQ 69

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007389 "pattern specification process" evidence=ISO

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

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

GO:0060349 "bone morphogenesis" evidence=IEA;ISO

UNIPROTKB|Q05095 Cdx1 "Homeobox protein CDX-1" [Rattus norvegicus (taxid:10116)]

 Score = 302 (111.4 bits), Expect = 7.3e-27, P = 7.3e-27
 Identities = 58/69 (84%), Positives = 65/69 (94%)

Query:     1 KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
             KTRTKDKYRVVY+D QRLELEKEFHYSRYITIRRK+ELA +LGL+ERQVKIWFQNRRAKE
Sbjct:     1 KTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKSELAANLGLTERQVKIWFQNRRAKE 60

Query:    61 RKQLKKREE 69
             RK  KK+++
Sbjct:    61 RKVNKKKQQ 69

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

GO:0005634 "nucleus" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q05095	CDX1_RAT	No assigned EC number	0.9032	0.3333	0.5040	no	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	186
pfam00046	57	pfam00046, Homeobox, Homeobox domain	1e-19
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	2e-16
smart00389	57	smart00389, HOX, Homeodomain	3e-16
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	2e-07

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

 Score = 77.5 bits (192), Expect = 1e-19
 Identities = 29/56 (51%), Positives = 40/56 (71%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          + R  ++ +Q  ELEKEF  +RY +   + ELA  LGL+ERQVK+WFQNRRAK ++
Sbjct: 2  RKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57

Length = 57

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

 Score = 69.6 bits (171), Expect = 2e-16
 Identities = 29/57 (50%), Positives = 39/57 (68%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
          + R  ++ +Q  ELEKEF  + Y +   + ELA  LGL+ERQVKIWFQNRRAK ++ 
Sbjct: 2  RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58

Length = 59

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 68.8 bits (169), Expect = 3e-16
 Identities = 29/55 (52%), Positives = 38/55 (69%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKER 61
          + R  ++ +Q  ELEKEF  + Y +   + ELA  LGLSERQVK+WFQNRRAK +
Sbjct: 3  RKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

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

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

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 24/71 (33%), Positives = 41/71 (57%)

Query: 9   RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKRE 68
           R   +D+Q + LE+EF  + Y +   + +L+  L +  + V+IWFQN+RAKE+K+   + 
Sbjct: 55  RRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKV 114

Query: 69  EVVIKDPSKDL 79
           E    +   DL
Sbjct: 115 EQRPGEEEADL 125

Length = 156

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	186
KOG0484|consensus	125		99.86
KOG0850|consensus	245		99.8
KOG2251|consensus	228		99.79
KOG0488|consensus	309		99.79
KOG0494|consensus	332		99.78
KOG0843|consensus	197		99.77
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.77
KOG0489|consensus	261		99.76
KOG0487|consensus	308		99.75
KOG0848|consensus	317		99.75
KOG0842|consensus	307		99.71
KOG0492|consensus	246		99.71
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.69
KOG0485|consensus	268		99.68
KOG0493|consensus	342		99.67
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.65
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.64
COG5576	156	Homeodomain-containing transcription factor [Trans	99.63
KOG0486|consensus	351		99.63
KOG0483|consensus	198		99.62
KOG0491|consensus	194		99.59
KOG0490|consensus	235		99.57
KOG0844|consensus	408		99.53
KOG3802|consensus	398		99.53
KOG4577|consensus	383		99.47
KOG0849|consensus	354		99.3
KOG0847|consensus	288		99.3
KOG0848|consensus	317		99.11
KOG0489|consensus	261		99.08
KOG1168|consensus	385		99.0
KOG0774|consensus	334		99.0
KOG0775|consensus	304		98.97
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.84
KOG2252|consensus	558		98.59
KOG0844|consensus	408		98.39
KOG0484|consensus	125		98.38
KOG0490|consensus	235		98.31
KOG0487|consensus	308		97.99
KOG0850|consensus	245		97.95
KOG1146|consensus	1406		97.76
KOG0488|consensus	309		97.62
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	97.52
KOG0494|consensus	332		97.51
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	97.43
KOG2251|consensus	228		97.42
KOG0842|consensus	307		97.06
KOG0485|consensus	268		96.9
KOG0773|consensus	342		96.83
KOG0491|consensus	194		96.63
COG5576	156	Homeodomain-containing transcription factor [Trans	96.58
KOG0843|consensus	197		96.52
KOG3623|consensus	1007		96.13
KOG0483|consensus	198		96.09
KOG4577|consensus	383		95.95
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	95.92
KOG0486|consensus	351		95.42
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	95.27
KOG0847|consensus	288		95.04
KOG0492|consensus	246		94.86
KOG0493|consensus	342		94.74
KOG0849|consensus	354		92.39
KOG0775|consensus	304		92.19
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	91.99
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	91.53
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	88.67
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	88.66
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	87.4
PF10668	60	Phage_terminase: Phage terminase small subunit; In	85.75
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	82.1
COG3413	215	Predicted DNA binding protein [General function pr	80.26

>KOG0484|consensus

Probab=99.86  E-value=3e-22  Score=131.00  Aligned_cols=66  Identities=38%  Similarity=0.610  Sum_probs=62.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhh
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR   67 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~   67 (186)
                      .+|+||.||.||+.|+.+||..|.+++|||+-.|++||.++.|++.+|+|||||||+|.+++.+-.
T Consensus        14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a   79 (125)
T KOG0484|consen   14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAA   79 (125)
T ss_pred             HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHH
Confidence            578999999999999999999999999999999999999999999999999999999999876643

>KOG0850|consensus

Probab=99.80  E-value=6.6e-20  Score=136.49  Aligned_cols=72  Identities=43%  Similarity=0.645  Sum_probs=66.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhhhhc
Q psy8536           1 KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVVI   72 (186)
Q Consensus         1 ~~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~~~~   72 (186)
                      |.||.||.||.|+..||..|+..|+.+.|.-..+|.+||..|||+..||+|||||||.|.||..+..+....
T Consensus       118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~~~e  189 (245)
T KOG0850|consen  118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSGPVE  189 (245)
T ss_pred             CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCCccc
Confidence            678999999999999999999999999999999999999999999999999999999999998875444333

>KOG2251|consensus

Probab=99.79  E-value=7.8e-20  Score=135.50  Aligned_cols=66  Identities=35%  Similarity=0.568  Sum_probs=63.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhh
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR   67 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~   67 (186)
                      +||.||.||.|+..|+++||+.|.++.|||+..|++||.+|+|.+.+|+|||.|||+|+++++...
T Consensus        34 pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   34 PRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             chhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            589999999999999999999999999999999999999999999999999999999999887754

>KOG0488|consensus

Probab=99.79  E-value=2e-19  Score=143.20  Aligned_cols=74  Identities=41%  Similarity=0.692  Sum_probs=67.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhhhhccCC
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVVIKDP   75 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~~~~~~~   75 (186)
                      +||+|+.||.||..|+..||+.|+...|.+..+|++||..|||+..||++||||||+|||++.....+......
T Consensus       169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~~~~~~~  242 (309)
T KOG0488|consen  169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGELLYQAG  242 (309)
T ss_pred             CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhccccccc
Confidence            57888999999999999999999999999999999999999999999999999999999999887554444333

>KOG0494|consensus

Probab=99.78  E-value=1.8e-19  Score=136.12  Aligned_cols=66  Identities=36%  Similarity=0.587  Sum_probs=59.9

Q ss_pred             CCCCCCC-CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhh
Q psy8536           2 TRTKDKY-RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR   67 (186)
Q Consensus         2 ~~~~rr~-r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~   67 (186)
                      ++++||. ||+||..|++.||+.|++.+|||...|+.||.++.|.|.+|+|||||||+||++.++.-
T Consensus       137 kk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w  203 (332)
T KOG0494|consen  137 KKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW  203 (332)
T ss_pred             cccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence            3444454 99999999999999999999999999999999999999999999999999999976643

>KOG0843|consensus

Probab=99.77  E-value=8.6e-19  Score=125.93  Aligned_cols=64  Identities=38%  Similarity=0.658  Sum_probs=61.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhh
Q psy8536           4 TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR   67 (186)
Q Consensus         4 ~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~   67 (186)
                      +-+|.||.||.+|+..||..|+.|+|-...+|+.||+.|+|++.||+|||||||.|.|+...+.
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~  164 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED  164 (197)
T ss_pred             CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence            6788999999999999999999999999999999999999999999999999999999987765

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.77  E-value=1.9e-18  Score=105.03  Aligned_cols=57  Identities=46%  Similarity=0.701  Sum_probs=54.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536           6 DKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus         6 rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      ||+|+.||.+|+.+|++.|..++||+..+++.||..+||+..+|.+||+|+|.++|+
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence            578899999999999999999999999999999999999999999999999999875

; 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 ....

>KOG0489|consensus

Probab=99.76  E-value=6.4e-19  Score=138.06  Aligned_cols=68  Identities=46%  Similarity=0.774  Sum_probs=62.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhhh
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEV   70 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~~   70 (186)
                      .+.||.||.||..|+.+||+.|..|.|.+...|.+||..|+|+|+||+|||||||+||||..+.....
T Consensus       157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~  224 (261)
T KOG0489|consen  157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ  224 (261)
T ss_pred             CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence            35688999999999999999999999999999999999999999999999999999999876654433

>KOG0487|consensus

Probab=99.75  E-value=6.6e-19  Score=138.32  Aligned_cols=65  Identities=52%  Similarity=0.818  Sum_probs=61.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhh
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR   67 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~   67 (186)
                      +..||||.-||+.|+.+||+.|.-|.|++.+.|.+|++.|+|+++||+|||||||+|+||..++.
T Consensus       233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~  297 (308)
T KOG0487|consen  233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN  297 (308)
T ss_pred             cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence            67889999999999999999999999999999999999999999999999999999999988643

>KOG0848|consensus

Probab=99.75  E-value=7.5e-19  Score=133.33  Aligned_cols=68  Identities=85%  Similarity=1.219  Sum_probs=64.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhh
Q psy8536           1 KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKRE   68 (186)
Q Consensus         1 ~~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~   68 (186)
                      |+|++-|-|.+||+.|+-+||+.|..+.|+++..+.+||..|||+|+||+|||||||+|++|..++..
T Consensus       195 KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~  262 (317)
T KOG0848|consen  195 KTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR  262 (317)
T ss_pred             eeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence            67888889999999999999999999999999999999999999999999999999999999877653

>KOG0842|consensus

Probab=99.71  E-value=4.8e-18  Score=133.43  Aligned_cols=71  Identities=44%  Similarity=0.688  Sum_probs=65.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhhhhc
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVVI   72 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~~~~   72 (186)
                      .+++||.|..||..|+-+||+.|....|.+..+|++||..|+|++.||+|||||||=|.||+.++......
T Consensus       150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~  220 (307)
T KOG0842|consen  150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEAL  220 (307)
T ss_pred             cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcc
Confidence            46788889999999999999999999999999999999999999999999999999999998887654443

>KOG0492|consensus

Probab=99.71  E-value=1.9e-17  Score=121.48  Aligned_cols=69  Identities=43%  Similarity=0.696  Sum_probs=63.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhh
Q psy8536           1 KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREE   69 (186)
Q Consensus         1 ~~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~   69 (186)
                      |-+..|+.||-||..|+..||..|....|.++.+|.+++..|.|++.||+|||||||+|.|+.+..+.+
T Consensus       140 Khk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~E  208 (246)
T KOG0492|consen  140 KHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELE  208 (246)
T ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHH
Confidence            345678889999999999999999999999999999999999999999999999999999987765443

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.69  E-value=2.7e-17  Score=98.73  Aligned_cols=53  Identities=15%  Similarity=0.389  Sum_probs=50.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCC----CCHHHHHHHHHHcCCChhHHHHHHHhhH
Q psy8536           5 KDKYRVVYSDQQRLELEKEFHYSRY----ITIRRKAELANSLGLSERQVKIWFQNRR   57 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f~~~~~----p~~~~r~~la~~~~l~~~~v~~WFqnrr   57 (186)
                      +||.||.||.+|++.|+..|..++|    ||..++++||..|||++.+|+|||||-+
T Consensus         1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            3788999999999999999999999    9999999999999999999999999953

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

>KOG0485|consensus

Probab=99.68  E-value=1.3e-16  Score=117.85  Aligned_cols=68  Identities=46%  Similarity=0.665  Sum_probs=62.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhhhh
Q psy8536           4 TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVV   71 (186)
Q Consensus         4 ~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~~~   71 (186)
                      ++||.||+|+..|+..||..|+...|.+..+|..||.+|.|+|.||+|||||||.|||++-....+..
T Consensus       103 RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ea~  170 (268)
T KOG0485|consen  103 RKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLEAA  170 (268)
T ss_pred             ccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhhhh
Confidence            56788999999999999999999999999999999999999999999999999999999876554443

>KOG0493|consensus

Probab=99.67  E-value=6.1e-17  Score=122.62  Aligned_cols=61  Identities=44%  Similarity=0.746  Sum_probs=57.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536           5 KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK   65 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~   65 (186)
                      -+|.||.||.+||..|++.|+.|.|.+...|++||.+|||.+.||+|||||+|+|.|+..-
T Consensus       246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTg  306 (342)
T KOG0493|consen  246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTG  306 (342)
T ss_pred             hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence            3578999999999999999999999999999999999999999999999999999987543

>smart00389 HOX Homeodomain

Probab=99.65  E-value=4.1e-16  Score=94.26  Aligned_cols=54  Identities=54%  Similarity=0.785  Sum_probs=51.6

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHH
Q psy8536           7 KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE   60 (186)
Q Consensus         7 r~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~   60 (186)
                      +.|+.|+.+|+.+|+..|..++||+..++..||..+||+..+|+.||+|+|.+.
T Consensus         2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~   55 (56)
T smart00389        2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKW   55 (56)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhcc
Confidence            567889999999999999999999999999999999999999999999999875

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

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

Probab=99.64  E-value=8.5e-16  Score=93.77  Aligned_cols=56  Identities=52%  Similarity=0.796  Sum_probs=53.5

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536           7 KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus         7 r~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      +.|..|+..|+.+|+++|..++||+..++..||..+||++.+|+.||+|+|.+.++
T Consensus         2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~   57 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR   57 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence            56789999999999999999999999999999999999999999999999999775

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.63  E-value=6.2e-16  Score=111.47  Aligned_cols=69  Identities=32%  Similarity=0.485  Sum_probs=62.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhhhh
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVV   71 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~~~   71 (186)
                      ...+++|++.|.+|+.+|+..|..|+||+...|..|+..|||+++-|+|||||+|++.++.........
T Consensus        49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~~~~  117 (156)
T COG5576          49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQR  117 (156)
T ss_pred             CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccchhcc
Confidence            456788999999999999999999999999999999999999999999999999999998776544433

>KOG0486|consensus

Probab=99.63  E-value=2.1e-16  Score=122.69  Aligned_cols=76  Identities=32%  Similarity=0.503  Sum_probs=67.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhhhhccCCCc
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVVIKDPSK   77 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~~~~~~~~~   77 (186)
                      ..|+||.|+.||..|+.+||.+|+++.|||...|++||..++|++.+|.+||.|||+||++.+........+....
T Consensus       109 i~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ae~~k~~f~  184 (351)
T KOG0486|consen  109 ISKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAELAKGGFG  184 (351)
T ss_pred             hhhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHHHHhhhcCCc
Confidence            3488999999999999999999999999999999999999999999999999999999999887766444444443

>KOG0483|consensus

Probab=99.62  E-value=2.9e-16  Score=116.94  Aligned_cols=81  Identities=31%  Similarity=0.432  Sum_probs=72.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhhhhccCCCcccccchhh
Q psy8536           6 DKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVVIKDPSKDLFLSNKV   85 (186)
Q Consensus         6 rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (186)
                      .+++.+||.+|+..||..|+.+.+.....+..||..|||.++||.||||||||+||..+.+.+...++.....+...+..
T Consensus        51 ~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~~~~  130 (198)
T KOG0483|consen   51 KGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSENDR  130 (198)
T ss_pred             ccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhhhH
Confidence            45567999999999999999999999999999999999999999999999999999999998888888887777766554


Q ss_pred             h
Q psy8536          86 M   86 (186)
Q Consensus        86 ~   86 (186)
                      .
T Consensus       131 L  131 (198)
T KOG0483|consen  131 L  131 (198)
T ss_pred             H
Confidence            3

>KOG0491|consensus

Probab=99.59  E-value=5.7e-16  Score=109.80  Aligned_cols=64  Identities=50%  Similarity=0.761  Sum_probs=60.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhh
Q psy8536           5 KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKRE   68 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~   68 (186)
                      +++-|++|+..|+..|++.|+...|.+-.+|.+||..|+|++.||+.||||||+|.|+.++...
T Consensus       100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~  163 (194)
T KOG0491|consen  100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ  163 (194)
T ss_pred             hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence            4567999999999999999999999999999999999999999999999999999999877654

>KOG0490|consensus

Probab=99.57  E-value=7e-16  Score=119.24  Aligned_cols=63  Identities=35%  Similarity=0.411  Sum_probs=59.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK   65 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~   65 (186)
                      .++|+.|+.|+..|+++|+.+|+.++|||...++.||..+++++..|++||||+|++++++..
T Consensus        58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~  120 (235)
T KOG0490|consen   58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER  120 (235)
T ss_pred             ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence            467889999999999999999999999999999999999999999999999999999998763

>KOG0844|consensus

Probab=99.53  E-value=2.1e-15  Score=116.67  Aligned_cols=71  Identities=38%  Similarity=0.628  Sum_probs=64.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhhhhccCC
Q psy8536           5 KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVVIKDP   75 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~~~~~~~   75 (186)
                      -||.||.||.+||..||+.|-...|-+...|.+||..|+|.|..|+|||||||+|+|++..-........+
T Consensus       181 mRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaWPhpaDP  251 (408)
T KOG0844|consen  181 MRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAWPHPADP  251 (408)
T ss_pred             HHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccCCCCCCh
Confidence            36789999999999999999999999999999999999999999999999999999998887665555443

>KOG3802|consensus

Probab=99.53  E-value=1.7e-15  Score=121.59  Aligned_cols=62  Identities=34%  Similarity=0.429  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536           4 TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK   65 (186)
Q Consensus         4 ~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~   65 (186)
                      ++||+||.|+...+..||++|..|+.|+..++..||++|+|...+|+|||||||.|+||...
T Consensus       293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            67889999999999999999999999999999999999999999999999999999997543

>KOG4577|consensus

Probab=99.47  E-value=5e-14  Score=108.33  Aligned_cols=63  Identities=30%  Similarity=0.490  Sum_probs=59.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHh
Q psy8536           4 TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK   66 (186)
Q Consensus         4 ~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~   66 (186)
                      ..+|+||.||..|++.|+.+|...+.|....|++|+.++||..+.|+|||||||+|+|+..+.
T Consensus       166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD  228 (383)
T KOG4577|consen  166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD  228 (383)
T ss_pred             ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence            357899999999999999999999999999999999999999999999999999999987654

>KOG0849|consensus

Probab=99.30  E-value=2.3e-12  Score=105.05  Aligned_cols=65  Identities=38%  Similarity=0.577  Sum_probs=60.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHh
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK   66 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~   66 (186)
                      .++.+|.|+.|+..|++.|++.|..++||++..|+.||.++|+++..|++||+|+|+++++....
T Consensus       173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~  237 (354)
T KOG0849|consen  173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD  237 (354)
T ss_pred             cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence            36778889999999999999999999999999999999999999999999999999999987743

>KOG0847|consensus

Probab=99.30  E-value=2.1e-12  Score=95.84  Aligned_cols=63  Identities=37%  Similarity=0.662  Sum_probs=57.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhh
Q psy8536           5 KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR   67 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~   67 (186)
                      ++--|-.|+-.|+..|+..|+...|+-..++.+||..+|+.+.+|+|||||||.||+++..-+
T Consensus       167 rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaE  229 (288)
T KOG0847|consen  167 RKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAE  229 (288)
T ss_pred             ccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccc
Confidence            334467899999999999999999999999999999999999999999999999999876533

>KOG0848|consensus

Probab=99.11  E-value=2.1e-11  Score=93.13  Aligned_cols=28  Identities=82%  Similarity=1.159  Sum_probs=25.9

Q ss_pred             cccCCCCCccccccchHHHHHHhhhhcC
Q psy8536         159 TRKTRTKDKYRVVYSDQQRLELEKEFHY  186 (186)
Q Consensus       159 ~~~~~~~~~~r~~~~~~q~~~l~~~f~~  186 (186)
                      ++++|+++++|++|||+|+||||||||+
T Consensus       193 ~~KtRTkDKYRvVYTDhQRLELEKEfh~  220 (317)
T KOG0848|consen  193 NVKTRTKDKYRVVYTDHQRLELEKEFHT  220 (317)
T ss_pred             CceeecccceeEEecchhhhhhhhhhcc
Confidence            5578999999999999999999999996

>KOG0489|consensus

Probab=99.08  E-value=5e-11  Score=93.62  Aligned_cols=36  Identities=33%  Similarity=0.469  Sum_probs=29.4

Q ss_pred             Ccccccccc-------ccCCCCCccccccchHHHHHHhhhhcC
Q psy8536         151 TSYILDIDT-------RKTRTKDKYRVVYSDQQRLELEKEFHY  186 (186)
Q Consensus       151 ~~~~~~~~~-------~~~~~~~~~r~~~~~~q~~~l~~~f~~  186 (186)
                      ..|+|+...       +.+++.||.||+||++||+||||||||
T Consensus       138 ~~~p~~~~~~~~~~~~~~~~~~kR~RtayT~~QllELEkEFhf  180 (261)
T KOG0489|consen  138 QIYPWMKSTANYLSSSETGGKSKRRRTAFTRYQLLELEKEFHF  180 (261)
T ss_pred             ccccchhhhhcccccccccCCCCCCCcccchhhhhhhhhhhcc
Confidence            466666543       335678999999999999999999997

>KOG1168|consensus

Probab=99.00  E-value=5.7e-11  Score=91.74  Aligned_cols=62  Identities=24%  Similarity=0.416  Sum_probs=58.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536           4 TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK   65 (186)
Q Consensus         4 ~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~   65 (186)
                      .++|+||.+-.-....||++|...+.|+.+....||++|.|....|+|||||+|.|.|+...
T Consensus       308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~  369 (385)
T KOG1168|consen  308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR  369 (385)
T ss_pred             ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence            46788999999999999999999999999999999999999999999999999999998544

>KOG0774|consensus

Probab=99.00  E-value=3.8e-10  Score=86.05  Aligned_cols=61  Identities=28%  Similarity=0.398  Sum_probs=56.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536           5 KDKYRVVYSDQQRLELEKEFH---YSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK   65 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f~---~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~   65 (186)
                      .||+|..|+..-.++|+++|.   .++||+.+.+++||.++|++..||..||.|+|-+.++..-
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~  251 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMG  251 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhh
Confidence            478899999999999999996   7899999999999999999999999999999999887543

>KOG0775|consensus

Probab=98.97  E-value=7.3e-10  Score=85.07  Aligned_cols=49  Identities=37%  Similarity=0.596  Sum_probs=45.5

Q ss_pred             HHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536          14 DQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus        14 ~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      +.-+.+|+++|..|+||+..++.+||+.+||+..||-.||.|||.++|-
T Consensus       185 ekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa  233 (304)
T KOG0775|consen  185 EKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA  233 (304)
T ss_pred             HhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence            3446799999999999999999999999999999999999999999983

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

Probab=98.84  E-value=4.7e-09  Score=58.43  Aligned_cols=34  Identities=38%  Similarity=0.632  Sum_probs=29.0

Q ss_pred             hcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536          26 YSRYITIRRKAELANSLGLSERQVKIWFQNRRAK   59 (186)
Q Consensus        26 ~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~   59 (186)
                      .+|||+..+++.||..+||+..||..||-|.|.+
T Consensus         7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR   40 (40)
T PF05920_consen    7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR   40 (40)
T ss_dssp             TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence            4799999999999999999999999999999864

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

>KOG2252|consensus

Probab=98.59  E-value=1.1e-07  Score=79.86  Aligned_cols=57  Identities=23%  Similarity=0.339  Sum_probs=53.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHH
Q psy8536           4 TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE   60 (186)
Q Consensus         4 ~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~   60 (186)
                      ..+|.|.+||..|+..|.++|+.+++|+.+..+.|+.+|||....|..||-|-|.+.
T Consensus       419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            356779999999999999999999999999999999999999999999999998885

>KOG0844|consensus

Probab=98.39  E-value=2.5e-07  Score=72.31  Aligned_cols=55  Identities=24%  Similarity=0.267  Sum_probs=42.7

Q ss_pred             CCCcccccchhhhhhcccceeeeeeeehhhhhhhhhhhcccccccCCCcccccccccc
Q psy8536          74 DPSKDLFLSNKVMYTYLVFQVKIWFQNRRAKERKQLKKREEVVIKDPSKDLFLSNKVM  131 (186)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~riq~WFqNrRak~~~~~~~~~~~~~~~p~~~~~~~~~~~  131 (186)
                      ..+.....+...+.++..+.|.|||||||+|+++|.-...++...+|.   ||..|-.
T Consensus       205 YVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaWPhpaDPa---fytymm~  259 (408)
T KOG0844|consen  205 YVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAWPHPADPA---FYTYMMN  259 (408)
T ss_pred             cccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccCCCCCChH---HHHHHHH
Confidence            344555677778888999999999999999999998877777766665   6666654

>KOG0484|consensus

Probab=98.38  E-value=6.1e-08  Score=64.01  Aligned_cols=56  Identities=32%  Similarity=0.466  Sum_probs=44.2

Q ss_pred             HHHHHhhhhhhccCCCcccccchhhhhhccc--ceeeeeeeehhhhhhhhhhhccccc
Q psy8536          61 RKQLKKREEVVIKDPSKDLFLSNKVMYTYLV--FQVKIWFQNRRAKERKQLKKREEVV  116 (186)
Q Consensus        61 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~riq~WFqNrRak~~~~~~~~~~~~  116 (186)
                      .-+.++.+..+.-.++.++......+..+.+  .+||||||||||+.++|+......+
T Consensus        26 S~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~~   83 (125)
T KOG0484|consen   26 SAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAKM   83 (125)
T ss_pred             HHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHHh
Confidence            3456677888888899999887776665554  5999999999999999988765543

>KOG0490|consensus

Probab=98.31  E-value=7.1e-07  Score=68.86  Aligned_cols=63  Identities=35%  Similarity=0.557  Sum_probs=58.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK   65 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~   65 (186)
                      .+.++.|+.++..|+..|...|..+++|+...++.|+..+|+++..|++||+|+|.+.++...
T Consensus       151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  151 KKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             cccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            456778999999999999999999999999999999999999999999999999999987655

>KOG0487|consensus

Probab=97.99  E-value=2.8e-06  Score=67.54  Aligned_cols=24  Identities=50%  Similarity=0.733  Sum_probs=20.7

Q ss_pred             CCCCccccccchHHHHHHhhhhcC
Q psy8536         163 RTKDKYRVVYSDQQRLELEKEFHY  186 (186)
Q Consensus       163 ~~~~~~r~~~~~~q~~~l~~~f~~  186 (186)
                      +..|+.|.-||.+||+||||||-|
T Consensus       233 ~~~RKKRcPYTK~QtlELEkEFlf  256 (308)
T KOG0487|consen  233 RRGRKKRCPYTKHQTLELEKEFLF  256 (308)
T ss_pred             cccccccCCchHHHHHHHHHHHHH
Confidence            455666999999999999999975

>KOG0850|consensus

Probab=97.95  E-value=1.2e-05  Score=60.77  Aligned_cols=39  Identities=44%  Similarity=0.523  Sum_probs=29.7

Q ss_pred             hhhhcccceeeeeeeehhhhhhhhhhhcccccccCCCcc
Q psy8536          85 VMYTYLVFQVKIWFQNRRAKERKQLKKREEVVIKDPSKD  123 (186)
Q Consensus        85 ~~~~~~~~riq~WFqNrRak~~~~~~~~~~~~~~~p~~~  123 (186)
                      ...++..++|.|||||||+|.++..+.+.....-+|...
T Consensus       157 AsLGLTQTQVKIWFQNrRSK~KKl~k~g~~~~e~~p~~~  195 (245)
T KOG0850|consen  157 ASLGLTQTQVKIWFQNRRSKFKKLKKQGSGPVEGDPSAS  195 (245)
T ss_pred             HHhCCchhHhhhhhhhhHHHHHHHHhcCCCccccCcccC
Confidence            334455579999999999999999997777666555543

>KOG1146|consensus

Probab=97.76  E-value=2.4e-05  Score=71.85  Aligned_cols=61  Identities=31%  Similarity=0.482  Sum_probs=57.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536           5 KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK   65 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~   65 (186)
                      +|..|+.+++.|+.+|...|....||...+.+.|...+++..+.|++||||-|++.++...
T Consensus       903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~  963 (1406)
T KOG1146|consen  903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL  963 (1406)
T ss_pred             hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence            4567999999999999999999999999999999999999999999999999999988655

>KOG0488|consensus

Probab=97.62  E-value=3.7e-05  Score=61.83  Aligned_cols=24  Identities=42%  Similarity=0.654  Sum_probs=22.1

Q ss_pred             CCCCccccccchHHHHHHhhhhcC
Q psy8536         163 RTKDKYRVVYSDQQRLELEKEFHY  186 (186)
Q Consensus       163 ~~~~~~r~~~~~~q~~~l~~~f~~  186 (186)
                      +++|+.||+||+.||.||||.|++
T Consensus       170 kK~RksRTaFT~~Ql~~LEkrF~~  193 (309)
T KOG0488|consen  170 KKRRKSRTAFSDHQLFELEKRFEK  193 (309)
T ss_pred             cccccchhhhhHHHHHHHHHHHHH
Confidence            678889999999999999999984

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=97.52  E-value=6e-05  Score=45.30  Aligned_cols=21  Identities=14%  Similarity=0.276  Sum_probs=19.4

Q ss_pred             CCccccccchHHHHHHhhhhc
Q psy8536         165 KDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       165 ~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      +||.||.||.+|+.+||++|+
T Consensus         1 ~kR~RT~Ft~~Q~~~Le~~fe   21 (58)
T TIGR01565         1 KKRRRTKFTAEQKEKMRDFAE   21 (58)
T ss_pred             CCCCCCCCCHHHHHHHHHHHH
Confidence            378899999999999999996

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

>KOG0494|consensus

Probab=97.51  E-value=4.8e-05  Score=58.51  Aligned_cols=24  Identities=29%  Similarity=0.610  Sum_probs=20.9

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      .+++|++||.||.||+.||||.|.
T Consensus       138 k~kRRh~RTiFT~~Qle~LEkaFk  161 (332)
T KOG0494|consen  138 KKKRRHFRTIFTSYQLEELEKAFK  161 (332)
T ss_pred             ccccccccchhhHHHHHHHHHHHh
Confidence            346777899999999999999994

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

Probab=97.43  E-value=0.00026  Score=41.88  Aligned_cols=40  Identities=25%  Similarity=0.362  Sum_probs=30.5

Q ss_pred             HHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhh
Q psy8536          17 RLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNR   56 (186)
Q Consensus        17 ~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnr   56 (186)
                      +..|+..|....++...+...|+.+.||+..||+.||-.+
T Consensus        10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~   49 (56)
T PF11569_consen   10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAER   49 (56)
T ss_dssp             -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHH
T ss_pred             hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHh
Confidence            4569999999999999999999999999999999999654

>KOG2251|consensus

Probab=97.42  E-value=6.8e-05  Score=56.47  Aligned_cols=53  Identities=34%  Similarity=0.567  Sum_probs=38.2

Q ss_pred             HHHHHHhhhhhhccCCCcccccchh--hhhhcccceeeeeeeehhhhhhhhhhhc
Q psy8536          60 ERKQLKKREEVVIKDPSKDLFLSNK--VMYTYLVFQVKIWFQNRRAKERKQLKKR  112 (186)
Q Consensus        60 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~riq~WFqNrRak~~~~~~~~  112 (186)
                      .+++....+..+.+..+.|+.....  ...++.+++|+|||.|||||++.+.+..
T Consensus        45 tr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   45 TRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             cHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            3445555566666666777766555  4456667999999999999999887753

>KOG0842|consensus

Probab=97.06  E-value=0.00037  Score=55.55  Aligned_cols=31  Identities=42%  Similarity=0.572  Sum_probs=23.5

Q ss_pred             hhhhhcccceeeeeeeehhhhhhhhhhhccc
Q psy8536          84 KVMYTYLVFQVKIWFQNRRAKERKQLKKREE  114 (186)
Q Consensus        84 ~~~~~~~~~riq~WFqNrRak~~~~~~~~~~  114 (186)
                      ....++..++|.|||||+|.|.+++......
T Consensus       187 A~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~  217 (307)
T KOG0842|consen  187 ASSLRLTPTQVKIWFQNRRYKTKRQQKDKAL  217 (307)
T ss_pred             HHhcCCCchheeeeeecchhhhhhhhhhhhh
Confidence            3445566689999999999998887665433

>KOG0485|consensus

Probab=96.90  E-value=0.00052  Score=51.62  Aligned_cols=30  Identities=40%  Similarity=0.513  Sum_probs=23.4

Q ss_pred             hhhhhcccceeeeeeeehhhhhhhhhhhcc
Q psy8536          84 KVMYTYLVFQVKIWFQNRRAKERKQLKKRE  113 (186)
Q Consensus        84 ~~~~~~~~~riq~WFqNrRak~~~~~~~~~  113 (186)
                      .....+..++|.|||||||.||+++.....
T Consensus       138 A~sLqLTETQVKIWFQNRRnKwKRq~aad~  167 (268)
T KOG0485|consen  138 AASLQLTETQVKIWFQNRRNKWKRQYAADL  167 (268)
T ss_pred             HHhhhhhhhhhhhhhhhhhHHHHHHHhhhh
Confidence            344456678999999999999999866543

>KOG0773|consensus

Probab=96.83  E-value=0.00077  Score=55.17  Aligned_cols=58  Identities=28%  Similarity=0.255  Sum_probs=49.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHH-h--hcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536           5 KDKYRVVYSDQQRLELEKEF-H--YSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f-~--~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      ..|++..+......+|+.+. .  ..+||+..++..||.++||+..||.+||-|.|.+.-+
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~  299 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWK  299 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCC
Confidence            44556789999999999884 3  3579999999999999999999999999999988554

>KOG0491|consensus

Probab=96.63  E-value=0.00069  Score=48.83  Aligned_cols=27  Identities=44%  Similarity=0.698  Sum_probs=22.1

Q ss_pred             hhcccceeeeeeeehhhhhhhhhhhcc
Q psy8536          87 YTYLVFQVKIWFQNRRAKERKQLKKRE  113 (186)
Q Consensus        87 ~~~~~~riq~WFqNrRak~~~~~~~~~  113 (186)
                      .++...+|..||||+|+|++++..+..
T Consensus       137 L~LS~~QVKTWFQNrRMK~Kk~~r~~~  163 (194)
T KOG0491|consen  137 LSLSETQVKTWFQNRRMKHKKQQRNNQ  163 (194)
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence            344446999999999999999988775

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=96.58  E-value=0.0012  Score=47.87  Aligned_cols=44  Identities=30%  Similarity=0.418  Sum_probs=27.0

Q ss_pred             hhhhccCCCcccccch--hhhhhcccceeeeeeeehhhhhhhhhhh
Q psy8536          68 EEVVIKDPSKDLFLSN--KVMYTYLVFQVKIWFQNRRAKERKQLKK  111 (186)
Q Consensus        68 ~~~~~~~~~~~~~~~~--~~~~~~~~~riq~WFqNrRak~~~~~~~  111 (186)
                      +..+...+..+....-  ....+...-.||+||||+|++.++....
T Consensus        67 ~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~  112 (156)
T COG5576          67 EREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG  112 (156)
T ss_pred             HHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence            3444455554444332  3333444569999999999998775443

>KOG0843|consensus

Probab=96.52  E-value=0.0016  Score=47.66  Aligned_cols=22  Identities=27%  Similarity=0.537  Sum_probs=20.8

Q ss_pred             CCCccccccchHHHHHHhhhhc
Q psy8536         164 TKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       164 ~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ..||.||+||..||+.||.+|.
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F~  122 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAFE  122 (197)
T ss_pred             CCCccccccCHHHHHHHHHHHh
Confidence            6899999999999999999996

>KOG3623|consensus

Probab=96.13  E-value=0.011  Score=52.01  Aligned_cols=48  Identities=21%  Similarity=0.309  Sum_probs=44.8

Q ss_pred             HHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536          17 RLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus        17 ~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      +.+|++.|..|..|+..+...+|...||+...|+.||++.++......
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~  615 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE  615 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence            788999999999999999999999999999999999999999877654

>KOG0483|consensus

Probab=96.09  E-value=0.00059  Score=51.31  Aligned_cols=23  Identities=39%  Similarity=0.575  Sum_probs=17.4

Q ss_pred             hcccceeeeeeeehhhhhhhhhh
Q psy8536          88 TYLVFQVKIWFQNRRAKERKQLK  110 (186)
Q Consensus        88 ~~~~~riq~WFqNrRak~~~~~~  110 (186)
                      ++..-+|.||||||||+|+...-
T Consensus        88 gL~pRQVavWFQNRRARwK~kql  110 (198)
T KOG0483|consen   88 GLQPRQVAVWFQNRRARWKTKQL  110 (198)
T ss_pred             CCChhHHHHHHhhccccccchhh
Confidence            33345999999999999876443

>KOG4577|consensus

Probab=95.95  E-value=0.0017  Score=50.97  Aligned_cols=17  Identities=59%  Similarity=1.068  Sum_probs=14.0

Q ss_pred             eeeeeeeehhhhhhhhh
Q psy8536          93 QVKIWFQNRRAKERKQL  109 (186)
Q Consensus        93 riq~WFqNrRak~~~~~  109 (186)
                      -|||||||||||.++..
T Consensus       210 VVQVWFQNRRAKEKRLK  226 (383)
T KOG4577|consen  210 VVQVWFQNRRAKEKRLK  226 (383)
T ss_pred             ehhhhhhhhhHHHHhhh
Confidence            68999999999966543

>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere

Probab=95.92  E-value=0.025  Score=33.33  Aligned_cols=47  Identities=21%  Similarity=0.376  Sum_probs=35.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhH
Q psy8536           6 DKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRR   57 (186)
Q Consensus         6 rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr   57 (186)
                      +|+|..+|-++...+-..++...     ...+||.++|++..+|..|..|+-
T Consensus         1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~   47 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD   47 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred             CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence            46789999999888888887666     578899999999999999998753

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

>KOG0486|consensus

Probab=95.42  E-value=0.016  Score=46.21  Aligned_cols=51  Identities=27%  Similarity=0.475  Sum_probs=34.6

Q ss_pred             HHHhhhhhhccCCCcccccchhhh--hhcccceeeeeeeehhhhhhhhhhhcc
Q psy8536          63 QLKKREEVVIKDPSKDLFLSNKVM--YTYLVFQVKIWFQNRRAKERKQLKKRE  113 (186)
Q Consensus        63 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~riq~WFqNrRak~~~~~~~~~  113 (186)
                      +..+.+..+...-+.+.....+.+  .++.+-+|.+||.||||+|++.+.+..
T Consensus       123 qlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~  175 (351)
T KOG0486|consen  123 QLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ  175 (351)
T ss_pred             HHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence            344445555555555554444433  345556999999999999999998877

>PF00046 Homeobox: Homeobox domain not present here

Probab=95.27  E-value=0.013  Score=34.69  Aligned_cols=20  Identities=25%  Similarity=0.391  Sum_probs=18.3

Q ss_pred             CccccccchHHHHHHhhhhc
Q psy8536         166 DKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       166 ~~~r~~~~~~q~~~l~~~f~  185 (186)
                      |+.|+.||.+|+..||..|.
T Consensus         1 kr~r~~~t~~q~~~L~~~f~   20 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQ   20 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHH
Confidence            56799999999999999995

; 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 ....

>KOG0847|consensus

Probab=95.04  E-value=0.0037  Score=47.17  Aligned_cols=24  Identities=50%  Similarity=0.693  Sum_probs=19.5

Q ss_pred             cccceeeeeeeehhhhhhhhhhhc
Q psy8536          89 YLVFQVKIWFQNRRAKERKQLKKR  112 (186)
Q Consensus        89 ~~~~riq~WFqNrRak~~~~~~~~  112 (186)
                      ...++|.|||||||-||++.+...
T Consensus       206 mteSqvkVWFQNRRTKWRKkhAaE  229 (288)
T KOG0847|consen  206 MTESQVKVWFQNRRTKWRKKHAAE  229 (288)
T ss_pred             ccHHHHHHHHhcchhhhhhhhccc
Confidence            345799999999999999976543

>KOG0492|consensus

Probab=94.86  E-value=0.021  Score=42.86  Aligned_cols=23  Identities=35%  Similarity=0.569  Sum_probs=20.4

Q ss_pred             CCCCccccccchHHHHHHhhhhc
Q psy8536         163 RTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       163 ~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ...|+.||.||..||+.||+.|+
T Consensus       142 k~nRkPRtPFTtqQLlaLErkfr  164 (246)
T KOG0492|consen  142 KPNRKPRTPFTTQQLLALERKFR  164 (246)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHh
Confidence            34678899999999999999996

>KOG0493|consensus

Probab=94.74  E-value=0.019  Score=44.62  Aligned_cols=22  Identities=23%  Similarity=0.454  Sum_probs=20.0

Q ss_pred             CCCccccccchHHHHHHhhhhc
Q psy8536         164 TKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       164 ~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      +.||.||+||.+||..|..||.
T Consensus       245 eeKRPRTAFtaeQL~RLK~EF~  266 (342)
T KOG0493|consen  245 EEKRPRTAFTAEQLQRLKAEFQ  266 (342)
T ss_pred             hhcCccccccHHHHHHHHHHHh
Confidence            3578999999999999999996

>KOG0849|consensus

Probab=92.39  E-value=0.1  Score=43.10  Aligned_cols=25  Identities=28%  Similarity=0.316  Sum_probs=22.4

Q ss_pred             cCCCCCccccccchHHHHHHhhhhc
Q psy8536         161 KTRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       161 ~~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      -+++.+|.||+||..|+.+||++|+
T Consensus       172 ~~~~~rr~rtsft~~Q~~~le~~f~  196 (354)
T KOG0849|consen  172 LQRGGRRNRTSFSPSQLEALEECFQ  196 (354)
T ss_pred             ccccccccccccccchHHHHHHHhc
Confidence            3577888899999999999999997

>KOG0775|consensus

Probab=92.19  E-value=0.21  Score=39.24  Aligned_cols=29  Identities=28%  Similarity=0.436  Sum_probs=22.4

Q ss_pred             chhhhhhcccceeeeeeeehhhhhhhhhh
Q psy8536          82 SNKVMYTYLVFQVKIWFQNRRAKERKQLK  110 (186)
Q Consensus        82 ~~~~~~~~~~~riq~WFqNrRak~~~~~~  110 (186)
                      +...++.+..++|..||.|||.+++....
T Consensus       208 eLA~aTgLt~tQVsNWFKNRRQRDRa~~a  236 (304)
T KOG0775|consen  208 ELAEATGLTITQVSNWFKNRRQRDRAAAA  236 (304)
T ss_pred             HHHHHhCCchhhhhhhhhhhhhhhhhccc
Confidence            34466677778999999999999985444

>smart00389 HOX Homeodomain

Probab=91.99  E-value=0.12  Score=30.19  Aligned_cols=20  Identities=40%  Similarity=0.592  Sum_probs=17.6

Q ss_pred             CccccccchHHHHHHhhhhc
Q psy8536         166 DKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       166 ~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ++.|+.||.+|+..||..|.
T Consensus         1 ~k~r~~~~~~~~~~L~~~f~   20 (56)
T smart00389        1 RRKRTSFTPEQLEELEKEFQ   20 (56)
T ss_pred             CCCCCcCCHHHHHHHHHHHH
Confidence            35688999999999999996

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

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

Probab=91.53  E-value=0.42  Score=28.08  Aligned_cols=40  Identities=28%  Similarity=0.302  Sum_probs=33.2

Q ss_pred             CCHHHHHHHHHHHhhcC--CCCHHHHHHHHHHcCCChhHHHH
Q psy8536          12 YSDQQRLELEKEFHYSR--YITIRRKAELANSLGLSERQVKI   51 (186)
Q Consensus        12 ~t~~q~~~L~~~f~~~~--~p~~~~r~~la~~~~l~~~~v~~   51 (186)
                      +|+.|.++|..++...=  +|-...-.+||.++|++...+..
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~   42 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSE   42 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence            58899999999987443  47788889999999999887654

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

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

Probab=88.67  E-value=0.72  Score=28.69  Aligned_cols=44  Identities=25%  Similarity=0.363  Sum_probs=29.8

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHH
Q psy8536           7 KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQ   54 (186)
Q Consensus         7 r~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFq   54 (186)
                      ++|..||.++...+-..+...    .....++|.++||+...|..|-.
T Consensus         2 ~~r~~ys~e~K~~~v~~~~~~----g~sv~~va~~~gi~~~~l~~W~~   45 (76)
T PF01527_consen    2 RKRRRYSPEFKLQAVREYLES----GESVSEVAREYGISPSTLYNWRK   45 (76)
T ss_dssp             -SS----HHHHHHHHHHHHHH----HCHHHHHHHHHTS-HHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHC----CCceEeeecccccccccccHHHH
Confidence            457899999888776666222    36788899999999999999974

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

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

Probab=88.66  E-value=2.4  Score=24.09  Aligned_cols=41  Identities=17%  Similarity=0.218  Sum_probs=31.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhh
Q psy8536          11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNR   56 (186)
Q Consensus        11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnr   56 (186)
                      .+++.+..+|...|..     ...-.++|..+|++...|..+...-
T Consensus         4 ~L~~~er~vi~~~y~~-----~~t~~eIa~~lg~s~~~V~~~~~~a   44 (50)
T PF04545_consen    4 QLPPREREVIRLRYFE-----GLTLEEIAERLGISRSTVRRILKRA   44 (50)
T ss_dssp             TS-HHHHHHHHHHHTS-----T-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHhcC-----CCCHHHHHHHHCCcHHHHHHHHHHH
Confidence            4788899999999932     2456788999999999999876543

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

>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=87.40  E-value=0.47  Score=27.83  Aligned_cols=19  Identities=42%  Similarity=0.597  Sum_probs=17.2

Q ss_pred             ccccccchHHHHHHhhhhc
Q psy8536         167 KYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       167 ~~r~~~~~~q~~~l~~~f~  185 (186)
                      +.|+.|+..|+..||+.|+
T Consensus         2 ~~r~~~~~~~~~~Le~~f~   20 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFE   20 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHH
Confidence            4588999999999999996

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

Probab=85.75  E-value=0.79  Score=27.66  Aligned_cols=21  Identities=29%  Similarity=0.624  Sum_probs=18.0

Q ss_pred             HHHHHHHHHcCCChhHHHHHH
Q psy8536          33 RRKAELANSLGLSERQVKIWF   53 (186)
Q Consensus        33 ~~r~~la~~~~l~~~~v~~WF   53 (186)
                      -.-.+||.+||+++.+|..|=
T Consensus        23 i~lkdIA~~Lgvs~~tIr~WK   43 (60)
T PF10668_consen   23 IKLKDIAEKLGVSESTIRKWK   43 (60)
T ss_pred             ccHHHHHHHHCCCHHHHHHHh
Confidence            345678999999999999995

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

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

Probab=82.10  E-value=3.5  Score=22.90  Aligned_cols=42  Identities=19%  Similarity=0.230  Sum_probs=31.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhH
Q psy8536          11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRR   57 (186)
Q Consensus        11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr   57 (186)
                      .++..+..++...|...     ..-.++|..+|++...|..|...-+
T Consensus        10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~   51 (55)
T cd06171          10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRAL   51 (55)
T ss_pred             hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            45777788887776422     3567789999999999999986543

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

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

Probab=80.26  E-value=2.8  Score=31.92  Aligned_cols=41  Identities=22%  Similarity=0.238  Sum_probs=34.6

Q ss_pred             CCCHHHHHHHHHHHhh--cCCCCHHHHHHHHHHcCCChhHHHH
Q psy8536          11 VYSDQQRLELEKEFHY--SRYITIRRKAELANSLGLSERQVKI   51 (186)
Q Consensus        11 ~~t~~q~~~L~~~f~~--~~~p~~~~r~~la~~~~l~~~~v~~   51 (186)
                      -+|+.|+++|..+|..  =.+|-...-.+||+++|++...+.-
T Consensus       155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~e  197 (215)
T COG3413         155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSE  197 (215)
T ss_pred             cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHH
Confidence            5999999999999973  4467788889999999999887653

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	186
1ftz_A	70	Nuclear Magnetic Resonance Solution Structure Of Th		2e-14
2r5y_A	88	Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO		1e-13
1ahd_P	68	Determination Of The Nmr Solution Structure Of An A		1e-13
1hom_A	68	Determination Of The Three-Dimensional Structure Of		1e-13
1san_A	62	The Des(1-6)antennapedia Homeodomain: Comparison Of		2e-13
9ant_A	62	Antennapedia Homeodomain-Dna Complex Length = 62		3e-13
1b8i_A	81	Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX		2e-12
2m34_A	71	Nmr Structure Of The Homeodomain Transcription Fact		3e-11
1puf_A	77	Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo		1e-10
1b72_A	97	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		1e-10
2lp0_A	60	The Solution Structure Of Homeodomain-Protein Compl		3e-10
2h1k_A	63	Crystal Structure Of The Pdx1 Homeodomain In Comple		3e-10
3hdd_A	60	Engrailed Homeodomain Dna Complex Length = 60		8e-10
1hdd_C	61	Crystal Structure Of An Engrailed Homeodomain-Dna C		9e-10
1enh_A	54	Structural Studies Of The Engrailed Homeodomain Len		1e-09
2djn_A	70	The Solution Structure Of The Homeobox Domain Of Hu		2e-09
1p7j_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		2e-09
1p7i_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		2e-09
2hdd_A	61	Engrailed Homeodomain Q50k Variant Dna Complex Leng		3e-09
1ig7_A	58	Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58		3e-09
1ztr_A	61	Solution Structure Of Engrailed Homeodomain L16a Mu		4e-09
1du0_A	57	Engrailed Homeodomain Q50a Variant Dna Complex Leng		5e-09
2e1o_A	70	Solution Structure Of Rsgi Ruh-028, A Homeobox Doma		2e-08
2hos_A	63	Phage-selected Homeodomain Bound To Unmodified Dna		3e-08
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		4e-08
1jgg_A	60	Even-Skipped Homeodomain Complexed To At-Rich Dna L		4e-08
2cra_A	70	Solution Structure Of The Homeobox Domain Of Human		4e-08
2ld5_A	67	Solution Nmr-Derived Complex Structure Of Hoxa13 Dn		5e-08
2l7z_A	73	Nmr Structure Of A13 Homedomain Length = 73		5e-08
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		5e-08
2dmt_A	80	Solution Structure Of The Homeobox Domain Of Homeob		1e-07
2p81_A	44	Engrailed Homeodomain Helix-Turn-Helix Motif Length		1e-07
2l9r_A	69	Solution Nmr Structure Of Homeobox Domain Of Homeob		2e-07
3a01_A	93	Crystal Structure Of Aristaless And Clawless Homeod		3e-07
3a02_A	60	Crystal Structure Of Aristaless Homeodomain Length		8e-07
3rkq_A	58	Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Lengt		1e-06
2kt0_A	84	Solution Structure Of Human Stem Cell Transcription		1e-06
2vi6_A	62	Crystal Structure Of The Nanog Homeodomain Length =		1e-06
1zq3_P	68	Nmr Solution Structure Of The Bicoid Homeodomain Bo		1e-06
3a03_A	56	Crystal Structure Of Hox11l1 Homeodomain Length = 5		2e-06
2l7f_P	68	Solution Structure Of The Pitx2 Homeodomain Length		3e-06
1fjl_A	81	Homeodomain From The Drosophila Paired Protein Boun		4e-06
1ftt_A	68	Thyroid Transcription Factor 1 Homeodomain (Rattus		4e-06
2l7m_P	68	Solution Structure Of The Pitx2 Homeodomain R24h Mu		1e-05
1nk2_P	77	VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES		2e-05
3cmy_A	61	Structure Of A Homeodomain In Complex With Dna Leng		5e-05
2dmu_A	70	Solution Structure Of The Homeobox Domain Of Homeob		5e-05
1qry_A	80	Homeobox Protein Vnd (Ventral Nervous System Defect		6e-05
2m0c_A	75	Solution Nmr Structure Of Homeobox Domain Of Human		1e-04
2cue_A	80	Solution Structure Of The Homeobox Domain Of The Hu		1e-04
4egc_A	559	Crystal Structure Of Mbp-fused Human Six1 Bound To		3e-04
2dmq_A	80	Solution Structure Of The Homeobox Domain Of LimHOM		5e-04

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

Iteration: 1
 Score = 75.1 bits (183), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 35/54 (64%), Positives = 44/54 (81%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          R  Y+  Q LELEKEFH++RYIT RR+ ++AN+L LSERQ+KIWFQNRR K +K
Sbjct: 7  RQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKK 60

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

Iteration: 1
 Score = 72.8 bits (177), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 46/57 (80%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65
          R  Y+  Q LELEKEFH++RY+T RR+ E+A++L L+ERQ+KIWFQNRR K +K+ K
Sbjct: 32 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEHK 88

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

Iteration: 1
 Score = 72.4 bits (176), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 35/61 (57%), Positives = 48/61 (78%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKRE 68
          R  Y+  Q LELEKEFH++RY+T RR+ E+A++L L+ERQ+KIWFQNRR K +K+ K + 
Sbjct: 6  RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTKG 65
Query: 69 E 69
          E
Sbjct: 66 E 66

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

Iteration: 1
 Score = 72.4 bits (176), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 35/61 (57%), Positives = 48/61 (78%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKRE 68
          R  Y+  Q LELEKEFH++RY+T RR+ E+A++L L+ERQ+KIWFQNRR K +K+ K + 
Sbjct: 6  RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKTKG 65
Query: 69 E 69
          E
Sbjct: 66 E 66

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

Iteration: 1
 Score = 72.0 bits (175), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 34/59 (57%), Positives = 47/59 (79%)
Query: 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREE 69
           Y+  Q LELEKEFH++RY+T RR+ E+A++L L+ERQ+KIWFQNRR K +K+ K + E
Sbjct: 2  TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTKGE 60

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

Iteration: 1
 Score = 71.2 bits (173), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 45/55 (81%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
          R  Y+  Q LELEKEFH++RY+T RR+ E+A++L L+ERQ+KIWFQNRR K +K+
Sbjct: 7  RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 32/57 (56%), Positives = 45/57 (78%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65
          R  Y+  Q LELEKEFH + Y+T RR+ E+A++L L+ERQ+KIWFQNRR K +K+++
Sbjct: 24 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEIQ 80

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

Iteration: 1
 Score = 64.7 bits (156), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 28/51 (54%), Positives = 41/51 (80%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59
          R  ++ +Q LELEKEFH  +Y+++  ++++A++L LSE QVKIWFQNRRAK
Sbjct: 11 RTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAK 61

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

Iteration: 1
 Score = 62.8 bits (151), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 33/61 (54%), Positives = 42/61 (68%)
Query: 2  TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKER 61
           R+  K R  Y+  Q LELEKEF ++ Y+T  R+ E+A  L L+ERQVKIWFQNRR K +
Sbjct: 10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMK 69
Query: 62 K 62
          K
Sbjct: 70 K 70

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

Iteration: 1
 Score = 62.4 bits (150), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 28/54 (51%), Positives = 42/54 (77%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          R  ++ +Q  ELEKEFH+++Y++  R+ E+A +L L+E QVKIWFQNRR K++K
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91

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

Iteration: 1
 Score = 61.6 bits (148), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 32/56 (57%), Positives = 40/56 (71%)
Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          K R  Y+  Q LELEKEF ++ Y+T  R+ E+A  L L+ERQVKIWFQNRR K +K
Sbjct: 3  KKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58

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

Iteration: 1
 Score = 61.2 bits (147), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/55 (54%), Positives = 40/55 (72%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
          R  Y+  Q LELEKEF +++YI+  R+ ELA  L L+ER +KIWFQNRR K +K+
Sbjct: 7  RTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61

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

Iteration: 1
 Score = 59.7 bits (143), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 26/51 (50%), Positives = 40/51 (78%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59
          R  +S +Q   L++EF+ +RY+T RR+ +L++ LGL+E Q+KIWFQN+RAK
Sbjct: 5  RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 55

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

Iteration: 1
 Score = 59.7 bits (143), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 26/51 (50%), Positives = 40/51 (78%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59
          R  +S +Q   L++EF+ +RY+T RR+ +L++ LGL+E Q+KIWFQN+RAK
Sbjct: 7  RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 57

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

Iteration: 1
 Score = 59.3 bits (142), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 26/51 (50%), Positives = 40/51 (78%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59
          R  +S +Q   L++EF+ +RY+T RR+ +L++ LGL+E Q+KIWFQN+RAK
Sbjct: 3  RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 27/56 (48%), Positives = 40/56 (71%)
Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          K R +YS  Q   L++ F  ++Y+ +  +AELA SLGL++ QVKIWFQN+R+K +K
Sbjct: 9  KPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 26/51 (50%), Positives = 39/51 (76%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59
          R  +S +Q   L++EF+ +RY+T RR+ +L++ LGL+E Q+KIWFQN RAK
Sbjct: 5  RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAK 55

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 26/51 (50%), Positives = 39/51 (76%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59
          R  +S +Q   L++EF+ +RY+T RR+ +L++ LGL+E Q+KIWFQN RAK
Sbjct: 5  RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 55

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 25/51 (49%), Positives = 40/51 (78%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59
          R  +S +Q   L++EF+ +RY+T RR+ +L++ LGL+E Q+KIWF+N+RAK
Sbjct: 7  RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAK 57

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

Iteration: 1
 Score = 57.8 bits (138), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 27/56 (48%), Positives = 40/56 (71%)
Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          K R  ++  Q L LE++F   +Y++I  +AE ++SL L+E QVKIWFQNRRAK ++
Sbjct: 2  KPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

Iteration: 1
 Score = 57.8 bits (138), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 41/54 (75%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          R  +S +Q    ++EF+ +RY+T RR+ +L++ LGL+E Q+KIWFQN+RAK R+
Sbjct: 7  RTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 25/51 (49%), Positives = 39/51 (76%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59
          R  +S +Q   L++EF+ +RY+T RR+ +L++ LGL+E Q+KIWF N+RAK
Sbjct: 3  RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAK 53

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 37/53 (69%)
Query: 10 VVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          V +S+ Q +ELEK+F   +Y++   +  LA  L LSERQVK WFQNRRAK R+
Sbjct: 12 VRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 25/51 (49%), Positives = 38/51 (74%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59
          R  +S +Q   L++EF+ +RY+T RR+ +L++ LGL+E QVK WF+N RAK
Sbjct: 8  RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAK 58

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 28/63 (44%), Positives = 41/63 (65%)
Query: 3  RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          R + +YR  ++  Q  ELEK F  + Y  +  + ELA  +GL+E ++++WFQNRRAK RK
Sbjct: 4  RKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 63
Query: 63 QLK 65
          Q K
Sbjct: 64 QEK 66

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 37/57 (64%)
Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
          +YR  ++  Q   LEKEF+   Y++  R+ ELA  L L E  +K+WFQNRR K+++Q
Sbjct: 3  RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 26/56 (46%), Positives = 40/56 (71%)
Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          K R+ YS  Q  ELE+E+  +++IT  ++ +++ +  LSERQ+ IWFQNRR KE+K
Sbjct: 9  KKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 28/60 (46%), Positives = 41/60 (68%)
Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK 66
          K RV Y+  Q  ELE+E+  +++IT  ++  ++ +  LSERQV IWFQNRR KE+K + K
Sbjct: 3  KKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINK 62

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 28/60 (46%), Positives = 41/60 (68%)
Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK 66
          K RV Y+  Q  ELE+E+  +++IT  ++  ++ +  LSERQV IWFQNRR KE+K + K
Sbjct: 9  KKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINK 68

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 38/57 (66%)
Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
          +YR  ++  Q  ELEK F  + Y  +  + ELA  +GL+E ++++WFQNRRAK RKQ
Sbjct: 1  RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 37/54 (68%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          R V+++ Q + LEK F   +Y++   + +LA SLGLS+ QVK W+QNRR K +K
Sbjct: 21 RTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKK 74

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 22/38 (57%), Positives = 33/38 (86%)
Query: 22 KEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59
          +EF+ +RY+T RR+ +L++ LGL+E Q+KIWFQN+RAK
Sbjct: 3  REFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 40

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/50 (54%), Positives = 38/50 (76%), Gaps = 1/50 (2%)
Query: 16 QRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK-ERKQL 64
          Q +ELE++F + +Y++   +A LA +L L+E QVKIWFQNRR K +RKQL
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQL 64

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 27/66 (40%), Positives = 38/66 (57%)
Query: 5  KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL 64
          + K R  ++  Q  ELEK FH  +Y+    +A LA  L +++ QVK WFQNRR K R+Q 
Sbjct: 17 RKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQT 76
Query: 65 KKREEV 70
           +  E 
Sbjct: 77 AEEREA 82

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

Iteration: 1
 Score = 50.1 bits (118), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 25/56 (44%), Positives = 37/56 (66%)
Query: 10 VVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65
          + ++  Q  ELEK F  + Y  +  + ELA  +GL+E ++++WFQNRRAK RKQ K
Sbjct: 4  MTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 59

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 26/55 (47%), Positives = 36/55 (65%)
Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKER 61
          K RV++S  Q  ELE+ F   RY++   + +LA+ L L+  QVKIWFQNRR K +
Sbjct: 4  KPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 36/58 (62%)
Query: 5  KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          K K R V+S  Q   L   F   +Y+++++  EL+N L LS +QVK WFQN+R K ++
Sbjct: 22 KQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKR 79

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 36/56 (64%)
Query: 4  TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59
          TK K R V+S  Q   L+  F   +Y+++++  EL++ L LS +QVK WFQN+R K
Sbjct: 2  TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMK 57

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 33/55 (60%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
          R  ++  Q  ELE+ F   RY+T  R A+L+  L L   QVKIWF+NRR + + Q
Sbjct: 6  RTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQ 60

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/52 (46%), Positives = 34/52 (65%)
Query: 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
          +S  Q LELE+ F   +Y+    +A LA +L +++ QVK WFQNRR K R+Q
Sbjct: 4  FSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/66 (40%), Positives = 40/66 (60%), Gaps = 4/66 (6%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKRE 68
          R  ++ QQ  ELE  F  +RY  +  + E+A    L+E +V++WF+NRRAK R    KRE
Sbjct: 7  RTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWR----KRE 62
Query: 69 EVVIKD 74
          E ++ D
Sbjct: 63 EFIVTD 68

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 38/61 (62%)
Query: 3  RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          R + + R  +S  Q  ELE+ F  ++Y  I  + ELA    L+E ++++WFQNRRA+ RK
Sbjct: 16 RKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK 75
Query: 63 Q 63
          Q
Sbjct: 76 Q 76

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/59 (42%), Positives = 37/59 (62%)
Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65
          K RV++S  Q  ELE+ F   +Y++   +  LA+ + L+  QVKIWFQN R K ++Q K
Sbjct: 4  KRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/66 (39%), Positives = 39/66 (59%), Gaps = 4/66 (6%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKRE 68
          R  ++ QQ  ELE  F  + Y  +  + E+A    L+E +V++WF+NRRAK R    KRE
Sbjct: 7  RTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWR----KRE 62
Query: 69 EVVIKD 74
          E ++ D
Sbjct: 63 EFIVTD 68

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 36/58 (62%)
Query: 5  KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          K K RV+++  Q  ELE+ F   RY++   +  LA+ + L+  QVKIWFQN R K ++
Sbjct: 9  KRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 34/55 (61%)
Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
          R  ++ +Q  ELE+ F  + Y  I  + ELA    L+E +V++WF NRRA+ RKQ
Sbjct: 6  RTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 37/56 (66%)
Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          ++R +++D+Q   LE  F  ++Y  +  + +LA  + L E +V++WF+NRRAK R+
Sbjct: 9  RHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRR 64

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 35/58 (60%)
Query: 5  KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          K K RV+++  Q  ELE+ F   RY++   +  L + + L+  QVKIWFQN R K ++
Sbjct: 12 KRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKR 69

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 35/58 (60%)
Query: 5  KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          K + R  ++  Q  ELEK F  + Y  +  + +LA    L+E +V++WFQNRRAK RK
Sbjct: 9  KRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRK 66

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 40/75 (53%)
Query: 4  TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
          +  + R  ++ +Q   LEKEF  + Y  +  +  LA  + L E ++++WF NRRAK R++
Sbjct: 6  SGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE 65
Query: 64 LKKREEVVIKDPSKD 78
           K R +     PS  
Sbjct: 66 EKLRNQRRQSGPSSG 80

>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human Eya2 Eya Domain Length = 559

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 20/58 (34%), Positives = 33/58 (56%)
Query: 12  YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREE 69
           + ++ R  L + + ++ Y + R K ELA + GL+  QV  WF+NRR ++R    K  E
Sbjct: 501 FKEKSRGVLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEAKERE 558

>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX Protein Lhx9 Length = 80

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 27/42 (64%)
Query: 37 ELANSLGLSERQVKIWFQNRRAKERKQLKKREEVVIKDPSKD 78
          +LA   GL++R +++WFQN RAK R+ L ++E   +  PS  
Sbjct: 39 QLAQKTGLTKRVLQVWFQNARAKFRRNLLRQENGGVSGPSSG 80

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	186
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	1e-23
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	2e-23
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	3e-23
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	1e-22
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	5e-22
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	8e-22
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	2e-21
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	3e-21
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	1e-20
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	2e-20
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	2e-20
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	2e-20
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	5e-20
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	6e-20
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	7e-20
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	1e-19
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	2e-19
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	2e-19
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	2e-19
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	9e-19
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	9e-19
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	1e-18
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	3e-18
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	3e-18
1e3o_C	160	Octamer-binding transcription factor 1; transcript	5e-17
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	2e-15
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	4e-15
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	2e-14
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	2e-13
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	2e-13
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	3e-13
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	1e-12
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	1e-12
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	1e-12
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	2e-12
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	6e-12
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	8e-12
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	9e-12
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	2e-11
1uhs_A	72	HOP, homeodomain only protein; structural genomics	3e-11
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	4e-11
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	4e-11
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	5e-11
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	6e-11
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	9e-11
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	2e-10
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	6e-10
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	9e-10
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	2e-09
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	4e-09
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	1e-08
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	4e-08
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	2e-06
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	6e-05
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	4e-04

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

 Score = 88.4 bits (219), Expect = 1e-23
 Identities = 34/59 (57%), Positives = 47/59 (79%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65
          + R  Y+  Q LELEKEFH++RY+T RR+ E+A++L L+ERQ+KIWFQNRR K +K+ K
Sbjct: 30 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEHK 88

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

 Score = 88.4 bits (219), Expect = 2e-23
 Identities = 28/61 (45%), Positives = 45/61 (73%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK 66
            R  ++ +Q  ELEKEFH+++Y++  R+ E+A +L L+E QVKIWFQNRR K++K+ ++
Sbjct: 36 GLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE 95

Query: 67 R 67
           
Sbjct: 96 G 96

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

 Score = 87.2 bits (216), Expect = 3e-23
 Identities = 32/59 (54%), Positives = 46/59 (77%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65
          + R  Y+  Q LELEKEFH + Y+T RR+ E+A++L L+ERQ+KIWFQNRR K +K+++
Sbjct: 22 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEIQ 80

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

 Score = 85.6 bits (212), Expect = 1e-22
 Identities = 26/67 (38%), Positives = 40/67 (59%)

Query: 1  KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
          K +   + R V+++ Q + LEK F   +Y++   + +LA SLGLS+ QVK W+QNRR K 
Sbjct: 13 KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKW 72

Query: 61 RKQLKKR 67
          +K     
Sbjct: 73 KKSGPSS 79

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

 Score = 83.6 bits (207), Expect = 5e-22
 Identities = 28/61 (45%), Positives = 38/61 (62%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK 66
            +V +S+ Q +ELEK+F   +Y++   +  LA  L LSERQVK WFQNRRAK R+    
Sbjct: 9  GGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGPS 68

Query: 67 R 67
           
Sbjct: 69 S 69

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

 Score = 83.8 bits (207), Expect = 8e-22
 Identities = 27/69 (39%), Positives = 38/69 (55%)

Query: 1  KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
              + K R  ++  Q  ELEK FH  +Y+    +A LA  L +++ QVK WFQNRR K 
Sbjct: 13 TPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKW 72

Query: 61 RKQLKKREE 69
          R+Q  +  E
Sbjct: 73 RRQTAEERE 81

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

 Score = 82.1 bits (203), Expect = 2e-21
 Identities = 24/63 (38%), Positives = 37/63 (58%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK 66
          + R  ++  Q  ELE+ F   RY+T  R A+L+  L L   QVKIWF+NRR + + Q  +
Sbjct: 4  RTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ 63

Query: 67 REE 69
           ++
Sbjct: 64 HKD 66

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

 Score = 81.7 bits (202), Expect = 3e-21
 Identities = 27/67 (40%), Positives = 41/67 (61%)

Query: 1  KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
             +  K R +YS  Q   L++ F  ++Y+ +  +AELA SLGL++ QVKIWFQN+R+K 
Sbjct: 3  SGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKI 62

Query: 61 RKQLKKR 67
          +K     
Sbjct: 63 KKSGPSS 69

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

 Score = 80.2 bits (198), Expect = 1e-20
 Identities = 35/63 (55%), Positives = 49/63 (77%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK 66
          + R  Y+  Q LELEKEFH++RY+T RR+ E+A++L L+ERQ+KIWFQNRR K +K+ K 
Sbjct: 4  RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKT 63

Query: 67 REE 69
          + E
Sbjct: 64 KGE 66

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

 Score = 79.7 bits (197), Expect = 2e-20
 Identities = 25/64 (39%), Positives = 39/64 (60%)

Query: 5  KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL 64
             +    S  Q +ELE++F + +Y++   +A LA +L L+E QVKIWFQNRR K +++ 
Sbjct: 4  HHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 63

Query: 65 KKRE 68
             E
Sbjct: 64 LSSE 67

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

 Score = 79.9 bits (197), Expect = 2e-20
 Identities = 35/69 (50%), Positives = 45/69 (65%)

Query: 1  KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
            R+  K R  Y+  Q LELEKEF ++ Y+T  R+ E+A  L L+ERQVKIWFQNRR K 
Sbjct: 9  HARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKM 68

Query: 61 RKQLKKREE 69
          +K  K R +
Sbjct: 69 KKINKDRAK 77

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

 Score = 79.8 bits (197), Expect = 2e-20
 Identities = 24/68 (35%), Positives = 38/68 (55%)

Query: 1  KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
              K K RV+++  Q  ELE+ F   RY++   +  LA+ + L+  QVKIWFQN R K 
Sbjct: 5  LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKT 64

Query: 61 RKQLKKRE 68
          ++   ++ 
Sbjct: 65 KRAQNEKG 72

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

 Score = 78.5 bits (194), Expect = 5e-20
 Identities = 26/54 (48%), Positives = 42/54 (77%)

Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          R  +S +Q   L++EF+ +RY+T RR+ +L++ LGL+E Q+KIWF+N+RAK +K
Sbjct: 7  RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

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

 Score = 78.2 bits (193), Expect = 6e-20
 Identities = 30/57 (52%), Positives = 41/57 (71%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
          + R  Y+  Q LELEKEF +++YI+  R+ ELA  L L+ER +KIWFQNRR K +K+
Sbjct: 5  RTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61

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

 Score = 77.7 bits (192), Expect = 7e-20
 Identities = 27/56 (48%), Positives = 40/56 (71%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          K R  ++  Q L LE++F   +Y++I  +AE ++SL L+E QVKIWFQNRRAK ++
Sbjct: 2  KPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

 Score = 77.3 bits (191), Expect = 1e-19
 Identities = 24/60 (40%), Positives = 38/60 (63%)

Query: 4  TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
          TK K R V+S  Q   L+  F   +Y+++++  EL++ L LS +QVK WFQN+R K ++ 
Sbjct: 2  TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW 61

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

 Score = 77.5 bits (191), Expect = 2e-19
 Identities = 25/65 (38%), Positives = 37/65 (56%)

Query: 1  KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
              K K R V+S  Q   L   F   +Y+++++  EL+N L LS +QVK WFQN+R K 
Sbjct: 18 VPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKS 77

Query: 61 RKQLK 65
          ++  K
Sbjct: 78 KRWQK 82

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

 Score = 76.8 bits (189), Expect = 2e-19
 Identities = 26/61 (42%), Positives = 40/61 (65%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK 66
          K R+ YS  Q  ELE+E+  +++IT  ++ +++ +  LSERQ+ IWFQNRR KE+K    
Sbjct: 9  KKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGPS 68

Query: 67 R 67
           
Sbjct: 69 S 69

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

 Score = 76.6 bits (189), Expect = 2e-19
 Identities = 25/57 (43%), Positives = 37/57 (64%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
          +YR  ++  Q   LEKEF+   Y++  R+ ELA  L L E  +K+WFQNRR K+++Q
Sbjct: 3  RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59

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

 Score = 75.0 bits (185), Expect = 9e-19
 Identities = 26/55 (47%), Positives = 36/55 (65%)

Query: 5  KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59
          + K RV++S  Q  ELE+ F   RY++   + +LA+ L L+  QVKIWFQNRR K
Sbjct: 2  RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYK 56

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

 Score = 75.1 bits (185), Expect = 9e-19
 Identities = 25/65 (38%), Positives = 39/65 (60%)

Query: 5  KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL 64
          + K RV++S  Q  ELE+ F   +Y++   +  LA+ + L+  QVKIWFQN R K ++Q 
Sbjct: 2  RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61

Query: 65 KKREE 69
          K +  
Sbjct: 62 KDKAA 66

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

 Score = 74.3 bits (183), Expect = 1e-18
 Identities = 24/53 (45%), Positives = 34/53 (64%)

Query: 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
           +S  Q LELE+ F   +Y+    +A LA +L +++ QVK WFQNRR K R+Q
Sbjct: 3  SFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

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

 Score = 74.1 bits (182), Expect = 3e-18
 Identities = 28/62 (45%), Positives = 42/62 (67%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK 66
          K RV Y+  Q  ELE+E+  +++IT  ++  ++ +  LSERQV IWFQNRR KE+K + K
Sbjct: 9  KKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINK 68

Query: 67 RE 68
           +
Sbjct: 69 LK 70

>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 = 73.4 bits (181), Expect = 3e-18
 Identities = 16/51 (31%), Positives = 28/51 (54%)

Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59
          +   S Q R  LE+ F   + +  + K E+A   G++  QV++WF N+R +
Sbjct: 9  KSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 59

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

 Score = 73.1 bits (179), Expect = 5e-17
 Identities = 17/61 (27%), Positives = 29/61 (47%)

Query: 2   TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKER 61
              + K R       R+ LEK F  ++  T      +A  L + +  +++WF NRR KE+
Sbjct: 98  LSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEK 157

Query: 62  K 62
           +
Sbjct: 158 R 158

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

 Score = 69.7 bits (170), Expect = 2e-15
 Identities = 18/60 (30%), Positives = 26/60 (43%)

Query: 7   KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK 66
           K R       +  LE  F      +      LA+SL L +  V++WF NRR KE++    
Sbjct: 101 KKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTPA 160

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

 Score = 65.9 bits (161), Expect = 4e-15
 Identities = 17/61 (27%), Positives = 26/61 (42%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK 66
           Y+   S +Q   L+  F  +++        L    GLS R+V+ WF +RR   R     
Sbjct: 10 IYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGS 69

Query: 67 R 67
          R
Sbjct: 70 R 70

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

 Score = 63.5 bits (155), Expect = 2e-14
 Identities = 19/63 (30%), Positives = 28/63 (44%)

Query: 3  RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
           +    R  ++D Q   L+  F  + Y       +L+N L L  R + +WFQN R K RK
Sbjct: 5  SSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64

Query: 63 QLK 65
             
Sbjct: 65 SGP 67

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

 Score = 61.7 bits (150), Expect = 2e-13
 Identities = 18/66 (27%), Positives = 34/66 (51%)

Query: 1  KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
          + +   + R   + +Q   L +++      T +    +A+ +GL +R V++WFQN RA+E
Sbjct: 13 EPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARE 72

Query: 61 RKQLKK 66
          RK    
Sbjct: 73 RKSGPS 78

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

 Score = 63.5 bits (154), Expect = 2e-13
 Identities = 17/58 (29%), Positives = 28/58 (48%)

Query: 5   KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
           K K R   S   +  LE+ F      + +    +A  L L +  V++WF NRR +E++
Sbjct: 87  KRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 144

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

 Score = 60.9 bits (148), Expect = 3e-13
 Identities = 20/69 (28%), Positives = 35/69 (50%)

Query: 8  YRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR 67
           R  +   Q   ++  F  +     +   +LA   GL++R +++WFQN RAK R+ L ++
Sbjct: 10 MRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQ 69

Query: 68 EEVVIKDPS 76
          E   +  PS
Sbjct: 70 ENGGVSGPS 78

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

 Score = 59.3 bits (144), Expect = 1e-12
 Identities = 16/57 (28%), Positives = 28/57 (49%)

Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65
          R   +D Q   L + F  +   +  +  E+A+  GL ++ +K WF+N   KER+   
Sbjct: 11 RTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGP 67

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

 Score = 59.4 bits (144), Expect = 1e-12
 Identities = 24/76 (31%), Positives = 41/76 (53%)

Query: 1  KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
             +  + R  ++  Q   LE  F  +RY  I  + E+A  + L E +V++WF+NRRAK 
Sbjct: 3  SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKC 62

Query: 61 RKQLKKREEVVIKDPS 76
          R+Q ++++      PS
Sbjct: 63 RQQQQQQQNGGQSGPS 78

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

 Score = 59.4 bits (144), Expect = 1e-12
 Identities = 15/62 (24%), Positives = 27/62 (43%), Gaps = 1/62 (1%)

Query: 9  RVVYSDQQRLELEKEFH-YSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR 67
              ++ Q   LE  F+  +++        +A   GL+E Q + WF+ R A+ R+     
Sbjct: 6  VSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLP 65

Query: 68 EE 69
           E
Sbjct: 66 SE 67

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

 Score = 58.9 bits (143), Expect = 2e-12
 Identities = 24/74 (32%), Positives = 40/74 (54%)

Query: 3  RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
           +  + R  ++ +Q   LEKEF  + Y  +  +  LA  + L E ++++WF NRRAK R+
Sbjct: 5  SSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRR 64

Query: 63 QLKKREEVVIKDPS 76
          + K R +     PS
Sbjct: 65 EEKLRNQRRQSGPS 78

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

 Score = 59.9 bits (144), Expect = 6e-12
 Identities = 16/67 (23%), Positives = 29/67 (43%)

Query: 3   RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
            T  K R+V++D QR  L   F  ++  +   +  ++  LGL    V  +F N R +   
Sbjct: 95  NTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLD 154

Query: 63  QLKKREE 69
           +  +   
Sbjct: 155 KWLEHHH 161

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

 Score = 56.9 bits (138), Expect = 8e-12
 Identities = 25/57 (43%), Positives = 37/57 (64%)

Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65
           + ++  Q  ELEK F  + Y  +  + ELA  +GL+E ++++WFQNRRAK RKQ K
Sbjct: 3  HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 59

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

 Score = 59.3 bits (143), Expect = 9e-12
 Identities = 16/60 (26%), Positives = 24/60 (40%)

Query: 3   RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
             K K R  ++ Q    L   F  +   T +   E+A  L      V++WF NRR   + 
Sbjct: 91  SKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN 150

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

 Score = 56.2 bits (136), Expect = 2e-11
 Identities = 20/61 (32%), Positives = 32/61 (52%)

Query: 8  YRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR 67
           R  ++  Q   LE  F  + Y  I    +LA  L L   +++IWFQNRRAK ++  ++ 
Sbjct: 4  PRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRES 63

Query: 68 E 68
          +
Sbjct: 64 Q 64

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

 Score = 55.9 bits (135), Expect = 3e-11
 Identities = 15/64 (23%), Positives = 28/64 (43%), Gaps = 1/64 (1%)

Query: 7  KYRVVYSDQQRLELEKEFH-YSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65
          +     ++ Q   LE  F+  +++        +A   GL+E Q + WF+ R A+ R+   
Sbjct: 3  EGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG 62

Query: 66 KREE 69
             E
Sbjct: 63 LPSE 66

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

 Score = 55.4 bits (134), Expect = 4e-11
 Identities = 17/59 (28%), Positives = 30/59 (50%)

Query: 8  YRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK 66
           R V +++Q   L   +  +       K +L    GLS R +++WFQN+R K++K+   
Sbjct: 6  VRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSIM 64

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

 Score = 55.4 bits (134), Expect = 4e-11
 Identities = 20/63 (31%), Positives = 38/63 (60%)

Query: 3  RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
           +  ++R +++D+Q   LE  F  ++Y  +  + +LA  + L E +V++WF+NRRAK R+
Sbjct: 5  SSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRR 64

Query: 63 QLK 65
             
Sbjct: 65 SGP 67

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

 Score = 55.0 bits (133), Expect = 5e-11
 Identities = 22/59 (37%), Positives = 37/59 (62%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65
          + R  ++ QQ  +LE  F  +RY  +  + E+A    L+E +V++WF+NRRAK RK+ +
Sbjct: 5  RQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREE 63

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

 Score = 57.0 bits (137), Expect = 6e-11
 Identities = 18/56 (32%), Positives = 31/56 (55%)

Query: 7   KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
           + R    ++ R  LE  F  S   ++++   +AN LGL +  V++WF NRR K ++
Sbjct: 98  RKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKR 153

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

 Score = 54.7 bits (132), Expect = 9e-11
 Identities = 25/63 (39%), Positives = 38/63 (60%)

Query: 3  RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          R + + R  +S  Q  ELE+ F  ++Y  I  + ELA    L+E ++++WFQNRRA+ RK
Sbjct: 16 RKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK 75

Query: 63 QLK 65
          Q  
Sbjct: 76 QHT 78

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

 Score = 54.2 bits (130), Expect = 2e-10
 Identities = 14/57 (24%), Positives = 20/57 (35%)

Query: 13 SDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREE 69
          +  Q   LE  F  S + T      L     LS R++  WF  RR       +   +
Sbjct: 21 TQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAVLD 77

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

 Score = 52.2 bits (125), Expect = 6e-10
 Identities = 12/57 (21%), Positives = 22/57 (38%)

Query: 13 SDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREE 69
          + +Q   LE  F  +          L +   ++ R++  WF  RR K   +  K+  
Sbjct: 15 APEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETKKSG 71

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

 Score = 52.3 bits (125), Expect = 9e-10
 Identities = 12/56 (21%), Positives = 24/56 (42%)

Query: 13 SDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKRE 68
          + +Q   L+  F  S  +T      L     L+ R++  WF  ++  +  + +K E
Sbjct: 19 TAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKME 74

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

 Score = 51.0 bits (122), Expect = 2e-09
 Identities = 12/56 (21%), Positives = 20/56 (35%), Gaps = 1/56 (1%)

Query: 9  RVVYSDQQRLELEKEFH-YSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
          R   S +    L+   H    Y        L+  L L +  +  +FQN+R   +  
Sbjct: 11 RTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS 66

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

 Score = 49.8 bits (119), Expect = 4e-09
 Identities = 11/60 (18%), Positives = 25/60 (41%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK 66
           +    + +Q   L+  F  S++        L    GL+  ++K WF + R + ++ +  
Sbjct: 6  HHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGIVH 65

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

 Score = 48.6 bits (116), Expect = 1e-08
 Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 3/59 (5%)

Query: 5  KDKYRVVYSDQQRLELEKEF-HYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          KD        +    LEK F   ++Y   +R   L+  L  S R+++ WF++RR +++ 
Sbjct: 10 KDSPVN--KVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKP 66

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

 Score = 48.1 bits (114), Expect = 4e-08
 Identities = 15/91 (16%), Positives = 34/91 (37%), Gaps = 15/91 (16%)

Query: 1  KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLG---------------LS 45
             +    R  +  +    +E  F+ ++Y    ++ E+AN+                 ++
Sbjct: 3  SGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVT 62

Query: 46 ERQVKIWFQNRRAKERKQLKKREEVVIKDPS 76
            +V  WF NRR + +++      +    PS
Sbjct: 63 SLKVYNWFANRRKEIKRRANIAAILESSGPS 93

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

 Score = 42.9 bits (101), Expect = 2e-06
 Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 20 LEKEF-HYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          LEK F   +++   +R   L+  L    R ++ WF+ RR +E+ 
Sbjct: 15 LEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 58

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

 Score = 39.4 bits (91), Expect = 6e-05
 Identities = 11/60 (18%), Positives = 23/60 (38%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK 66
                + +Q   L+  F  +++ +     +LA   GL+   +  WF + R   +    K
Sbjct: 27 GKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNLK 86

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

 Score = 36.7 bits (84), Expect = 4e-04
 Identities = 10/53 (18%), Positives = 22/53 (41%)

Query: 10 VVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          +         LE+ +   + +      +L+ +  LS +QV  WF +R  +  +
Sbjct: 11 IPPPPPDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSRLPQPAE 63

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	186
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.86
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.86
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.86
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.86
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.86
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.86
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.86
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.86
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.86
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.85
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.85
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.85
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.85
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.85
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.85
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.85
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.85
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.85
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.85
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.85
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.85
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.84
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.84
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.84
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.84
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.84
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.84
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.84
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.84
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.84
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.84
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.84
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.83
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.83
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.83
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.83
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.83
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.83
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.83
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.83
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.83
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.82
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.82
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.81
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.81
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.81
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.8
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.8
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.8
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.8
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.8
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.8
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.79
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.79
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.79
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.79
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.78
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.78
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.78
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.78
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.77
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.77
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.76
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.76
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.76
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.76
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.76
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.75
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.73
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.73
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.71
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.7
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.62
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.61
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.59
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.55
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.36
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.68
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	98.28
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	98.21
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.07
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	97.85
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	97.85
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	97.8
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	97.78
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	97.74
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	97.73
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	97.65
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	97.65
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	97.6
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	97.56
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	97.55
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	97.52
2e19_A	64	Transcription factor 8; homeobox domain, structura	97.52
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	97.5
1uhs_A	72	HOP, homeodomain only protein; structural genomics	97.49
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	97.49
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	97.46
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	97.46
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	97.45
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	97.44
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	97.44
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	97.42
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	97.41
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	97.39
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	97.38
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	97.37
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	97.36
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	97.36
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	97.35
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	97.33
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	97.32
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	97.29
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	97.27
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	97.27
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	97.23
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	97.19
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	97.19
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	97.19
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	97.18
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	97.15
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	97.15
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	97.13
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	97.11
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	97.05
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	97.03
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	97.02
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	96.99
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	96.96
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	96.91
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	96.91
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	96.9
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	96.9
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	96.9
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	96.89
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	96.84
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	96.82
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	96.67
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	96.66
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	96.62
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	96.54
1lfb_A	99	Liver transcription factor (LFB1); transcription r	96.52
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	96.31
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	96.28
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	96.25
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	96.19
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	96.09
1e3o_C	160	Octamer-binding transcription factor 1; transcript	96.05
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	95.93
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	95.66
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	95.6
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	95.53
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	95.37
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	95.26
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	95.1
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	95.03
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	94.74
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	91.18
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	90.71
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	88.83
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	82.12
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	80.2

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

Probab=99.86  E-value=1.7e-21  Score=125.57  Aligned_cols=68  Identities=32%  Similarity=0.573  Sum_probs=62.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhhh
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEV   70 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~~   70 (186)
                      .+.+|.|+.||.+|+.+||..|..++||+..++.+||..+||++.+|++||||||+++++........
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~~~~   72 (80)
T 2cue_A            5 SSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQR   72 (80)
T ss_dssp             CSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhhhcc
Confidence            56788999999999999999999999999999999999999999999999999999999987665543

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

Probab=99.86  E-value=1.5e-21  Score=124.96  Aligned_cols=66  Identities=36%  Similarity=0.659  Sum_probs=61.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhh
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR   67 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~   67 (186)
                      +++.++.|+.||..|+.+||..|..++||+..++++||..+||++.+|++||||||+++++.....
T Consensus         6 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~~   71 (77)
T 1nk2_P            6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEK   71 (77)
T ss_dssp             SCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhccc
Confidence            467788899999999999999999999999999999999999999999999999999999876543

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

Probab=99.86  E-value=2e-21  Score=125.32  Aligned_cols=67  Identities=27%  Similarity=0.479  Sum_probs=62.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhh
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKRE   68 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~   68 (186)
                      ..+.+|.|+.||.+|+.+|+..|..++||+..+++.||..+||++.+|++||||||+++++......
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~   70 (80)
T 2dmq_A            4 GSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQE   70 (80)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHHHh
Confidence            3567889999999999999999999999999999999999999999999999999999999766543

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

Probab=99.86  E-value=1.5e-21  Score=120.23  Aligned_cols=60  Identities=50%  Similarity=0.833  Sum_probs=55.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536           4 TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus         4 ~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~   63 (186)
                      +.+|.|+.||..|+.+|+..|..++||+..++.+||..+||++.+|++||||+|+++++.
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   61 (63)
T 2h1k_A            2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE   61 (63)
T ss_dssp             ---CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhh
Confidence            467889999999999999999999999999999999999999999999999999999975

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

Probab=99.86  E-value=1.8e-21  Score=117.98  Aligned_cols=57  Identities=47%  Similarity=0.807  Sum_probs=55.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536           6 DKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus         6 rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      |+.|+.||.+|+.+|+..|..++||+..++.+||..+||++.+|++||||+|+++++
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            578999999999999999999999999999999999999999999999999999986

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

Probab=99.86  E-value=1e-21  Score=120.17  Aligned_cols=58  Identities=45%  Similarity=0.818  Sum_probs=53.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536           5 KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      .+|.|+.||.+|+.+||..|..++||+..++++||..+||++.+|++||||+|+++++
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            5688999999999999999999999999999999999999999999999999999885

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

Probab=99.86  E-value=6.1e-22  Score=121.23  Aligned_cols=61  Identities=30%  Similarity=0.487  Sum_probs=48.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536           1 KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKER   61 (186)
Q Consensus         1 ~~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~   61 (186)
                      |.++.++.|+.||.+|+.+|+.+|..++||+..++.+||..+||++.+|++||+|+|++++
T Consensus         1 kk~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            1 KKEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             -----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            5678889999999999999999999999999999999999999999999999999999864

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

Probab=99.86  E-value=1.5e-21  Score=129.24  Aligned_cols=71  Identities=38%  Similarity=0.586  Sum_probs=62.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhhhhc
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVVI   72 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~~~~   72 (186)
                      +.+.++.|+.||.+|+.+||..|..++||+..++.+||..+||++.+|++||||||+++++..........
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~~~~~   84 (93)
T 3a01_A           14 PPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEEREAER   84 (93)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC-----
T ss_pred             CCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHHHHHHH
Confidence            35678889999999999999999999999999999999999999999999999999999998766544433

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

Probab=99.86  E-value=1.2e-21  Score=126.23  Aligned_cols=62  Identities=40%  Similarity=0.696  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~   63 (186)
                      .++.+|.|+.||.+|+.+||..|..++||+..++++||..|||++.+|++||||||+++++.
T Consensus        14 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~   75 (80)
T 2dmt_A           14 AKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKS   75 (80)
T ss_dssp             CCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcc
Confidence            46778899999999999999999999999999999999999999999999999999999864

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

Probab=99.85  E-value=3e-21  Score=123.55  Aligned_cols=65  Identities=52%  Similarity=0.774  Sum_probs=61.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHh
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK   66 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~   66 (186)
                      .++.++.|+.||..|+.+||..|..++||+..++++||..+||++.+|++||||||+++++....
T Consensus        10 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k~   74 (77)
T 1puf_A           10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhhh
Confidence            35678899999999999999999999999999999999999999999999999999999987654

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

Probab=99.85  E-value=2.6e-21  Score=121.66  Aligned_cols=62  Identities=32%  Similarity=0.594  Sum_probs=58.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      .+.+|.|+.||.+|+.+||..|..++||+..++++||..+||++.+|++||||+|+++++..
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~   66 (70)
T 2dmu_A            5 SSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSG   66 (70)
T ss_dssp             TSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccC
Confidence            46788899999999999999999999999999999999999999999999999999999753

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

Probab=99.85  E-value=1.1e-21  Score=126.44  Aligned_cols=65  Identities=34%  Similarity=0.514  Sum_probs=60.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHh
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK   66 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~   66 (186)
                      .++.+|.|+.||.+|+.+||..|..++||+..++++||..+||++.+|++||||||+++++....
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~   68 (80)
T 2dms_A            4 GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQ   68 (80)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHc
Confidence            35778899999999999999999999999999999999999999999999999999999986543

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

Probab=99.85  E-value=5e-22  Score=121.97  Aligned_cols=60  Identities=40%  Similarity=0.663  Sum_probs=52.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536           4 TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus         4 ~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~   63 (186)
                      +.++.|+.||.+|+.+||..|..++||+..++.+||..+||++.+|++||||+|+++++.
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            467889999999999999999999999999999999999999999999999999998863

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

Probab=99.85  E-value=1.2e-21  Score=123.15  Aligned_cols=62  Identities=42%  Similarity=0.701  Sum_probs=58.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~   63 (186)
                      ..+.++.|+.||.+|+.+||..|..++||+..++++||..+||++.+|++||||||+++++.
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~   65 (70)
T 2cra_A            4 GSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKS   65 (70)
T ss_dssp             SCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSS
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhccc
Confidence            35678899999999999999999999999999999999999999999999999999998864

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

Probab=99.85  E-value=2.9e-21  Score=120.68  Aligned_cols=63  Identities=38%  Similarity=0.637  Sum_probs=59.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhh
Q psy8536           5 KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR   67 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~   67 (186)
                      .++.|+.||.+|+.+|+..|..++||+..++..||..+||++.+|++||||||+++++.....
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~~   64 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQH   64 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhccc
Confidence            467899999999999999999999999999999999999999999999999999999876543

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

Probab=99.85  E-value=4.3e-21  Score=123.99  Aligned_cols=64  Identities=39%  Similarity=0.642  Sum_probs=59.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK   65 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~   65 (186)
                      .++.++.|+.||..|+.+|+..|..++||+..++..||..+||++.+|++||||||++++++..
T Consensus        15 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~   78 (81)
T 1fjl_A           15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   78 (81)
T ss_dssp             --CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhcc
Confidence            3567889999999999999999999999999999999999999999999999999999998764

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

Probab=99.85  E-value=2.8e-21  Score=121.50  Aligned_cols=62  Identities=31%  Similarity=0.429  Sum_probs=58.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~   63 (186)
                      ..+.++.|+.||.+|+.+||..|..++||+..++++||..+||++.+|++||||+|+++++.
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   65 (70)
T 2da2_A            4 GSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKS   65 (70)
T ss_dssp             SCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhc
Confidence            45778899999999999999999999999999999999999999999999999999999864

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

Probab=99.85  E-value=2.8e-21  Score=120.71  Aligned_cols=61  Identities=56%  Similarity=0.917  Sum_probs=57.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536           5 KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK   65 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~   65 (186)
                      ++|.|+.||.+|+.+||..|..++||+..++.+||..+||++.+|++||||||+++++...
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~   62 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK   62 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhcc
Confidence            4678999999999999999999999999999999999999999999999999999998653

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

Probab=99.85  E-value=4e-21  Score=117.16  Aligned_cols=58  Identities=43%  Similarity=0.777  Sum_probs=55.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536           6 DKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus         6 rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~   63 (186)
                      ||.|+.||.+|+.+|+..|..++||+..++.+||..+||++.+|++||||+|++++++
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   59 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHhHhhcc
Confidence            5789999999999999999999999999999999999999999999999999999874

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

Probab=99.85  E-value=2.3e-21  Score=121.86  Aligned_cols=62  Identities=26%  Similarity=0.386  Sum_probs=58.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~   63 (186)
                      .++.++.|+.||.+|+.+|+..|..++||+..++.+||..+||++.+|++||||+|+++++.
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   65 (70)
T 2da1_A            4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQS   65 (70)
T ss_dssp             SCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhh
Confidence            35678899999999999999999999999999999999999999999999999999999874

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

Probab=99.85  E-value=6.7e-21  Score=119.71  Aligned_cols=62  Identities=45%  Similarity=0.664  Sum_probs=58.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      .+.++.|++||.+|+.+||..|..++||+..++++||..+||++.+|++||||||+++++..
T Consensus         5 ~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~   66 (70)
T 2e1o_A            5 SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSG   66 (70)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCC
Confidence            45677899999999999999999999999999999999999999999999999999999754

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

Probab=99.84  E-value=3.8e-21  Score=121.78  Aligned_cols=62  Identities=44%  Similarity=0.691  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      .+.++.|+.||.+|+.+||..|..++||+..++.+||..+||++.+|++||||||+++++..
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   66 (73)
T 2l7z_A            5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVI   66 (73)
T ss_dssp             SCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHh
Confidence            56788999999999999999999999999999999999999999999999999999998753

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

Probab=99.84  E-value=5.8e-21  Score=119.31  Aligned_cols=61  Identities=41%  Similarity=0.694  Sum_probs=57.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536           5 KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK   65 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~   65 (186)
                      +++.|+.||.+|+.+|+..|..++||+..++.+||..+||++.+|++||||+|+++++...
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~   62 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK   62 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhh
Confidence            5678999999999999999999999999999999999999999999999999999998654

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

Probab=99.84  E-value=2.6e-21  Score=120.25  Aligned_cols=60  Identities=28%  Similarity=0.493  Sum_probs=56.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536           4 TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus         4 ~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~   63 (186)
                      +.+|.|+.||.+|+.+|+..|..++||+..+++.||..+||++.+|++||||+|+++++.
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   61 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR   61 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHH
Confidence            467889999999999999999999999999999999999999999999999999998764

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

Probab=99.84  E-value=1.7e-21  Score=121.75  Aligned_cols=63  Identities=35%  Similarity=0.578  Sum_probs=59.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHh
Q psy8536           4 TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK   66 (186)
Q Consensus         4 ~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~   66 (186)
                      +.++.|+.||.+|+.+|+..|..++||+..++.+||..+||++.+|++||||+|+++++....
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~~   64 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEF   64 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhhc
Confidence            567889999999999999999999999999999999999999999999999999999986543

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

Probab=99.84  E-value=2.5e-21  Score=121.68  Aligned_cols=62  Identities=44%  Similarity=0.731  Sum_probs=58.3

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~   63 (186)
                      ..+.++.|+.||.+|+.+||..|..++||+..++++||..+||++.+|++||||+|+++++.
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   65 (70)
T 2djn_A            4 GSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKS   65 (70)
T ss_dssp             CCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhccc
Confidence            35678889999999999999999999999999999999999999999999999999998763

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

Probab=99.84  E-value=2.2e-21  Score=124.78  Aligned_cols=59  Identities=10%  Similarity=0.223  Sum_probs=56.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhh----cCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHY----SRYITIRRKAELANSLGLSERQVKIWFQNRRAKER   61 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~----~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~   61 (186)
                      ++.||.||.||.+|+.+|+..|..    ++||+..++++||..|||++.+|+|||||+|+|.+
T Consensus        15 ~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~   77 (80)
T 1wh5_A           15 GIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGP   77 (80)
T ss_dssp             CCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSS
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCC
Confidence            567889999999999999999999    99999999999999999999999999999999865

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

Probab=99.84  E-value=7.3e-21  Score=115.25  Aligned_cols=57  Identities=46%  Similarity=0.761  Sum_probs=54.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536           5 KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKER   61 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~   61 (186)
                      +++.|+.||..|+.+|+..|..++||+..++++||..+||++.+|++||||+|+++|
T Consensus         2 ~rr~Rt~~t~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~k   58 (58)
T 3rkq_A            2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK   58 (58)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHC
T ss_pred             cCCCCCCcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhhccCC
Confidence            467899999999999999999999999999999999999999999999999999874

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

Probab=99.84  E-value=3.2e-21  Score=124.37  Aligned_cols=62  Identities=29%  Similarity=0.483  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~   63 (186)
                      .++.+|.|+.||.+|+.+|+..|..++||+..++++||..|||++.+|++||||||+++++.
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   75 (80)
T 2da3_A           14 PQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKS   75 (80)
T ss_dssp             CCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhh
Confidence            45678899999999999999999999999999999999999999999999999999999874

>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.84  E-value=9.6e-21  Score=119.40  Aligned_cols=58  Identities=16%  Similarity=0.191  Sum_probs=54.7

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536           7 KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus         7 r~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      ..|..||.+|+.+|+..|..++||+..++++||..+||++.+|++||||+|+++|+..
T Consensus         5 ~~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~   62 (76)
T 2ecc_A            5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ   62 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHH
Confidence            4578899999999999999999999999999999999999999999999999998753

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

Probab=99.84  E-value=5e-21  Score=123.38  Aligned_cols=62  Identities=23%  Similarity=0.309  Sum_probs=58.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhc----CCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYS----RYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~----~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~   63 (186)
                      .++.+|.|+.||.+|+.+|+.+|..+    +||+..++++||.++||++.+|++||||+|+++++.
T Consensus         5 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~   70 (80)
T 2da4_A            5 SSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLM   70 (80)
T ss_dssp             CCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhc
Confidence            35678889999999999999999999    999999999999999999999999999999999884

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

Probab=99.84  E-value=4.7e-21  Score=124.67  Aligned_cols=62  Identities=39%  Similarity=0.631  Sum_probs=58.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~   63 (186)
                      .++.+|.|+.||..|+.+||..|..++||+..++..||..+||++.+|++||||||+++++.
T Consensus        19 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~   80 (84)
T 2kt0_A           19 PVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRW   80 (84)
T ss_dssp             CSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence            35678889999999999999999999999999999999999999999999999999998864

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

Probab=99.83  E-value=3.6e-21  Score=119.93  Aligned_cols=61  Identities=33%  Similarity=0.512  Sum_probs=57.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536           5 KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK   65 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~   65 (186)
                      .||.|+.||.+|+.+|+..|..++||+..++..||..+||++.+|++||||+|+++++...
T Consensus         1 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~   61 (67)
T 2k40_A            1 GRRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR   61 (67)
T ss_dssp             CCCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCC
T ss_pred             CcCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhch
Confidence            3678999999999999999999999999999999999999999999999999999987543

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

Probab=99.83  E-value=4.5e-21  Score=123.82  Aligned_cols=61  Identities=52%  Similarity=0.847  Sum_probs=53.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~   63 (186)
                      .+.+|.|+.||.+|+.+||..|..++||+..++++||..+||++.+|++||||||+++++.
T Consensus        18 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   78 (81)
T 1b8i_A           18 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE   78 (81)
T ss_dssp             ------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhh
Confidence            4567889999999999999999999999999999999999999999999999999999875

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

Probab=99.83  E-value=1.4e-20  Score=113.11  Aligned_cols=54  Identities=44%  Similarity=0.733  Sum_probs=50.9

Q ss_pred             CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536          10 VVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus        10 ~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~   63 (186)
                      |.||.+|+.+||..|..++||+..++.+||..+||++.+|++||||||++++++
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~   55 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ   55 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhhccc
Confidence            679999999999999999999999999999999999999999999999999975

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

Probab=99.83  E-value=2.2e-20  Score=117.98  Aligned_cols=59  Identities=24%  Similarity=0.303  Sum_probs=56.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHhh-cCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536           6 DKYRVVYSDQQRLELEKEFHY-SRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus         6 rr~r~~~t~~q~~~L~~~f~~-~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      .+.|+.||.+|+.+||..|.. ++||+..++++||..+||++.+|++||||||+++++..
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~   61 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhc
Confidence            467899999999999999996 99999999999999999999999999999999999865

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

Probab=99.83  E-value=1.3e-20  Score=119.96  Aligned_cols=63  Identities=38%  Similarity=0.572  Sum_probs=59.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      .+++++.|+.||..|+.+|+..|..++||+..++++||..+||++.+|++||||+|+++++..
T Consensus         6 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   68 (75)
T 2m0c_A            6 KGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRE   68 (75)
T ss_dssp             CSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHH
Confidence            456778899999999999999999999999999999999999999999999999999998753

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

Probab=99.83  E-value=1e-20  Score=115.29  Aligned_cols=57  Identities=42%  Similarity=0.660  Sum_probs=50.7

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536           8 YRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus         8 ~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      .|+.||.+|+.+|+..|..++||+..++.+||..+||++.+|++||||||+++++..
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~   58 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE   58 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC---
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhc
Confidence            479999999999999999999999999999999999999999999999999998764

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

Probab=99.83  E-value=2.5e-20  Score=118.04  Aligned_cols=61  Identities=23%  Similarity=0.249  Sum_probs=57.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhh-cCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536           5 KDKYRVVYSDQQRLELEKEFHY-SRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK   65 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f~~-~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~   65 (186)
                      .++.|+.||.+|+.+||..|.. ++||+..++++||..+||++.+|++||||||+++++...
T Consensus         2 ~~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~~   63 (73)
T 2hi3_A            2 SAQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   63 (73)
T ss_dssp             CCSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhcc
Confidence            3567899999999999999995 999999999999999999999999999999999998663

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

Probab=99.83  E-value=1.9e-20  Score=113.59  Aligned_cols=57  Identities=21%  Similarity=0.197  Sum_probs=54.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhh-cCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHY-SRYITIRRKAELANSLGLSERQVKIWFQNRRAK   59 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~-~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~   59 (186)
                      ++.+|.||.|+.+|+.+|+.+|+. ++|||...|+.||.++||++++|++||||+|--
T Consensus         5 ~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~   62 (71)
T 1wi3_A            5 SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYH   62 (71)
T ss_dssp             CCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceee
Confidence            567889999999999999999999 999999999999999999999999999999964

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

Probab=99.83  E-value=1.5e-20  Score=123.31  Aligned_cols=61  Identities=54%  Similarity=0.911  Sum_probs=54.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~   63 (186)
                      .+.+|.|+.||.+|+.+||..|..++||+..++++||..+||++.+|++||||||+++++.
T Consensus        26 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~   86 (88)
T 2r5y_A           26 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   86 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhh
Confidence            4567889999999999999999999999999999999999999999999999999999874

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

Probab=99.82  E-value=2.3e-20  Score=124.52  Aligned_cols=62  Identities=45%  Similarity=0.805  Sum_probs=56.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536           4 TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK   65 (186)
Q Consensus         4 ~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~   65 (186)
                      +.++.|+.||.+|+.+||..|..++||+..++.+||..+||++.+|++||||||+++++...
T Consensus        33 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   94 (97)
T 1b72_A           33 SPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   94 (97)
T ss_dssp             ----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhc
Confidence            45788999999999999999999999999999999999999999999999999999998764

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

Probab=99.82  E-value=6.6e-21  Score=122.32  Aligned_cols=58  Identities=16%  Similarity=0.334  Sum_probs=54.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhh-----cCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHY-----SRYITIRRKAELANSLGLSERQVKIWFQNRRAKER   61 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~-----~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~   61 (186)
                      .++||.||.||.+|+.+|+ .|..     ++||+..++++||.+|||++.+|+|||||+|+|.+
T Consensus        15 ~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~   77 (80)
T 1wh7_A           15 GTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGP   77 (80)
T ss_dssp             CCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSC
T ss_pred             CCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCC
Confidence            5678889999999999999 7999     99999999999999999999999999999999865

>1puf_B PRE-B-cell leukemia transcription factor-1; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Homo sapiens} SCOP: a.4.1.1 PDB: 1b8i_B* 2r5y_B* 2r5z_B*

Probab=99.81  E-value=5e-20  Score=116.64  Aligned_cols=62  Identities=29%  Similarity=0.437  Sum_probs=57.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHH---hhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHh
Q psy8536           5 KDKYRVVYSDQQRLELEKEF---HYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK   66 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f---~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~   66 (186)
                      .||+|+.||.+|+.+|+.+|   ..++||+..++..||..+||++.+|++||+|+|+++++....
T Consensus         1 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~   65 (73)
T 1puf_B            1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGK   65 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTT
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccccccc
Confidence            36789999999999999999   899999999999999999999999999999999999876543

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

Probab=99.81  E-value=7e-20  Score=121.73  Aligned_cols=65  Identities=20%  Similarity=0.353  Sum_probs=61.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcC---------------CChhHHHHHHHhhHHHHHHHHHh
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLG---------------LSERQVKIWFQNRRAKERKQLKK   66 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~---------------l~~~~v~~WFqnrr~~~~~~~~~   66 (186)
                      .++++|.|+.||..|+.+||..|..++||+..++++||..+|               |++.+|++||||||+++++....
T Consensus         4 ~~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~~   83 (95)
T 2cuf_A            4 GSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANI   83 (95)
T ss_dssp             SSCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhhc
Confidence            357788999999999999999999999999999999999999               99999999999999999987765

>1x2n_A Homeobox protein pknox1; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.81  E-value=1.2e-19  Score=114.87  Aligned_cols=62  Identities=21%  Similarity=0.213  Sum_probs=58.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHY---SRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~---~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      ++.++.|+.|+.+|+.+|+.+|..   ++||+..++++||..+||++.+|++||+|+|+++++..
T Consensus         5 ~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~   69 (73)
T 1x2n_A            5 SSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSG   69 (73)
T ss_dssp             SSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhccccc
Confidence            567788999999999999999976   99999999999999999999999999999999998753

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

Probab=99.80  E-value=1.1e-19  Score=115.59  Aligned_cols=59  Identities=19%  Similarity=0.230  Sum_probs=55.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536           6 DKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus         6 rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      .++|+.||.+|+.+||..|..++||+..++.+||..+||++.+|++||||||+++++..
T Consensus         8 ~~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~   66 (75)
T 2da5_A            8 PTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEE   66 (75)
T ss_dssp             SCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSS
T ss_pred             CCCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhh
Confidence            45678899999999999999999999999999999999999999999999999999754

>1b72_B Protein (PBX1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1 PDB: 1lfu_P

Probab=99.80  E-value=1.3e-19  Score=118.60  Aligned_cols=63  Identities=29%  Similarity=0.424  Sum_probs=58.2

Q ss_pred             CCCCCCCCHHHHHHHHHHH---hhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhh
Q psy8536           6 DKYRVVYSDQQRLELEKEF---HYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKRE   68 (186)
Q Consensus         6 rr~r~~~t~~q~~~L~~~f---~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~   68 (186)
                      ||+|+.|+.+|+.+|+.+|   ..++||+..++++||..+||++.+|++||+|+|+++++......
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~~   67 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQ   67 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGGGH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhcccccc
Confidence            6789999999999999999   89999999999999999999999999999999999998765443

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

Probab=99.80  E-value=1e-19  Score=115.53  Aligned_cols=61  Identities=20%  Similarity=0.307  Sum_probs=57.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536           4 TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus         4 ~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      ..++.|+.||.+|+.+|+..|..++||+..++++||..+||++.+|++||||+|+++++..
T Consensus         5 ~~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   65 (74)
T 2ly9_A            5 DSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSK   65 (74)
T ss_dssp             CCCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTT
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhC
Confidence            3467899999999999999999999999999999999999999999999999999998753

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

Probab=99.80  E-value=1.4e-19  Score=110.27  Aligned_cols=55  Identities=27%  Similarity=0.395  Sum_probs=52.9

Q ss_pred             CCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536           8 YRVVYSDQQRLELEKEFHY---SRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus         8 ~r~~~t~~q~~~L~~~f~~---~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      +|+.||.+|+.+|+.+|..   ++||+..++++||..+||++.+|++||+|+|+++++
T Consensus         1 rr~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk   58 (60)
T 1k61_A            1 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             CCCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CcCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHccccc
Confidence            4689999999999999999   999999999999999999999999999999999885

>2da6_A Hepatocyte nuclear factor 1-beta; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=4.4e-19  Score=117.63  Aligned_cols=67  Identities=18%  Similarity=0.266  Sum_probs=62.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHc---------------------CCChhHHHHHHHhhHHHH
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSL---------------------GLSERQVKIWFQNRRAKE   60 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~---------------------~l~~~~v~~WFqnrr~~~   60 (186)
                      .+++||.|+.|+..|+.+|+..|..++||+..+|++||..+                     +|++.+|++||||||+++
T Consensus         3 ~~~~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k~   82 (102)
T 2da6_A            3 SGSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEE   82 (102)
T ss_dssp             TCCSCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHHH
Confidence            56788999999999999999999999999999999999999                     799999999999999999


Q ss_pred             HHHHHhhh
Q psy8536          61 RKQLKKRE   68 (186)
Q Consensus        61 ~~~~~~~~   68 (186)
                      ++......
T Consensus        83 kr~~~~~~   90 (102)
T 2da6_A           83 AFRQKLAM   90 (102)
T ss_dssp             HHHHHHHH
T ss_pred             HHhhHhhh
Confidence            98766543

>2dmn_A Homeobox protein TGIF2LX; TGFB-induced factor 2-like protein, X-linked TGF(beta) induced transcription factor 2-like protein, TGIF-like on the X; NMR {Homo sapiens}

Probab=99.80  E-value=1.8e-19  Score=116.65  Aligned_cols=65  Identities=18%  Similarity=0.185  Sum_probs=59.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhh
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHY---SRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR   67 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~---~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~   67 (186)
                      .+++++|+.|+.+|+.+|+.+|..   ++||+..++++||..+||++.||++||+|+|++.++.....
T Consensus         5 ~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~~~   72 (83)
T 2dmn_A            5 SSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQ   72 (83)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHTCC
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHHHh
Confidence            456788999999999999999987   69999999999999999999999999999999998765543

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

Probab=99.79  E-value=3.8e-20  Score=114.27  Aligned_cols=59  Identities=27%  Similarity=0.344  Sum_probs=55.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHH---hhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536           4 TKDKYRVVYSDQQRLELEKEF---HYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus         4 ~~rr~r~~~t~~q~~~L~~~f---~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      ..++.|+.|+.+|+.+|+.+|   ..++||+..++++||..+||++.+|++||+|+|+++++
T Consensus         2 ~~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A            2 SGHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             CCCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            457889999999999999999   89999999999999999999999999999999998764

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

Probab=99.79  E-value=1e-19  Score=116.04  Aligned_cols=59  Identities=27%  Similarity=0.402  Sum_probs=55.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536           6 DKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus         6 rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      .+.|+.||.+|+.+||..|..++||+..++++||..+||++.+|++||||||+++++..
T Consensus         9 ~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~   67 (76)
T 2dn0_A            9 SIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLK   67 (76)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCC
T ss_pred             CCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhc
Confidence            45689999999999999999999999999999999999999999999999999988743

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

Probab=99.79  E-value=9.4e-20  Score=118.77  Aligned_cols=57  Identities=18%  Similarity=0.250  Sum_probs=53.4

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536           9 RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK   65 (186)
Q Consensus         9 r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~   65 (186)
                      ...||.+|+.+||..|..++||+..++++||..|||++.||+|||||||+++++...
T Consensus        15 ~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~   71 (89)
T 2ecb_A           15 FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEE   71 (89)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCS
T ss_pred             hccCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHH
Confidence            348999999999999999999999999999999999999999999999999987544

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

Probab=99.79  E-value=1.8e-19  Score=119.99  Aligned_cols=62  Identities=16%  Similarity=0.202  Sum_probs=56.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      ...+++|+.||..|+.+|+..|..++||+..++++||..+||++.+|++||||||+++|+..
T Consensus        23 ~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   84 (96)
T 3nar_A           23 SGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGN   84 (96)
T ss_dssp             ----CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTC
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhc
Confidence            34567899999999999999999999999999999999999999999999999999999754

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

Probab=99.78  E-value=2.3e-19  Score=116.32  Aligned_cols=60  Identities=25%  Similarity=0.309  Sum_probs=54.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536           6 DKYRVVYSDQQRLELEKEFHY---SRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK   65 (186)
Q Consensus         6 rr~r~~~t~~q~~~L~~~f~~---~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~   65 (186)
                      +++|++|+.+|+.+|+.+|..   ++||+..++.+||..+||++.+|++||||+|+++++...
T Consensus         3 ~krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~~   65 (83)
T 1le8_B            3 PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITI   65 (83)
T ss_dssp             --CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHcccccccc
Confidence            455677999999999999999   999999999999999999999999999999999987543

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

Probab=99.78  E-value=4.4e-19  Score=108.01  Aligned_cols=53  Identities=21%  Similarity=0.380  Sum_probs=50.1

Q ss_pred             CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536          12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus        12 ~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      -|.+|+.+|+..|..++||+..++.+||..+||++.+|++||||||+++++-.
T Consensus        11 ~~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg~   63 (66)
T 3nau_A           11 KTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGI   63 (66)
T ss_dssp             CCHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhccC
Confidence            37899999999999999999999999999999999999999999999998643

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

Probab=99.78  E-value=5e-19  Score=115.73  Aligned_cols=58  Identities=29%  Similarity=0.391  Sum_probs=55.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536           4 TKDKYRVVYSDQQRLELEKEFHY---SRYITIRRKAELANSLGLSERQVKIWFQNRRAKER   61 (186)
Q Consensus         4 ~~rr~r~~~t~~q~~~L~~~f~~---~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~   61 (186)
                      +++++|+.|+.+|+.+|+.+|..   ++||+..+++.||..+||++.+|++||+|+|+++|
T Consensus        26 ~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k   86 (87)
T 1mnm_C           26 TKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK   86 (87)
T ss_dssp             SSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcc
Confidence            45667999999999999999999   99999999999999999999999999999999986

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

Probab=99.78  E-value=1e-19  Score=114.57  Aligned_cols=58  Identities=28%  Similarity=0.430  Sum_probs=54.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHH-hhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536           5 KDKYRVVYSDQQRLELEKEF-HYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f-~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      ..+.|.+++.+|+.+||..| ..++||+..++++||..+||++.+|++||||||+++++
T Consensus         8 g~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~   66 (72)
T 2cqx_A            8 GIKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKP   66 (72)
T ss_dssp             CCCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCC
Confidence            45677889999999999999 99999999999999999999999999999999999885

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

Probab=99.77  E-value=5.5e-19  Score=126.17  Aligned_cols=60  Identities=28%  Similarity=0.449  Sum_probs=54.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      +++||.|+.||..|+.+||..|..++||+..++.+||..+||++.+|++||||||+++|+
T Consensus        85 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr  144 (146)
T 1au7_A           85 ERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR  144 (146)
T ss_dssp             ----CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhc
Confidence            567788999999999999999999999999999999999999999999999999999886

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

Probab=99.77  E-value=9.4e-19  Score=125.80  Aligned_cols=61  Identities=26%  Similarity=0.397  Sum_probs=58.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      ..++||+|+.||..|+.+|+..|..++||+..++.+||..+||++.+|++||||||+++|+
T Consensus        90 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           90 PSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            3567889999999999999999999999999999999999999999999999999999875

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

Probab=99.76  E-value=5.5e-19  Score=117.62  Aligned_cols=63  Identities=22%  Similarity=0.379  Sum_probs=53.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHH------------------cC---CChhHHHHHHHhhHHHH
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANS------------------LG---LSERQVKIWFQNRRAKE   60 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~------------------~~---l~~~~v~~WFqnrr~~~   60 (186)
                      .++.||.|+.|+..|+.+||..|..++||+..+|++||..                  ||   |++.+|++||||||+++
T Consensus         6 ~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k~   85 (99)
T 1lfb_A            6 TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEE   85 (99)
T ss_dssp             -------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHHH
Confidence            4677889999999999999999999999999999999999                  88   99999999999999987


Q ss_pred             HHHH
Q psy8536          61 RKQL   64 (186)
Q Consensus        61 ~~~~   64 (186)
                      ++..
T Consensus        86 k~k~   89 (99)
T 1lfb_A           86 AFRH   89 (99)
T ss_dssp             SCCC
T ss_pred             HHhc
Confidence            6543

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

Probab=99.76  E-value=2.6e-19  Score=111.46  Aligned_cols=55  Identities=44%  Similarity=0.717  Sum_probs=52.0

Q ss_pred             CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536          10 VVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus        10 ~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      ..+|..|+.+||..|..++||+..++.+||..+||++.+|++||||||+++|+..
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~   63 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ   63 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSS
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhh
Confidence            4689999999999999999999999999999999999999999999999988754

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

Probab=99.76  E-value=1.5e-18  Score=113.77  Aligned_cols=58  Identities=24%  Similarity=0.240  Sum_probs=53.4

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536           8 YRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK   65 (186)
Q Consensus         8 ~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~   65 (186)
                      ++..||.+|+.+||..|..++||+..++++||..+||++.+|++||||||+|+++...
T Consensus        16 k~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~   73 (89)
T 2dmp_A           16 KFKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQ   73 (89)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCS
T ss_pred             ccccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhH
Confidence            3455999999999999999999999999999999999999999999999999886543

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

Probab=99.76  E-value=9.4e-19  Score=126.89  Aligned_cols=60  Identities=28%  Similarity=0.496  Sum_probs=54.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      .++||.|+.||..|+.+||..|..++||+..++.+||..+||++.+|++||||||+++|+
T Consensus        99 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr  158 (160)
T 1e3o_C           99 SRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR  158 (160)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTS
T ss_pred             CCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhc
Confidence            467888999999999999999999999999999999999999999999999999999986

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

Probab=99.76  E-value=7.3e-19  Score=127.74  Aligned_cols=62  Identities=31%  Similarity=0.393  Sum_probs=51.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      +++||+|+.||..|+.+||..|..++||+..++.+||..+||++.+|++||||||+|+|+..
T Consensus        97 ~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~  158 (164)
T 2xsd_C           97 GRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMT  158 (164)
T ss_dssp             ---------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSC
T ss_pred             ccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhcc
Confidence            56788899999999999999999999999999999999999999999999999999999754

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

Probab=99.75  E-value=1.6e-18  Score=106.63  Aligned_cols=54  Identities=17%  Similarity=0.171  Sum_probs=50.7

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536           9 RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus         9 r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      +...+.+|+.+||..|..++||+..++.+||..+||++.+|++||||||+|.++
T Consensus         7 ~~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~   60 (64)
T 2e19_A            7 GQPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS   60 (64)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSC
T ss_pred             CCCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCC
Confidence            466789999999999999999999999999999999999999999999998654

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

Probab=99.73  E-value=3.4e-18  Score=123.25  Aligned_cols=61  Identities=30%  Similarity=0.558  Sum_probs=57.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~   63 (186)
                      .++||.|+.|+..|+.+|+..|..++||+..++.+||..+||++.+|++||||||+++|+.
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             cCCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            3677889999999999999999999999999999999999999999999999999999863

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

Probab=99.73  E-value=2.7e-18  Score=104.73  Aligned_cols=49  Identities=29%  Similarity=0.471  Sum_probs=45.9

Q ss_pred             HHHHHHHHHHH-hhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536          14 DQQRLELEKEF-HYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus        14 ~~q~~~L~~~f-~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      ..|+.+||..| ..++||+..++.+||..|||+++||++||||||+++|+
T Consensus         9 ~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~   58 (64)
T 1x2m_A            9 AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   58 (64)
T ss_dssp             SCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             chHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCC
Confidence            46899999999 67999999999999999999999999999999999874

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

Probab=99.71  E-value=7e-18  Score=122.91  Aligned_cols=62  Identities=26%  Similarity=0.364  Sum_probs=54.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      .+.||.|+.||.+|+.+|+..|..++||+..++++||..+||++.+|++||||||++.++..
T Consensus        95 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~  156 (164)
T 2d5v_A           95 NTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKW  156 (164)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC-
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccC
Confidence            35688899999999999999999999999999999999999999999999999999987643

>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding, transcription, nucleus, phosphoprotein, DNA bindi protein; 1.95A {Homo sapiens} SCOP: a.4.1.1

Probab=99.70  E-value=1.9e-17  Score=102.84  Aligned_cols=56  Identities=21%  Similarity=0.300  Sum_probs=50.0

Q ss_pred             CCCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536          10 VVYSDQQRLELEKEFH---YSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK   65 (186)
Q Consensus        10 ~~~t~~q~~~L~~~f~---~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~   65 (186)
                      ..|+.+|+.+|+.+|.   .++||+..++++||..+||++.||++||+|+|++.++...
T Consensus         3 g~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~   61 (67)
T 3k2a_A            3 GIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMI   61 (67)
T ss_dssp             ---CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC-
T ss_pred             CcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHH
Confidence            4799999999999999   9999999999999999999999999999999999886543

>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=8.9e-16  Score=93.82  Aligned_cols=46  Identities=17%  Similarity=0.299  Sum_probs=44.2

Q ss_pred             HHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536          14 DQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK   59 (186)
Q Consensus        14 ~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~   59 (186)
                      ++|+.+|+++|..|++|+..++..||..+||++++|++||||+|+.
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~   59 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVY   59 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhcccc
Confidence            5789999999999999999999999999999999999999999974

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

Probab=99.61  E-value=2.6e-16  Score=116.68  Aligned_cols=59  Identities=19%  Similarity=0.345  Sum_probs=53.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcC---------------------CChhHHHHHHHhhHHHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLG---------------------LSERQVKIWFQNRRAKER   61 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~---------------------l~~~~v~~WFqnrr~~~~   61 (186)
                      ++.||.|+.|+..|+.+|+..|..++||+...|++||..+|                     |++.+|++||||||++.+
T Consensus       113 ~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~~k  192 (194)
T 1ic8_A          113 KKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEA  192 (194)
T ss_dssp             ----CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHHCC
T ss_pred             ccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhhhh
Confidence            57788999999999999999999999999999999999999                     999999999999999865

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

Probab=99.59  E-value=4.1e-15  Score=96.17  Aligned_cols=58  Identities=22%  Similarity=0.239  Sum_probs=53.4

Q ss_pred             CCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhh
Q psy8536          10 VVYSDQQRLELEKEFHY---SRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR   67 (186)
Q Consensus        10 ~~~t~~q~~~L~~~f~~---~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~   67 (186)
                      ..|+.+++.+|+.+|..   ++||+..++++||..+||++.||++||+|+|.+.++.....
T Consensus        10 ~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~~~   70 (89)
T 2lk2_A           10 HMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRK   70 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHHHh
Confidence            46899999999999987   99999999999999999999999999999999998865544

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

Probab=99.55  E-value=5.4e-15  Score=110.73  Aligned_cols=58  Identities=17%  Similarity=0.342  Sum_probs=52.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcC---------------------CChhHHHHHHHhhHHH
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLG---------------------LSERQVKIWFQNRRAK   59 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~---------------------l~~~~v~~WFqnrr~~   59 (186)
                      .++.||.|+.|+..|+.+|+..|..++||+..+|++||..+|                     |++.+|++||+|||+.
T Consensus       139 ~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~~  217 (221)
T 2h8r_A          139 NKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKE  217 (221)
T ss_dssp             ---CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHTT
T ss_pred             cCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhhh
Confidence            467888999999999999999999999999999999999988                     8999999999999975

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

Probab=99.36  E-value=2.7e-13  Score=111.48  Aligned_cols=55  Identities=29%  Similarity=0.504  Sum_probs=51.4

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536           7 KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKER   61 (186)
Q Consensus         7 r~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~   61 (186)
                      +.++.++..|+..|+..|..++||+..+|++||.++||+++||++||||||+|+|
T Consensus       367 ~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          367 AAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            3467899999999999999999999999999999999999999999999998753

>2nzz_A Penetratin conjugated GAS (374-394) peptide; conformational analysis, G protein, GAS subunit, A2A adenosine receptor, cell-penetrating peptides; NMR {Synthetic} PDB: 2o00_A

Probab=98.68  E-value=7.4e-10  Score=59.38  Aligned_cols=26  Identities=50%  Similarity=0.820  Sum_probs=21.1

Q ss_pred             hHHHHHHHhhHHHHHHHHHhhhhhhc
Q psy8536          47 RQVKIWFQNRRAKERKQLKKREEVVI   72 (186)
Q Consensus        47 ~~v~~WFqnrr~~~~~~~~~~~~~~~   72 (186)
                      +||+|||||||+|+|+.........+
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~~~~~~   26 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFNDARDII   26 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHHTTTSS
T ss_pred             CCceeccHHHHHHHHHHhHHHHHHHH
Confidence            48999999999999998877554443

>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=98.28  E-value=2.7e-07  Score=58.82  Aligned_cols=38  Identities=34%  Similarity=0.394  Sum_probs=20.4

Q ss_pred             CCCCccccccccccCCCCCccccccchHHHHHHhhhhc
Q psy8536         148 TTATSYILDIDTRKTRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ++.+.++|+...+..+..++.||.||..|+.+||++|.
T Consensus         3 s~~~~~p~~~~~~~~~~~rr~Rt~ft~~Ql~~Le~~F~   40 (81)
T 1b8i_A            3 SNHTFYPWMAIAGTNGLRRRGRQTYTRYQTLELEKEFH   40 (81)
T ss_dssp             ----CCTTCC-----------CCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCccccCCCCCCCCCCCcccCHHHHHHHHHHHh
Confidence            34455666666666778899999999999999999995

>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=98.21  E-value=5e-08  Score=64.44  Aligned_cols=71  Identities=24%  Similarity=0.302  Sum_probs=35.6

Q ss_pred             HcCCChhHHHHHHHhhHHHHHH---------------------HHHhhhhhhccCCCcccccchh--hhhhcccceeeee
Q psy8536          41 SLGLSERQVKIWFQNRRAKERK---------------------QLKKREEVVIKDPSKDLFLSNK--VMYTYLVFQVKIW   97 (186)
Q Consensus        41 ~~~l~~~~v~~WFqnrr~~~~~---------------------~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~riq~W   97 (186)
                      ++|++..+|..||++.|...+.                     +....+..+....+.+......  ...++...+|++|
T Consensus         2 ~~~~~~~~~~~W~~~~r~~~~~~~~~~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vW   81 (97)
T 1b72_A            2 EPNTPTARTFDWMKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIW   81 (97)
T ss_dssp             ------CCCCGGGGC--------------------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHH
T ss_pred             CCCCCCcccccccccccCCCCCCCCCCCCCCCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHH
Confidence            4667778888899988765332                     1122233343444433333322  3334445699999


Q ss_pred             eeehhhhhhhhhhh
Q psy8536          98 FQNRRAKERKQLKK  111 (186)
Q Consensus        98 FqNrRak~~~~~~~  111 (186)
                      |||+|+++++....
T Consensus        82 FqNRR~k~kk~~~~   95 (97)
T 1b72_A           82 FQNRRMKQKKRERE   95 (97)
T ss_dssp             HHHHHHHHHHHHTC
T ss_pred             HHHHhHHHhHHhcc
Confidence            99999999987643

>2nzz_A Penetratin conjugated GAS (374-394) peptide; conformational analysis, G protein, GAS subunit, A2A adenosine receptor, cell-penetrating peptides; NMR {Synthetic} PDB: 2o00_A

Probab=98.07  E-value=3.4e-07  Score=48.98  Aligned_cols=20  Identities=55%  Similarity=0.911  Sum_probs=17.8

Q ss_pred             eeeeeeeehhhhhhhhhhhc
Q psy8536          93 QVKIWFQNRRAKERKQLKKR  112 (186)
Q Consensus        93 riq~WFqNrRak~~~~~~~~  112 (186)
                      +|.||||||||++++.....
T Consensus         2 QVkIWFQNRRaK~Kk~~~~~   21 (37)
T 2nzz_A            2 QIKIWFQNRRMKWKKRVFND   21 (37)
T ss_dssp             CTTTTTTCSHHHHTSSHHHH
T ss_pred             CceeccHHHHHHHHHHhHHH
Confidence            68999999999999987764

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

Probab=97.85  E-value=8.3e-07  Score=53.78  Aligned_cols=52  Identities=15%  Similarity=0.248  Sum_probs=34.7

Q ss_pred             HHHHHHHHHhhhhhhccCCCcccccchh--hhhhcccceeeeeeeehhhhhhhh
Q psy8536          57 RAKERKQLKKREEVVIKDPSKDLFLSNK--VMYTYLVFQVKIWFQNRRAKERKQ  108 (186)
Q Consensus        57 r~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~riq~WFqNrRak~~~~  108 (186)
                      |.+.+.+....+..+....+.+......  ...++...+|++||||+|+++++.
T Consensus         9 ~~~~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg   62 (66)
T 3nau_A            9 RKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRG   62 (66)
T ss_dssp             --CCHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhcc
Confidence            4445556666666666666666655544  444555679999999999998753

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

Probab=97.85  E-value=9.3e-06  Score=52.39  Aligned_cols=24  Identities=46%  Similarity=0.688  Sum_probs=17.4

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      .+..++.||.||..|+.+||++|+
T Consensus        25 ~~~~rr~Rt~ft~~Ql~~Le~~F~   48 (88)
T 2r5y_A           25 NGETKRQRTSYTRYQTLELEKEFH   48 (88)
T ss_dssp             ------CCCCCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCcCHHHHHHHHHHHh
Confidence            456788899999999999999996

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

Probab=97.80  E-value=3.8e-06  Score=54.30  Aligned_cols=44  Identities=9%  Similarity=0.128  Sum_probs=27.8

Q ss_pred             hhhccCCCcccccch--hhhhhcccceeeeeeeehhhhhhhhhhhc
Q psy8536          69 EVVIKDPSKDLFLSN--KVMYTYLVFQVKIWFQNRRAKERKQLKKR  112 (186)
Q Consensus        69 ~~~~~~~~~~~~~~~--~~~~~~~~~riq~WFqNrRak~~~~~~~~  112 (186)
                      ..+....+.+.....  ....++...+|+|||||||+++++.....
T Consensus        28 ~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~~~   73 (89)
T 2ecb_A           28 ASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKM   73 (89)
T ss_dssp             HHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCC
T ss_pred             HHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHHHh
Confidence            333334444433333  34445556799999999999998865543

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

Probab=97.78  E-value=2.7e-05  Score=49.68  Aligned_cols=24  Identities=33%  Similarity=0.426  Sum_probs=21.6

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      .+..++.||.||..|+.+||++|+
T Consensus        19 ~~~~rr~Rt~ft~~Q~~~Le~~F~   42 (84)
T 2kt0_A           19 PVKKQKTRTVFSSTQLCVLNDRFQ   42 (84)
T ss_dssp             CSCSCCCSSCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHH
Confidence            456788899999999999999995

>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=97.74  E-value=2.3e-05  Score=49.58  Aligned_cols=24  Identities=17%  Similarity=0.416  Sum_probs=20.8

Q ss_pred             cCCCCCccccccchHHHHHHhhhhc
Q psy8536         161 KTRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       161 ~~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      .....+|.||+||.+|+.+|| +|+
T Consensus        13 ~~~~~rR~Rt~ft~~Ql~~Le-~F~   36 (80)
T 1wh7_A           13 SGGTTKRFRTKFTAEQKEKML-AFA   36 (80)
T ss_dssp             CCCCSSCCCCCCCHHHHHHHH-HHH
T ss_pred             CCCCCCCCCccCCHHHHHHHH-HHH
Confidence            345678999999999999999 886

>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=97.73  E-value=2.7e-05  Score=49.28  Aligned_cols=24  Identities=8%  Similarity=0.140  Sum_probs=21.5

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      .+..+|.||+||.+|+.+||++|+
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le~~f~   37 (80)
T 1wh5_A           14 GGIRKRHRTKFTAEQKERMLALAE   37 (80)
T ss_dssp             CCCSCCCSCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHH
Confidence            356788999999999999999996

>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=97.65  E-value=7.2e-06  Score=53.06  Aligned_cols=29  Identities=17%  Similarity=0.268  Sum_probs=22.3

Q ss_pred             hhhhhcccceeeeeeeehhhhhhhhhhhc
Q psy8536          84 KVMYTYLVFQVKIWFQNRRAKERKQLKKR  112 (186)
Q Consensus        84 ~~~~~~~~~riq~WFqNrRak~~~~~~~~  112 (186)
                      .....+...+|++||||||+++++.....
T Consensus        47 a~~~~l~~~qV~vWFqNRR~k~r~~~~~~   75 (89)
T 2dmp_A           47 RVETKLSRREIDSWFSERRKLRDSMEQAV   75 (89)
T ss_dssp             HHHHTCCHHHHHHHHHHHHHHHHTSCSCC
T ss_pred             HHHhCCCHHhccHhhHhHHHHHHHHhHhh
Confidence            34445556799999999999998876544

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

Probab=97.65  E-value=6.1e-06  Score=48.59  Aligned_cols=25  Identities=48%  Similarity=0.610  Sum_probs=19.8

Q ss_pred             hhhhhcccceeeeeeeehhhhhhhh
Q psy8536          84 KVMYTYLVFQVKIWFQNRRAKERKQ  108 (186)
Q Consensus        84 ~~~~~~~~~riq~WFqNrRak~~~~  108 (186)
                      ....++...+|++||||+|++++++
T Consensus        31 A~~l~l~~~qV~~WFqNRR~k~kr~   55 (56)
T 3a03_A           31 AKALRMTDAQVKTWFQNRRTKWRRQ   55 (56)
T ss_dssp             HHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhCcCHHHhhHhhHHhhhhhccc
Confidence            3444556679999999999999875

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

Probab=97.60  E-value=4.7e-06  Score=51.25  Aligned_cols=27  Identities=41%  Similarity=0.555  Sum_probs=20.4

Q ss_pred             hhhhhcccceeeeeeeehhhhhhhhhh
Q psy8536          84 KVMYTYLVFQVKIWFQNRRAKERKQLK  110 (186)
Q Consensus        84 ~~~~~~~~~riq~WFqNrRak~~~~~~  110 (186)
                      ....++...+|++||||||+++++...
T Consensus        38 A~~l~Lte~qVqvWFqNRRak~kr~~~   64 (69)
T 2l9r_A           38 AKNLKLTETQVKIWFQNRRYKTKRKQL   64 (69)
T ss_dssp             HHHTTCCHHHHHHHHHHHHHHSCCSSS
T ss_pred             HHHhCCChhheeecchhhhhhhhhhhh
Confidence            344455567999999999999987644

>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=97.56  E-value=1.4e-05  Score=49.87  Aligned_cols=37  Identities=8%  Similarity=-0.001  Sum_probs=25.2

Q ss_pred             ccCCCccccc--chhhhhhcccceeeeeeeehhhhhhhh
Q psy8536          72 IKDPSKDLFL--SNKVMYTYLVFQVKIWFQNRRAKERKQ  108 (186)
Q Consensus        72 ~~~~~~~~~~--~~~~~~~~~~~riq~WFqNrRak~~~~  108 (186)
                      ...++.+...  ......++...+|++||||+|+++++.
T Consensus        23 ~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~   61 (76)
T 2ecc_A           23 LQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             HHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             HHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHH
Confidence            3344444433  334555666679999999999998875

>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=97.55  E-value=6.8e-05  Score=47.35  Aligned_cols=24  Identities=29%  Similarity=0.552  Sum_probs=21.5

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ....++.||+||..|+.+||++|.
T Consensus        14 ~~~~rr~Rt~ft~~Q~~~Le~~F~   37 (80)
T 2dmt_A           14 AKKGRRSRTVFTELQLMGLEKRFE   37 (80)
T ss_dssp             CCCCCCSCCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHH
Confidence            456788899999999999999995

>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=97.52  E-value=7e-06  Score=49.60  Aligned_cols=29  Identities=21%  Similarity=0.422  Sum_probs=21.4

Q ss_pred             ccchhhhhhcccceeeeeeeehhhhhhhh
Q psy8536          80 FLSNKVMYTYLVFQVKIWFQNRRAKERKQ  108 (186)
Q Consensus        80 ~~~~~~~~~~~~~riq~WFqNrRak~~~~  108 (186)
                      ........++...+|++||||||++++..
T Consensus        31 r~~LA~~l~LterQVkvWFqNRR~k~k~~   59 (64)
T 1x2m_A           31 LEGLSKQLDWDVRSIQRWFRQRRNQEKPS   59 (64)
T ss_dssp             HHHHHHHHCSCHHHHHHHHHHHHHHSCCS
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHhccCCC
Confidence            33444555666679999999999998753

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

Probab=97.52  E-value=9.1e-06  Score=49.22  Aligned_cols=40  Identities=13%  Similarity=0.056  Sum_probs=24.4

Q ss_pred             hhhhccCCCcccccch--hhhhhcccceeeeeeeehhhhhhh
Q psy8536          68 EEVVIKDPSKDLFLSN--KVMYTYLVFQVKIWFQNRRAKERK  107 (186)
Q Consensus        68 ~~~~~~~~~~~~~~~~--~~~~~~~~~riq~WFqNrRak~~~  107 (186)
                      +..+....+.+.....  ....++...+|++|||||||+..+
T Consensus        19 e~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~   60 (64)
T 2e19_A           19 KAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS   60 (64)
T ss_dssp             HHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSC
T ss_pred             HHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCC
Confidence            3334444444333333  344455567999999999998765

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

Probab=97.50  E-value=1.6e-05  Score=52.03  Aligned_cols=24  Identities=25%  Similarity=0.483  Sum_probs=19.8

Q ss_pred             cccceeeeeeeehhhhhhhhhhhc
Q psy8536          89 YLVFQVKIWFQNRRAKERKQLKKR  112 (186)
Q Consensus        89 ~~~~riq~WFqNrRak~~~~~~~~  112 (186)
                      +...+|++||||+|+++++.....
T Consensus        61 ls~~qV~~WFqNRR~k~kr~~~~~   84 (95)
T 2cuf_A           61 VTSLKVYNWFANRRKEIKRRANIA   84 (95)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             CCHHHHHHHHHHHHHHHHHHhhcc
Confidence            455689999999999999886653

>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=97.49  E-value=1.7e-05  Score=49.13  Aligned_cols=27  Identities=22%  Similarity=0.228  Sum_probs=21.3

Q ss_pred             hhhhhcccceeeeeeeehhhhhhhhhh
Q psy8536          84 KVMYTYLVFQVKIWFQNRRAKERKQLK  110 (186)
Q Consensus        84 ~~~~~~~~~riq~WFqNrRak~~~~~~  110 (186)
                      ....++...+|++||||+|+++++...
T Consensus        36 A~~l~l~~~qV~~WFqNRR~k~rk~~~   62 (72)
T 1uhs_A           36 AAEAGLTEEQTQKWFKQRLAEWRRSEG   62 (72)
T ss_dssp             HHHHTCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHCcCHHHhhHHhHHHHHHHhhhcc
Confidence            344455567999999999999998764

>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=97.49  E-value=1.5e-05  Score=50.84  Aligned_cols=30  Identities=17%  Similarity=0.286  Sum_probs=22.4

Q ss_pred             hhhhhhcccceeeeeeeehhhhhhhhhhhc
Q psy8536          83 NKVMYTYLVFQVKIWFQNRRAKERKQLKKR  112 (186)
Q Consensus        83 ~~~~~~~~~~riq~WFqNrRak~~~~~~~~  112 (186)
                      .....++...+|++||||+|+++.+.....
T Consensus        43 LA~~~gLs~~qV~~WFqNrR~r~k~~~~~~   72 (83)
T 2dmn_A           43 LSEKTNLSLLQISNWFINARRRILPDMLQQ   72 (83)
T ss_dssp             HHHHHCCCHHHHHHHHHHHHHHTHHHHTCC
T ss_pred             HHHHHCcCHHHhhHHhhhhHhhhcHHHHHh
Confidence            344555666799999999999998765443

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

Probab=97.46  E-value=9.9e-06  Score=48.33  Aligned_cols=26  Identities=42%  Similarity=0.615  Sum_probs=18.6

Q ss_pred             hhhhhcccceeeeeeeehhhhhhhhh
Q psy8536          84 KVMYTYLVFQVKIWFQNRRAKERKQL  109 (186)
Q Consensus        84 ~~~~~~~~~riq~WFqNrRak~~~~~  109 (186)
                      ....++...+|++||||+|+++++..
T Consensus        33 a~~l~l~~~qV~~WFqNrR~k~rk~~   58 (60)
T 3a02_A           33 AMKIGLTEARIQVWFQNRRAKWRKQE   58 (60)
T ss_dssp             HHHHTSCHHHHHHHHHHHHHHHC---
T ss_pred             HHHHCcCHHHHHHHhhhhhhhhHhhc
Confidence            44445666799999999999998764

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

Probab=97.46  E-value=7.3e-05  Score=47.20  Aligned_cols=24  Identities=29%  Similarity=0.466  Sum_probs=21.8

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ++..++.||.||..|+.+||++|+
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~   27 (80)
T 2cue_A            4 GSSGQRNRTSFTQEQIEALEKEFE   27 (80)
T ss_dssp             CCSSCCCCCCSCHHHHHHHHHHHT
T ss_pred             CCCCCCCCCccCHHHHHHHHHHHh
Confidence            457888999999999999999996

>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=97.45  E-value=1.2e-05  Score=50.28  Aligned_cols=42  Identities=17%  Similarity=0.133  Sum_probs=26.8

Q ss_pred             hhccCCCcccccc--hhhhhhcccceeeeeeeehhhhhhhhhhh
Q psy8536          70 VVIKDPSKDLFLS--NKVMYTYLVFQVKIWFQNRRAKERKQLKK  111 (186)
Q Consensus        70 ~~~~~~~~~~~~~--~~~~~~~~~~riq~WFqNrRak~~~~~~~  111 (186)
                      .+....+.+....  .....++...+|++||||+|+++++....
T Consensus        25 ~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~~   68 (75)
T 2da5_A           25 SFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETK   68 (75)
T ss_dssp             HHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSCS
T ss_pred             HHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhhc
Confidence            3333444433333  33444555679999999999999987653

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

Probab=97.44  E-value=7.3e-05  Score=45.92  Aligned_cols=24  Identities=25%  Similarity=0.440  Sum_probs=21.5

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ++..++.||.||..|+.+||++|.
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~   27 (70)
T 2dmu_A            4 GSSGRRHRTIFTDEQLEALENLFQ   27 (70)
T ss_dssp             TTSSCCCCCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHH
Confidence            456788899999999999999995

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

Probab=97.44  E-value=8.2e-05  Score=45.69  Aligned_cols=24  Identities=29%  Similarity=0.430  Sum_probs=21.7

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ++..++.||.||..|+.+||++|.
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~   27 (70)
T 2djn_A            4 GSSGRKPRTIYSSFQLAALQRRFQ   27 (70)
T ss_dssp             CCCCCCSSCSSCHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHc
Confidence            456788899999999999999996

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

Probab=97.42  E-value=2.1e-05  Score=48.89  Aligned_cols=27  Identities=22%  Similarity=0.228  Sum_probs=21.6

Q ss_pred             hhhhhcccceeeeeeeehhhhhhhhhh
Q psy8536          84 KVMYTYLVFQVKIWFQNRRAKERKQLK  110 (186)
Q Consensus        84 ~~~~~~~~~riq~WFqNrRak~~~~~~  110 (186)
                      ....++...+|++||||+|+++++...
T Consensus        37 A~~~~l~~~qV~~WFqNRR~k~rk~~~   63 (73)
T 2hi3_A           37 AAEAGLTEEQTQKWFKQRLAEWRRSEG   63 (73)
T ss_dssp             HHHHTSCHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHCcCHHHHHHHHHHHHHHHHHhcc
Confidence            444455667999999999999998764

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

Probab=97.41  E-value=1.7e-05  Score=48.34  Aligned_cols=29  Identities=31%  Similarity=0.565  Sum_probs=21.9

Q ss_pred             hhhhhcccceeeeeeeehhhhhhhhhhhc
Q psy8536          84 KVMYTYLVFQVKIWFQNRRAKERKQLKKR  112 (186)
Q Consensus        84 ~~~~~~~~~riq~WFqNrRak~~~~~~~~  112 (186)
                      ....++...+|++||||+|+++++.....
T Consensus        35 a~~l~l~~~qV~~WFqNrR~k~kr~~~~~   63 (67)
T 2k40_A           35 AQKLNLELDRIQIWFQNRRAKLKRSHRES   63 (67)
T ss_dssp             HHHHTCCHHHHHHHHHHHHHHHHCSCCTT
T ss_pred             HHHHCcCHHHhhHhhHhHHHHHhHhchhc
Confidence            34445556799999999999999875543

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

Probab=97.39  E-value=6.4e-06  Score=51.15  Aligned_cols=25  Identities=20%  Similarity=0.588  Sum_probs=19.5

Q ss_pred             hhhhhcccceeeeeeeehhhhhhhh
Q psy8536          84 KVMYTYLVFQVKIWFQNRRAKERKQ  108 (186)
Q Consensus        84 ~~~~~~~~~riq~WFqNrRak~~~~  108 (186)
                      ....++...+|++||||||++++..
T Consensus        43 A~~l~l~e~qVqvWFqNRR~k~r~~   67 (72)
T 2cqx_A           43 SKQLDWSVRKIQCWFRHRRNQDKPS   67 (72)
T ss_dssp             HHHTTCCHHHHHHHHHHHHHHHSSC
T ss_pred             HHHhCCChhhcchhhhhcccCCCCC
Confidence            3444555679999999999998864

>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=97.38  E-value=9.4e-05  Score=45.43  Aligned_cols=24  Identities=38%  Similarity=0.494  Sum_probs=21.5

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ++..++.||.||..|+.+||++|+
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~   27 (70)
T 2cra_A            4 GSSGRKKRIPYSKGQLRELEREYA   27 (70)
T ss_dssp             SCCCCCSCCCSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHH
Confidence            456788899999999999999995

>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=97.37  E-value=0.0001  Score=45.27  Aligned_cols=24  Identities=21%  Similarity=0.214  Sum_probs=21.6

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ++..++.||.||..|+.+||++|+
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~   27 (70)
T 2da1_A            4 GSSGKRPRTRITDDQLRVLRQYFD   27 (70)
T ss_dssp             SCCCCSCSCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHH
Confidence            457888999999999999999995

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

Probab=97.36  E-value=6.9e-05  Score=45.04  Aligned_cols=22  Identities=45%  Similarity=0.679  Sum_probs=18.1

Q ss_pred             CCCccccccchHHHHHHhhhhc
Q psy8536         164 TKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       164 ~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      +.++.||.||..|+.+||++|+
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~   23 (63)
T 2h1k_A            2 SNKRTRTAYTRAQLLELEKEFL   23 (63)
T ss_dssp             ---CCCCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCHHHHHHHHHHHh
Confidence            4678899999999999999995

>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=97.36  E-value=0.00011  Score=45.97  Aligned_cols=25  Identities=36%  Similarity=0.586  Sum_probs=21.8

Q ss_pred             cCCCCCccccccchHHHHHHhhhhc
Q psy8536         161 KTRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       161 ~~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      .....++.||.||..|+.+||++|+
T Consensus         5 ~~~~~rr~Rt~ft~~Q~~~Le~~F~   29 (77)
T 1nk2_P            5 LPNKKRKRRVLFTKAQTYELERRFR   29 (77)
T ss_dssp             CSCCCCCCCCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHh
Confidence            3456788899999999999999996

>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=97.35  E-value=0.00011  Score=45.13  Aligned_cols=24  Identities=21%  Similarity=0.216  Sum_probs=21.6

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ++..++.||.||..|+.+||++|.
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~   27 (70)
T 2da2_A            4 GSSGRSSRTRFTDYQLRVLQDFFD   27 (70)
T ss_dssp             SCCSCCCCCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHH
Confidence            457788899999999999999995

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

Probab=97.33  E-value=0.00013  Score=45.97  Aligned_cols=24  Identities=21%  Similarity=0.256  Sum_probs=21.5

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      .+..++.||+||..|+.+||++|+
T Consensus         5 ~~~~rr~Rt~ft~~Q~~~Le~~F~   28 (80)
T 2da4_A            5 SSGALQDRTQFSDRDLATLKKYWD   28 (80)
T ss_dssp             CCCCCCSSCCCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHH
Confidence            356788899999999999999996

>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=97.32  E-value=3.3e-05  Score=49.62  Aligned_cols=30  Identities=30%  Similarity=0.418  Sum_probs=22.7

Q ss_pred             hhhhhcccceeeeeeeehhhhhhhhhhhcc
Q psy8536          84 KVMYTYLVFQVKIWFQNRRAKERKQLKKRE  113 (186)
Q Consensus        84 ~~~~~~~~~riq~WFqNrRak~~~~~~~~~  113 (186)
                      ....++...+|++||||+|+++++......
T Consensus        38 a~~~~l~~~qV~~WFqNrR~r~kk~~~~~~   67 (87)
T 1b72_B           38 AKKCGITVSQVSNWFGNKRIRYKKNIGKFQ   67 (87)
T ss_dssp             HHHHTSCHHHHHHHHHHHHHHHHHCGGGGH
T ss_pred             HHHHCcCHHHHHHHHHHHHHHhhhcccccc
Confidence            344455667999999999999988765543

>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=97.29  E-value=0.00014  Score=45.89  Aligned_cols=24  Identities=13%  Similarity=0.257  Sum_probs=21.5

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      +...++.||.||.+|+.+||++|.
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~   27 (80)
T 2dmq_A            4 GSSGKRMRTSFKHHQLRTMKSYFA   27 (80)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHH
Confidence            456788999999999999999995

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

Probab=97.27  E-value=8.8e-05  Score=44.40  Aligned_cols=22  Identities=41%  Similarity=0.591  Sum_probs=15.4

Q ss_pred             CCCccccccchHHHHHHhhhhc
Q psy8536         164 TKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       164 ~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ..++.||+||..|+.+||++|+
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~   23 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQ   23 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHH
Confidence            4678899999999999999995

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

Probab=97.27  E-value=0.00015  Score=45.77  Aligned_cols=24  Identities=21%  Similarity=0.207  Sum_probs=21.6

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ++..++.||.||..|+.+||++|+
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~   27 (80)
T 2dms_A            4 GSSGRRERTTFTRAQLDVLEALFA   27 (80)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHH
Confidence            457888999999999999999996

>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=97.23  E-value=0.00017  Score=43.96  Aligned_cols=22  Identities=27%  Similarity=0.487  Sum_probs=20.3

Q ss_pred             CCCccccccchHHHHHHhhhhc
Q psy8536         164 TKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       164 ~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ..++.||.||..|+.+||++|+
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~   23 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQ   23 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHH
Confidence            5788899999999999999996

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

Probab=97.19  E-value=0.00029  Score=45.79  Aligned_cols=24  Identities=38%  Similarity=0.528  Sum_probs=21.2

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ....++.||.||.+|+.+||++|.
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~F~   37 (93)
T 3a01_A           14 PPKRKKPRTSFTRIQVAELEKRFH   37 (93)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCCCHHHHHHHHHHHH
Confidence            346788899999999999999995

>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=97.19  E-value=0.00019  Score=45.10  Aligned_cols=24  Identities=13%  Similarity=0.194  Sum_probs=21.3

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ....++.||.||..|+.+||++|.
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~f~   37 (80)
T 2da3_A           14 PQRDKRLRTTITPEQLEILYQKYL   37 (80)
T ss_dssp             CCCCTTCCSSCCTTTHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHH
Confidence            356788899999999999999995

>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=97.19  E-value=0.00021  Score=43.86  Aligned_cols=24  Identities=33%  Similarity=0.502  Sum_probs=21.1

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      +...++.|+.||..|+.+||++|.
T Consensus         4 ~~~~~r~R~~ft~~q~~~Le~~F~   27 (70)
T 2e1o_A            4 GSSGKGGQVRFSNDQTIELEKKFE   27 (70)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHH
Confidence            456778899999999999999995

>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=97.18  E-value=0.00025  Score=44.37  Aligned_cols=24  Identities=50%  Similarity=0.711  Sum_probs=21.5

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      .+..++.||.||..|+.+||++|.
T Consensus        10 ~~~~rr~Rt~ft~~Q~~~Le~~F~   33 (77)
T 1puf_A           10 ARSTRKKRCPYTKHQTLELEKEFL   33 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHh
Confidence            456788899999999999999995

>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=97.15  E-value=4.8e-05  Score=48.43  Aligned_cols=27  Identities=30%  Similarity=0.338  Sum_probs=20.9

Q ss_pred             hhhhhcccceeeeeeeehhhhhhhhhh
Q psy8536          84 KVMYTYLVFQVKIWFQNRRAKERKQLK  110 (186)
Q Consensus        84 ~~~~~~~~~riq~WFqNrRak~~~~~~  110 (186)
                      ....++...+|++||||+|+++++...
T Consensus        39 a~~~gLt~~qV~~WFqNrR~r~kk~~~   65 (83)
T 1le8_B           39 MKNTSLSRIQIKNWVAARRAKEKTITI   65 (83)
T ss_dssp             HHHHCCCHHHHHHHHHHHHHHHTTSCC
T ss_pred             HHHHCCCHHHcccccHHHHcccccccc
Confidence            344456667999999999999988643

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

Probab=97.15  E-value=0.00026  Score=43.90  Aligned_cols=24  Identities=33%  Similarity=0.444  Sum_probs=21.4

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ++..++.||.||..|+.+||++|+
T Consensus         6 ~~~~rr~Rt~ft~~q~~~Le~~F~   29 (75)
T 2m0c_A            6 KGKKRRNRTTFTSYQLEELEKVFQ   29 (75)
T ss_dssp             CSCCCSCSCSSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHH
Confidence            456788899999999999999995

>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=97.13  E-value=4.7e-05  Score=45.30  Aligned_cols=25  Identities=32%  Similarity=0.430  Sum_probs=19.4

Q ss_pred             hhhhhcccceeeeeeeehhhhhhhh
Q psy8536          84 KVMYTYLVFQVKIWFQNRRAKERKQ  108 (186)
Q Consensus        84 ~~~~~~~~~riq~WFqNrRak~~~~  108 (186)
                      ....++...+|++||+|+|+++++.
T Consensus        35 a~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A           35 MKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             HHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHCcCHHHHHHHHHHHHcccccC
Confidence            3444566679999999999998763

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

Probab=97.11  E-value=0.00025  Score=43.22  Aligned_cols=21  Identities=29%  Similarity=0.464  Sum_probs=19.5

Q ss_pred             CCccccccchHHHHHHhhhhc
Q psy8536         165 KDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       165 ~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      +++.||.||..|+.+||++|.
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~   22 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFL   22 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHT
T ss_pred             cCCCCCCcCHHHHHHHHHHHh
Confidence            578899999999999999996

>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=97.05  E-value=0.00025  Score=43.20  Aligned_cols=21  Identities=52%  Similarity=0.792  Sum_probs=19.3

Q ss_pred             CCccccccchHHHHHHhhhhc
Q psy8536         165 KDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       165 ~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      +++.||.||..|+.+||++|+
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~   22 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFH   22 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCcCHHHHHHHHHHHc
Confidence            477899999999999999996

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

Probab=97.03  E-value=0.00035  Score=43.21  Aligned_cols=23  Identities=39%  Similarity=0.468  Sum_probs=20.8

Q ss_pred             CCCCccccccchHHHHHHhhhhc
Q psy8536         163 RTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       163 ~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ...++.||.||..|+.+||++|+
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~   27 (73)
T 2l7z_A            5 LEGRKKRVPYTKVQLKELEREYA   27 (73)
T ss_dssp             SCCCCCCCCSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHh
Confidence            46788899999999999999996

>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=97.02  E-value=0.00011  Score=45.53  Aligned_cols=28  Identities=32%  Similarity=0.465  Sum_probs=21.7

Q ss_pred             hhhhhcccceeeeeeeehhhhhhhhhhh
Q psy8536          84 KVMYTYLVFQVKIWFQNRRAKERKQLKK  111 (186)
Q Consensus        84 ~~~~~~~~~riq~WFqNrRak~~~~~~~  111 (186)
                      ....++...+|++||||+|+++++....
T Consensus        38 a~~~~L~~~qV~~WFqNrR~r~kk~~~~   65 (73)
T 1puf_B           38 AKKCGITVSQVSNWFGNKRIRYKKNIGK   65 (73)
T ss_dssp             HHHHTSCHHHHHHHHHHHHHHHHHCTTT
T ss_pred             HHHHCcCHHHHHHHHHHHHhhccccccc
Confidence            3445566679999999999999886554

>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=96.99  E-value=0.00025  Score=42.18  Aligned_cols=22  Identities=27%  Similarity=0.540  Sum_probs=16.4

Q ss_pred             CCCccccccchHHHHHHhhhhc
Q psy8536         164 TKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       164 ~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ..++.||.||..|+.+||++|.
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~   23 (61)
T 2hdd_A            2 AEKRPRTAFSSEQLARLKREFN   23 (61)
T ss_dssp             -----CCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHH
Confidence            3578899999999999999995

>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=96.96  E-value=0.00039  Score=42.04  Aligned_cols=22  Identities=18%  Similarity=0.294  Sum_probs=20.0

Q ss_pred             CCCccccccchHHHHHHhhhhc
Q psy8536         164 TKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       164 ~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ..++.||.||..|+.+||+.|+
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~   23 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYA   23 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHh
Confidence            4678899999999999999995

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

Probab=96.91  E-value=0.00048  Score=40.34  Aligned_cols=21  Identities=43%  Similarity=0.683  Sum_probs=19.3

Q ss_pred             CCccccccchHHHHHHhhhhc
Q psy8536         165 KDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       165 ~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      +++.||.||..|+.+||++|+
T Consensus         2 ~rr~Rt~~t~~q~~~Le~~F~   22 (58)
T 3rkq_A            2 RRKPRVLFSQAQVYELERRFK   22 (58)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHT
T ss_pred             cCCCCCCcCHHHHHHHHHHHH
Confidence            567899999999999999996

>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=96.91  E-value=0.00023  Score=46.85  Aligned_cols=23  Identities=35%  Similarity=0.465  Sum_probs=18.3

Q ss_pred             ccceeeeeeeehhhhhhhhhhhc
Q psy8536          90 LVFQVKIWFQNRRAKERKQLKKR  112 (186)
Q Consensus        90 ~~~riq~WFqNrRak~~~~~~~~  112 (186)
                      ...+|++||||||+++.......
T Consensus        67 te~~V~~WFqNRR~k~kr~~~~~   89 (102)
T 2da6_A           67 TEVRVYNWFANRRKEEAFRQKLA   89 (102)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccceeeeecchHHHHHHhhHhh
Confidence            34589999999999998765544

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

Probab=96.90  E-value=0.0005  Score=41.65  Aligned_cols=24  Identities=17%  Similarity=0.014  Sum_probs=22.0

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ++.++|.||+||..||..||.+|+
T Consensus         4 ~~~~kR~RT~~s~eQL~~Lqs~f~   27 (71)
T 1wi3_A            4 GSSGPRSRTKISLEALGILQSFIH   27 (71)
T ss_dssp             CCCCCCCCCCCCSHHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHH
Confidence            467899999999999999999996

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

Probab=96.90  E-value=0.0004  Score=40.81  Aligned_cols=20  Identities=35%  Similarity=0.546  Sum_probs=18.3

Q ss_pred             CccccccchHHHHHHhhhhc
Q psy8536         166 DKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       166 ~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ++.||.||..|+.+||++|.
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~   20 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFR   20 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHh
Confidence            46799999999999999995

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

Probab=96.90  E-value=0.00035  Score=45.63  Aligned_cols=24  Identities=13%  Similarity=-0.013  Sum_probs=17.9

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ....++.||.||..|+.+||++|.
T Consensus        22 ~~~~~r~Rt~ft~~Ql~~Le~~F~   45 (96)
T 3nar_A           22 KSGSTGKICKKTPEQLHMLKSAFV   45 (96)
T ss_dssp             -----CCSSSSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHH
Confidence            345667899999999999999995

>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=96.89  E-value=0.00044  Score=43.63  Aligned_cols=24  Identities=33%  Similarity=0.509  Sum_probs=20.4

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      .+..++.||.||..|+.+||+.|.
T Consensus        15 ~~~~rr~Rt~ft~~Q~~~Le~~F~   38 (81)
T 1fjl_A           15 KRKQRRSRTTFSASQLDELERAFE   38 (81)
T ss_dssp             --CCCCCCCCCCHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHH
Confidence            456788899999999999999995

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

Probab=96.84  E-value=0.00045  Score=40.94  Aligned_cols=20  Identities=40%  Similarity=0.632  Sum_probs=17.9

Q ss_pred             CccccccchHHHHHHhhhhc
Q psy8536         166 DKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       166 ~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ++.||.||..|+.+||++|+
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~   21 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEFY   21 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHH
Confidence            57799999999999999995

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

Probab=96.82  E-value=0.00054  Score=41.71  Aligned_cols=21  Identities=43%  Similarity=0.703  Sum_probs=19.2

Q ss_pred             CCccccccchHHHHHHhhhhc
Q psy8536         165 KDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       165 ~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      +++.||.||..|+.+||++|+
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~   22 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFK   22 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHH
T ss_pred             CCCCCCccCHHHHHHHHHHHH
Confidence            567899999999999999995

>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=96.67  E-value=0.00014  Score=44.31  Aligned_cols=26  Identities=23%  Similarity=0.369  Sum_probs=20.1

Q ss_pred             hhhhhcccceeeeeeeehhhhhhhhh
Q psy8536          84 KVMYTYLVFQVKIWFQNRRAKERKQL  109 (186)
Q Consensus        84 ~~~~~~~~~riq~WFqNrRak~~~~~  109 (186)
                      ....++...+|++||+|+|++..+..
T Consensus        35 a~~~~l~~~qV~~WFqNrR~r~kk~~   60 (67)
T 3k2a_A           35 AQDTGLTILQVNNWFINARRRIVQPM   60 (67)
T ss_dssp             HHHHTCCHHHHHHHHHHHHHHHHSCC
T ss_pred             HHHhCcCHHHhhhhhHHHHHHHhHHH
Confidence            34445666799999999999988653

>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=96.66  E-value=0.00059  Score=40.50  Aligned_cols=23  Identities=30%  Similarity=0.251  Sum_probs=13.4

Q ss_pred             CCCCccccccchHHHHHHhhhhc
Q psy8536         163 RTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       163 ~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ...++.||.||..|+.+||..|.
T Consensus         3 ~k~rr~Rt~ft~~q~~~Le~~f~   25 (61)
T 1akh_A            3 EKSPKGKSSISPQARAFLEEVFR   25 (61)
T ss_dssp             ---------CCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHH
Confidence            45778899999999999999995

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

Probab=96.62  E-value=0.0012  Score=40.97  Aligned_cols=22  Identities=23%  Similarity=0.215  Sum_probs=19.1

Q ss_pred             CCCccccccchHHHHHHhhhhc
Q psy8536         164 TKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       164 ~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ...+.|+.||.+|+.+||++|.
T Consensus         7 ~~~~~R~~ft~~Ql~~Le~~F~   28 (76)
T 2dn0_A            7 GASIYKNKKSHEQLSALKGSFC   28 (76)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCccCCHHHHHHHHHHHh
Confidence            4555699999999999999995

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

Probab=96.54  E-value=0.0048  Score=37.35  Aligned_cols=40  Identities=23%  Similarity=0.310  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHH
Q psy8536          15 QQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQ   54 (186)
Q Consensus        15 ~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFq   54 (186)
                      .-.+.|+..|.........+...|+.+.+|+..+|+.||-
T Consensus        16 ~~~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa   55 (70)
T 2ys9_A           16 PDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFD   55 (70)
T ss_dssp             CCCHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHH
T ss_pred             CcchHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHH
Confidence            3457899999999999999999999999999999999994

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

Probab=96.52  E-value=0.00018  Score=47.26  Aligned_cols=20  Identities=35%  Similarity=0.534  Sum_probs=16.2

Q ss_pred             cccceeeeeeeehhhhhhhh
Q psy8536          89 YLVFQVKIWFQNRRAKERKQ  108 (186)
Q Consensus        89 ~~~~riq~WFqNrRak~~~~  108 (186)
                      +...+|++||||+|++....
T Consensus        69 lse~qV~vWFqNRR~k~k~k   88 (99)
T 1lfb_A           69 VTEVRVYNWFANRRKEEAFR   88 (99)
T ss_dssp             CCHHHHHHHHHHHHHTTSCC
T ss_pred             cCcceeeeccHHHHHHHHHh
Confidence            55679999999999987553

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

Probab=96.31  E-value=0.0018  Score=39.91  Aligned_cols=22  Identities=18%  Similarity=0.128  Sum_probs=19.5

Q ss_pred             CCCccccccchHHHHHHhhhhc
Q psy8536         164 TKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       164 ~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ..++.||.||..|+.+||++|.
T Consensus         5 ~~~~~Rt~ft~~Ql~~Le~~F~   26 (74)
T 2ly9_A            5 DSFGIRAKKTKEQLAELKVSYL   26 (74)
T ss_dssp             CCCCTTCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCcCCCHHHHHHHHHHHH
Confidence            4567799999999999999995

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

Probab=96.28  E-value=0.0014  Score=48.25  Aligned_cols=24  Identities=13%  Similarity=0.230  Sum_probs=18.3

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      .+..||.||+||..|+.+||++|+
T Consensus       112 ~~k~rr~R~~ft~~ql~~Le~~F~  135 (194)
T 1ic8_A          112 TKKGRRNRFKWGPASQQILFQAYE  135 (194)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHH
T ss_pred             cccCCCCCcccCHHHHHHHHHHHH
Confidence            356788999999999999999996

>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=96.25  E-value=0.0016  Score=45.79  Aligned_cols=24  Identities=29%  Similarity=0.307  Sum_probs=18.1

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      .+.++|.||+||..|+.+||++|+
T Consensus        84 ~~~~rr~Rt~ft~~Q~~~Le~~F~  107 (146)
T 1au7_A           84 NERKRKRRTTISIAAKDALERHFG  107 (146)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCccHHHHHHHHHHHH
Confidence            456788899999999999999996

>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=96.19  E-value=0.0033  Score=38.61  Aligned_cols=24  Identities=8%  Similarity=0.014  Sum_probs=20.9

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ++..++.|+.||..|+.+||+.|.
T Consensus         4 ~~~~rr~R~~~~~~q~~~Le~~f~   27 (73)
T 1x2n_A            4 GSSGKNKRGVLPKHATNVMRSWLF   27 (73)
T ss_dssp             CSSSCCSSCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHH
Confidence            356788899999999999999993

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

Probab=96.09  E-value=0.00057  Score=43.83  Aligned_cols=30  Identities=20%  Similarity=0.263  Sum_probs=22.3

Q ss_pred             hhhhhhcccceeeeeeeehhhhhhhhhhhc
Q psy8536          83 NKVMYTYLVFQVKIWFQNRRAKERKQLKKR  112 (186)
Q Consensus        83 ~~~~~~~~~~riq~WFqNrRak~~~~~~~~  112 (186)
                      .....++...+|.+||+|+|.+........
T Consensus        41 LA~~tgLt~~QV~~WF~NrR~R~kk~~~~~   70 (89)
T 2lk2_A           41 LSQQTHLSTLQVCNWFINARRRLLPDMLRK   70 (89)
T ss_dssp             HHHHSSSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHCcCHHHHHHHHHHHHHHhhhHHHHh
Confidence            344555666799999999999988765433

>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=96.05  E-value=0.0022  Score=45.82  Aligned_cols=23  Identities=30%  Similarity=0.411  Sum_probs=17.3

Q ss_pred             CCCCccccccchHHHHHHhhhhc
Q psy8536         163 RTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       163 ~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      +.++|.||+||..|+.+||++|+
T Consensus        99 ~~~rr~Rt~ft~~Q~~~Le~~F~  121 (160)
T 1e3o_C           99 SRRRKKRTSIETNIRVALEKSFM  121 (160)
T ss_dssp             -----CCCCCCHHHHHHHHHHHH
T ss_pred             CCCCcCccccCHHHHHHHHHHHh
Confidence            46788899999999999999995

>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=95.93  E-value=0.004  Score=43.94  Aligned_cols=23  Identities=26%  Similarity=0.296  Sum_probs=20.7

Q ss_pred             CCCCccccccchHHHHHHhhhhc
Q psy8536         163 RTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       163 ~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      +.++|.||.||..|+.+||++|+
T Consensus        91 ~~~rr~Rt~ft~~q~~~Le~~F~  113 (151)
T 3d1n_I           91 SKKRKRRTSFTPQAIEALNAYFE  113 (151)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCcccCHHHHHHHHHHHH
Confidence            46778899999999999999996

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

Probab=95.66  E-value=0.0038  Score=44.73  Aligned_cols=24  Identities=25%  Similarity=0.170  Sum_probs=13.5

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      .+..+|.||+||..|+.+||++|+
T Consensus        96 ~~~~rr~Rt~ft~~Ql~~LE~~F~  119 (164)
T 2xsd_C           96 QGRKRKKRTSIEVGVKGALESHFL  119 (164)
T ss_dssp             ----------CCHHHHHHHHHHHH
T ss_pred             cccCCCCceeccHHHHHHHHHHHh
Confidence            356788899999999999999996

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

Probab=95.60  E-value=0.0043  Score=44.38  Aligned_cols=24  Identities=38%  Similarity=0.492  Sum_probs=17.4

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      +...+|.||.||..|+.+||++|+
T Consensus        94 ~~~~rr~Rt~ft~~q~~~Le~~F~  117 (164)
T 2d5v_A           94 GNTPKKPRLVFTDVQRRTLHAIFK  117 (164)
T ss_dssp             ------CCCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHh
Confidence            346788899999999999999996

>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=95.53  E-value=0.0059  Score=38.88  Aligned_cols=23  Identities=22%  Similarity=0.120  Sum_probs=19.5

Q ss_pred             CCCCccccccchHHHHHHhhhhc
Q psy8536         163 RTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       163 ~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ..+++.|+.||..|+.+||+.|.
T Consensus        25 ~~~~k~r~~ft~~q~~~Le~~f~   47 (87)
T 1mnm_C           25 STKPYRGHRFTKENVRILESWFA   47 (87)
T ss_dssp             ESSCCTTCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHH
Confidence            34556699999999999999995

>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=95.37  E-value=0.0013  Score=40.05  Aligned_cols=22  Identities=23%  Similarity=0.306  Sum_probs=16.2

Q ss_pred             hhhhhhcccceeeeeeeehhhh
Q psy8536          83 NKVMYTYLVFQVKIWFQNRRAK  104 (186)
Q Consensus        83 ~~~~~~~~~~riq~WFqNrRak  104 (186)
                      -....++..-.|++||+|+|+.
T Consensus        38 LA~~lgL~~~VVrVWFqNrRa~   59 (71)
T 2da7_A           38 ISIAVGLPQEFVKEWFEQRKVY   59 (71)
T ss_dssp             HHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHhCCCHHHHHHHHhhcccc
Confidence            3444455566999999999974

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

Probab=95.26  E-value=0.0075  Score=45.09  Aligned_cols=24  Identities=8%  Similarity=0.214  Sum_probs=20.0

Q ss_pred             CCCCCccccccchHHHHHHhhhhc
Q psy8536         162 TRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       162 ~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      .+..+|.|++||..|+.+||++|+
T Consensus       139 ~~k~RR~R~~ft~~ql~~Le~~F~  162 (221)
T 2h8r_A          139 NKKMRRNRFKWGPASQQILYQAYD  162 (221)
T ss_dssp             ---CCCCCCCCCHHHHHHHHHHHH
T ss_pred             cCCCCCCCcCCCHHHHHHHHHHHH
Confidence            456889999999999999999996

>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=95.10  E-value=0.011  Score=41.91  Aligned_cols=23  Identities=22%  Similarity=0.383  Sum_probs=20.6

Q ss_pred             CCCCccccccchHHHHHHhhhhc
Q psy8536         163 RTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       163 ~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      +.++|.||.||..|+.+||+.|+
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~  116 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFL  116 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTT
T ss_pred             cCCCCCCcccCHHHHHHHHHHHc
Confidence            45677899999999999999996

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

Probab=95.03  E-value=0.01  Score=35.33  Aligned_cols=21  Identities=14%  Similarity=-0.007  Sum_probs=18.9

Q ss_pred             CCCccccccchHHHHHHhhhh
Q psy8536         164 TKDKYRVVYSDQQRLELEKEF  184 (186)
Q Consensus       164 ~~~~~r~~~~~~q~~~l~~~f  184 (186)
                      .+++.|+.||..|+.+||+.|
T Consensus         2 ~~rr~R~~ft~~q~~~Le~~f   22 (64)
T 1du6_A            2 SGHIEGRHMNKQATEILNEYF   22 (64)
T ss_dssp             CCCCCCCSSTTTHHHHHHHHH
T ss_pred             CCCCCCCcCCHHHHHHHHHHH
Confidence            356779999999999999999

>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=94.74  E-value=0.0028  Score=51.51  Aligned_cols=39  Identities=23%  Similarity=0.359  Sum_probs=24.3

Q ss_pred             hhhhccCCCccc--ccchhhhhhcccceeeeeeeehhhhhh
Q psy8536          68 EEVVIKDPSKDL--FLSNKVMYTYLVFQVKIWFQNRRAKER  106 (186)
Q Consensus        68 ~~~~~~~~~~~~--~~~~~~~~~~~~~riq~WFqNrRak~~  106 (186)
                      +..+...++.+.  ........++...+|++||||||++++
T Consensus       381 e~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          381 EQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             HHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            344444444433  333444555666799999999998863

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

Probab=91.18  E-value=0.52  Score=27.09  Aligned_cols=45  Identities=16%  Similarity=0.366  Sum_probs=32.6

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHH
Q psy8536           9 RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQ   54 (186)
Q Consensus         9 r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFq   54 (186)
                      |..|+.+........+.. .........++|.++|++...|..|..
T Consensus         3 r~~ys~efK~~~~~~~~~-g~s~~~~~~~vA~~~gIs~~tl~~W~~   47 (59)
T 2glo_A            3 RRIFTPHFKLQVLESYRN-DNDCKGNQRATARKYNIHRRQIQKWLQ   47 (59)
T ss_dssp             CCCCCHHHHHHHHHHHHH-CTTTTTCHHHHHHHTTSCHHHHHHHHT
T ss_pred             CCcCCHHHHHHHHHHHHc-CCCcchHHHHHHHHHCcCHHHHHHHHH
Confidence            567999988777554443 332222367899999999999999975

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

Probab=90.71  E-value=0.84  Score=28.48  Aligned_cols=46  Identities=15%  Similarity=0.328  Sum_probs=33.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHH
Q psy8536           4 TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQ   54 (186)
Q Consensus         4 ~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFq   54 (186)
                      ++++.+..|+.++....-..+.. .    ....++|..+|++...|..|..
T Consensus        15 ~~~~~~~~ys~e~k~~~v~~~~~-g----~s~~~iA~~~gIs~sTl~rW~k   60 (87)
T 2elh_A           15 KGKRPLRSLTPRDKIHAIQRIHD-G----ESKASVARDIGVPESTLRGWCK   60 (87)
T ss_dssp             CCSSCCSSCCHHHHHHHHHHHHH-T----CCHHHHHHHHTCCHHHHHHHHH
T ss_pred             cCCCCCCCCCHHHHHHHHHHHHC-C----CCHHHHHHHHCcCHHHHHHHHH
Confidence            34456778999986655555542 2    2356889999999999999974

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

Probab=88.83  E-value=1.6  Score=29.00  Aligned_cols=50  Identities=16%  Similarity=0.232  Sum_probs=38.5

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536           7 KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK   59 (186)
Q Consensus         7 r~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~   59 (186)
                      ++|..||.++...+-..+..+....   ..+||+.+|++...|..|..++...
T Consensus         3 ~~r~~~t~e~K~~iv~~~~~~g~~~---~~~~A~~~gvs~stl~~~~~~~~~~   52 (131)
T 1hlv_A            3 PKRRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNKRAI   52 (131)
T ss_dssp             CSSCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTHHHH
T ss_pred             CcceeCCHHHHHHHHHHHHHCCCCc---HHHHHHHhCCCHHHHHHHHhchhhh
Confidence            3578999999987777775555443   3368999999999999999776654

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

Probab=82.12  E-value=6.2  Score=24.44  Aligned_cols=49  Identities=22%  Similarity=0.306  Sum_probs=35.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536          11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus        11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      .++..+..+|.-.|...     ..-.++|..+|++...|+.+...-+.+.++..
T Consensus        37 ~L~~~~r~vl~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l   85 (92)
T 3hug_A           37 QLSAEHRAVIQRSYYRG-----WSTAQIATDLGIAEGTVKSRLHYAVRALRLTL   85 (92)
T ss_dssp             TSCHHHHHHHHHHHTSC-----CCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            35677777777655333     24678899999999999998876666665544

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

Probab=80.20  E-value=4.7  Score=21.09  Aligned_cols=40  Identities=15%  Similarity=0.282  Sum_probs=29.1

Q ss_pred             CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHH
Q psy8536          10 VVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQ   54 (186)
Q Consensus        10 ~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFq   54 (186)
                      ..++.++...+...+... .    ...++|+.+|++...|..|..
T Consensus         4 ~~l~~~~~~~i~~~~~~g-~----s~~~IA~~lgis~~Tv~~~~~   43 (51)
T 1tc3_C            4 SALSDTERAQLDVMKLLN-V----SLHEMSRKISRSRHCIRVYLK   43 (51)
T ss_dssp             CCCCHHHHHHHHHHHHTT-C----CHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHcC-C----CHHHHHHHHCcCHHHHHHHHh
Confidence            357787775555555432 2    366889999999999999985

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	186
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	7e-19
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	1e-17
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	3e-17
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	1e-15
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	1e-15
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	1e-15
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	1e-14
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	2e-14
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	2e-14
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	2e-14
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	3e-14
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	3e-14
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	6e-14
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	8e-14
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	1e-13
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	2e-13
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	3e-13
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	4e-13
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	8e-13
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	1e-12
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	2e-12
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	2e-12
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	6e-12
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	1e-11
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	2e-11
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	2e-11
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	6e-11
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	2e-10
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	2e-09
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	4e-09
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	2e-08
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	6e-07

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

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

 Score = 74.5 bits (183), Expect = 7e-19
 Identities = 35/69 (50%), Positives = 45/69 (65%)

Query: 1  KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
            R+  K R  Y+  Q LELEKEF ++ Y+T  R+ E+A  L L+ERQVKIWFQNRR K 
Sbjct: 9  HARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKM 68

Query: 61 RKQLKKREE 69
          +K  K R +
Sbjct: 69 KKINKDRAK 77

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

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

 Score = 71.0 bits (174), Expect = 1e-17
 Identities = 33/55 (60%), Positives = 45/55 (81%)

Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
          R  Y+  Q LELEKEFH++RY+T RR+ E+A++L L+ERQ+KIWFQNRR K +K+
Sbjct: 1  RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 55

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Length = 68

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

 Score = 70.2 bits (172), Expect = 3e-17
 Identities = 22/63 (34%), Positives = 37/63 (58%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK 66
          + R  ++ +Q   LEKEF  + Y  +  +  LA  + L E ++++WF NRRAK R++ K 
Sbjct: 3  RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL 62

Query: 67 REE 69
          R +
Sbjct: 63 RNQ 65

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58

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

 Score = 65.7 bits (160), Expect = 1e-15
 Identities = 26/56 (46%), Positives = 40/56 (71%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          K R+ YS  Q  ELE+E+  +++IT  ++ +++ +  LSERQ+ IWFQNRR KE+K
Sbjct: 3  KKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 58

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

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

 Score = 66.6 bits (162), Expect = 1e-15
 Identities = 28/66 (42%), Positives = 46/66 (69%)

Query: 1  KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
             +    R  ++ +Q  ELEKEFH+++Y++  R+ E+A +L L+E QVKIWFQNRR K+
Sbjct: 23 GLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQ 82

Query: 61 RKQLKK 66
          +K+ ++
Sbjct: 83 KKRERE 88

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 53

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

 Score = 65.3 bits (159), Expect = 1e-15
 Identities = 26/53 (49%), Positives = 40/53 (75%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59
          + R  +S +Q   L++EF+ +RY+T RR+ +L++ LGL+E Q+KIWFQN RAK
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

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

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

 Score = 63.4 bits (154), Expect = 1e-14
 Identities = 24/63 (38%), Positives = 37/63 (58%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK 66
          + R  ++  Q  ELE+ F   RY+T  R A+L+  L L   QVKIWF+NRR + + Q  +
Sbjct: 3  RTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ 62

Query: 67 REE 69
           ++
Sbjct: 63 HKD 65

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

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

 Score = 62.4 bits (152), Expect = 2e-14
 Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 13 SDQQRLELEKEF-HYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          + Q    LEK F   +++   +R   L+  L    R ++ WF+ RR +E+ 
Sbjct: 1  TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 51

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57

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

 Score = 62.6 bits (152), Expect = 2e-14
 Identities = 25/57 (43%), Positives = 37/57 (64%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
          +YR  ++  Q   LEKEF+   Y++  R+ ELA  L L E  +K+WFQNRR K+++Q
Sbjct: 1  RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 57

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Length = 57

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

 Score = 62.5 bits (152), Expect = 2e-14
 Identities = 28/54 (51%), Positives = 38/54 (70%)

Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          +V +S+ Q +ELEK+F   +Y++   +  LA  L LSERQVK WFQNRRAK R+
Sbjct: 4  QVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 57

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

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

 Score = 62.2 bits (151), Expect = 3e-14
 Identities = 14/49 (28%), Positives = 24/49 (48%)

Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRR 57
          R+V++D QR  L   F  ++  +   +  ++  LGL    V  +F N R
Sbjct: 2  RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 77

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

 Score = 62.8 bits (152), Expect = 3e-14
 Identities = 24/68 (35%), Positives = 38/68 (55%)

Query: 1  KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60
              K K RV+++  Q  ELE+ F   RY++   +  LA+ + L+  QVKIWFQN R K 
Sbjct: 5  LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKT 64

Query: 61 RKQLKKRE 68
          ++   ++ 
Sbjct: 65 KRAQNEKG 72

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

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

 Score = 61.3 bits (149), Expect = 6e-14
 Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 1/56 (1%)

Query: 7  KYRVVYSDQQRLELEKEF-HYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKER 61
          K   V   +    LEK F   ++Y   +R   L+  L  S R+++ WF++RR +++
Sbjct: 3  KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

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

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

 Score = 61.0 bits (148), Expect = 8e-14
 Identities = 17/57 (29%), Positives = 31/57 (54%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
          + R V +++Q   L   +  +       K +L    GLS R +++WFQN+R K++K+
Sbjct: 5  RVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 68

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

 Score = 60.7 bits (147), Expect = 1e-13
 Identities = 25/64 (39%), Positives = 39/64 (60%)

Query: 5  KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL 64
          + K RV++S  Q  ELE+ F   +Y++   +  LA+ + L+  QVKIWFQN R K ++Q 
Sbjct: 2  RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61

Query: 65 KKRE 68
          K + 
Sbjct: 62 KDKA 65

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 58

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

 Score = 59.9 bits (145), Expect = 2e-13
 Identities = 27/56 (48%), Positives = 40/56 (71%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          K R  ++  Q L LE++F   +Y++I  +AE ++SL L+E QVKIWFQNRRAK ++
Sbjct: 2  KPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 65

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

 Score = 59.5 bits (144), Expect = 3e-13
 Identities = 24/59 (40%), Positives = 36/59 (61%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65
          + R  +S  Q  ELE+ F  ++Y  I  + ELA    L+E ++++WFQNRRA+ RKQ  
Sbjct: 4  RSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT 62

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.2 bits (143), Expect = 4e-13
 Identities = 22/57 (38%), Positives = 36/57 (63%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
          + R  ++ QQ  +LE  F  +RY  +  + E+A    L+E +V++WF+NRRAK RK+
Sbjct: 3  RQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 59

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

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

 Score = 58.9 bits (142), Expect = 8e-13
 Identities = 13/74 (17%), Positives = 29/74 (39%), Gaps = 15/74 (20%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELAN---------------SLGLSERQVKI 51
            R  +  +    +E  F+ ++Y    ++ E+AN                  ++  +V  
Sbjct: 2  GSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYN 61

Query: 52 WFQNRRAKERKQLK 65
          WF NRR + +++  
Sbjct: 62 WFANRRKEIKRRAN 75

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

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

 Score = 57.6 bits (139), Expect = 1e-12
 Identities = 16/53 (30%), Positives = 29/53 (54%)

Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKER 61
          +   S Q R  LE+ F   + +  + K E+A   G++  QV++WF N+R + +
Sbjct: 1  KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 58

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

 Score = 57.6 bits (139), Expect = 2e-12
 Identities = 16/57 (28%), Positives = 27/57 (47%)

Query: 7  KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
          K R   S   +  LE+ F      + +    +A  L L +  V++WF NRR +E++ 
Sbjct: 1  KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV 57

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

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

 Score = 57.3 bits (138), Expect = 2e-12
 Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 1/64 (1%)

Query: 7  KYRVVYSDQQRLELEKEFHYS-RYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65
          +     ++ Q   LE  F+   ++        +A   GL+E Q + WF+ R A+ R+   
Sbjct: 3  EGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG 62

Query: 66 KREE 69
             E
Sbjct: 63 LPSE 66

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

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

 Score = 56.5 bits (136), Expect = 6e-12
 Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 3/66 (4%)

Query: 7  KYRVVYSDQQRLELEK---EFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
          + R  ++ Q    L +       + Y +   K ELA   G++  QV  WF N+R + +K 
Sbjct: 3  RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN 62

Query: 64 LKKREE 69
          + K +E
Sbjct: 63 IGKFQE 68

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

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

 Score = 55.8 bits (134), Expect = 1e-11
 Identities = 17/62 (27%), Positives = 32/62 (51%)

Query: 2  TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKER 61
           + + + R    ++ R  LE  F      ++++   +AN LGL +  V++WF NRR K +
Sbjct: 5  VQARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGK 64

Query: 62 KQ 63
          + 
Sbjct: 65 RS 66

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

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

 Score = 54.8 bits (132), Expect = 2e-11
 Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 3/54 (5%)

Query: 12 YSDQQRLELEKEFHYSR---YITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
          ++ +    LE  F  +    Y+  +    L  +  LS  Q+K W  NRR KE+ 
Sbjct: 5  FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.6 bits (131), Expect = 2e-11
 Identities = 16/55 (29%), Positives = 27/55 (49%)

Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
          R       R+ LEK F  ++  T      +A  L + +  +++WF NRR KE++ 
Sbjct: 2  RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI 56

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

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

 Score = 53.6 bits (129), Expect = 6e-11
 Identities = 13/59 (22%), Positives = 19/59 (32%), Gaps = 3/59 (5%)

Query: 7  KYRVVYSDQQRLELEKEF---HYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62
            R V        +           Y T   K ++A    L+  QV  WF N R +  +
Sbjct: 4  NKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQ 62

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

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

 Score = 52.7 bits (126), Expect = 2e-10
 Identities = 8/67 (11%), Positives = 23/67 (34%), Gaps = 4/67 (5%)

Query: 1  KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIR----RKAELANSLGLSERQVKIWFQNR 56
             T  ++R  ++ +Q+ ++        +   +       +     G+  + +KIW  N 
Sbjct: 13 SGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNN 72

Query: 57 RAKERKQ 63
          +      
Sbjct: 73 KNSGPSS 79

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

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

 Score = 50.1 bits (119), Expect = 2e-09
 Identities = 12/58 (20%), Positives = 21/58 (36%), Gaps = 1/58 (1%)

Query: 7  KYRVVYSDQQRLELEKEFH-YSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63
          + R   S +    L+   H    Y        L+  L L +  +  +FQN+R   +  
Sbjct: 9  RSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS 66

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Zinc fingers and homeoboxes protein 1, ZHX1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.3 bits (117), Expect = 4e-09
 Identities = 12/57 (21%), Positives = 24/57 (42%)

Query: 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKRE 68
           + +Q   L+  F  S  +T      L     L+ R++  WF  ++  +  + +K E
Sbjct: 11 KTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKME 67

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

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

 Score = 47.1 bits (111), Expect = 2e-08
 Identities = 12/78 (15%), Positives = 24/78 (30%), Gaps = 21/78 (26%)

Query: 9  RVVYSDQQRLELEKEFHYSRYITIRRKAELANSL---------------------GLSER 47
          R  +    +  L + +   +  +   +  L                          ++E 
Sbjct: 1  RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 48 QVKIWFQNRRAKERKQLK 65
          +V  WF NRR +E  + K
Sbjct: 61 RVYNWFANRRKEEAFRHK 78

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]} Length = 76

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

 Score = 43.2 bits (101), Expect = 6e-07
 Identities = 12/65 (18%), Positives = 22/65 (33%)

Query: 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVV 71
           + +Q   L+  F   ++       +L    GL   ++  WF + R   +    K     
Sbjct: 10 KTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLKWFRDN 69

Query: 72 IKDPS 76
             PS
Sbjct: 70 ASGPS 74

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	186
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.9
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.9
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.9
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.9
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.9
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.89
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.89
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.89
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.89
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.89
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.88
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.88
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.87
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.87
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.86
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.86
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.85
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.85
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.85
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.84
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.84
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.82
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.82
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.79
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.79
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.79
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.77
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.75
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.73
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.73
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.73
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.73
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	97.95
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	97.9
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	97.72
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	97.71
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	97.64
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	97.55
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	97.53
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	97.45
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	97.39
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	97.34
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	97.31
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	97.26
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	97.26
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	97.22
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	97.19
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	97.18
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	97.18
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	97.17
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	97.08
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	97.06
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	97.01
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	96.98
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	96.8
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	96.78
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	96.68
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	96.63
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	96.5
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	96.43
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	96.31
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	96.12
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	95.02
d1hlva1	66	DNA-binding domain of centromere binding protein B	90.7
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	90.36
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	88.26
d1iufa1	78	Ars-binding protein 1, ABP1 {Fission yeast (Schizo	88.1

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

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

Probab=99.90  E-value=9.2e-25  Score=129.87  Aligned_cols=58  Identities=45%  Similarity=0.747  Sum_probs=55.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536           5 KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      +||+|+.||.+|+.+||..|..|+||+..++++||..|||++.+|++||||+|+++++
T Consensus         1 Grr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           1 GRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            4678999999999999999999999999999999999999999999999999998764

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

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

Probab=99.90  E-value=5.3e-24  Score=127.08  Aligned_cols=57  Identities=47%  Similarity=0.807  Sum_probs=55.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536           6 DKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus         6 rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      ||.|++||.+|+.+|+..|+.|+||+..++++||..|||++.+|++||||+|+++++
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            567999999999999999999999999999999999999999999999999999986

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

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

Probab=99.90  E-value=1.2e-23  Score=132.03  Aligned_cols=66  Identities=53%  Similarity=0.786  Sum_probs=61.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhh
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR   67 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~   67 (186)
                      .+.+|++|++||.+|+.+||..|..++||+..++++||..|||++.+|+|||||+|+++++.....
T Consensus        10 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~~   75 (77)
T d1pufa_          10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDR   75 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHHh
Confidence            356778899999999999999999999999999999999999999999999999999999876543

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

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

Probab=99.90  E-value=5.7e-24  Score=126.34  Aligned_cols=56  Identities=43%  Similarity=0.790  Sum_probs=54.5

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536           7 KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus         7 r~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      |.|+.||.+|+.+||..|..++||+..++++||..+||++.+|++||||+|+++|+
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk   56 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR   56 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhc
Confidence            57899999999999999999999999999999999999999999999999999986

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

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

Probab=99.90  E-value=1e-23  Score=125.20  Aligned_cols=57  Identities=49%  Similarity=0.746  Sum_probs=54.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536           6 DKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus         6 rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      ++.|++||.+|+.+|+..|..|+||+..++++||..+||++.+|++||||+|+++|+
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k~kk   57 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR   57 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhhccC
Confidence            467899999999999999999999999999999999999999999999999999885

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

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

Probab=99.89  E-value=1.9e-23  Score=127.35  Aligned_cols=62  Identities=39%  Similarity=0.637  Sum_probs=58.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536           4 TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK   65 (186)
Q Consensus         4 ~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~   65 (186)
                      ++||.|+.||.+|+.+|+.+|..|+||+..++++||..+||++.+|++||||+|++++++..
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~   62 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   62 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhccc
Confidence            46778999999999999999999999999999999999999999999999999999998654

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

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

Probab=99.89  E-value=1.2e-23  Score=123.79  Aligned_cols=55  Identities=60%  Similarity=1.005  Sum_probs=53.4

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536           9 RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus         9 r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~   63 (186)
                      ||.||.+|+.+||..|..|+||+..++++||..|||++++|+|||||||+++|++
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk~   55 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   55 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhhc
Confidence            7999999999999999999999999999999999999999999999999999874

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

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

Probab=99.89  E-value=1.4e-23  Score=128.66  Aligned_cols=61  Identities=39%  Similarity=0.658  Sum_probs=57.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHh
Q psy8536           6 DKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK   66 (186)
Q Consensus         6 rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~   66 (186)
                      ||.|++||.+|+.+|+..|..++||+..++.+||..|||++.+|+|||||+|++++++...
T Consensus         2 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~~   62 (67)
T d1zq3p1           2 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ   62 (67)
T ss_dssp             SCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhhh
Confidence            4678999999999999999999999999999999999999999999999999999986654

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

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

Probab=99.89  E-value=1.3e-23  Score=123.04  Aligned_cols=53  Identities=49%  Similarity=0.851  Sum_probs=51.4

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536           7 KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK   59 (186)
Q Consensus         7 r~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~   59 (186)
                      |.|+.||.+|+.+||..|..++||+..++.+||..|||++.+|++||||||+|
T Consensus         1 R~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~lgL~~~qV~vWFqNrRaK   53 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK   53 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             CCCccCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChHHhhhcccccCCC
Confidence            57899999999999999999999999999999999999999999999999985

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

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

Probab=99.89  E-value=3.9e-23  Score=126.95  Aligned_cols=63  Identities=35%  Similarity=0.608  Sum_probs=58.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhh
Q psy8536           5 KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR   67 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~   67 (186)
                      +||.|++||.+|+.+|+..|..|+||+..++++||..+||++.+|++||||+|++.++.....
T Consensus         1 grR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~~   63 (68)
T d2cuea1           1 GQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLR   63 (68)
T ss_dssp             SCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhhhh
Confidence            467899999999999999999999999999999999999999999999999999999865543

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

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

Probab=99.88  E-value=5.7e-23  Score=126.13  Aligned_cols=60  Identities=40%  Similarity=0.687  Sum_probs=57.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536           5 KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      +||.|++||..|+.+|++.|..|+||+..++.+||..+||++.+|++||||+|+++++..
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~   61 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA   61 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhcc
Confidence            467899999999999999999999999999999999999999999999999999998753

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=2.4e-23  Score=125.06  Aligned_cols=59  Identities=37%  Similarity=0.637  Sum_probs=56.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536           5 KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~   63 (186)
                      +||.|++||.+|+.+|+..|..|+||+..+++.||..+||++.+|++||+|+|++.++.
T Consensus         1 Qrr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1           1 QRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             SSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            46889999999999999999999999999999999999999999999999999999875

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

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

Probab=99.87  E-value=1.1e-22  Score=130.89  Aligned_cols=63  Identities=44%  Similarity=0.787  Sum_probs=56.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK   65 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~   65 (186)
                      .+.+|.|+.||.+|+.+|+..|..|+||+..++++||..|||++.+|++||||+|+++|+...
T Consensus        25 ~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~~   87 (88)
T d1b72a_          25 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   87 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhcc
Confidence            345778999999999999999999999999999999999999999999999999999998653

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

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

Probab=99.87  E-value=2.5e-22  Score=124.18  Aligned_cols=60  Identities=23%  Similarity=0.292  Sum_probs=55.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhh-cCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536           5 KDKYRVVYSDQQRLELEKEFHY-SRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f~~-~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      +++.|+.||.+|+.+|+..|.. ++||+...+++||..+||++++|++||||||+++++..
T Consensus         1 g~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~   61 (72)
T d1uhsa_           1 GSEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhcc
Confidence            3678999999999999999986 67999999999999999999999999999999998754

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

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

Probab=99.86  E-value=2.7e-23  Score=130.62  Aligned_cols=62  Identities=39%  Similarity=0.685  Sum_probs=58.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536           2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus         2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~   63 (186)
                      +.+++|.|++||.+|+.+|+..|..|+||+..++++||..+||++.+|++||||+|++.++.
T Consensus         6 p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   67 (77)
T d1vnda_           6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRA   67 (77)
T ss_dssp             SSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHH
Confidence            45678889999999999999999999999999999999999999999999999999997753

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

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

Probab=99.86  E-value=2.5e-22  Score=122.59  Aligned_cols=60  Identities=28%  Similarity=0.493  Sum_probs=56.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536           4 TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus         4 ~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~   63 (186)
                      +.+|.|++||.+|+.+|+..|..|+||+..++++||.++||++.+|++||||+|++.++.
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~   61 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR   61 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSC
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHH
Confidence            456889999999999999999999999999999999999999999999999999997753

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

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

Probab=99.85  E-value=5.1e-22  Score=118.21  Aligned_cols=56  Identities=29%  Similarity=0.462  Sum_probs=54.0

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536           7 KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus         7 r~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      |+|+.|+.+|+++|+..|..|+||+..++.+||..+||++.+|++||||+|+++++
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr   56 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR   56 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHh
Confidence            57899999999999999999999999999999999999999999999999999875

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

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

Probab=99.85  E-value=2.3e-22  Score=122.96  Aligned_cols=60  Identities=28%  Similarity=0.540  Sum_probs=56.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      ..++|+|++||.+|+.+|+..|..|+||+..++++||..+||++.+|++||||+|+++|+
T Consensus         6 ~~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk   65 (67)
T d1ocpa_           6 QARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR   65 (67)
T ss_dssp             CCSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSS
T ss_pred             hccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhc
Confidence            456788999999999999999999999999999999999999999999999999998765

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

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

Probab=99.85  E-value=5.6e-22  Score=115.87  Aligned_cols=53  Identities=30%  Similarity=0.547  Sum_probs=51.2

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536           9 RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKER   61 (186)
Q Consensus         9 r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~   61 (186)
                      |++||++|+.+|++.|..|+||+..++.+||..+||++.+|++||||+|++.|
T Consensus         1 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~K   53 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   53 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTTC
T ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhccC
Confidence            68999999999999999999999999999999999999999999999999854

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

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

Probab=99.84  E-value=3.1e-21  Score=122.77  Aligned_cols=60  Identities=22%  Similarity=0.399  Sum_probs=56.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcC---------------CChhHHHHHHHhhHHHHHHHHH
Q psy8536           6 DKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLG---------------LSERQVKIWFQNRRAKERKQLK   65 (186)
Q Consensus         6 rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~---------------l~~~~v~~WFqnrr~~~~~~~~   65 (186)
                      ||.|+.||.+|+.+||.+|..|+||+..+|++||..+|               |++.+|++||||||+++|++..
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~   75 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRAN   75 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhh
Confidence            67899999999999999999999999999999999875               9999999999999999998654

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=2.7e-21  Score=114.55  Aligned_cols=55  Identities=29%  Similarity=0.509  Sum_probs=53.5

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536           8 YRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus         8 ~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      +||+|+.+|+.+|+..|..++||+..++++||.++||++.+|++||||+|+++|+
T Consensus         1 kRT~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk   55 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR   55 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTS
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHc
Confidence            5899999999999999999999999999999999999999999999999999886

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

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

Probab=99.82  E-value=6.7e-21  Score=118.08  Aligned_cols=60  Identities=20%  Similarity=0.204  Sum_probs=55.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHh-hcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFH-YSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~-~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      ...++.|++||.+|+.+|+++|. .++||+..++++||.++||++.+|++||||+|++.|+
T Consensus         5 ~~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk   65 (71)
T d1wi3a_           5 SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             CCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhcc
Confidence            34678899999999999999997 4899999999999999999999999999999999774

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

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

Probab=99.82  E-value=4.3e-21  Score=110.95  Aligned_cols=50  Identities=28%  Similarity=0.402  Sum_probs=48.8

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhH
Q psy8536           8 YRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRR   57 (186)
Q Consensus         8 ~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr   57 (186)
                      +|++||.+|+.+|+..|..++||+..++.+||.++||++++|++||||+|
T Consensus         1 PRt~ft~~Q~~~Le~~F~~n~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1           1 PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             CCSCCCHHHHHHHHHHTTSSCSSTHHHHHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhhcCCcCc
Confidence            58999999999999999999999999999999999999999999999987

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

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

Probab=99.79  E-value=1.6e-19  Score=112.40  Aligned_cols=59  Identities=29%  Similarity=0.447  Sum_probs=55.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536           6 DKYRVVYSDQQRLELEKEFH---YSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus         6 rr~r~~~t~~q~~~L~~~f~---~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      ||+|+.|+.+|+.+|+++|.   .++||+..++++||..+||++.+|++||+|+|++.++..
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~   63 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccc
Confidence            67889999999999999997   488999999999999999999999999999999988643

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Zinc fingers and homeoboxes protein 1, ZHX1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=4.2e-20  Score=115.87  Aligned_cols=56  Identities=18%  Similarity=0.247  Sum_probs=51.3

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536           9 RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL   64 (186)
Q Consensus         9 r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~   64 (186)
                      +..+|.+|+.+|+.+|..|+||+..++++||..+||++.+|++||||+|++.++..
T Consensus         8 ~k~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~   63 (76)
T d2ecba1           8 FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE   63 (76)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCC
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHh
Confidence            34569999999999999999999999999999999999999999999998876543

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

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

Probab=99.79  E-value=3.9e-20  Score=117.03  Aligned_cols=59  Identities=14%  Similarity=0.263  Sum_probs=53.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhh----cCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536           3 RTKDKYRVVYSDQQRLELEKEFHY----SRYITIRRKAELANSLGLSERQVKIWFQNRRAKER   61 (186)
Q Consensus         3 ~~~rr~r~~~t~~q~~~L~~~f~~----~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~   61 (186)
                      .++||.|++||.+|+++|+.+|+.    ++||+..++++||.+|||++.+|++||||+|.+.+
T Consensus        15 ~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k   77 (80)
T d1wh7a_          15 GTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGP   77 (80)
T ss_dssp             CCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSC
T ss_pred             cCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCC
Confidence            456788999999999999999886    89999999999999999999999999999996543

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=99.77  E-value=4.8e-19  Score=111.02  Aligned_cols=57  Identities=16%  Similarity=0.204  Sum_probs=53.5

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536           7 KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus         7 r~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~   63 (186)
                      ..++++|.+|+.+|+++|..|+||+..+++.||..+||++.+|++||+|+|++.|+.
T Consensus         5 s~~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~   61 (76)
T d2ecca1           5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhc
Confidence            345678999999999999999999999999999999999999999999999999874

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

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

Probab=99.75  E-value=4.6e-19  Score=102.69  Aligned_cols=50  Identities=28%  Similarity=0.465  Sum_probs=46.3

Q ss_pred             CHHHHHHHHHHHhh-cCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536          13 SDQQRLELEKEFHY-SRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus        13 t~~q~~~L~~~f~~-~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      |.+|..+||..|.. ++||+..++++||..+||++++|++||||||+++|+
T Consensus         1 T~~q~~iLE~~F~~~~~~P~~~~~~~LA~~~~ls~~qV~~WFqNrR~k~k~   51 (52)
T d1x2ma1           1 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   51 (52)
T ss_dssp             SSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             ChhHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccCc
Confidence            46799999999986 789999999999999999999999999999999763

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

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

Probab=99.73  E-value=6.4e-18  Score=100.92  Aligned_cols=53  Identities=28%  Similarity=0.428  Sum_probs=48.9

Q ss_pred             CCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536          10 VVYSDQQRLELEKEFHY---SRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK   62 (186)
Q Consensus        10 ~~~t~~q~~~L~~~f~~---~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~   62 (186)
                      .+|+.+|+.+|+.+|..   +|||+..++++||..+||++.+|++||+|+|++.|.
T Consensus         3 ~Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           3 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             CSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            45999999999999975   479999999999999999999999999999998763

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

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

Probab=99.73  E-value=9.2e-18  Score=100.76  Aligned_cols=57  Identities=23%  Similarity=0.239  Sum_probs=52.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536           5 KDKYRVVYSDQQRLELEKEFHY---SRYITIRRKAELANSLGLSERQVKIWFQNRRAKER   61 (186)
Q Consensus         5 ~rr~r~~~t~~q~~~L~~~f~~---~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~   61 (186)
                      .|++|+.|+.+++.+|+.+|..   +|||+..++..||..+||+..||++||+|+|.+..
T Consensus         2 ~krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R~l   61 (62)
T d1x2na1           2 GKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRIL   61 (62)
T ss_dssp             SCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhc
Confidence            4567889999999999999984   89999999999999999999999999999998754

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

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

Probab=99.73  E-value=1e-18  Score=109.39  Aligned_cols=55  Identities=20%  Similarity=0.343  Sum_probs=51.7

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcC---------------------CChhHHHHHHHhhHHHHHHH
Q psy8536           9 RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLG---------------------LSERQVKIWFQNRRAKERKQ   63 (186)
Q Consensus         9 r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~---------------------l~~~~v~~WFqnrr~~~~~~   63 (186)
                      |++||.+|+.+|+..|..|+||+..+|+.||.+++                     |++.+|++||+|||++.++.
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr~   76 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFR   76 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCC
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHHh
Confidence            68999999999999999999999999999999994                     89999999999999997753

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

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

Probab=99.73  E-value=1.2e-18  Score=103.51  Aligned_cols=55  Identities=29%  Similarity=0.471  Sum_probs=51.2

Q ss_pred             CCCCCCCHHHHHHHHHHHhh-cCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536           7 KYRVVYSDQQRLELEKEFHY-SRYITIRRKAELANSLGLSERQVKIWFQNRRAKER   61 (186)
Q Consensus         7 r~r~~~t~~q~~~L~~~f~~-~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~   61 (186)
                      +.+.+++.++..+||.+|.. ++||+..++++||..+||++++|++||||||+++|
T Consensus         3 k~~~~~k~~~~~iLE~~F~~~~~yPs~~~~~~LA~~lgls~~qV~~WFqNrR~k~r   58 (59)
T d2cqxa1           3 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK   58 (59)
T ss_dssp             CCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCccccHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccC
Confidence            56788999999999999985 68999999999999999999999999999999875

>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=97.95  E-value=4e-07  Score=52.21  Aligned_cols=41  Identities=29%  Similarity=0.263  Sum_probs=25.7

Q ss_pred             hhhhccCCCcccccch--hhhhhcccceeeeeeeehhhhhhhh
Q psy8536          68 EEVVIKDPSKDLFLSN--KVMYTYLVFQVKIWFQNRRAKERKQ  108 (186)
Q Consensus        68 ~~~~~~~~~~~~~~~~--~~~~~~~~~riq~WFqNrRak~~~~  108 (186)
                      +..+...++.+.....  +...++..-+|++||||+|++++++
T Consensus        13 e~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk~   55 (56)
T d9anta_          13 EKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   55 (56)
T ss_dssp             HHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhhc
Confidence            3334444444443333  3444555569999999999998874

>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=97.90  E-value=4.5e-06  Score=51.36  Aligned_cols=27  Identities=11%  Similarity=0.234  Sum_probs=22.3

Q ss_pred             cccCCCCCccccccchHHHHHHhhhhc
Q psy8536         159 TRKTRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       159 ~~~~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ++.+...||.||+||.+|+.+||.+|+
T Consensus        11 ~~~~~~~kR~Rt~ft~~Q~~~L~~~fe   37 (80)
T d1wh7a_          11 SSSGGTTKRFRTKFTAEQKEKMLAFAE   37 (80)
T ss_dssp             CCCCCCSSCCCCCCCHHHHHHHHHHHH
T ss_pred             CCCccCCCCccccCCHHHHHHHHHHHH
Confidence            334556788999999999999988885

>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=97.72  E-value=2.7e-06  Score=51.25  Aligned_cols=32  Identities=19%  Similarity=0.133  Sum_probs=23.5

Q ss_pred             cccchhhhhhcccceeeeeeeehhhhhhhhhh
Q psy8536          79 LFLSNKVMYTYLVFQVKIWFQNRRAKERKQLK  110 (186)
Q Consensus        79 ~~~~~~~~~~~~~~riq~WFqNrRak~~~~~~  110 (186)
                      .........++...+|++||||+||+++++..
T Consensus        31 ~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~~   62 (72)
T d1uhsa_          31 TLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   62 (72)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHHHHHhccC
Confidence            33334455566667999999999999988654

>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=97.71  E-value=2.7e-06  Score=50.53  Aligned_cols=44  Identities=25%  Similarity=0.327  Sum_probs=27.3

Q ss_pred             hhhhccCCCcccccchhh--hhhcccceeeeeeeehhhhhhhhhhh
Q psy8536          68 EEVVIKDPSKDLFLSNKV--MYTYLVFQVKIWFQNRRAKERKQLKK  111 (186)
Q Consensus        68 ~~~~~~~~~~~~~~~~~~--~~~~~~~riq~WFqNrRak~~~~~~~  111 (186)
                      +..+...++.+.......  ..++...+|+|||||+|++++++...
T Consensus        17 e~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~~   62 (67)
T d1zq3p1          17 EQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ   62 (67)
T ss_dssp             HHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhhh
Confidence            334444444444433333  33444568999999999999886543

>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=97.64  E-value=1.1e-05  Score=50.49  Aligned_cols=23  Identities=39%  Similarity=0.582  Sum_probs=17.4

Q ss_pred             CCCCccccccchHHHHHHhhhhc
Q psy8536         163 RTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       163 ~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      +..++.||+||++|+.+||++|.
T Consensus        25 ~~~kr~Rt~ft~~Ql~~Le~~F~   47 (88)
T d1b72a_          25 GSPSGLRTNFTTRQLTELEKEFH   47 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHT
T ss_pred             CCCCCCCcCCCHHHHHHHHHHHH
Confidence            34578899999999999999996

>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=97.55  E-value=1.8e-05  Score=48.15  Aligned_cols=26  Identities=35%  Similarity=0.551  Sum_probs=22.3

Q ss_pred             ccCCCCCccccccchHHHHHHhhhhc
Q psy8536         160 RKTRTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       160 ~~~~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      |.....++.||+||.+|+.+||..|.
T Consensus         4 g~p~k~rr~Rt~ft~~Q~~~Le~~F~   29 (77)
T d1vnda_           4 GLPNKKRKRRVLFTKAQTYELERRFR   29 (77)
T ss_dssp             CCSSSSCSSCCCCCTTHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHH
Confidence            44456788899999999999999995

>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=97.53  E-value=1.7e-05  Score=45.53  Aligned_cols=21  Identities=43%  Similarity=0.561  Sum_probs=18.8

Q ss_pred             CCccccccchHHHHHHhhhhc
Q psy8536         165 KDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       165 ~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      +++.||.||++|+.+||++|.
T Consensus         1 Grr~Rt~ft~~Q~~~Le~~F~   21 (58)
T d2craa1           1 GRKKRIPYSKGQLRELEREYA   21 (58)
T ss_dssp             CCCSCCCSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHh
Confidence            467799999999999999995

>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=97.45  E-value=2.3e-05  Score=44.97  Aligned_cols=20  Identities=35%  Similarity=0.546  Sum_probs=18.3

Q ss_pred             CccccccchHHHHHHhhhhc
Q psy8536         166 DKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       166 ~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ||.||.||.+|+.+||++|.
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~   20 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFR   20 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHH
Confidence            56799999999999999995

>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=97.39  E-value=5.1e-05  Score=46.05  Aligned_cols=23  Identities=52%  Similarity=0.733  Sum_probs=20.5

Q ss_pred             CCCCccccccchHHHHHHhhhhc
Q psy8536         163 RTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       163 ~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      +..++.||.||..|+.+||++|+
T Consensus        11 ~~~rr~Rt~ft~~Ql~~Le~~F~   33 (77)
T d1pufa_          11 RSTRKKRCPYTKHQTLELEKEFL   33 (77)
T ss_dssp             CTTSCCCCCCCHHHHHHHHHHHH
T ss_pred             CcCCCCCCCCCHHHHHHHHHHHH
Confidence            45678899999999999999996

>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=97.34  E-value=1.4e-05  Score=47.42  Aligned_cols=45  Identities=27%  Similarity=0.412  Sum_probs=29.4

Q ss_pred             hhhhhhccCCCcccccch--hhhhhcccceeeeeeeehhhhhhhhhh
Q psy8536          66 KREEVVIKDPSKDLFLSN--KVMYTYLVFQVKIWFQNRRAKERKQLK  110 (186)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~--~~~~~~~~~riq~WFqNrRak~~~~~~  110 (186)
                      ..+..+...++.+.....  +...++...+|++||||+|++++++..
T Consensus        15 ~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~   61 (68)
T d2cuea1          15 ALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK   61 (68)
T ss_dssp             HHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhh
Confidence            344445555555554443  344455557999999999999987654

>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=97.31  E-value=4.5e-05  Score=45.16  Aligned_cols=21  Identities=43%  Similarity=0.703  Sum_probs=19.2

Q ss_pred             CCccccccchHHHHHHhhhhc
Q psy8536         165 KDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       165 ~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      +||.||.||+.|+.+||++|.
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~   22 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFK   22 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHH
Confidence            467899999999999999995

>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=97.26  E-value=5.5e-05  Score=43.18  Aligned_cols=20  Identities=40%  Similarity=0.617  Sum_probs=18.4

Q ss_pred             CccccccchHHHHHHhhhhc
Q psy8536         166 DKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       166 ~~~r~~~~~~q~~~l~~~f~  185 (186)
                      |+.|+.||+.|+.+||.+|+
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~   20 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFE   20 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHH
Confidence            56799999999999999996

>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=97.26  E-value=1.8e-05  Score=48.05  Aligned_cols=27  Identities=7%  Similarity=0.293  Sum_probs=19.8

Q ss_pred             hhhhhcccceeeeeeeehhhhhhhhhh
Q psy8536          84 KVMYTYLVFQVKIWFQNRRAKERKQLK  110 (186)
Q Consensus        84 ~~~~~~~~~riq~WFqNrRak~~~~~~  110 (186)
                      ....++...+|++||||+|++.+....
T Consensus        38 A~~l~l~~~~V~~WFqNrR~r~k~~~~   64 (76)
T d2ecba1          38 RAQTKLTRREIDAWFTEKKKSKALKEE   64 (76)
T ss_dssp             HHHTCCCHHHHHHHHHHHHHHHHSCCS
T ss_pred             HHHhCCCHHHHHHhHHHHHHHHHHHhH
Confidence            344455556999999999998776544

>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=97.22  E-value=1.2e-05  Score=48.86  Aligned_cols=34  Identities=9%  Similarity=0.176  Sum_probs=23.1

Q ss_pred             CCcccccchhhhhhcccceeeeeeeehhhhhhhh
Q psy8536          75 PSKDLFLSNKVMYTYLVFQVKIWFQNRRAKERKQ  108 (186)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~riq~WFqNrRak~~~~  108 (186)
                      +............++...+|++||+|+|++.+..
T Consensus        28 Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~   61 (76)
T d2ecca1          28 ARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             CCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhc
Confidence            3333333344555566679999999999998864

>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=97.19  E-value=6.7e-05  Score=42.13  Aligned_cols=19  Identities=32%  Similarity=0.585  Sum_probs=17.5

Q ss_pred             ccccccchHHHHHHhhhhc
Q psy8536         167 KYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       167 ~~r~~~~~~q~~~l~~~f~  185 (186)
                      |.||+||.+|+.+||.+|.
T Consensus         1 R~Rt~ft~~Q~~~Le~~F~   19 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREFN   19 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHH
Confidence            5699999999999999995

>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=97.18  E-value=2e-05  Score=48.58  Aligned_cols=24  Identities=25%  Similarity=0.483  Sum_probs=19.0

Q ss_pred             cccceeeeeeeehhhhhhhhhhhc
Q psy8536          89 YLVFQVKIWFQNRRAKERKQLKKR  112 (186)
Q Consensus        89 ~~~~riq~WFqNrRak~~~~~~~~  112 (186)
                      +....|++||||+|++.++.....
T Consensus        54 l~~~~V~vWFqNRR~k~kk~~~~a   77 (82)
T d2cufa1          54 VTSLKVYNWFANRRKEIKRRANIA   77 (82)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             CCHHHHHHHHhhhHHHHHHhhhHH
Confidence            444689999999999999865543

>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=97.18  E-value=1.1e-05  Score=45.57  Aligned_cols=26  Identities=23%  Similarity=0.381  Sum_probs=18.6

Q ss_pred             ccchhhhhhcccceeeeeeeehhhhh
Q psy8536          80 FLSNKVMYTYLVFQVKIWFQNRRAKE  105 (186)
Q Consensus        80 ~~~~~~~~~~~~~riq~WFqNrRak~  105 (186)
                      ........++...+|++||||+|++.
T Consensus        27 ~~~LA~~lgl~~~qV~~WFqNrR~k~   52 (53)
T d1le8a_          27 KEEVAKKCGITPLQVRVWFINKRMRS   52 (53)
T ss_dssp             HHHHHHHTTSCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHCCCHHHHHHHHHhhhhcc
Confidence            33334444556679999999999875

>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=97.17  E-value=7.1e-05  Score=42.68  Aligned_cols=19  Identities=42%  Similarity=0.670  Sum_probs=17.6

Q ss_pred             ccccccchHHHHHHhhhhc
Q psy8536         167 KYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       167 ~~r~~~~~~q~~~l~~~f~  185 (186)
                      |.||+||+.|+.+||+.|.
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~   19 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFY   19 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHH
Confidence            5699999999999999995

>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=97.08  E-value=0.00012  Score=42.17  Aligned_cols=20  Identities=30%  Similarity=0.486  Sum_probs=18.6

Q ss_pred             CccccccchHHHHHHhhhhc
Q psy8536         166 DKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       166 ~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ||.||+||++|+.+||..|.
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~   21 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQ   21 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCHHHHHHHHHHHH
Confidence            67799999999999999996

>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=97.06  E-value=1.8e-05  Score=45.26  Aligned_cols=27  Identities=26%  Similarity=0.443  Sum_probs=20.0

Q ss_pred             chhhhhhcccceeeeeeeehhhhhhhh
Q psy8536          82 SNKVMYTYLVFQVKIWFQNRRAKERKQ  108 (186)
Q Consensus        82 ~~~~~~~~~~~riq~WFqNrRak~~~~  108 (186)
                      ......++...+|++||||+|+++++.
T Consensus        30 ~LA~~lgL~~~qV~~WFqNrR~k~kk~   56 (57)
T d1e3oc1          30 LIAEQLNMEKEVIRVWFSNRRQKEKRI   56 (57)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHcc
Confidence            334444555679999999999998753

>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=97.01  E-value=8.2e-06  Score=45.87  Aligned_cols=27  Identities=22%  Similarity=0.426  Sum_probs=19.6

Q ss_pred             cchhhhhhcccceeeeeeeehhhhhhh
Q psy8536          81 LSNKVMYTYLVFQVKIWFQNRRAKERK  107 (186)
Q Consensus        81 ~~~~~~~~~~~~riq~WFqNrRak~~~  107 (186)
                      .......++...+|++||||+|++++.
T Consensus        25 ~~LA~~~~ls~~qV~~WFqNrR~k~k~   51 (52)
T d1x2ma1          25 EGLSKQLDWDVRSIQRWFRQRRNQEKP   51 (52)
T ss_dssp             HHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHCcCHHHHHHHHHhhhcccCc
Confidence            333444556667999999999998763

>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=96.98  E-value=0.00017  Score=42.13  Aligned_cols=21  Identities=33%  Similarity=0.504  Sum_probs=19.2

Q ss_pred             CCccccccchHHHHHHhhhhc
Q psy8536         165 KDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       165 ~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      .|+.||.||++|+.+||..|.
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~   22 (65)
T d1fjla_           2 QRRSRTTFSASQLDELERAFE   22 (65)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHH
Confidence            577899999999999999995

>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=96.80  E-value=0.00034  Score=41.08  Aligned_cols=22  Identities=23%  Similarity=0.377  Sum_probs=19.8

Q ss_pred             CCCccccccchHHHHHHhhhhc
Q psy8536         164 TKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       164 ~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      .++|.||.||+.|+..||++|+
T Consensus         7 ~~rr~Rt~~t~~q~~~Le~~F~   28 (67)
T d1ocpa_           7 ARKRKRTSIENRVRWSLETMFL   28 (67)
T ss_dssp             CSSSCCSSCCHHHHHHHHHHHS
T ss_pred             ccCCCCCCCCHHHHHHHHHHHH
Confidence            4577899999999999999996

>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=96.78  E-value=6.2e-05  Score=45.22  Aligned_cols=31  Identities=26%  Similarity=0.291  Sum_probs=23.0

Q ss_pred             ccchhhhhhcccceeeeeeeehhhhhhhhhh
Q psy8536          80 FLSNKVMYTYLVFQVKIWFQNRRAKERKQLK  110 (186)
Q Consensus        80 ~~~~~~~~~~~~~riq~WFqNrRak~~~~~~  110 (186)
                      ........++...+|++||+|+|++..+...
T Consensus        34 k~~La~~~gl~~~qv~~WF~N~R~r~k~~~~   64 (73)
T d1pufb_          34 KEELAKKCGITVSQVSNWFGNKRIRYKKNIG   64 (73)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHCcCHHHhHHHHHHHHHHhcccch
Confidence            3344555666777999999999999886543

>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=96.68  E-value=0.00036  Score=38.45  Aligned_cols=18  Identities=39%  Similarity=0.567  Sum_probs=16.9

Q ss_pred             cccccchHHHHHHhhhhc
Q psy8536         168 YRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       168 ~r~~~~~~q~~~l~~~f~  185 (186)
                      .||.||.+|+..||++|+
T Consensus         1 PRt~ft~~Q~~~Le~~F~   18 (50)
T d1s7ea1           1 PRLVFTDVQRRTLHAIFK   18 (50)
T ss_dssp             CCSCCCHHHHHHHHHHTT
T ss_pred             CCCCCCHHHHHHHHHHHH
Confidence            499999999999999996

>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=96.63  E-value=3.2e-05  Score=44.50  Aligned_cols=25  Identities=20%  Similarity=0.559  Sum_probs=18.4

Q ss_pred             chhhhhhcccceeeeeeeehhhhhh
Q psy8536          82 SNKVMYTYLVFQVKIWFQNRRAKER  106 (186)
Q Consensus        82 ~~~~~~~~~~~riq~WFqNrRak~~  106 (186)
                      ......++...+|++||+|+|++++
T Consensus        34 ~LA~~lgls~~qV~~WFqNrR~k~r   58 (59)
T d2cqxa1          34 GLSKQLDWSVRKIQCWFRHRRNQDK   58 (59)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHCcCHHHHHHHHHhhhcccC
Confidence            3344455566799999999998864

>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=96.50  E-value=0.00061  Score=39.82  Aligned_cols=22  Identities=18%  Similarity=0.294  Sum_probs=19.8

Q ss_pred             CCCccccccchHHHHHHhhhhc
Q psy8536         164 TKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       164 ~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ..+|.||.||+.|+..||..|.
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~   23 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYA   23 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHH
T ss_pred             CCCCCCcCcCHHHHHHHHHHHH
Confidence            3678899999999999999995

>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=96.43  E-value=0.00069  Score=40.16  Aligned_cols=23  Identities=17%  Similarity=0.030  Sum_probs=20.1

Q ss_pred             CCCCccccccchHHHHHHhhhhc
Q psy8536         163 RTKDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       163 ~~~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      ...++.|+.||+.|+..||+.|+
T Consensus         5 ~~~~r~R~~~t~~Q~~~Le~~F~   27 (71)
T d1wi3a_           5 SSGPRSRTKISLEALGILQSFIH   27 (71)
T ss_dssp             CCCCCCCCCCCSHHHHHHHHHHH
T ss_pred             CCCCCCCccCCHHHHHHHHHHHH
Confidence            45677899999999999999994

>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=96.31  E-value=0.00015  Score=41.75  Aligned_cols=26  Identities=31%  Similarity=0.411  Sum_probs=19.3

Q ss_pred             chhhhhhcccceeeeeeeehhhhhhh
Q psy8536          82 SNKVMYTYLVFQVKIWFQNRRAKERK  107 (186)
Q Consensus        82 ~~~~~~~~~~~riq~WFqNrRak~~~  107 (186)
                      ......++...+|++||+|+|++.+.
T Consensus        33 ~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_          33 NLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             HHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHCcCHHHHhHHhHhhcccccc
Confidence            34445556667999999999987754

>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=96.12  E-value=0.00011  Score=44.67  Aligned_cols=24  Identities=29%  Similarity=0.343  Sum_probs=18.1

Q ss_pred             hhhhcccceeeeeeeehhhhhhhh
Q psy8536          85 VMYTYLVFQVKIWFQNRRAKERKQ  108 (186)
Q Consensus        85 ~~~~~~~~riq~WFqNrRak~~~~  108 (186)
                      ....+...+|++||+|||++....
T Consensus        53 ~~~~vt~~~V~~WF~NRR~~~kr~   76 (78)
T d1lfba_          53 GSNLVTEVRVYNWFANRRKEEAFR   76 (78)
T ss_dssp             GGGCCCHHHHHHHHHHHHHTTSCC
T ss_pred             cccCCCHHHHHHHHHHHHHHHHHh
Confidence            333455568999999999987754

>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=95.02  E-value=0.0054  Score=34.59  Aligned_cols=19  Identities=32%  Similarity=0.324  Sum_probs=17.2

Q ss_pred             ccccccchHHHHHHhhhhc
Q psy8536         167 KYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       167 ~~r~~~~~~q~~~l~~~f~  185 (186)
                      |.||.||..|+..||..|.
T Consensus         1 r~Rt~~s~~q~~~Le~~F~   19 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFG   19 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHH
Confidence            4599999999999999995

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

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

Probab=90.70  E-value=0.78  Score=25.92  Aligned_cols=49  Identities=16%  Similarity=0.240  Sum_probs=39.2

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536           8 YRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK   59 (186)
Q Consensus         8 ~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~   59 (186)
                      +|..+|-.+...+-..++..+...   ..+||..+|++...|..|..|+..-
T Consensus         4 kRk~LT~~eK~~ii~~~e~g~k~s---q~eIA~~fGv~~STvs~IlKnK~ki   52 (66)
T d1hlva1           4 KRRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNKRAI   52 (66)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTHHHH
T ss_pred             ccccCCHHHHHHHHHHHHcCCcch---HHHHHHHhCCChhHHHHHHHHHHHH
Confidence            456789988888888888776443   5679999999999999999886544

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=90.36  E-value=0.43  Score=25.10  Aligned_cols=40  Identities=10%  Similarity=0.240  Sum_probs=34.1

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHH
Q psy8536           9 RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWF   53 (186)
Q Consensus         9 r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WF   53 (186)
                      +..+|++|++...+.+....     ...+||..+|++...|-.||
T Consensus         3 ~~~lt~~q~~~a~~l~~~G~-----s~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_           3 PRAINKHEQEQISRLLEKGH-----PRQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             CCSSCHHHHHHHHHHHHTTC-----CHHHHHHHHTCCHHHHHHHS
T ss_pred             CCcCCHHHHHHHHHHHHCCC-----CHHHHHHHHCcCHHHHHhhC
Confidence            46799999999999997542     37889999999999998887

>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=88.26  E-value=0.14  Score=28.85  Aligned_cols=21  Identities=10%  Similarity=0.012  Sum_probs=17.6

Q ss_pred             CCccccccchHHHHHHhhhhc
Q psy8536         165 KDKYRVVYSDQQRLELEKEFH  185 (186)
Q Consensus       165 ~~~~r~~~~~~q~~~l~~~f~  185 (186)
                      +|+.|+.|+.+|+..||..|.
T Consensus         2 ~krkR~~~~~~~~~iL~~wf~   22 (62)
T d1x2na1           2 GKNKRGVLPKHATNVMRSWLF   22 (62)
T ss_dssp             SCCSSCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHH
Confidence            345588999999999999884