Psyllid ID: psy526

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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-------190-------200-------210-------220-------230-------240-------250-------260-------270----
Protein Sequence
MDSMKDSEEYYKKINNNNITNNTMSYYGKKDIRDARDLPKPAALSNLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGKLLPPAPSMANSLYYYPLFYNMHSLYGTQGKLLPPAPSMANSLYYYPLFYNMHSNYGAQLTSPVLTTVTSTTYNEDDGESSGSGEGEEGDGGEIVDVCNDVEEDDQPSSSNLSE
Secondary Structure (PSIPRED)
ccccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHccccccHHHHHHHHHHcccccHHHHHHHHccHHHHHHHHHHHHHccccccccccccccEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHEccccHHHHHHHHHHHcccHHHHHHHHHHHHHcccHcHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEcccccccccccccccccc
Coil and Loop (DISEMBL)
MDSMKDSEEYYKKINnnnitnntmsyygkkdirdardlpkpaalsnlpglaqsqpptgrkkrsraAFSHAQVYELEKRFNaqkylsgperadVAKSLKLTETQVKIWFQNRRYKTKRKQLQLLEgslntpsagngkKVAVKILVReshpygsdylygtqgkllppapsmanslyyyplfynmhslygtqgkllppapsmanslyyyplfynmhsnygaqltspvlttvtsttyneddgessgsgegeegdggeivdvcndveeddqpsssnlse
Flexible Loop (DISEMBL)
MDSMKDSEEYYKKinnnnitnntmSYYGKKDIRDARDLpkpaalsnlpglaqsqpptgrkKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVakslkltetqvkiwfqnrryktkRKQLQLlegslntpsagngkKVAVKILVRESHPYGSDYLYGTQGKLLPPAPSMANSLYYYPLFYNMHSLYGTQGKLLPPAPSMANSLYYYPLFYNMHSNYGAQLTSPVLTTVTSTTYneddgessgsgegeegdgGEIVDVCNDveeddqpsssnlse
Low Complexity Region (SEG)
MDSMKDSeeyykkinnnnitnntMSYYGKKDIRDARDLPKPAALSNLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGKLLPPAPSMANSLYYYPLFYNMHSLYGTQGKLLPPAPSMANSLYYYPLFYNMHSNYGAQltspvlttvtsttYNeddgessgsgegeegdggeIVDVCNDVEEDDQPSSSNLSE
Disordered region (IsUnstruct)
***********************************************************************VYELEKRFNAQKYL*******VAKSLKLTETQVKIWFQNRRYKTKRKQLQLL************KKVAVKILVRESHPYGSDYLYGTQGKLLPPAPSMANSLYYYPLFYNMHSLYGTQGKLLPPAPSMANSLYYYPLFYNMHSNYGAQLTSPVLTTVT*********************************************
Disordered Region (DISOPRED)
*******************************************************************SHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYK***********************************************************YYYPLFYN*********************************************************************************************
Disordered Region (DISEMBL)
********EYYKKINNNNITNNTMSYYGKKDIRDARDLPKPAALSNLPGL****************FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGKLLPPAPSMANSLYYYPLFYNMHSLYGTQGKLLPPAPSMANSLYYYPLFYNMHSNYGAQLTSPVLTTVTSTT******************GGEIVDVCNDVE************
Disordered Region (DISPRO)
***************************************************************RAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK*********************VKI*****HPYGSDYLYGTQGKLLPPAPSMANSLYYYPLFYNMHSLYGTQGKLLPPAPSMANSLYYYPLFYNMHSNYGAQLTSPVLTTVTSTTY*ED*************DGGEIVDVCNDVE************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDSMKDSEEYYKKINNNNITNNTMSYYGKKDIRDARDLPKPAALSNLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGKLLPPAPSMANSLYYYPLFYNMHSLYGTQGKLLPPAPSMANSLYYYPLFYNMHSNYGAQLTSPVLTTVTSTTYNEDDGESSGSGEGEEGDGGEIVDVCNDVEEDDQPSSSNLSE
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	274	2.2.26 [Sep-21-2011]
P78367	333	Homeobox protein Nkx-3.2	yes	N/A	0.390	0.321	0.626	1e-31
P97503	333	Homeobox protein Nkx-3.2	yes	N/A	0.390	0.321	0.626	1e-31
P22809	382	Homeobox protein bagpipe	yes	N/A	0.306	0.219	0.715	1e-30
O93590	224	Homeobox protein zampogna	N/A	N/A	0.430	0.526	0.550	7e-29
P70061	329	Homeobox protein Nkx-3.2	N/A	N/A	0.244	0.203	0.835	1e-27
Q9W7E8	213	Homeobox protein koza OS=	N/A	N/A	0.405	0.521	0.537	3e-24
Q99801	234	Homeobox protein Nkx-3.1	no	N/A	0.262	0.307	0.743	3e-23
P97436	237	Homeobox protein Nkx-3.1	no	N/A	0.273	0.316	0.687	6e-23
P52952	324	Homeobox protein Nkx-2.5	no	N/A	0.317	0.268	0.573	9e-20
Q90788	294	Homeobox protein Nkx-2.5	yes	N/A	0.306	0.285	0.572	1e-19

>sp|P78367|NKX32_HUMAN Homeobox protein Nkx-3.2 OS=Homo sapiens GN=NKX3-2 PE=2 SV=2

 Score =  137 bits (344), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 79/126 (62%), Positives = 89/126 (70%), Gaps = 19/126 (15%)

Query: 59  RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
           RKKRSRAAFSHAQV+ELE+RFN Q+YLSGPERAD+A SLKLTETQVKIWFQNRRYKTKR+
Sbjct: 205 RKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQNRRYKTKRR 264

Query: 119 QL--QLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGK---LLPPAPSMANSL 173
           Q+   LL       SA   KKVAVK+LVR+       YL G   +   LLP  PS     
Sbjct: 265 QMAADLLA------SAPAAKKVAVKVLVRDDQ---RQYLPGEVLRPPSLLPLQPS----- 310

Query: 174 YYYPLF 179
           YYYP +
Sbjct: 311 YYYPYY 316

Transcriptional repressor that acts as a negative regulator of chondrocyte maturation. PLays a role in distal stomach development; required for proper antral-pyloric morphogenesis and development of antral-type epithelium. In concert with GSC, defines the structural components of the middle ear; required for tympanic ring and gonium development and in the regulation of the width of the malleus.
Homo sapiens (taxid: 9606)

>sp|P97503|NKX32_MOUSE Homeobox protein Nkx-3.2 OS=Mus musculus GN=Nkx3-2 PE=1 SV=2

 Score =  136 bits (343), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 79/126 (62%), Positives = 89/126 (70%), Gaps = 19/126 (15%)

Query: 59  RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
           RKKRSRAAFSHAQV+ELE+RFN Q+YLSGPERAD+A SLKLTETQVKIWFQNRRYKTKR+
Sbjct: 205 RKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQNRRYKTKRR 264

Query: 119 QL--QLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGK---LLPPAPSMANSL 173
           Q+   LL       SA   KKVAVK+LVR+       YL G   +   LLP  PS     
Sbjct: 265 QMAADLLA------SAPAAKKVAVKVLVRDDQ---RQYLPGEVLRPPSLLPLQPS----- 310

Query: 174 YYYPLF 179
           YYYP +
Sbjct: 311 YYYPYY 316

Transcriptional repressor that acts as a negative regulator of chondrocyte maturation. PLays a role in distal stomach development; required for proper antral-pyloric morphogenesis and development of antral-type epithelium. In concert with GSC, defines the structural components of the middle ear; required for tympanic ring and gonium development and in the regulation of the width of the malleus.

Mus musculus (taxid: 10090)

>sp|P22809|BAGP_DROME Homeobox protein bagpipe OS=Drosophila melanogaster GN=bap PE=2 SV=3

 Score =  133 bits (335), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 63/88 (71%), Positives = 75/88 (85%), Gaps = 4/88 (4%)

Query: 59  RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
           RKKRSRAAFSHAQV+ELE+RF  Q+YLSGPER+++AKSL+LTETQVKIWFQNRRYKTKRK
Sbjct: 174 RKKRSRAAFSHAQVFELERRFAQQRYLSGPERSEMAKSLRLTETQVKIWFQNRRYKTKRK 233

Query: 119 QLQLLEGSLNTPSAGNGKKVAVKILVRE 146
           Q+Q  E +L     G  K+V V++LVRE
Sbjct: 234 QIQQHEAAL----LGASKRVPVQVLVRE 257

Involved in the determination of cell fates in the dorsal mesoderm.

Drosophila melanogaster (taxid: 7227)

>sp|O93590|ZAX_XENLA Homeobox protein zampogna OS=Xenopus laevis GN=zax PE=2 SV=1

 Score =  127 bits (320), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 71/129 (55%), Positives = 87/129 (67%), Gaps = 11/129 (8%)

Query: 56  PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115
           P   KKRSRAAFSHAQVYELE+RF+ Q+YLSGPERAD+A SLKLTETQVKIWFQNRRYKT
Sbjct: 96  PKSSKKRSRAAFSHAQVYELERRFSLQRYLSGPERADLAASLKLTETQVKIWFQNRRYKT 155

Query: 116 KRKQL--QLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGKLLPPAPSMANSL 173
           KRK +  Q    S   P+    +KVAV++LV++         Y  +  L P   S+ ++ 
Sbjct: 156 KRKLIATQTAPKSSLVPT----RKVAVRVLVKDDQ-----RQYCPEDMLSPSLLSLYHAY 206

Query: 174 YYYPLFYNM 182
            YYP  Y +
Sbjct: 207 QYYPYMYCL 215

Xenopus laevis (taxid: 8355)

>sp|P70061|NKX32_XENLA Homeobox protein Nkx-3.2 OS=Xenopus laevis GN=nkx3-2 PE=2 SV=1

 Score =  124 bits (310), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 56/67 (83%), Positives = 63/67 (94%)

Query: 54  QPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRY 113
           +PP  RKKRSRAAFSHAQV+ELE+RFN Q+YLSGPERAD+A SLKLTETQVKIWFQNRRY
Sbjct: 196 EPPKQRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQNRRY 255

Query: 114 KTKRKQL 120
           KTKR+Q+
Sbjct: 256 KTKRRQM 262

Xenopus laevis (taxid: 8355)

>sp|Q9W7E8|KOZA_XENLA Homeobox protein koza OS=Xenopus laevis GN=koza PE=2 SV=1

 Score =  112 bits (279), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 65/121 (53%), Positives = 85/121 (70%), Gaps = 10/121 (8%)

Query: 3   SMKDSEEYY--KKINNNNITNNTMSYYGKKDIRDARDLPKP-AALSNLPGLAQSQPPTGR 59
           S++D+EE Y  +K+ +++        + + D     D  +P  A+ N   LA+ Q     
Sbjct: 49  SLRDTEEKYASEKLQSSSQPAEIHHSHMEADENLELDTAQPITAVEN--KLAKQQ----- 101

Query: 60  KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
           +KRSRAAFSH+QV ELE++F++QKYLS PERA +AKSLKLTETQVKIWFQNRRYKTKRKQ
Sbjct: 102 QKRSRAAFSHSQVIELERKFSSQKYLSAPERAQLAKSLKLTETQVKIWFQNRRYKTKRKQ 161

Query: 120 L 120
           L
Sbjct: 162 L 162

May regulate cell proliferation in a tissue-specific manner.

Xenopus laevis (taxid: 8355)

>sp|Q99801|NKX31_HUMAN Homeobox protein Nkx-3.1 OS=Homo sapiens GN=NKX3-1 PE=1 SV=2

 Score =  109 bits (272), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 55/74 (74%), Positives = 62/74 (83%), Gaps = 2/74 (2%)

Query: 47  LPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKI 106
           LP L Q+  P   +KRSRAAFSH QV ELE++F+ QKYLS PERA +AK+LKLTETQVKI
Sbjct: 113 LPRLPQT--PKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKI 170

Query: 107 WFQNRRYKTKRKQL 120
           WFQNRRYKTKRKQL
Sbjct: 171 WFQNRRYKTKRKQL 184

Transcription factor, which binds preferentially the consensus sequence 5'-TAAGT[AG]-3' and can behave as a transcriptional repressor. Play an important role in normal prostate development, regulating proliferation of glandular epithelium and in the formation of ducts in prostate. Act as a tumor suppressor controlling prostate carcinogenesis, as shown by the ability to inhibit proliferation and invasion activities of PC-3 prostate cancer cells.

Homo sapiens (taxid: 9606)

>sp|P97436|NKX31_MOUSE Homeobox protein Nkx-3.1 OS=Mus musculus GN=Nkx3-1 PE=1 SV=1

 Score =  108 bits (269), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 55/80 (68%), Positives = 65/80 (81%), Gaps = 5/80 (6%)

Query: 41  PAALSNLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLT 100
           P  L++ P + + QP    +KRSRAAFSH QV ELE++F+ QKYLS PERA +AK+LKLT
Sbjct: 111 PGDLASAPQVTK-QP----QKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLT 165

Query: 101 ETQVKIWFQNRRYKTKRKQL 120
           ETQVKIWFQNRRYKTKRKQL
Sbjct: 166 ETQVKIWFQNRRYKTKRKQL 185

Transcription factor, which binds preferentially the consensus sequence 5'-TAAGT[AG]-3' and can behave as a transcriptional repressor (By similarity). Plays an important role in normal prostate development, regulating proliferation of glandular epithelium and in the formation of ducts in prostate. Act as a tumor suppressor controlling prostate carcinogenesis, as shown by the ability to suppress growth and tumorigenicity of prostate carcinoma cells. Plays a role in the formation of minor salivary glands (particularly palatine and lingual glands). Essential for appropriate differentiation and secretory function of the bulbourethral gland.

Mus musculus (taxid: 10090)

>sp|P52952|NKX25_HUMAN Homeobox protein Nkx-2.5 OS=Homo sapiens GN=NKX2-5 PE=1 SV=1

 Score = 97.4 bits (241), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 51/89 (57%), Positives = 60/89 (67%), Gaps = 2/89 (2%)

Query: 67  FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR-KQLQLLE- 124
           FS AQVYELE+RF  Q+YLS PER  +A  LKLT TQVKIWFQNRRYK KR +Q Q LE 
Sbjct: 145 FSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKCKRQRQDQTLEL 204

Query: 125 GSLNTPSAGNGKKVAVKILVRESHPYGSD 153
             L  P     +++AV +LVR+  P   D
Sbjct: 205 VGLPPPPPPPARRIAVPVLVRDGKPCLGD 233

Implicated in commitment to and/or differentiation of the myocardial lineage. Acts as a transcriptional activator of ANF in cooperation with GATA4.

Homo sapiens (taxid: 9606)

>sp|Q90788|NKX25_CHICK Homeobox protein Nkx-2.5 OS=Gallus gallus GN=NKX-2.5 PE=2 SV=1

 Score = 97.1 bits (240), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 55/96 (57%), Positives = 62/96 (64%), Gaps = 12/96 (12%)

Query: 67  FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR-KQLQLLEG 125
           FS AQVYELE+RF  QKYLS PER  +A  LKLT TQVKIWFQNRRYK KR +Q Q LE 
Sbjct: 126 FSQAQVYELERRFKQQKYLSAPERDHLANVLKLTSTQVKIWFQNRRYKCKRQRQDQTLEM 185

Query: 126 SLNTPSAGNGKKVAVKILVR-------ESHPYGSDY 154
               P     +++AV +LVR       ES PY S Y
Sbjct: 186 VGIPPP----RRIAVPVLVRDGKPCLGESSPYSSPY 217

Implicated in commitment to and/or differentiation of the myocardial lineage.

Gallus gallus (taxid: 9031)

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	274
357614147	385	putative Homeobox protein bagpipe [Danau	0.416	0.296	0.641	2e-32
410914283	260	PREDICTED: homeobox protein Nkx-3.2-like	0.423	0.446	0.625	2e-31
166796884	245	NK3 homeobox 2 [Danio rerio]	0.423	0.473	0.617	3e-31
30023832	245	homeobox protein Nkx-3.2 [Danio rerio] g	0.423	0.473	0.617	3e-31
432877095	265	PREDICTED: homeobox protein Nkx-3.2-like	0.423	0.437	0.617	3e-31
91091010	279	PREDICTED: similar to Homeobox protein b	0.379	0.372	0.669	3e-31
348515405	261	PREDICTED: homeobox protein Nkx-3.2-like	0.423	0.444	0.617	3e-31
259013466	272	NK3 homeobox 2-like [Saccoglossus kowale	0.445	0.448	0.542	5e-31
242018176	266	Homeobox protein Nkx-3.1, putative [Pedi	0.427	0.439	0.577	5e-31
157113790	431	nk homeobox protein [Aedes aegypti] gi|1	0.529	0.336	0.487	2e-30

>gi|357614147|gb|EHJ68936.1| putative Homeobox protein bagpipe [Danaus plexippus]

 Score =  145 bits (365), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 75/117 (64%), Positives = 87/117 (74%), Gaps = 3/117 (2%)

Query: 57  TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116
           +GRKKRSRAAFSHAQVYELE+RF+ Q+YLSGPERAD+A SLKLTETQVKIWFQNRRYKTK
Sbjct: 159 SGRKKRSRAAFSHAQVYELERRFSQQRYLSGPERADLAVSLKLTETQVKIWFQNRRYKTK 218

Query: 117 RKQLQLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGKLLPPAPSMANSL 173
           RKQ+QL E  L    A + +KVAVK+LV    P    Y    +   L P P + NS+
Sbjct: 219 RKQMQLQESGL---LANHARKVAVKVLVNGQLPDIKAYQAPCKNPALFPPPMLDNSI 272

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|410914283|ref|XP_003970617.1| PREDICTED: homeobox protein Nkx-3.2-like [Takifugu rubripes]

 Score =  141 bits (356), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 80/128 (62%), Positives = 95/128 (74%), Gaps = 12/128 (9%)

Query: 56  PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115
           P  RKKRSRAAFSHAQV+ELE+RFN Q+YLSGPERAD+A SLKLTETQVKIWFQNRRYKT
Sbjct: 132 PKQRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQNRRYKT 191

Query: 116 KRKQLQLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGKLL-PPAPSMANSLY 174
           KR+Q+   +   +TP+A   KKVAVK+LVR+      D    + G+LL PP  S+  S Y
Sbjct: 192 KRRQM-AADLMASTPAA---KKVAVKVLVRD------DQRQYSPGELLRPPLLSLQPS-Y 240

Query: 175 YYPLFYNM 182
           YYP  Y +
Sbjct: 241 YYPYAYCL 248

Source: Takifugu rubripes

Species: Takifugu rubripes

Genus: Takifugu

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|166796884|gb|AAI59242.1| NK3 homeobox 2 [Danio rerio]

 Score =  141 bits (356), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 79/128 (61%), Positives = 92/128 (71%), Gaps = 12/128 (9%)

Query: 56  PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115
           P  RKKRSRAAFSHAQV+ELE+RFN Q+YLSGPERAD+A SLKLTETQVKIWFQNRRYKT
Sbjct: 116 PKQRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQNRRYKT 175

Query: 116 KRKQLQLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGKLL-PPAPSMANSLY 174
           KR+Q+     +    SA   KKVAVK+LVR+      D    + G+LL PP  S+  S Y
Sbjct: 176 KRRQM----AADLLASAPAAKKVAVKVLVRD------DRRQYSPGELLRPPLLSLQPS-Y 224

Query: 175 YYPLFYNM 182
           YYP  Y +
Sbjct: 225 YYPYTYCL 232

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|30023832|ref|NP_835233.1| homeobox protein Nkx-3.2 [Danio rerio] gi|28273598|gb|AAO33928.1| bagpipe homeobox transcription factor Bapx1 [Danio rerio] gi|190336857|gb|AAI62299.1| NK3 homeobox 2 [Danio rerio] gi|190337902|gb|AAI62289.1| NK3 homeobox 2 [Danio rerio]

 Score =  141 bits (356), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 79/128 (61%), Positives = 92/128 (71%), Gaps = 12/128 (9%)

Query: 56  PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115
           P  RKKRSRAAFSHAQV+ELE+RFN Q+YLSGPERAD+A SLKLTETQVKIWFQNRRYKT
Sbjct: 116 PKQRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQNRRYKT 175

Query: 116 KRKQLQLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGKLL-PPAPSMANSLY 174
           KR+Q+     +    SA   KKVAVK+LVR+      D    + G+LL PP  S+  S Y
Sbjct: 176 KRRQM----AADLLASAPAAKKVAVKVLVRD------DRRQYSPGELLRPPLLSLQPS-Y 224

Query: 175 YYPLFYNM 182
           YYP  Y +
Sbjct: 225 YYPYTYCL 232

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|432877095|ref|XP_004073104.1| PREDICTED: homeobox protein Nkx-3.2-like [Oryzias latipes]

 Score =  141 bits (356), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 79/128 (61%), Positives = 95/128 (74%), Gaps = 12/128 (9%)

Query: 56  PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115
           P  RKKRSRAAFSHAQV+ELE+RFN Q+YLSGPERAD+A SLKLTETQVKIWFQNRRYKT
Sbjct: 137 PKQRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQNRRYKT 196

Query: 116 KRKQLQLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGKLL-PPAPSMANSLY 174
           KR+Q+   +   +TP+A   KKVAVK+LVR+      D    + G++L PP  S+  S Y
Sbjct: 197 KRRQM-AADLMASTPAA---KKVAVKVLVRD------DQRQYSPGEILRPPLLSLQPS-Y 245

Query: 175 YYPLFYNM 182
           YYP  Y +
Sbjct: 246 YYPYAYCL 253

Source: Oryzias latipes

Species: Oryzias latipes

Genus: Oryzias

Family: Adrianichthyidae

Order: Beloniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|91091010|ref|XP_975015.1| PREDICTED: similar to Homeobox protein bagpipe (NK-3) [Tribolium castaneum] gi|270014047|gb|EFA10495.1| hypothetical protein TcasGA2_TC012743 [Tribolium castaneum]

 Score =  141 bits (355), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 73/109 (66%), Positives = 88/109 (80%), Gaps = 5/109 (4%)

Query: 41  PAALSNLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLT 100
           P + S   G   SQP  GRKKRSRAAF+HAQV+ELE+RF+ Q+YLSGPERAD+A++LKLT
Sbjct: 91  PPSQSEESGREPSQP--GRKKRSRAAFTHAQVFELERRFSQQRYLSGPERADLAQALKLT 148

Query: 101 ETQVKIWFQNRRYKTKRKQLQLLEGSLNTPSAGNGKKVAVKILVRESHP 149
           ETQVKIW+QNRRYKTKRKQLQ+ E SL   SA   +KVAVK+LV++  P
Sbjct: 149 ETQVKIWYQNRRYKTKRKQLQMQESSLMGQSA---RKVAVKVLVKDDVP 194

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|348515405|ref|XP_003445230.1| PREDICTED: homeobox protein Nkx-3.2-like [Oreochromis niloticus]

 Score =  141 bits (355), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 79/128 (61%), Positives = 95/128 (74%), Gaps = 12/128 (9%)

Query: 56  PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115
           P  RKKRSRAAFSHAQV+ELE+RFN Q+YLSGPERAD+A SLKLTETQVKIWFQNRRYKT
Sbjct: 133 PKQRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQNRRYKT 192

Query: 116 KRKQLQLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGKLL-PPAPSMANSLY 174
           KR+Q+   +   +TP+A   KKVAVK+LVR+      D    + G++L PP  S+  S Y
Sbjct: 193 KRRQM-AADLMASTPAA---KKVAVKVLVRD------DQRQYSPGEILRPPLLSLQPS-Y 241

Query: 175 YYPLFYNM 182
           YYP  Y +
Sbjct: 242 YYPYAYCL 249

Source: Oreochromis niloticus

Species: Oreochromis niloticus

Genus: Oreochromis

Family: Cichlidae

Order: Perciformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|259013466|ref|NP_001158476.1| NK3 homeobox 2-like [Saccoglossus kowalevskii] gi|197734645|gb|ACH73218.1| bagpipe-like homeobox protein [Saccoglossus kowalevskii]

 Score =  140 bits (354), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 77/142 (54%), Positives = 93/142 (65%), Gaps = 20/142 (14%)

Query: 52  QSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNR 111
           Q Q P  RKKRSRAAFSHAQV+ELE+RFN Q+YLSGPERAD+A +LKLTE Q+KIWFQNR
Sbjct: 133 QLQTPKQRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAIALKLTEQQIKIWFQNR 192

Query: 112 RYKTKRKQLQLLEGSLNTPSAGNGKKVAVKILVRESH-----------PYGSDYLYGTQG 160
           RYKTKR+QLQ     L+ P +   KKVA+K+LVR+             P+  + L    G
Sbjct: 193 RYKTKRRQLQAA-AELSAPMS--AKKVAIKVLVRDDQRQYTPDDMFRPPFTYNMLLPAYG 249

Query: 161 KLLPPAPSMANSLYYYPLFYNM 182
             +PP P      Y  PLF N+
Sbjct: 250 YHIPPRP------YPGPLFSNL 265

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|242018176|ref|XP_002429556.1| Homeobox protein Nkx-3.1, putative [Pediculus humanus corporis] gi|212514510|gb|EEB16818.1| Homeobox protein Nkx-3.1, putative [Pediculus humanus corporis]

 Score =  140 bits (353), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 71/123 (57%), Positives = 91/123 (73%), Gaps = 6/123 (4%)

Query: 59  RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
           RKKRSRAAFSH+QVYELE+RFN Q+YLSG ER D+A +LKLTETQVKIWFQNRRYKTKRK
Sbjct: 95  RKKRSRAAFSHSQVYELERRFNQQRYLSGSERTDLANALKLTETQVKIWFQNRRYKTKRK 154

Query: 119 QLQLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGKLLP--PAPSMANSLYYY 176
           Q+Q+ + + +  ++  G+KVAVK+LV ++       + G   K++   P P +    YYY
Sbjct: 155 QMQMADVNGSVRNSNAGRKVAVKVLVHDNQ----QNVNGESDKVMTSFPYPHIPLPYYYY 210

Query: 177 PLF 179
           PLF
Sbjct: 211 PLF 213

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157113790|ref|XP_001657903.1| nk homeobox protein [Aedes aegypti] gi|108877578|gb|EAT41803.1| AAEL006597-PA [Aedes aegypti]

 Score =  138 bits (348), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 79/162 (48%), Positives = 101/162 (62%), Gaps = 17/162 (10%)

Query: 46  NLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVK 105
           +LPG     P   RKKRSRAAFSH+QV+ELE+RF  Q+YLSGPER+++AKSL+LTETQVK
Sbjct: 187 SLPG--DDAPTAARKKRSRAAFSHSQVFELERRFAQQRYLSGPERSELAKSLRLTETQVK 244

Query: 106 IWFQNRRYKTKRKQLQLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGKLLPP 165
           IWFQNRRYKTKRKQ+Q  E ++ + +    K+V V++LVRE   YG   +   Q      
Sbjct: 245 IWFQNRRYKTKRKQIQQHEAAILSAT----KRVPVQVLVREDGTYGPAAMLAGQ------ 294

Query: 166 APSMANSLYYYPLFYNMHSLYGTQGKLLPPAPSMANSLYYYP 207
            P  A+ L    L    H +    G  +PP P      Y+YP
Sbjct: 295 -PHYASGLDPALLNVYRHQIQMAYGMPVPPMPFS----YFYP 331

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

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	274
ZFIN|ZDB-GENE-030127-1	245	nkx3.2 "NK3 homeobox 2" [Danio	0.416	0.465	0.626	2.6e-31
UNIPROTKB|P70061	329	nkx3-2 "Homeobox protein Nkx-3	0.510	0.425	0.525	3.3e-31
UNIPROTKB|E1B710	330	NKX3-2 "Uncharacterized protei	0.419	0.348	0.612	6.9e-31
UNIPROTKB|E2RDY4	333	NKX3-2 "Uncharacterized protei	0.419	0.345	0.612	6.9e-31
UNIPROTKB|P78367	333	NKX3-2 "Homeobox protein Nkx-3	0.419	0.345	0.612	6.9e-31
UNIPROTKB|I3LTH9	337	NKX3-2 "Uncharacterized protei	0.419	0.341	0.612	6.9e-31
MGI|MGI:108015	333	Nkx3-2 "NK3 homeobox 2" [Mus m	0.419	0.345	0.612	6.9e-31
ZFIN|ZDB-GENE-050306-27	240	nkx3.3 "NK3 homeobox 3" [Danio	0.430	0.491	0.576	1.1e-30
FB|FBgn0004862	382	bap "bagpipe" [Drosophila mela	0.562	0.403	0.491	1.3e-29
UNIPROTKB|O93590	224	zax "Homeobox protein zampogna	0.437	0.535	0.556	1.9e-28

ZFIN|ZDB-GENE-030127-1 nkx3.2 "NK3 homeobox 2" [Danio rerio (taxid:7955)]

 Score = 344 (126.2 bits), Expect = 2.6e-31, P = 2.6e-31
 Identities = 79/126 (62%), Positives = 93/126 (73%)

Query:    56 PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115
             P  RKKRSRAAFSHAQV+ELE+RFN Q+YLSGPERAD+A SLKLTETQVKIWFQNRRYKT
Sbjct:   116 PKQRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQNRRYKT 175

Query:   116 KRKQLQLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGKLL-PPAPSMANSLY 174
             KR+Q+   +   + P+A   KKVAVK+LVR+       Y   + G+LL PP  S+  S Y
Sbjct:   176 KRRQMAA-DLLASAPAA---KKVAVKVLVRDDR---RQY---SPGELLRPPLLSLQPS-Y 224

Query:   175 YYPLFY 180
             YYP  Y
Sbjct:   225 YYPYTY 230

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

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0048703 "embryonic viscerocranium morphogenesis" evidence=IGI;IMP

UNIPROTKB|P70061 nkx3-2 "Homeobox protein Nkx-3.2" [Xenopus laevis (taxid:8355)]

 Score = 343 (125.8 bits), Expect = 3.3e-31, P = 3.3e-31
 Identities = 82/156 (52%), Positives = 101/156 (64%)

Query:    28 GKKDIRDARDLPKPAALSNLPGLAQS--QPPTGRKKRSRAAFSHAQVYELEKRFNAQKYL 85
             G  D      +P P+     P   Q   +PP  RKKRSRAAFSHAQV+ELE+RFN Q+YL
Sbjct:   168 GCSDCEIGASVPDPSPPDEDPKCEQLMLEPPKQRKKRSRAAFSHAQVFELERRFNHQRYL 227

Query:    86 SGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL--QLLEGSLNTPSAGNGKKVAVKIL 143
             SGPERAD+A SLKLTETQVKIWFQNRRYKTKR+Q+   LL  +   P+A   KKVAVK+L
Sbjct:   228 SGPERADLAASLKLTETQVKIWFQNRRYKTKRRQMATDLLAAA---PAA---KKVAVKVL 281

Query:   144 VRESHPYGSDYLYGTQGKLLPPAPSMANSLYYYPLF 179
             VR+       Y     G++L P+     + Y+YP +
Sbjct:   282 VRDDQ---RQY---HPGEVLHPSLLPLQAPYFYPYY 311

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=NAS

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

UNIPROTKB|E1B710 NKX3-2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 340 (124.7 bits), Expect = 6.9e-31, P = 6.9e-31
 Identities = 76/124 (61%), Positives = 89/124 (71%)

Query:    56 PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115
             P  RKKRSRAAFSHAQV+ELE+RFN Q+YLSGPERAD+A SLKLTETQVKIWFQNRRYKT
Sbjct:   199 PKPRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQNRRYKT 258

Query:   116 KRKQLQLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGKLLPPAPSMANSLYY 175
             KR+Q+   +   + P+A   KKVAVK+LVR+       YL G    L PP+       YY
Sbjct:   259 KRRQMAA-DLLASAPAA---KKVAVKVLVRDDQ---RQYLPGEV--LRPPSLLPLQPSYY 309

Query:   176 YPLF 179
             YP +
Sbjct:   310 YPYY 313

GO:0005634 "nucleus" evidence=IEA

GO:0060576 "intestinal epithelial cell development" evidence=IEA

GO:0048706 "embryonic skeletal system development" evidence=IEA

GO:0048705 "skeletal system morphogenesis" evidence=IEA

GO:0048645 "organ formation" evidence=IEA

GO:0048536 "spleen development" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0042474 "middle ear morphogenesis" evidence=IEA

GO:0032331 "negative regulation of chondrocyte differentiation" evidence=IEA

GO:0031016 "pancreas development" evidence=IEA

GO:0007368 "determination of left/right symmetry" evidence=IEA

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

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

UNIPROTKB|E2RDY4 NKX3-2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 340 (124.7 bits), Expect = 6.9e-31, P = 6.9e-31
 Identities = 76/124 (61%), Positives = 89/124 (71%)

Query:    56 PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115
             P  RKKRSRAAFSHAQV+ELE+RFN Q+YLSGPERAD+A SLKLTETQVKIWFQNRRYKT
Sbjct:   202 PKPRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQNRRYKT 261

Query:   116 KRKQLQLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGKLLPPAPSMANSLYY 175
             KR+Q+   +   + P+A   KKVAVK+LVR+       YL G    L PP+       YY
Sbjct:   262 KRRQMAA-DLLASAPAA---KKVAVKVLVRDDQ---RQYLPGEV--LRPPSLLPLQPSYY 312

Query:   176 YPLF 179
             YP +
Sbjct:   313 YPYY 316

GO:0005634 "nucleus" evidence=IEA

GO:0060576 "intestinal epithelial cell development" evidence=IEA

GO:0048706 "embryonic skeletal system development" evidence=IEA

GO:0048705 "skeletal system morphogenesis" evidence=IEA

GO:0048645 "organ formation" evidence=IEA

GO:0048536 "spleen development" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0042474 "middle ear morphogenesis" evidence=IEA

GO:0032331 "negative regulation of chondrocyte differentiation" evidence=IEA

GO:0031016 "pancreas development" evidence=IEA

GO:0007368 "determination of left/right symmetry" evidence=IEA

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

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

UNIPROTKB|P78367 NKX3-2 "Homeobox protein Nkx-3.2" [Homo sapiens (taxid:9606)]

 Score = 340 (124.7 bits), Expect = 6.9e-31, P = 6.9e-31
 Identities = 76/124 (61%), Positives = 89/124 (71%)

Query:    56 PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115
             P  RKKRSRAAFSHAQV+ELE+RFN Q+YLSGPERAD+A SLKLTETQVKIWFQNRRYKT
Sbjct:   202 PKPRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQNRRYKT 261

Query:   116 KRKQLQLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGKLLPPAPSMANSLYY 175
             KR+Q+   +   + P+A   KKVAVK+LVR+       YL G    L PP+       YY
Sbjct:   262 KRRQMAA-DLLASAPAA---KKVAVKVLVRDDQ---RQYLPGEV--LRPPSLLPLQPSYY 312

Query:   176 YPLF 179
             YP +
Sbjct:   313 YPYY 316

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

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

GO:0007368 "determination of left/right symmetry" evidence=IEA

GO:0031016 "pancreas development" evidence=IEA

GO:0042474 "middle ear morphogenesis" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0048536 "spleen development" evidence=IEA

GO:0048645 "organ formation" evidence=IEA

GO:0048705 "skeletal system morphogenesis" evidence=IEA

GO:0048706 "embryonic skeletal system development" evidence=IEA

GO:0060576 "intestinal epithelial cell development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0032331 "negative regulation of chondrocyte differentiation" evidence=ISS

GO:0001501 "skeletal system development" evidence=TAS

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

UNIPROTKB|I3LTH9 NKX3-2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 340 (124.7 bits), Expect = 6.9e-31, P = 6.9e-31
 Identities = 76/124 (61%), Positives = 89/124 (71%)

Query:    56 PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115
             P  RKKRSRAAFSHAQV+ELE+RFN Q+YLSGPERAD+A SLKLTETQVKIWFQNRRYKT
Sbjct:   206 PKPRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQNRRYKT 265

Query:   116 KRKQLQLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGKLLPPAPSMANSLYY 175
             KR+Q+   +   + P+A   KKVAVK+LVR+       YL G    L PP+       YY
Sbjct:   266 KRRQMAA-DLLASAPAA---KKVAVKVLVRDDQ---RQYLPGEV--LRPPSLLPLQPSYY 316

Query:   176 YPLF 179
             YP +
Sbjct:   317 YPYY 320

GO:0005634 "nucleus" evidence=IEA

GO:0060576 "intestinal epithelial cell development" evidence=IEA

GO:0048706 "embryonic skeletal system development" evidence=IEA

GO:0048705 "skeletal system morphogenesis" evidence=IEA

GO:0048645 "organ formation" evidence=IEA

GO:0048536 "spleen development" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0042474 "middle ear morphogenesis" evidence=IEA

GO:0032331 "negative regulation of chondrocyte differentiation" evidence=IEA

GO:0031016 "pancreas development" evidence=IEA

GO:0007368 "determination of left/right symmetry" evidence=IEA

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

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

MGI|MGI:108015 Nkx3-2 "NK3 homeobox 2" [Mus musculus (taxid:10090)]

 Score = 340 (124.7 bits), Expect = 6.9e-31, P = 6.9e-31
 Identities = 76/124 (61%), Positives = 89/124 (71%)

Query:    56 PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115
             P  RKKRSRAAFSHAQV+ELE+RFN Q+YLSGPERAD+A SLKLTETQVKIWFQNRRYKT
Sbjct:   202 PKPRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQNRRYKT 261

Query:   116 KRKQLQLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGKLLPPAPSMANSLYY 175
             KR+Q+   +   + P+A   KKVAVK+LVR+       YL G    L PP+       YY
Sbjct:   262 KRRQMAA-DLLASAPAA---KKVAVKVLVRDDQ---RQYLPGEV--LRPPSLLPLQPSYY 312

Query:   176 YPLF 179
             YP +
Sbjct:   313 YPYY 316

GO:0001501 "skeletal system development" evidence=IMP

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0007368 "determination of left/right symmetry" evidence=IMP

GO:0031016 "pancreas development" evidence=IMP

GO:0032331 "negative regulation of chondrocyte differentiation" evidence=IMP

GO:0042474 "middle ear morphogenesis" evidence=IMP

GO:0043066 "negative regulation of apoptotic process" evidence=IMP

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

GO:0048513 "organ development" evidence=IMP

GO:0048536 "spleen development" evidence=IMP

GO:0048645 "organ formation" evidence=IMP

GO:0048705 "skeletal system morphogenesis" evidence=IMP

GO:0048706 "embryonic skeletal system development" evidence=IMP

GO:0055123 "digestive system development" evidence=IMP

GO:0060576 "intestinal epithelial cell development" evidence=IGI

ZFIN|ZDB-GENE-050306-27 nkx3.3 "NK3 homeobox 3" [Danio rerio (taxid:7955)]

 Score = 338 (124.0 bits), Expect = 1.1e-30, P = 1.1e-30
 Identities = 72/125 (57%), Positives = 85/125 (68%)

Query:    56 PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115
             P   KKRSRAAFSHAQVYELE+RFN Q+YLSGPERAD+A +LKLTETQVKIWFQNRRYKT
Sbjct:   107 PKSSKKRSRAAFSHAQVYELERRFNLQRYLSGPERADLAGALKLTETQVKIWFQNRRYKT 166

Query:   116 KRKQLQLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGKLLPPAPSMANSLYY 175
             KR+Q+     +  TP+    K+VAVK+LVR          Y T+    P  P +  S  Y
Sbjct:   167 KRRQMAAELAT--TPTTTLAKRVAVKVLVRNDQRQ-----YNTEDLPSPSVPPLYQSFPY 219

Query:   176 YPLFY 180
             YP  +
Sbjct:   220 YPYMF 224

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

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

FB|FBgn0004862 bap "bagpipe" [Drosophila melanogaster (taxid:7227)]

 Score = 328 (120.5 bits), Expect = 1.3e-29, P = 1.3e-29
 Identities = 87/177 (49%), Positives = 105/177 (59%)

Query:    37 DLPKPAALSNLPG---LAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADV 93
             D   P  LS+ P    L+       RKKRSRAAFSHAQV+ELE+RF  Q+YLSGPER+++
Sbjct:   149 DCDSPPPLSSSPSESPLSHDGSGLSRKKRSRAAFSHAQVFELERRFAQQRYLSGPERSEM 208

Query:    94 AKSLKLTETQVKIWFQNRRYKTKRKQLQLLEGSLNTPSAGNGKKVAVKILVRESHPYGSD 153
             AKSL+LTETQVKIWFQNRRYKTKRKQ+Q  E +L     G  K+V V++LVRE    GS 
Sbjct:   209 AKSLRLTETQVKIWFQNRRYKTKRKQIQQHEAAL----LGASKRVPVQVLVRED---GST 261

Query:   154 YLYGTQGKLLPPAPSMANSLYYYPLFYNM--HSLYGTQGKLLPPAPSMANSL-YYYP 207
                 T   +   AP   + L   P   N+  H L    G L  P P M     Y+YP
Sbjct:   262 ----TYAHMA--APGAGHGLD--PALINIYRHQLQLAYGGL--PLPQMQMPFPYFYP 308

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

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

GO:0003677 "DNA binding" evidence=NAS

GO:0045165 "cell fate commitment" evidence=NAS

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

GO:0007494 "midgut development" evidence=TAS

GO:0007522 "visceral muscle development" evidence=NAS

GO:0007498 "mesoderm development" evidence=IEP

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

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

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

GO:0007507 "heart development" evidence=NAS

GO:0001710 "mesodermal cell fate commitment" evidence=TAS

UNIPROTKB|O93590 zax "Homeobox protein zampogna" [Xenopus laevis (taxid:8355)]

 Score = 317 (116.6 bits), Expect = 1.9e-28, P = 1.9e-28
 Identities = 74/133 (55%), Positives = 89/133 (66%)

Query:    50 LAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQ 109
             LA S  P   KKRSRAAFSHAQVYELE+RF+ Q+YLSGPERAD+A SLKLTETQVKIWFQ
Sbjct:    92 LADS--PKSSKKRSRAAFSHAQVYELERRFSLQRYLSGPERADLAASLKLTETQVKIWFQ 149

Query:   110 NRRYKTKRKQL--QLLEGSLNTPSAGNGKKVAVKILVRESHPYGSDYLYGTQGKLLPPAP 167
             NRRYKTKRK +  Q    S   P+    +KVAV++LV++         Y  +  L P   
Sbjct:   150 NRRYKTKRKLIATQTAPKSSLVPT----RKVAVRVLVKDDQRQ-----YCPEDMLSPSLL 200

Query:   168 SMANSLYYYPLFY 180
             S+ ++  YYP  Y
Sbjct:   201 SLYHAYQYYPYMY 213

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=NAS

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by 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	274
pfam00046	57	pfam00046, Homeobox, Homeobox domain	1e-25
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	2e-22
smart00389	57	smart00389, HOX, Homeodomain	5e-22
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	3e-08

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

 Score = 95.6 bits (239), Expect = 1e-25
 Identities = 31/57 (54%), Positives = 38/57 (66%)

Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           +R R  F+  Q+ ELEK F   +Y S  ER ++AK L LTE QVK+WFQNRR K KR
Sbjct: 1   RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57

Length = 57

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

 Score = 87.3 bits (217), Expect = 2e-22
 Identities = 32/59 (54%), Positives = 38/59 (64%)

Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
           +R R  F+  Q+ ELEK F    Y S  ER ++AK L LTE QVKIWFQNRR K KR +
Sbjct: 1   RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59

Length = 59

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 86.2 bits (214), Expect = 5e-22
 Identities = 30/57 (52%), Positives = 38/57 (66%)

Query: 60  KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116
           K+R R +F+  Q+ ELEK F    Y S  ER ++AK L L+E QVK+WFQNRR K K
Sbjct: 1   KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

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

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

 Score = 51.7 bits (124), Expect = 3e-08
 Identities = 23/77 (29%), Positives = 36/77 (46%)

Query: 43  ALSNLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTET 102
           A  +   L + Q  +   K  R   +  Q+  LE+ F    Y S   R  ++  L +   
Sbjct: 34  AADSEMKLERKQDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPK 93

Query: 103 QVKIWFQNRRYKTKRKQ 119
            V+IWFQN+R K K+K+
Sbjct: 94  SVQIWFQNKRAKEKKKR 110

Length = 156

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	274
KOG3802|consensus	398		99.96
KOG0842|consensus	307		99.84
KOG0484|consensus	125		99.81
KOG0486|consensus	351		99.8
KOG2251|consensus	228		99.78
KOG1168|consensus	385		99.78
KOG0489|consensus	261		99.77
KOG0488|consensus	309		99.75
KOG0843|consensus	197		99.71
KOG0494|consensus	332		99.71
KOG0487|consensus	308		99.71
KOG0850|consensus	245		99.7
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.7
KOG0485|consensus	268		99.69
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.65
KOG0492|consensus	246		99.65
KOG0848|consensus	317		99.6
KOG4577|consensus	383		99.59
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.56
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.56
KOG0491|consensus	194		99.55
KOG0493|consensus	342		99.55
KOG0844|consensus	408		99.53
COG5576	156	Homeodomain-containing transcription factor [Trans	99.46
KOG0483|consensus	198		99.45
KOG0847|consensus	288		99.33
KOG0490|consensus	235		99.31
KOG0849|consensus	354		99.23
KOG0775|consensus	304		99.07
KOG0774|consensus	334		98.82
KOG2252|consensus	558		98.46
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.45
KOG0490|consensus	235		98.4
KOG1146|consensus	1406		98.1
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	96.97
KOG0773|consensus	342		96.53
PF00157	75	Pou: Pou domain - N-terminal to homeobox domain; I	96.51
KOG3623|consensus	1007		96.39
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	95.28
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	87.6
smart00352	75	POU Found in Pit-Oct-Unc transcription factors.	86.81
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	80.17

>KOG3802|consensus

Probab=99.96  E-value=3.2e-30  Score=241.35  Aligned_cols=108  Identities=23%  Similarity=0.314  Sum_probs=89.9

Q ss_pred             HHHhCCCCCcccccCcccCCCCcCCCCCCCccCCCC------------CCCCCCCCCCCCCCCCCCcCCHHHHHHHHHHH
Q psy526           12 KKINNNNITNNTMSYYGKKDIRDARDLPKPAALSNL------------PGLAQSQPPTGRKKRSRAAFSHAQVYELEKRF   79 (274)
Q Consensus        12 ~~~~g~~~sqttis~fe~~~ls~~~~~~~~~~~~~~------------~~~~~~~~~~~k~rR~RT~ft~~Ql~~Le~~F   79 (274)
                      -++|||+||||||||||+|+|++++|+.-...+..|            ....+......|||||||+|+...+..||++|
T Consensus       234 G~lyGn~FSQTTIcRFEALqLSFKNMCKLKPLL~KWLeEAes~~~~~~~~~~e~i~a~~RkRKKRTSie~~vr~aLE~~F  313 (398)
T KOG3802|consen  234 GALYGNVFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAESRESTGSPNSIEKIGAQSRKRKKRTSIEVNVRGALEKHF  313 (398)
T ss_pred             HhhhCcccchhhhhHhHhhccCHHHHhhhHHHHHHHHHHHhcccccCCCCCHHHhhccccccccccceeHHHHHHHHHHH
Confidence            479999999999999999999999994322222111            11122233445889999999999999999999


Q ss_pred             hhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           80 NAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        80 ~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      .+|++|+.+|+.+||++|+|.++||||||||||+|.||..
T Consensus       314 ~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~  353 (398)
T KOG3802|consen  314 LKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT  353 (398)
T ss_pred             HhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence            9999999999999999999999999999999999999953

>KOG0842|consensus

Probab=99.84  E-value=6.5e-21  Score=175.41  Aligned_cols=96  Identities=53%  Similarity=0.809  Sum_probs=85.4

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHHHhcCCCCCCCCCCC
Q psy526           57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQLLEGSLNTPSAGNGK  136 (274)
Q Consensus        57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~~~~~~~~~~~~~~~  136 (274)
                      .++|||.|..|++.|.-+||+.|.+++|.+..||++||..|+|+++||+|||||||.|+||+++............+..+
T Consensus       150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~~~~~~~~r  229 (307)
T KOG0842|consen  150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALLLASSPPPR  229 (307)
T ss_pred             cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcccCCCCCccc
Confidence            56778889999999999999999999999999999999999999999999999999999999887766655555555557


Q ss_pred             ccceeccccCCCCCCC
Q psy526          137 KVAVKILVRESHPYGS  152 (274)
Q Consensus       137 ~~~~~~l~~~~~p~~~  152 (274)
                      .+.++.+.++..+|..
T Consensus       230 ~v~vpvlvrd~kp~~~  245 (307)
T KOG0842|consen  230 RVAVPVLVRDGKPCSG  245 (307)
T ss_pred             ccCCceeccCCCcccC
Confidence            8999999999999854

>KOG0484|consensus

Probab=99.81  E-value=4.7e-20  Score=143.66  Aligned_cols=69  Identities=33%  Similarity=0.595  Sum_probs=64.6

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHHHh
Q psy526           56 PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQLLE  124 (274)
Q Consensus        56 ~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~~~  124 (274)
                      .++|+||-||.||..||.+||+.|...+||++-.|++||.+|.|++.+|||||||||+|.||+.+....
T Consensus        13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~   81 (125)
T KOG0484|consen   13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIA   81 (125)
T ss_pred             HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            457889999999999999999999999999999999999999999999999999999999998766543

>KOG0486|consensus

Probab=99.80  E-value=3.3e-19  Score=162.49  Aligned_cols=66  Identities=32%  Similarity=0.600  Sum_probs=62.7

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHHH
Q psy526           58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQLL  123 (274)
Q Consensus        58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~~  123 (274)
                      .|+||.||.|+.+||.+||..|.+|+||++..|+|||..++|++.+|+|||+|||+||||+++.+.
T Consensus       110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~  175 (351)
T KOG0486|consen  110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ  175 (351)
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence            378899999999999999999999999999999999999999999999999999999999877665

>KOG2251|consensus

Probab=99.78  E-value=3.6e-19  Score=155.58  Aligned_cols=68  Identities=34%  Similarity=0.562  Sum_probs=64.7

Q ss_pred             CCCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526           55 PPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL  122 (274)
Q Consensus        55 ~~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~  122 (274)
                      ...+|+||.||+|+..|+++||+.|.+.+||+...|++||.+|+|.+.+|+|||+|||+|+|++++++
T Consensus        32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            45678999999999999999999999999999999999999999999999999999999999988775

>KOG1168|consensus

Probab=99.78  E-value=3e-20  Score=167.58  Aligned_cols=103  Identities=26%  Similarity=0.394  Sum_probs=86.0

Q ss_pred             CCCcccccCcccCCCCcCCCCCCCccCCCCCCCCC-------------CCCCCCCCCCCCCcCCHHHHHHHHHHHhhCCC
Q psy526           18 NITNNTMSYYGKKDIRDARDLPKPAALSNLPGLAQ-------------SQPPTGRKKRSRAAFSHAQVYELEKRFNAQKY   84 (274)
Q Consensus        18 ~~sqttis~fe~~~ls~~~~~~~~~~~~~~~~~~~-------------~~~~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~   84 (274)
                      .+||+||||||.+.|+.++|+.-...+..|...++             +--..+.||||||++-.-+.+.||++|...+.
T Consensus       254 sLSQSTICRFESLTLSHNNMiALKPILqaWLEeAE~a~keK~~~pd~~~l~~~~ekKRKRTSIAAPEKRsLEayFavQPR  333 (385)
T KOG1168|consen  254 SLSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAAMKEKDTKPDINELLPGGEKKRKRTSIAAPEKRSLEAYFAVQPR  333 (385)
T ss_pred             cccccceeeeeeeccccCcchhhhHHHHHHHHHHHHHHHhhccCCchhhccCccccccccccccCcccccHHHHhccCCC
Confidence            46999999999999999999655444444322111             12234578899999999999999999999999


Q ss_pred             CCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526           85 LSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL  120 (274)
Q Consensus        85 Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~  120 (274)
                      |+.+.+..||++|.|.+.||+|||||+|+|.||...
T Consensus       334 PS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~  369 (385)
T KOG1168|consen  334 PSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR  369 (385)
T ss_pred             CchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence            999999999999999999999999999999999643

>KOG0489|consensus

Probab=99.77  E-value=2.2e-19  Score=163.75  Aligned_cols=66  Identities=48%  Similarity=0.779  Sum_probs=61.9

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526           57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL  122 (274)
Q Consensus        57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~  122 (274)
                      .++.||.||.||..|+.+||+.|+.|+|.++..|.|||..|.|+++||+|||||||+||||..+..
T Consensus       156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~  221 (261)
T KOG0489|consen  156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAK  221 (261)
T ss_pred             cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccc
Confidence            356789999999999999999999999999999999999999999999999999999999976554

>KOG0488|consensus

Probab=99.75  E-value=1e-18  Score=162.59  Aligned_cols=69  Identities=52%  Similarity=0.763  Sum_probs=63.5

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHHHh
Q psy526           56 PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQLLE  124 (274)
Q Consensus        56 ~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~~~  124 (274)
                      ..+|+||.||.||..||..||+.|++..|.+..+|.+||..|||+..||++||||||+||||......+
T Consensus       168 ~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~  236 (309)
T KOG0488|consen  168 TPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGE  236 (309)
T ss_pred             CCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhc
Confidence            336778889999999999999999999999999999999999999999999999999999998766433

>KOG0843|consensus

Probab=99.71  E-value=7.8e-18  Score=143.03  Aligned_cols=64  Identities=52%  Similarity=0.796  Sum_probs=61.3

Q ss_pred             CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526           59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL  122 (274)
Q Consensus        59 k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~  122 (274)
                      |.||.||.|+.+||..||..|+.++|-.-.+|++||..|+|++.||+|||||||.|.||.+...
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            7899999999999999999999999999999999999999999999999999999999987654

>KOG0494|consensus

Probab=99.71  E-value=9.4e-18  Score=149.55  Aligned_cols=64  Identities=31%  Similarity=0.541  Sum_probs=59.2

Q ss_pred             CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526           59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL  122 (274)
Q Consensus        59 k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~  122 (274)
                      |+|+.||.||..|++.||+.|....||+...|+.||.++.|.+++|+|||||||+||||.++..
T Consensus       140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w  203 (332)
T KOG0494|consen  140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW  203 (332)
T ss_pred             ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence            4444599999999999999999999999999999999999999999999999999999987654

>KOG0487|consensus

Probab=99.71  E-value=5.1e-18  Score=156.41  Aligned_cols=65  Identities=40%  Similarity=0.682  Sum_probs=61.4

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526           58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL  122 (274)
Q Consensus        58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~  122 (274)
                      ++.||||..+|+.|+.+||+.|..|.|.+++.|.||++.|+|++|||+|||||||.|.||..++.
T Consensus       233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~  297 (308)
T KOG0487|consen  233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN  297 (308)
T ss_pred             cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence            56788899999999999999999999999999999999999999999999999999999987644

>KOG0850|consensus

Probab=99.70  E-value=2.1e-16  Score=139.02  Aligned_cols=67  Identities=46%  Similarity=0.704  Sum_probs=62.1

Q ss_pred             CCCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHH
Q psy526           55 PPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQ  121 (274)
Q Consensus        55 ~~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~  121 (274)
                      +..+|.||.||.++.-||..|.+.|++++|.-..||.+||..|||+.+||+|||||||.|.||..++
T Consensus       117 gk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~  183 (245)
T KOG0850|consen  117 GKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQ  183 (245)
T ss_pred             CCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhc
Confidence            4445667789999999999999999999999999999999999999999999999999999998763

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.70  E-value=3.1e-17  Score=115.54  Aligned_cols=57  Identities=51%  Similarity=0.733  Sum_probs=55.4

Q ss_pred             CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        61 rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      ||+|+.|+.+|+.+|+.+|..++||+..++++||..|||+..+|++||+|||+++||
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            678999999999999999999999999999999999999999999999999999986

; 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 ....

>KOG0485|consensus

Probab=99.69  E-value=6e-17  Score=141.25  Aligned_cols=68  Identities=59%  Similarity=0.845  Sum_probs=63.2

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHHHh
Q psy526           57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQLLE  124 (274)
Q Consensus        57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~~~  124 (274)
                      ..||||.||+|+..|+..||..|+..+|.+..+|.-||.+|.|++.||+|||||||.||||+.....+
T Consensus       101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~e  168 (268)
T KOG0485|consen  101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLE  168 (268)
T ss_pred             ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhh
Confidence            35888999999999999999999999999999999999999999999999999999999998655544

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.65  E-value=1.4e-16  Score=113.21  Aligned_cols=54  Identities=20%  Similarity=0.360  Sum_probs=51.6

Q ss_pred             CCCCCCcCCHHHHHHHHHHHhhCCC----CCHHHHHHHHHHhCCCcccchhhhhhhhh
Q psy526           60 KKRSRAAFSHAQVYELEKRFNAQKY----LSGPERADVAKSLKLTETQVKIWFQNRRY  113 (274)
Q Consensus        60 ~rR~RT~ft~~Ql~~Le~~F~~~~~----Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~  113 (274)
                      +||.||.||.+|++.||.+|++++|    |+..+|++||..|||++++|+|||||.++
T Consensus         1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k~   58 (58)
T TIGR01565         1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNKK   58 (58)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCCC
Confidence            4789999999999999999999999    99999999999999999999999999763

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.

>KOG0492|consensus

Probab=99.65  E-value=1.7e-16  Score=137.61  Aligned_cols=65  Identities=52%  Similarity=0.794  Sum_probs=60.7

Q ss_pred             CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHHHh
Q psy526           60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQLLE  124 (274)
Q Consensus        60 ~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~~~  124 (274)
                      .|+.||.||.+||..||+.|.+.+|.++.+|.+++..|.|+++||+|||||||+|.||.+....+
T Consensus       144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~E  208 (246)
T KOG0492|consen  144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELE  208 (246)
T ss_pred             CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHH
Confidence            36679999999999999999999999999999999999999999999999999999998766554

>KOG0848|consensus

Probab=99.60  E-value=4.9e-16  Score=139.14  Aligned_cols=63  Identities=38%  Similarity=0.681  Sum_probs=58.5

Q ss_pred             CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526           60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL  122 (274)
Q Consensus        60 ~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~  122 (274)
                      |-|-|.++|..|+.+||+.|..++|.++..+.|||..|+|++|||+|||||||+|+||..++.
T Consensus       199 kDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk  261 (317)
T KOG0848|consen  199 KDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK  261 (317)
T ss_pred             ccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence            345588999999999999999999999999999999999999999999999999999976655

>KOG4577|consensus

Probab=99.59  E-value=1.5e-14  Score=130.90  Aligned_cols=65  Identities=28%  Similarity=0.431  Sum_probs=60.7

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526           58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL  122 (274)
Q Consensus        58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~  122 (274)
                      ...||+||+||..||+.|+.+|...++|-+..||+|+.++||..+||||||||||+|+||.++..
T Consensus       165 ~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDA  229 (383)
T KOG4577|consen  165 ASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDA  229 (383)
T ss_pred             cccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhc
Confidence            34689999999999999999999999999999999999999999999999999999999976544

>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=99.56  E-value=5.7e-15  Score=103.84  Aligned_cols=57  Identities=56%  Similarity=0.815  Sum_probs=54.3

Q ss_pred             CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        61 rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      ++.|+.|+..|+.+|+++|..++||+..+++.||.++||++.+|++||+|||.+.++
T Consensus         1 ~~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~   57 (59)
T cd00086           1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR   57 (59)
T ss_pred             CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence            356889999999999999999999999999999999999999999999999999876

>smart00389 HOX Homeodomain

Probab=99.56  E-value=4.2e-15  Score=103.83  Aligned_cols=56  Identities=50%  Similarity=0.764  Sum_probs=52.7

Q ss_pred             CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHH
Q psy526           61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK  116 (274)
Q Consensus        61 rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~K  116 (274)
                      ++.|+.|+.+|+.+|+..|..++||+..++.+||..+||+..+|++||+|||.+.|
T Consensus         1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~   56 (56)
T smart00389        1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK   56 (56)
T ss_pred             CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence            46688899999999999999999999999999999999999999999999998753

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

>KOG0491|consensus

Probab=99.55  E-value=1.8e-15  Score=126.94  Aligned_cols=64  Identities=53%  Similarity=0.866  Sum_probs=60.5

Q ss_pred             CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526           59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL  122 (274)
Q Consensus        59 k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~  122 (274)
                      ++||-||+|+..|+..||+.|+..+|.+-.+|.|||..|+|++.||+.||||||+|.||+++..
T Consensus        99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~  162 (194)
T KOG0491|consen   99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNN  162 (194)
T ss_pred             HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence            5677899999999999999999999999999999999999999999999999999999987664

>KOG0493|consensus

Probab=99.55  E-value=4.9e-15  Score=132.39  Aligned_cols=58  Identities=43%  Similarity=0.781  Sum_probs=56.2

Q ss_pred             CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        61 rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      ||.||.||.+||..|+..|..|+|.+.+.|.+||.+|+|.+.||+|||||+|+|.||.
T Consensus       247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs  304 (342)
T KOG0493|consen  247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS  304 (342)
T ss_pred             cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence            5789999999999999999999999999999999999999999999999999999984

>KOG0844|consensus

Probab=99.53  E-value=2.9e-15  Score=136.32  Aligned_cols=63  Identities=46%  Similarity=0.825  Sum_probs=59.5

Q ss_pred             CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHH
Q psy526           59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQ  121 (274)
Q Consensus        59 k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~  121 (274)
                      .-||-||.||.+|+..||+.|-+..|-++..|.|||..|||.+..|+|||||||+|+||++..
T Consensus       180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla  242 (408)
T KOG0844|consen  180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA  242 (408)
T ss_pred             HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence            457889999999999999999999999999999999999999999999999999999997654

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.46  E-value=7.2e-14  Score=118.21  Aligned_cols=64  Identities=31%  Similarity=0.490  Sum_probs=58.2

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHH
Q psy526           58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQ  121 (274)
Q Consensus        58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~  121 (274)
                      ...+++|+..+..|+.+|++.|..++||+...|.+|+..|+|+++-||+||||||++.|+....
T Consensus        49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~  112 (156)
T COG5576          49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG  112 (156)
T ss_pred             CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence            4456667777999999999999999999999999999999999999999999999999987644

>KOG0483|consensus

Probab=99.45  E-value=5.3e-14  Score=123.02  Aligned_cols=61  Identities=39%  Similarity=0.552  Sum_probs=55.8

Q ss_pred             CCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526           62 RSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL  122 (274)
Q Consensus        62 R~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~  122 (274)
                      +++..|+.+|...||+.|+.+.|....++..||.+|||.++||.|||||||+|||.++...
T Consensus        52 ~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~  112 (198)
T KOG0483|consen   52 GKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEK  112 (198)
T ss_pred             cccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhh
Confidence            3344589999999999999999999999999999999999999999999999999887554

>KOG0847|consensus

Probab=99.33  E-value=6.8e-13  Score=116.18  Aligned_cols=64  Identities=48%  Similarity=0.917  Sum_probs=60.2

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHH
Q psy526           58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQ  121 (274)
Q Consensus        58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~  121 (274)
                      +++|..|-+|+-.|+..||+.|++.+|+--.+|.+||..+|+++.+|+|||||||.||||+-..
T Consensus       165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa  228 (288)
T KOG0847|consen  165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA  228 (288)
T ss_pred             ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence            6777789999999999999999999999999999999999999999999999999999997543

>KOG0490|consensus

Probab=99.31  E-value=1e-12  Score=116.16  Aligned_cols=64  Identities=31%  Similarity=0.415  Sum_probs=61.2

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526           57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL  120 (274)
Q Consensus        57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~  120 (274)
                      ..++||.||.|+..|+++||+.|.+.+||+...|+.||..++|++..|+|||||||+||++...
T Consensus        57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~  120 (235)
T KOG0490|consen   57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER  120 (235)
T ss_pred             hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence            5678999999999999999999999999999999999999999999999999999999999764

>KOG0849|consensus

Probab=99.23  E-value=5.1e-11  Score=113.16  Aligned_cols=67  Identities=34%  Similarity=0.514  Sum_probs=62.1

Q ss_pred             CCCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHH
Q psy526           55 PPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQ  121 (274)
Q Consensus        55 ~~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~  121 (274)
                      ..+++.||.||+|+..|+..||+.|++++||+...|++||.+++|++..|+|||+|||+|++|...+
T Consensus       171 ~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~  237 (354)
T KOG0849|consen  171 ALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD  237 (354)
T ss_pred             cccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence            3456778889999999999999999999999999999999999999999999999999999997643

>KOG0775|consensus

Probab=99.07  E-value=4.7e-10  Score=101.31  Aligned_cols=51  Identities=31%  Similarity=0.478  Sum_probs=47.5

Q ss_pred             CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      |...-+..|..+|.+++||+..++.+||+.+||+..||-.||+|||+|+|-
T Consensus       183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa  233 (304)
T KOG0775|consen  183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA  233 (304)
T ss_pred             hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence            555568899999999999999999999999999999999999999999983

>KOG0774|consensus

Probab=98.82  E-value=1.6e-08  Score=90.97  Aligned_cols=63  Identities=29%  Similarity=0.447  Sum_probs=57.1

Q ss_pred             CCCCCCcCCHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526           60 KKRSRAAFSHAQVYELEKRFN---AQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL  122 (274)
Q Consensus        60 ~rR~RT~ft~~Ql~~Le~~F~---~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~  122 (274)
                      .||+|..|++...++|..+|.   .++||+.+.+++||.++|++..||..||.|+|-+.||.--..
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~  253 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKN  253 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhh
Confidence            367889999999999999995   589999999999999999999999999999999999865443

>KOG2252|consensus

Probab=98.46  E-value=1.9e-07  Score=91.66  Aligned_cols=58  Identities=24%  Similarity=0.327  Sum_probs=54.5

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHH
Q psy526           58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT  115 (274)
Q Consensus        58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~  115 (274)
                      -+.||.|.+||..|++.|.+.|+.+++|+.++.+.|+.+|||....|..||-|.|.|.
T Consensus       418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            4567889999999999999999999999999999999999999999999999988664

>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=98.45  E-value=1.2e-07  Score=62.60  Aligned_cols=34  Identities=32%  Similarity=0.557  Sum_probs=29.1

Q ss_pred             hCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhH
Q psy526           81 AQKYLSGPERADVAKSLKLTETQVKIWFQNRRYK  114 (274)
Q Consensus        81 ~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k  114 (274)
                      .+|||+.+++++||.++||+..||..||-|.|.|
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.

>KOG0490|consensus

Probab=98.40  E-value=2.7e-07  Score=81.55  Aligned_cols=66  Identities=30%  Similarity=0.562  Sum_probs=61.1

Q ss_pred             CCCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526           55 PPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL  120 (274)
Q Consensus        55 ~~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~  120 (274)
                      ....+.++.|+.|...|+..|+..|...++|+...++.|+..+|+..++|+|||+|+|++.++...
T Consensus       148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  148 PSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             CCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            344677889999999999999999999999999999999999999999999999999999998654

>KOG1146|consensus

Probab=98.10  E-value=3.8e-06  Score=89.43  Aligned_cols=63  Identities=24%  Similarity=0.370  Sum_probs=59.3

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526           58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL  120 (274)
Q Consensus        58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~  120 (274)
                      -.+|+.||.++..||+.|...|....||..++.|.|-..++|.+++|+|||||.|+|.|+...
T Consensus       901 ~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~  963 (1406)
T KOG1146|consen  901 MGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL  963 (1406)
T ss_pred             hhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence            356788999999999999999999999999999999999999999999999999999998765

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

Probab=96.97  E-value=0.00067  Score=47.80  Aligned_cols=43  Identities=21%  Similarity=0.403  Sum_probs=31.8

Q ss_pred             HHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhH
Q psy526           72 VYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYK  114 (274)
Q Consensus        72 l~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k  114 (274)
                      +..|+++|...+++...+...|..+.+|+..+|+.||-.|+.+
T Consensus        10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e   52 (56)
T PF11569_consen   10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE   52 (56)
T ss_dssp             -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred             hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence            4569999999999999999999999999999999999876543

>KOG0773|consensus

Probab=96.53  E-value=0.0019  Score=61.00  Aligned_cols=60  Identities=27%  Similarity=0.331  Sum_probs=50.8

Q ss_pred             CCCCCCCcCCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           59 RKKRSRAAFSHAQVYELEKRFNA---QKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        59 k~rR~RT~ft~~Ql~~Le~~F~~---~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      .++|++..|......+|+.+..+   .+||+..++..||.++||+..||..||-|.|-|..+-
T Consensus       238 ~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p  300 (342)
T KOG0773|consen  238 SKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKP  300 (342)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCc
Confidence            35556678999999999987543   5799999999999999999999999999999886653

>PF00157 Pou: Pou domain - N-terminal to homeobox domain; InterPro: IPR000327 POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain

Probab=96.51  E-value=0.00019  Score=53.63  Aligned_cols=27  Identities=4%  Similarity=0.123  Sum_probs=24.0

Q ss_pred             HHHHhCCCCCcccccCcccCCCCcCCC
Q psy526           11 YKKINNNNITNNTMSYYGKKDIRDARD   37 (274)
Q Consensus        11 ~~~~~g~~~sqttis~fe~~~ls~~~~   37 (274)
                      -..+||++|||++|||||+++|+.+++
T Consensus        34 l~~~~G~~~SQttI~RFE~L~LS~kn~   60 (75)
T PF00157_consen   34 LGRLYGKEFSQTTICRFEALQLSFKNM   60 (75)
T ss_dssp             HHHHHSSGGSHHHHHHHHTTTSCHHHH
T ss_pred             HHHhcCccccchhhhhhHhcccCHHHH
Confidence            356899999999999999999997765

The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system [] and the development of an organism []. Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) [, ], and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1). The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (IPR000327 from INTERPRO), while the C-terminal subunit is a homeobox domain (IPR007103 from INTERPRO). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions []. The subdomains are connected by a flexible linker [, , ]. In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [, ]. This entry represents the POU-specific subunit of the POU domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3D1N_O 1AU7_A 3L1P_A 2XSD_C 1O4X_A 1HF0_B 1GT0_C 1POU_A 1CQT_B 1E3O_C ....

>KOG3623|consensus

Probab=96.39  E-value=0.0034  Score=64.09  Aligned_cols=48  Identities=19%  Similarity=0.274  Sum_probs=45.2

Q ss_pred             HHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           72 VYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        72 l~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      +..|+.+|..|..|+..+...||.++||..++|++||.+++++..+..
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            788999999999999999999999999999999999999999887754

>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=95.28  E-value=0.038  Score=38.34  Aligned_cols=46  Identities=22%  Similarity=0.452  Sum_probs=35.5

Q ss_pred             CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhh
Q psy526           61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNR  111 (274)
Q Consensus        61 rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNr  111 (274)
                      ||+|..+|-++...+-..++...     ...+||.++|+...+|..|..|+
T Consensus         1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k   46 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK   46 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred             CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence            57899999999888888887666     57789999999999999999885

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

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

Probab=87.60  E-value=1.3  Score=29.62  Aligned_cols=46  Identities=13%  Similarity=0.214  Sum_probs=34.7

Q ss_pred             cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHH
Q psy526           66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK  116 (274)
Q Consensus        66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~K  116 (274)
                      .++..+..+|...|-     ......+||..+|++...|+.+...-..|.|
T Consensus         4 ~L~~~er~vi~~~y~-----~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR   49 (50)
T PF04545_consen    4 QLPPREREVIRLRYF-----EGLTLEEIAERLGISRSTVRRILKRALKKLR   49 (50)
T ss_dssp             TS-HHHHHHHHHHHT-----ST-SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHhc-----CCCCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence            467889999999982     2334778999999999999998766665554

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 ....

>smart00352 POU Found in Pit-Oct-Unc transcription factors

Probab=86.81  E-value=0.074  Score=39.75  Aligned_cols=25  Identities=4%  Similarity=0.086  Sum_probs=22.6

Q ss_pred             HhCCCCCcccccCcccCCCCcCCCC
Q psy526           14 INNNNITNNTMSYYGKKDIRDARDL   38 (274)
Q Consensus        14 ~~g~~~sqttis~fe~~~ls~~~~~   38 (274)
                      +||..++|++|||||..+|+.++++
T Consensus        37 ~~g~i~SQstISR~Es~~ls~~n~~   61 (75)
T smart00352       37 LYGPDFSQTTICRFEALQLSFKNMC   61 (75)
T ss_pred             cccCcCCHHHHHHHHhcCccHHHHH
Confidence            6889999999999999999988764

>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=80.17  E-value=2.1  Score=27.64  Aligned_cols=44  Identities=14%  Similarity=0.177  Sum_probs=33.0

Q ss_pred             cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhH
Q psy526           66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYK  114 (274)
Q Consensus        66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k  114 (274)
                      .++..+..++...|...     ....+||..+|++...|..|....+.+
T Consensus        10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~   53 (55)
T cd06171          10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK   53 (55)
T ss_pred             hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            46777888888776422     346778999999999999998665443

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	274
2l9r_A	69	Solution Nmr Structure Of Homeobox Domain Of Homeob		4e-18
3rkq_A	58	Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Lengt		1e-16
1nk2_P	77	VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES		9e-16
1ftt_A	68	Thyroid Transcription Factor 1 Homeodomain (Rattus		1e-15
1qry_A	80	Homeobox Protein Vnd (Ventral Nervous System Defect		2e-15
2m34_A	71	Nmr Structure Of The Homeodomain Transcription Fact		7e-15
3a01_A	93	Crystal Structure Of Aristaless And Clawless Homeod		2e-13
2dmt_A	80	Solution Structure Of The Homeobox Domain Of Homeob		1e-12
2h1k_A	63	Crystal Structure Of The Pdx1 Homeodomain In Comple		2e-12
1b72_A	97	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		2e-12
3a03_A	56	Crystal Structure Of Hox11l1 Homeodomain Length = 5		6e-12
2e1o_A	70	Solution Structure Of Rsgi Ruh-028, A Homeobox Doma		2e-11
1ig7_A	58	Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58		2e-11
2djn_A	70	The Solution Structure Of The Homeobox Domain Of Hu		5e-11
2r5y_A	88	Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO		2e-10
9ant_A	62	Antennapedia Homeodomain-Dna Complex Length = 62		2e-10
1b8i_A	81	Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX		3e-10
1hom_A	68	Determination Of The Three-Dimensional Structure Of		4e-10
1ahd_P	68	Determination Of The Nmr Solution Structure Of An A		4e-10
1ftz_A	70	Nuclear Magnetic Resonance Solution Structure Of Th		6e-10
1jgg_A	60	Even-Skipped Homeodomain Complexed To At-Rich Dna L		3e-09
2vi6_A	62	Crystal Structure Of The Nanog Homeodomain Length =		1e-08
2lp0_A	60	The Solution Structure Of Homeodomain-Protein Compl		2e-08
1puf_A	77	Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo		2e-08
1zq3_P	68	Nmr Solution Structure Of The Bicoid Homeodomain Bo		2e-08
1san_A	62	The Des(1-6)antennapedia Homeodomain: Comparison Of		3e-08
1ztr_A	61	Solution Structure Of Engrailed Homeodomain L16a Mu		3e-08
1hdd_C	61	Crystal Structure Of An Engrailed Homeodomain-Dna C		3e-08
3hdd_A	60	Engrailed Homeodomain Dna Complex Length = 60		3e-08
1p7j_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		5e-08
1p7i_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		8e-08
2hdd_A	61	Engrailed Homeodomain Q50k Variant Dna Complex Leng		9e-08
2kt0_A	84	Solution Structure Of Human Stem Cell Transcription		1e-07
2cra_A	70	Solution Structure Of The Homeobox Domain Of Human		2e-07
1fjl_A	81	Homeodomain From The Drosophila Paired Protein Boun		2e-07
2l7f_P	68	Solution Structure Of The Pitx2 Homeodomain Length		3e-07
1enh_A	54	Structural Studies Of The Engrailed Homeodomain Len		3e-07
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		5e-07
2l7m_P	68	Solution Structure Of The Pitx2 Homeodomain R24h Mu		5e-07
1du0_A	57	Engrailed Homeodomain Q50a Variant Dna Complex Leng		5e-07
2l7z_A	73	Nmr Structure Of A13 Homedomain Length = 73		6e-07
2ld5_A	67	Solution Nmr-Derived Complex Structure Of Hoxa13 Dn		8e-07
2hos_A	63	Phage-selected Homeodomain Bound To Unmodified Dna		2e-06
2dms_A	80	Solution Structure Of The Homeobox Domain Of Homeob		2e-06
3cmy_A	61	Structure Of A Homeodomain In Complex With Dna Leng		3e-06
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		3e-06
2m0c_A	75	Solution Nmr Structure Of Homeobox Domain Of Human		3e-06
3a02_A	60	Crystal Structure Of Aristaless Homeodomain Length		9e-06
2k40_A	67	Nmr Structure Of Hesx-1 Homeodomain Double Mutant R		3e-05
2cue_A	80	Solution Structure Of The Homeobox Domain Of The Hu		3e-05
2dmu_A	70	Solution Structure Of The Homeobox Domain Of Homeob		6e-05
2p81_A	44	Engrailed Homeodomain Helix-Turn-Helix Motif Length		2e-04
2dmq_A	80	Solution Structure Of The Homeobox Domain Of LimHOM		8e-04

>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 = 88.6 bits (218), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 41/51 (80%), Positives = 46/51 (90%)
Query: 70  AQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120
            QV ELE++F+ QKYLS PERA +AK+LKLTETQVKIWFQNRRYKTKRKQL
Sbjct: 14  TQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQL 64

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

Iteration: 1
 Score = 83.6 bits (205), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 41/59 (69%), Positives = 46/59 (77%), Gaps = 1/59 (1%)
Query: 58  GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116
           GR+K  R  FS AQVYELE+RF  Q+YLS PER  +A  LKLT TQVKIWFQNRRYK+K
Sbjct: 1   GRRK-PRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

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

Iteration: 1
 Score = 80.5 bits (197), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 37/61 (60%), Positives = 46/61 (75%)
Query: 59  RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
           +K++ R  F+ AQ YELE+RF  Q+YLS PER  +A  ++LT TQVKIWFQN RYKTKR 
Sbjct: 8   KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRA 67
Query: 119 Q 119
           Q
Sbjct: 68  Q 68

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

Iteration: 1
 Score = 80.1 bits (196), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 40/60 (66%), Positives = 45/60 (75%), Gaps = 1/60 (1%)
Query: 59  RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
           R+KR R  FS AQVYELE+RF  QKYLS PER  +A  + LT TQVKIWFQN RYK KR+
Sbjct: 2   RRKR-RVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60

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

Iteration: 1
 Score = 79.3 bits (194), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 36/61 (59%), Positives = 45/61 (73%)
Query: 59  RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
           +K++ R  F+ AQ YELE+RF  Q+YLS PER  +   ++LT TQVKIWFQN RYKTKR 
Sbjct: 11  KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRA 70
Query: 119 Q 119
           Q
Sbjct: 71  Q 71

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

Iteration: 1
 Score = 77.8 bits (190), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 36/62 (58%), Positives = 46/62 (74%)
Query: 56  PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115
           P G+ +R R AF+  Q+ ELEK F+ +KYLS  ER+ +A +LKL+E QVKIWFQNRR K 
Sbjct: 3   PGGKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKW 62
Query: 116 KR 117
           KR
Sbjct: 63  KR 64

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

Iteration: 1
 Score = 73.2 bits (178), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 51/74 (68%), Gaps = 1/74 (1%)
Query: 52  QSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNR 111
           Q++ P  RKK  R +F+  QV ELEKRF+ QKYL+  ERA +A+ LK+T+ QVK WFQNR
Sbjct: 10  QNRTPPKRKK-PRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNR 68
Query: 112 RYKTKRKQLQLLEG 125
           R K +R+  +  E 
Sbjct: 69  RTKWRRQTAEEREA 82

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

Iteration: 1
 Score = 69.7 bits (169), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 36/66 (54%), Positives = 46/66 (69%), Gaps = 2/66 (3%)
Query: 54  QPPTGRKK--RSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNR 111
           +P T  KK  RSR  F+  Q+  LEKRF  QKYLS P+R D+A+SL L++ QVK W+QNR
Sbjct: 9   EPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNR 68
Query: 112 RYKTKR 117
           R K K+
Sbjct: 69  RMKWKK 74

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

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 32/62 (51%), Positives = 43/62 (69%)
Query: 58  GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           G  KR+R A++ AQ+ ELEK F   KY+S P R ++A  L LTE  +KIWFQNRR K K+
Sbjct: 1   GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60
Query: 118 KQ 119
           ++
Sbjct: 61  EE 62

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 40/84 (47%), Positives = 53/84 (63%), Gaps = 8/84 (9%)
Query: 36  RDLPKPAALSNLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAK 95
           R+ PK A +S  PGL     P+G     R  F+  Q+ ELEK F+  KYLS   R ++A 
Sbjct: 18  RNPPKTAKVSE-PGLGS---PSG----LRTNFTTRQLTELEKEFHFNKYLSRARRVEIAA 69
Query: 96  SLKLTETQVKIWFQNRRYKTKRKQ 119
           +L+L ETQVKIWFQNRR K K+++
Sbjct: 70  TLELNETQVKIWFQNRRMKQKKRE 93

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

Iteration: 1
 Score = 67.8 bits (164), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 31/53 (58%), Positives = 42/53 (79%)
Query: 66  AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
           +FS +QV ELE+RF  QKYL+  ERA +AK+L++T+ QVK WFQNRR K +R+
Sbjct: 3   SFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/51 (62%), Positives = 38/51 (74%)
Query: 67  FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           FS+ Q  ELEK+F  QKYLS PER  +AK L+L+E QVK WFQNRR K +R
Sbjct: 14  FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64

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

Iteration: 1
 Score = 65.9 bits (159), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 32/57 (56%), Positives = 42/57 (73%)
Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           ++ R  F+ AQ+  LE++F  ++YLS  ERA+ + SL LTETQVKIWFQNRR K KR
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

Iteration: 1
 Score = 64.7 bits (156), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 32/61 (52%), Positives = 45/61 (73%), Gaps = 2/61 (3%)
Query: 57  TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116
           +GRK R+   +S  Q+  L++RF   +YL+ PERA++A SL LT+TQVKIWFQN+R K K
Sbjct: 6   SGRKPRT--IYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIK 63
Query: 117 R 117
           +
Sbjct: 64  K 64

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

Iteration: 1
 Score = 62.8 bits (151), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 29/62 (46%), Positives = 41/62 (66%)
Query: 58  GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           G  KR R +++  Q  ELEK F+  +YL+   R ++A +L LTE Q+KIWFQNRR K K+
Sbjct: 26  GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 85
Query: 118 KQ 119
           + 
Sbjct: 86  EH 87

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

Iteration: 1
 Score = 62.4 bits (150), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 28/59 (47%), Positives = 40/59 (67%)
Query: 60  KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
           +KR R  ++  Q  ELEK F+  +YL+   R ++A +L LTE Q+KIWFQNRR K K++
Sbjct: 3   RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61

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

Iteration: 1
 Score = 62.0 bits (149), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 28/61 (45%), Positives = 40/61 (65%)
Query: 58  GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           G ++R R  ++  Q  ELEK F+   YL+   R ++A +L LTE Q+KIWFQNRR K K+
Sbjct: 18  GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKK 77
Query: 118 K 118
           +
Sbjct: 78  E 78

>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 = 61.6 bits (148), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 28/59 (47%), Positives = 40/59 (67%)
Query: 60  KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
           +KR R  ++  Q  ELEK F+  +YL+   R ++A +L LTE Q+KIWFQNRR K K++
Sbjct: 2   RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 60

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

Iteration: 1
 Score = 61.6 bits (148), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 28/59 (47%), Positives = 40/59 (67%)
Query: 60  KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
           +KR R  ++  Q  ELEK F+  +YL+   R ++A +L LTE Q+KIWFQNRR K K++
Sbjct: 2   RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 60

>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 = 61.2 bits (147), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 27/59 (45%), Positives = 41/59 (69%)
Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
           KR+R  ++  Q  ELEK F+  +Y++   R D+A +L L+E Q+KIWFQNRR K+K+ +
Sbjct: 4   KRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKDR 62

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

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 27/59 (45%), Positives = 39/59 (66%)
Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
           +R R AF+  Q+  LEK F  + Y+S P R ++A  L L E+ +K+WFQNRR K KR++
Sbjct: 2   RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQR 60

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 29/62 (46%), Positives = 39/62 (62%)
Query: 58  GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           G K++ R  FS AQ+  L+ RF  QKYLS  +  +++  L L+  QVK WFQN+R K KR
Sbjct: 1   GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
Query: 118 KQ 119
            Q
Sbjct: 61  WQ 62

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 28/57 (49%), Positives = 36/57 (63%)
Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           ++ R  ++  Q  ELEK F    YL+   R +VA+ L LTE QVKIWFQNRR K K+
Sbjct: 2   RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 28/57 (49%), Positives = 36/57 (63%)
Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           ++ R  ++  Q  ELEK F    YL+   R +VA+ L LTE QVKIWFQNRR K K+
Sbjct: 14  RKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70

>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 = 55.8 bits (133), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 25/56 (44%), Positives = 37/56 (66%)
Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116
           +R+R  F+ +Q+ ELE+ F   +YL+ P  AD++  L L   QVKIWF+NRR + K
Sbjct: 3   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58

>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 = 55.8 bits (133), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 25/52 (48%), Positives = 36/52 (69%)
Query: 67  FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
           ++  Q  ELEK F+  +YL+   R ++A +L LTE Q+KIWFQNRR K K++
Sbjct: 3   YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 54

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 26/60 (43%), Positives = 37/60 (61%)
Query: 58  GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           G +KR R AFS  Q+   ++ FN  +YL+   R  ++  L L E Q+KIWFQN+R K +R
Sbjct: 1   GDEKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 26/58 (44%), Positives = 37/58 (63%)
Query: 60  KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           +KR R AFS  Q+  L++ FN  +YL+   R  ++  L L E Q+KIWFQN+R K K+
Sbjct: 3   EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 26/58 (44%), Positives = 37/58 (63%)
Query: 60  KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           +KR R AFS  Q+  L++ FN  +YL+   R  ++  L L E Q+KIWFQN+R K K+
Sbjct: 1   EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 26/58 (44%), Positives = 36/58 (62%)
Query: 60  KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           +KR R AFS  Q+  L++ FN  +YL+   R  ++  L L E Q+KIWFQN R K K+
Sbjct: 1   EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 26/58 (44%), Positives = 36/58 (62%)
Query: 60  KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           +KR R AFS  Q+  L++ FN  +YL+   R  ++  L L E Q+KIWFQN R K K+
Sbjct: 1   EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 25/58 (43%), Positives = 37/58 (63%)
Query: 60  KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           +KR R AFS  Q+  L++ FN  +YL+   R  ++  L L E Q+KIWF+N+R K K+
Sbjct: 3   EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/80 (37%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 40  KPAALSNLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKL 99
           +P +  N     + + P  +K+++R  FS  Q+  L  RF  QKYLS  +  +++  L L
Sbjct: 3   QPTSAENSVAKKEDKVPV-KKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNL 61
Query: 100 TETQVKIWFQNRRYKTKRKQ 119
           +  QVK WFQN+R K+KR Q
Sbjct: 62  SYKQVKTWFQNQRMKSKRWQ 81

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/65 (40%), Positives = 41/65 (63%), Gaps = 2/65 (3%)
Query: 53  SQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRR 112
           S   +GRKKR    +S  Q+ ELE+ + A K+++  +R  ++ +  L+E Q+ IWFQNRR
Sbjct: 2   SSGSSGRKKR--IPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRR 59
Query: 113 YKTKR 117
            K K+
Sbjct: 60  VKEKK 64

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 25/72 (34%), Positives = 45/72 (62%), Gaps = 4/72 (5%)
Query: 48  PGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIW 107
           PG+A  +    +++RSR  FS +Q+ ELE+ F   +Y     R ++A+   LTE ++++W
Sbjct: 10  PGIALKR----KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVW 65
Query: 108 FQNRRYKTKRKQ 119
           FQNRR + +++ 
Sbjct: 66  FQNRRARLRKQH 77

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 22/62 (35%), Positives = 37/62 (59%)
Query: 58  GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           G ++R R  F+  Q+ ELE  F   +Y     R ++A    LTE +V++WF+NRR K ++
Sbjct: 1   GSQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Query: 118 KQ 119
           ++
Sbjct: 61  RE 62

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 24/53 (45%), Positives = 33/53 (62%)
Query: 62  RSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYK 114
           R R AFS  Q+  L++ FN  +YL+   R  ++  L L E Q+KIWFQN+R K
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 23/64 (35%), Positives = 40/64 (62%)
Query: 56  PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115
           P  +++R R  F+  Q+ ELEK F+   Y     R ++A  + LTE ++++WFQNRR K 
Sbjct: 2   PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKW 61
Query: 116 KRKQ 119
           ++++
Sbjct: 62  RKQE 65

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 22/62 (35%), Positives = 36/62 (58%)
Query: 58  GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           G ++R R  F+  Q+ ELE  F    Y     R ++A    LTE +V++WF+NRR K ++
Sbjct: 1   GSQRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Query: 118 KQ 119
           ++
Sbjct: 61  RE 62

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 24/56 (42%), Positives = 34/56 (60%)
Query: 62  RSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           R R AFS  Q+  L++ FN  +YL+   R  ++  L L E Q+KIWF N+R K K+
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 24/60 (40%), Positives = 38/60 (63%), Gaps = 2/60 (3%)
Query: 58  GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           GRKKR    ++  Q+ ELE+ +   K+++  +R  ++ +  L+E QV IWFQNRR K K+
Sbjct: 7   GRKKR--VPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 24/60 (40%), Positives = 38/60 (63%), Gaps = 2/60 (3%)
Query: 58  GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           GRKKR    ++  Q+ ELE+ +   K+++  +R  ++ +  L+E QV IWFQNRR K K+
Sbjct: 1   GRKKR--VPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/58 (43%), Positives = 35/58 (60%)
Query: 60  KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           +KR R AFS  Q+  L++ FN  +YL+   R  ++  L L E QVK WF+N R K K+
Sbjct: 4   EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 27/73 (36%), Positives = 43/73 (58%)
Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120
           +R R  F+ AQ+  LE  F   +Y     R +VA  + L E++V++WF+NRR K +++Q 
Sbjct: 8   RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQ 67
Query: 121 QLLEGSLNTPSAG 133
           Q   G  + PS+G
Sbjct: 68  QQQNGGQSGPSSG 80

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 22/59 (37%), Positives = 37/59 (62%)
Query: 60  KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
           ++RSR  F+  Q+ ELE+ F    Y     R ++A+  KLTE +V++WF NRR + +++
Sbjct: 2   QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 22/58 (37%), Positives = 36/58 (62%)
Query: 62  RSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
           R R  F+  Q+ ELEK F+   Y     R ++A  + LTE ++++WFQNRR K ++++
Sbjct: 1   RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58

>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 = 48.9 bits (115), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/62 (40%), Positives = 38/62 (61%)
Query: 58  GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           G+K+R+R  F+  Q+ ELEK F    Y     R  +A    LTE +V++WFQNRR K ++
Sbjct: 7   GKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRK 66
Query: 118 KQ 119
           ++
Sbjct: 67  RE 68

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 21/57 (36%), Positives = 35/57 (61%)
Query: 63  SRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
           S   F+  Q+ ELEK F+   Y     R ++A  + LTE ++++WFQNRR K ++++
Sbjct: 2   SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 23/59 (38%), Positives = 31/59 (52%)
Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
           +R R AF+  Q+  LE  F    Y       D+A+ L L   +++IWFQNRR K KR  
Sbjct: 2   RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSH 60

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 23/73 (31%), Positives = 40/73 (54%)
Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120
           +R+R +F+  Q+  LEK F    Y     R  +A  + L E ++++WF NRR K +R++ 
Sbjct: 8   QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 67
Query: 121 QLLEGSLNTPSAG 133
              +   + PS+G
Sbjct: 68  LRNQRRQSGPSSG 80

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 21/57 (36%), Positives = 32/57 (56%)
Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           +R R  F+  Q+  LE  F   KY     R  +A+ + L E +V++WF+NRR K +R
Sbjct: 8   RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRR 64

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 18/42 (42%), Positives = 27/42 (64%)
Query: 76  EKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           ++ FN  +YL+   R  ++  L L E Q+KIWFQN+R K K+
Sbjct: 2   KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43

>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 = 8e-04,   Method: Compositional matrix adjust.
 Identities = 22/73 (30%), Positives = 38/73 (52%)
Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120
           KR R +F H Q+  ++  F         +   +A+   LT+  +++WFQN R K +R  L
Sbjct: 8   KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLL 67
Query: 121 QLLEGSLNTPSAG 133
           +   G ++ PS+G
Sbjct: 68  RQENGGVSGPSSG 80

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	274
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	6e-39
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	2e-38
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	4e-37
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	7e-37
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	3e-36
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	4e-35
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	4e-35
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	8e-35
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	8e-34
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	9e-34
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	4e-32
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	1e-30
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	4e-29
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	4e-26
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	7e-25
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	7e-24
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	7e-24
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	1e-23
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	6e-22
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	6e-22
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	2e-21
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	3e-20
1e3o_C	160	Octamer-binding transcription factor 1; transcript	7e-20
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	1e-19
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	3e-19
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	3e-19
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	9e-19
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	7e-18
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	2e-17
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	1e-16
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	4e-16
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	4e-16
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	9e-16
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	2e-15
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	3e-15
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	3e-15
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	7e-15
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	2e-14
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	2e-14
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	2e-14
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	4e-14
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	8e-14
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	2e-13
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	2e-13
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	3e-13
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	4e-13
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	2e-12
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	3e-12
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	7e-12
1uhs_A	72	HOP, homeodomain only protein; structural genomics	6e-11
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	1e-10
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	1e-10
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	3e-09
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	6e-09
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	2e-08
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	7e-08
1lfb_A	99	Liver transcription factor (LFB1); transcription r	1e-07
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	5e-06
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	7e-06
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	6e-04

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

 Score =  129 bits (327), Expect = 6e-39
 Identities = 44/64 (68%), Positives = 50/64 (78%)

Query: 58  GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           G      +  SH QV ELE++F+ QKYLS PERA +AK+LKLTETQVKIWFQNRRYKTKR
Sbjct: 2   GHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61

Query: 118 KQLQ 121
           KQL 
Sbjct: 62  KQLS 65

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

 Score =  128 bits (323), Expect = 2e-38
 Identities = 29/62 (46%), Positives = 39/62 (62%)

Query: 58  GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           G K++ R  FS AQ+  L+ RF  QKYLS  +  +++  L L+  QVK WFQN+R K KR
Sbjct: 1   GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60

Query: 118 KQ 119
            Q
Sbjct: 61  WQ 62

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

 Score =  125 bits (315), Expect = 4e-37
 Identities = 37/62 (59%), Positives = 44/62 (70%)

Query: 60  KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
           +++ R  FS AQVYELE+RF  QKYLS PER  +A  + LT TQVKIWFQN RYK KR+ 
Sbjct: 2   RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61

Query: 120 LQ 121
             
Sbjct: 62  KD 63

>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 =  124 bits (314), Expect = 7e-37
 Identities = 40/78 (51%), Positives = 51/78 (65%), Gaps = 2/78 (2%)

Query: 53  SQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRR 112
           S     +K++ R  F+ AQ YELE+RF  Q+YLS PER  +A  ++LT TQVKIWFQN R
Sbjct: 2   SDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHR 61

Query: 113 YKTKRKQLQLLEGSLNTP 130
           YKTKR Q +  +G    P
Sbjct: 62  YKTKRAQNE--KGYEGHP 77

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

 Score =  122 bits (308), Expect = 3e-36
 Identities = 38/57 (66%), Positives = 45/57 (78%)

Query: 60  KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116
           +++ R  FS AQVYELE+RF  Q+YLS PER  +A  LKLT TQVKIWFQNRRYK+K
Sbjct: 2   RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

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

 Score =  120 bits (303), Expect = 4e-35
 Identities = 35/83 (42%), Positives = 50/83 (60%)

Query: 49  GLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWF 108
           G         ++K+ R +F+  QV ELEKRF+ QKYL+  ERA +A+ LK+T+ QVK WF
Sbjct: 6   GHPYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWF 65

Query: 109 QNRRYKTKRKQLQLLEGSLNTPS 131
           QNRR K +R+  +  E      +
Sbjct: 66  QNRRTKWRRQTAEEREAERQAAN 88

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

 Score =  119 bits (301), Expect = 4e-35
 Identities = 32/57 (56%), Positives = 42/57 (73%)

Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           ++ R  F+ AQ+  LE++F  ++YLS  ERA+ + SL LTETQVKIWFQNRR K KR
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

 Score =  119 bits (300), Expect = 8e-35
 Identities = 30/81 (37%), Positives = 46/81 (56%), Gaps = 1/81 (1%)

Query: 39  PKPAALSNLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLK 98
            +P +  N     + + P  +K+++R  FS  Q+  L  RF  QKYLS  +  +++  L 
Sbjct: 2   KQPTSAENSVAKKEDKVP-VKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILN 60

Query: 99  LTETQVKIWFQNRRYKTKRKQ 119
           L+  QVK WFQN+R K+KR Q
Sbjct: 61  LSYKQVKTWFQNQRMKSKRWQ 81

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

 Score =  116 bits (293), Expect = 8e-34
 Identities = 29/64 (45%), Positives = 42/64 (65%)

Query: 56  PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115
                ++ R  +S  Q+  L++RF   +YL+ PERA++A SL LT+TQVKIWFQN+R K 
Sbjct: 3   SGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKI 62

Query: 116 KRKQ 119
           K+  
Sbjct: 63  KKSG 66

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

 Score =  115 bits (291), Expect = 9e-34
 Identities = 31/53 (58%), Positives = 42/53 (79%)

Query: 66  AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
           +FS +QV ELE+RF  QKYL+  ERA +AK+L++T+ QVK WFQNRR K +R+
Sbjct: 3   SFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

>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 =  112 bits (281), Expect = 4e-32
 Identities = 33/65 (50%), Positives = 40/65 (61%)

Query: 55  PPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYK 114
                 K  +  FS+ Q  ELEK+F  QKYLS PER  +AK L+L+E QVK WFQNRR K
Sbjct: 2   SSGSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAK 61

Query: 115 TKRKQ 119
            +R  
Sbjct: 62  WRRSG 66

>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 =  108 bits (272), Expect = 1e-30
 Identities = 33/75 (44%), Positives = 46/75 (61%)

Query: 45  SNLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQV 104
           S+     +      + +RSR  F+  Q+  LEKRF  QKYLS P+R D+A+SL L++ QV
Sbjct: 2   SSGSSGGEPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQV 61

Query: 105 KIWFQNRRYKTKRKQ 119
           K W+QNRR K K+  
Sbjct: 62  KTWYQNRRMKWKKSG 76

>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 =  104 bits (261), Expect = 4e-29
 Identities = 27/66 (40%), Positives = 41/66 (62%)

Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120
           +R+R  F+ +Q+ ELE+ F   +YL+ P  AD++  L L   QVKIWF+NRR + K +  
Sbjct: 3   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 62

Query: 121 QLLEGS 126
           Q  + S
Sbjct: 63  QHKDQS 68

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

 Score = 96.5 bits (241), Expect = 4e-26
 Identities = 17/58 (29%), Positives = 34/58 (58%)

Query: 59  RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116
           +  + +++ S      LE+ F  ++ L+  E+ +VAK   +T  QV++WF N+R ++K
Sbjct: 4   KSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61

>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 = 93.2 bits (232), Expect = 7e-25
 Identities = 27/59 (45%), Positives = 39/59 (66%)

Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
           +R R AF+  Q+  LEK F  + Y+S P R ++A  L L E+ +K+WFQNRR K KR++
Sbjct: 2   RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQR 60

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

 Score = 90.5 bits (225), Expect = 7e-24
 Identities = 25/58 (43%), Positives = 37/58 (63%)

Query: 60  KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           +KR R AFS  Q+  L++ FN  +YL+   R  ++  L L E Q+KIWF+N+R K K+
Sbjct: 3   EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

>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 = 91.5 bits (227), Expect = 7e-24
 Identities = 33/68 (48%), Positives = 44/68 (64%)

Query: 52  QSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNR 111
            S+P  G     R  F+  Q+ ELEK F+  KYLS   R ++A +L+L ETQVKIWFQNR
Sbjct: 26  VSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNR 85

Query: 112 RYKTKRKQ 119
           R K K+++
Sbjct: 86  RMKQKKRE 93

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

 Score = 90.1 bits (224), Expect = 1e-23
 Identities = 32/62 (51%), Positives = 43/62 (69%)

Query: 58  GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           G  KR+R A++ AQ+ ELEK F   KY+S P R ++A  L LTE  +KIWFQNRR K K+
Sbjct: 1   GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60

Query: 118 KQ 119
           ++
Sbjct: 61  EE 62

>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 = 86.0 bits (213), Expect = 6e-22
 Identities = 28/68 (41%), Positives = 40/68 (58%)

Query: 52  QSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNR 111
                 G ++R R  ++  Q  ELEK F+   YL+   R ++A +L LTE Q+KIWFQNR
Sbjct: 12  AIAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNR 71

Query: 112 RYKTKRKQ 119
           R K K++ 
Sbjct: 72  RMKLKKEI 79

>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 = 85.5 bits (212), Expect = 6e-22
 Identities = 28/60 (46%), Positives = 40/60 (66%)

Query: 60  KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
           +KR R  ++  Q  ELEK F+  +YL+   R ++A +L LTE Q+KIWFQNRR K K++ 
Sbjct: 2   RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61

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

 Score = 85.3 bits (211), Expect = 2e-21
 Identities = 29/69 (42%), Positives = 42/69 (60%)

Query: 51  AQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQN 110
             +    G  KR R +++  Q  ELEK F+  +YL+   R ++A +L LTE Q+KIWFQN
Sbjct: 19  TSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQN 78

Query: 111 RRYKTKRKQ 119
           RR K K++ 
Sbjct: 79  RRMKWKKEH 87

>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 = 81.4 bits (201), Expect = 3e-20
 Identities = 21/65 (32%), Positives = 37/65 (56%)

Query: 55  PPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYK 114
                 ++ R  +S  Q+ ELE+ + A K+++  +R  ++ +  L+E Q+ IWFQNRR K
Sbjct: 2   SSGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVK 61

Query: 115 TKRKQ 119
            K+  
Sbjct: 62  EKKSG 66

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

 Score = 83.1 bits (205), Expect = 7e-20
 Identities = 20/90 (22%), Positives = 38/90 (42%), Gaps = 2/90 (2%)

Query: 30  KDIRDARDLPKPAALSNLPGL--AQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSG 87
           K + DA       +  + P    +       R+++ R +        LEK F   +  + 
Sbjct: 69  KWLNDAEANLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTS 128

Query: 88  PERADVAKSLKLTETQVKIWFQNRRYKTKR 117
            +   +A+ L + +  +++WF NRR K KR
Sbjct: 129 EDITLIAEQLNMEKEVIRVWFSNRRQKEKR 158

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

 Score = 79.5 bits (196), Expect = 1e-19
 Identities = 20/59 (33%), Positives = 36/59 (61%)

Query: 59  RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
             ++ R  ++  Q+ ELE+ +   K+++  +R  ++ +  L+E QV IWFQNRR K K+
Sbjct: 6   EGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64

>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 = 78.7 bits (194), Expect = 3e-19
 Identities = 28/65 (43%), Positives = 36/65 (55%)

Query: 55  PPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYK 114
                 ++ R  ++  Q  ELEK F    YL+   R +VA+ L LTE QVKIWFQNRR K
Sbjct: 8   LHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMK 67

Query: 115 TKRKQ 119
            K+  
Sbjct: 68  MKKIN 72

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

 Score = 81.2 bits (200), Expect = 3e-19
 Identities = 22/66 (33%), Positives = 30/66 (45%)

Query: 52  QSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNR 111
                 GRK++ R +        LE  F      S  E   +A SL+L +  V++WF NR
Sbjct: 91  DKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNR 150

Query: 112 RYKTKR 117
           R K KR
Sbjct: 151 RQKEKR 156

>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 = 79.6 bits (196), Expect = 9e-19
 Identities = 21/68 (30%), Positives = 32/68 (47%)

Query: 52  QSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNR 111
           +      RK++ R   S A    LE+ F      S  E   +A+ L L +  V++WF NR
Sbjct: 79  EKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNR 138

Query: 112 RYKTKRKQ 119
           R + KR +
Sbjct: 139 RQREKRVK 146

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

 Score = 75.1 bits (185), Expect = 7e-18
 Identities = 23/85 (27%), Positives = 39/85 (45%), Gaps = 9/85 (10%)

Query: 49  GLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWF 108
           G + S   +  K +     SH Q+  L+  F   ++    E   + K   L+  +V+ WF
Sbjct: 1   GSSGSSGASIYKNK----KSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWF 56

Query: 109 QNRRYKTKRKQLQLLEGSLNTPSAG 133
            +RRY  +      L+GS + PS+G
Sbjct: 57  SDRRYHCRN-----LKGSRSGPSSG 76

>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 = 73.9 bits (182), Expect = 2e-17
 Identities = 17/61 (27%), Positives = 28/61 (45%)

Query: 59  RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
             + SR  F+  Q+  L+  F+A  Y    E   ++  L L    + +WFQN R K ++ 
Sbjct: 6   SGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKS 65

Query: 119 Q 119
            
Sbjct: 66  G 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 = 71.7 bits (176), Expect = 1e-16
 Identities = 11/65 (16%), Positives = 26/65 (40%)

Query: 58  GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
                     +  Q+  L+  F   ++    E   + +   L  +++K WF + RY+ +R
Sbjct: 2   AHHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR 61

Query: 118 KQLQL 122
             + +
Sbjct: 62  GIVHI 66

>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 = 70.5 bits (173), Expect = 4e-16
 Identities = 27/75 (36%), Positives = 43/75 (57%)

Query: 59  RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
             +R R  F+ AQ+  LE  F   +Y     R +VA  + L E++V++WF+NRR K +++
Sbjct: 6   SGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQ 65

Query: 119 QLQLLEGSLNTPSAG 133
           Q Q   G  + PS+G
Sbjct: 66  QQQQQNGGQSGPSSG 80

>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 = 70.6 bits (173), Expect = 4e-16
 Identities = 22/75 (29%), Positives = 38/75 (50%)

Query: 59  RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
             KR R +F H Q+  ++  F         +   +A+   LT+  +++WFQN R K +R 
Sbjct: 6   SGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRN 65

Query: 119 QLQLLEGSLNTPSAG 133
            L+   G ++ PS+G
Sbjct: 66  LLRQENGGVSGPSSG 80

>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 = 71.6 bits (175), Expect = 9e-16
 Identities = 19/103 (18%), Positives = 35/103 (33%)

Query: 15  NNNNITNNTMSYYGKKDIRDARDLPKPAALSNLPGLAQSQPPTGRKKRSRAAFSHAQVYE 74
              +IT  +         +   +            +        +K++ R +F+   +  
Sbjct: 48  EKLDITPKSAQKLKPVLEKWLNEAELRNQEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEA 107

Query: 75  LEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           L   F      +G E  ++AK L      V++WF NRR   K 
Sbjct: 108 LNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN 150

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

 Score = 68.6 bits (168), Expect = 2e-15
 Identities = 24/82 (29%), Positives = 42/82 (51%), Gaps = 6/82 (7%)

Query: 55  PPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPE---RADVAKSLKLTETQVKIWFQNR 111
                 +R+R +F+  Q+  LEK F    Y   P+   R  +A  + L E ++++WF NR
Sbjct: 2   SSGSSGQRNRTSFTQEQIEALEKEFERTHY---PDVFARERLAAKIDLPEARIQVWFSNR 58

Query: 112 RYKTKRKQLQLLEGSLNTPSAG 133
           R K +R++    +   + PS+G
Sbjct: 59  RAKWRREEKLRNQRRQSGPSSG 80

>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 = 70.5 bits (172), Expect = 3e-15
 Identities = 22/73 (30%), Positives = 35/73 (47%)

Query: 46  NLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVK 105
           NL  +++S+     +KR R +  +   + LE  F      S  +   +A  L L +  V+
Sbjct: 82  NLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVR 141

Query: 106 IWFQNRRYKTKRK 118
           +WF NRR K KR 
Sbjct: 142 VWFSNRRQKGKRS 154

>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 = 68.3 bits (167), Expect = 3e-15
 Identities = 16/80 (20%), Positives = 33/80 (41%), Gaps = 2/80 (2%)

Query: 42  AALSNLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTE 101
            +  +  G    +P   R KR R   +  Q+  L +++      +      +A  + L +
Sbjct: 1   GSSGSSGGTGGEEPQ--RDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKK 58

Query: 102 TQVKIWFQNRRYKTKRKQLQ 121
             V++WFQN R + ++    
Sbjct: 59  RVVQVWFQNTRARERKSGPS 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 = 67.0 bits (164), Expect = 7e-15
 Identities = 14/62 (22%), Positives = 27/62 (43%)

Query: 58  GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
              KR R   +  Q+  L + F+     S  +  ++A    L +  +K WF+N  +K ++
Sbjct: 5   SSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQ 64

Query: 118 KQ 119
             
Sbjct: 65  SG 66

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

 Score = 65.9 bits (161), Expect = 2e-14
 Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 1/60 (1%)

Query: 61  KRSRAAFSHAQVYELEKRFN-AQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
            ++ +  +  QV  LE  FN   K+        +A    LTE Q + WF+ R  + +R +
Sbjct: 3   AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 62

>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 = 65.8 bits (161), Expect = 2e-14
 Identities = 22/69 (31%), Positives = 41/69 (59%), Gaps = 6/69 (8%)

Query: 58  GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPE---RADVAKSLKLTETQVKIWFQNRRYK 114
           G ++R R  F+  Q+ +LE  F   +Y   P+   R ++A    LTE +V++WF+NRR K
Sbjct: 1   GSQRRQRTHFTSQQLQQLEATFQRNRY---PDMSTREEIAVWTNLTEARVRVWFKNRRAK 57

Query: 115 TKRKQLQLL 123
            ++++  ++
Sbjct: 58  WRKREEFIV 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 = 66.6 bits (162), Expect = 2e-14
 Identities = 20/93 (21%), Positives = 36/93 (38%), Gaps = 15/93 (16%)

Query: 56  PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSL---------------KLT 100
                + SR  +    +  +E  FN  +Y    +R ++A +                ++T
Sbjct: 3   SGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVT 62

Query: 101 ETQVKIWFQNRRYKTKRKQLQLLEGSLNTPSAG 133
             +V  WF NRR + KR+         + PS+G
Sbjct: 63  SLKVYNWFANRRKEIKRRANIAAILESSGPSSG 95

>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 = 64.7 bits (158), Expect = 4e-14
 Identities = 13/64 (20%), Positives = 30/64 (46%)

Query: 59  RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
           +  R R   +  Q++ L   + A        +  + +   L+   +++WFQN+R K K++
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

Query: 119 QLQL 122
            + +
Sbjct: 62  SIMM 65

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

 Score = 63.9 bits (156), Expect = 8e-14
 Identities = 26/65 (40%), Positives = 33/65 (50%), Gaps = 8/65 (12%)

Query: 58  GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPE---RADVAKSLKLTETQVKIWFQNRRYK 114
           GR  R R AF+  Q+  LE  F    Y   P      D+A+ L L   +++IWFQNRR K
Sbjct: 1   GR--RPRTAFTQNQIEVLENVFRVNCY---PGIDILEDLAQKLNLELDRIQIWFQNRRAK 55

Query: 115 TKRKQ 119
            KR  
Sbjct: 56  LKRSH 60

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

 Score = 65.7 bits (159), Expect = 2e-13
 Identities = 20/120 (16%), Positives = 39/120 (32%), Gaps = 11/120 (9%)

Query: 2   DSMKDSEEYYKKINNNNITNNTMSYYGKKDIRDARDLPKPAALSNLPGLAQSQPPTGRKK 61
             +K   E ++++               ++    R      A          +      K
Sbjct: 50  SKLKSGRETFRRMWKW-----------LQEPEFQRMSALRLAACKRKEQEHGKDRGNTPK 98

Query: 62  RSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQ 121
           + R  F+  Q   L   F   K  S   +  +++ L L  + V  +F N R ++  K L+
Sbjct: 99  KPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWLE 158

>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 = 62.9 bits (153), Expect = 2e-13
 Identities = 14/61 (22%), Positives = 23/61 (37%), Gaps = 1/61 (1%)

Query: 58  GRKKRSRAAFSHAQVYELEKRF-NAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116
               RSR   S   +  L+    +   Y        ++  L L +  +  +FQN+RY  K
Sbjct: 5   SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVK 64

Query: 117 R 117
            
Sbjct: 65  H 65

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

 Score = 62.8 bits (153), Expect = 3e-13
 Identities = 26/74 (35%), Positives = 45/74 (60%), Gaps = 9/74 (12%)

Query: 52  QSQPPTGRKK---RSRAAFSHAQVYELEKRFNAQKYLSGPE---RADVAKSLKLTETQVK 105
           +S+P    K+   RSR  FS +Q+ ELE+ F   +Y   P+   R ++A+   LTE +++
Sbjct: 7   ESEPGIALKRKQRRSRTTFSASQLDELERAFERTQY---PDIYTREELAQRTNLTEARIQ 63

Query: 106 IWFQNRRYKTKRKQ 119
           +WFQNRR + +++ 
Sbjct: 64  VWFQNRRARLRKQH 77

>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 = 62.4 bits (152), Expect = 4e-13
 Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 6/64 (9%)

Query: 59  RKKRSRAAFSHAQVYELEKRFNAQKYLSGPE---RADVAKSLKLTETQVKIWFQNRRYKT 115
             +R R  F+  Q+  LE  F   KY   P+   R  +A+ + L E +V++WF+NRR K 
Sbjct: 6   SGRRHRTIFTDEQLEALENLFQETKY---PDVGTREQLARKVHLREEKVEVWFKNRRAKW 62

Query: 116 KRKQ 119
           +R  
Sbjct: 63  RRSG 66

>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 = 60.3 bits (146), Expect = 2e-12
 Identities = 18/71 (25%), Positives = 28/71 (39%), Gaps = 5/71 (7%)

Query: 49  GLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWF 108
           G + S  PT  K+R+       Q+  LE  F         E   +    K+T  ++  WF
Sbjct: 1   GSSGSSGPTKYKERAPE-----QLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWF 55

Query: 109 QNRRYKTKRKQ 119
             RR K   ++
Sbjct: 56  SERRKKVNAEE 66

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

 Score = 59.2 bits (144), Expect = 3e-12
 Identities = 22/60 (36%), Positives = 37/60 (61%), Gaps = 6/60 (10%)

Query: 63  SRAAFSHAQVYELEKRFNAQKYLSGPE---RADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
           S   F+  Q+ ELEK F+   Y   P+   R ++A  + LTE ++++WFQNRR K ++++
Sbjct: 2   SHMTFTSFQLEELEKAFSRTHY---PDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58

>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 = 59.2 bits (143), Expect = 7e-12
 Identities = 16/77 (20%), Positives = 30/77 (38%), Gaps = 5/77 (6%)

Query: 56  PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115
           P   K++++      QV  LE  F    + +  E   +    KL+  ++  WF  RR   
Sbjct: 14  PQKFKEKTQG-----QVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLR 68

Query: 116 KRKQLQLLEGSLNTPSA 132
              +  +L+   +  S 
Sbjct: 69  DSMEQAVLDSMGSGKSG 85

>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 = 56.2 bits (136), Expect = 6e-11
 Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 62  RSRAAFSHAQVYELEKRFN-AQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
              A  +  QV  LE  FN   K+        +A    LTE Q + WF+ R  + +R +
Sbjct: 3   EGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 61

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

 Score = 58.3 bits (140), Expect = 1e-10
 Identities = 23/119 (19%), Positives = 41/119 (34%), Gaps = 21/119 (17%)

Query: 21  NNTMSYYGKKDIRDARDLPKPAALSNLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFN 80
               ++Y +K    A+          +      + PT + +R+R  +  A    L + + 
Sbjct: 76  AALYTWYVRKQREVAQQFTHAGQGGLIEEPTGDELPTKKGRRNRFKWGPASQQILFQAYE 135

Query: 81  AQKYLSGPERADVAK---------------------SLKLTETQVKIWFQNRRYKTKRK 118
            QK  S  ER  + +                     S  +TE +V  WF NRR +   +
Sbjct: 136 RQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFR 194

>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 = 55.8 bits (134), Expect = 1e-10
 Identities = 15/80 (18%), Positives = 30/80 (37%), Gaps = 5/80 (6%)

Query: 55  PPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYK 114
            P   K+++       Q+  L+  F     L+  E   +    KLT  ++  WF  ++  
Sbjct: 11  TPQKFKEKTAE-----QLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKS 65

Query: 115 TKRKQLQLLEGSLNTPSAGN 134
              K+ ++     N  S+  
Sbjct: 66  KALKEEKMEIDESNAGSSSG 85

>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 = 52.5 bits (125), Expect = 3e-09
 Identities = 20/80 (25%), Positives = 30/80 (37%)

Query: 45  SNLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQV 104
           S L  L Q   P           +  Q++ L+  F   ++ S  E   +AK   L  T +
Sbjct: 10  SGLEVLFQGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDI 69

Query: 105 KIWFQNRRYKTKRKQLQLLE 124
             WF + RY  K   L+   
Sbjct: 70  VSWFGDTRYAWKNGNLKWYY 89

>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 Length = 76

 Score = 50.8 bits (121), Expect = 6e-09
 Identities = 16/76 (21%), Positives = 31/76 (40%)

Query: 58  GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           G    S    +  Q+  L+  F   ++    +   + +   L   ++  WF + RY  K 
Sbjct: 1   GSSGSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH 60

Query: 118 KQLQLLEGSLNTPSAG 133
            QL+    + + PS+G
Sbjct: 61  GQLKWFRDNASGPSSG 76

>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 = 49.4 bits (118), Expect = 2e-08
 Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 5/59 (8%)

Query: 59  RKKRSRAAFSHAQVYELEKRFNAQ-KYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116
               ++          LEK F +  KY        ++K L  +  +++ WF++RR + K
Sbjct: 11  DSPVNKVE----PNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 65

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

 Score = 50.8 bits (120), Expect = 7e-08
 Identities = 20/87 (22%), Positives = 34/87 (39%), Gaps = 21/87 (24%)

Query: 53  SQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAK----------------- 95
           S+P   + +R+R  +  A    L + ++ QK  S  ER  + +                 
Sbjct: 135 SEPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKA 194

Query: 96  ----SLKLTETQVKIWFQNRRYKTKRK 118
               S  +TE +V  WF NRR +   +
Sbjct: 195 HGLGSNLVTEVRVYNWFANRRKEEAFR 221

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

 Score = 48.3 bits (114), Expect = 1e-07
 Identities = 20/85 (23%), Positives = 32/85 (37%), Gaps = 21/85 (24%)

Query: 56  PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAK-------------------- 95
           PT + +R+R  +  A    L + +  QK  S  ER  + +                    
Sbjct: 5   PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGL 64

Query: 96  -SLKLTETQVKIWFQNRRYKTKRKQ 119
            S  +TE +V  WF NRR +   + 
Sbjct: 65  GSNLVTEVRVYNWFANRRKEEAFRH 89

>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 = 42.5 bits (100), Expect = 5e-06
 Identities = 16/60 (26%), Positives = 23/60 (38%), Gaps = 4/60 (6%)

Query: 58  GRKKRSRAAFSHAQVYELEKRFNAQ-KYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116
           G    S  A        LEK F A  K+        ++K L      ++ WF+ RR + K
Sbjct: 1   GSSGSSGTA---QPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 57

>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 42.6 bits (99), Expect = 7e-06
 Identities = 14/68 (20%), Positives = 26/68 (38%), Gaps = 4/68 (5%)

Query: 58  GRKKRSRAAFSHAQVYELEKRF----NAQKYLSGPERADVAKSLKLTETQVKIWFQNRRY 113
               + R  FS   +  L+K +     +   +   +   VA  L +    V+ W  NRR 
Sbjct: 6   SGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRR 65

Query: 114 KTKRKQLQ 121
           K +   ++
Sbjct: 66  KYRLMGIE 73

>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 Length = 87

 Score = 37.1 bits (86), Expect = 6e-04
 Identities = 20/81 (24%), Positives = 28/81 (34%), Gaps = 5/81 (6%)

Query: 40  KPAALSNLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQK---YLSGPERADVAKS 96
           K A       + Q       K      F+   V  LE  F       YL      ++ K+
Sbjct: 7   KSADGLVFNVVTQDMINKSTKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKN 66

Query: 97  LKLTETQVKIWFQN--RRYKT 115
             L+  Q+K W  N  R+ KT
Sbjct: 67  TSLSRIQIKNWVSNRRRKEKT 87

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	274
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.91
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.9
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.9
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.88
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.88
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.84
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.83
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.83
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.83
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.83
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.82
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.82
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.82
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.82
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.82
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.81
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.81
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.81
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.81
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.81
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.81
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.81
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.81
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.81
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.81
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.81
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.8
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.8
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.8
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.8
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.8
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.8
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.8
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.8
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.79
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.79
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.79
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.79
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.78
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.78
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.78
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.78
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.78
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.78
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.77
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.77
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.77
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.77
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.77
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.76
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.75
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.75
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.75
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.75
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.75
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.75
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.74
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.74
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.74
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.73
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.72
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.72
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.71
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.71
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.7
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.7
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.7
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.67
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.67
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.66
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.65
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.58
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.57
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.56
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.48
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.43
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.35
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.67
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	95.4
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	85.24
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	83.83
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	83.68
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	82.68

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

Probab=99.91  E-value=2.7e-26  Score=194.55  Aligned_cols=110  Identities=24%  Similarity=0.296  Sum_probs=77.3

Q ss_pred             HHHHHhCCCCCcccccCcccCCCCcCCCC----------CCCccCCCCCCCCCCCCCCCCCCCCCCcCCHHHHHHHHHHH
Q psy526           10 YYKKINNNNITNNTMSYYGKKDIRDARDL----------PKPAALSNLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRF   79 (274)
Q Consensus        10 ~~~~~~g~~~sqttis~fe~~~ls~~~~~----------~~~~~~~~~~~~~~~~~~~~k~rR~RT~ft~~Ql~~Le~~F   79 (274)
                      ..-.+||++|+|+||||||+++++..++.          .+.................+++||+||.|+..|+.+||..|
T Consensus        39 alg~l~g~~~Sqtti~rFE~l~ls~kn~~klkPlL~~wl~eae~~~~~~~~~~~~~~~~~~rr~Rt~ft~~Ql~~LE~~F  118 (164)
T 2xsd_C           39 ALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPLLNKWLEETDSSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHF  118 (164)
T ss_dssp             HHHHHHSCCCCHHHHHHHHTTCSBHHHHHHHHHHHHHHHHHHCC-----------------------CCHHHHHHHHHHH
T ss_pred             ccccccCCCcCcchhhhhhccCCCHHHHHHcchhHHHHHhhhccccCCCcccccccccccCCCCceeccHHHHHHHHHHH
Confidence            34679999999999999999999976662          11111111111222223456788899999999999999999


Q ss_pred             hhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           80 NAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        80 ~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      ..++||+..+|++||..|||++++|+|||||||+|+||..
T Consensus       119 ~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~  158 (164)
T 2xsd_C          119 LKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMT  158 (164)
T ss_dssp             HHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSC
T ss_pred             hcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhcc
Confidence            9999999999999999999999999999999999999854

>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=99.90  E-value=5.4e-26  Score=190.95  Aligned_cols=108  Identities=22%  Similarity=0.306  Sum_probs=84.8

Q ss_pred             HHHHhCCCCCcccccCcccCCCCcCCCCC----------CCccCCCCCCCCCCCCCCCCCCCCCCcCCHHHHHHHHHHHh
Q psy526           11 YKKINNNNITNNTMSYYGKKDIRDARDLP----------KPAALSNLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFN   80 (274)
Q Consensus        11 ~~~~~g~~~sqttis~fe~~~ls~~~~~~----------~~~~~~~~~~~~~~~~~~~k~rR~RT~ft~~Ql~~Le~~F~   80 (274)
                      -..+||++|||+||||||+++++..++..          +.................+++||+||.|+..|+.+||..|.
T Consensus        37 l~~l~G~~~Sqtti~rfE~l~ls~~nm~kLkPlL~~Wl~eae~~~~~~~~~~~~~~~~~~rr~Rt~ft~~Q~~~Le~~F~  116 (155)
T 3l1p_A           37 LGVLFGKVFSQTTISRFEALQLSLKNMSKLRPLLEKWVEEADNNENLQEISKSETLVQARKRKRTSIENRVRWSLETMFL  116 (155)
T ss_dssp             HHHHHSCCCCHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHHTTCHHHHHSSCC---CCCSCCCCCCCCHHHHHHHHTTTT
T ss_pred             HHhhcCcccccccccccccccCChhhHhhcchHHHHHhhhhhcccCccccccccccccCCCCCCcccCHHHHHHHHHHHc
Confidence            34689999999999999999999877521          11100111111112222257788999999999999999999


Q ss_pred             hCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           81 AQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        81 ~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      .++||+..+|++||.+|||++++|+|||||||+|+||.
T Consensus       117 ~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A          117 KSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             TCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             cCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            99999999999999999999999999999999999984

>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=99.90  E-value=1.6e-25  Score=186.36  Aligned_cols=107  Identities=21%  Similarity=0.328  Sum_probs=81.2

Q ss_pred             HHHHHhCCCCCcccccCcccCCCCcCCCCC----------CCccCCCCCCCCCCCCCCCCCCCCCCcCCHHHHHHHHHHH
Q psy526           10 YYKKINNNNITNNTMSYYGKKDIRDARDLP----------KPAALSNLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRF   79 (274)
Q Consensus        10 ~~~~~~g~~~sqttis~fe~~~ls~~~~~~----------~~~~~~~~~~~~~~~~~~~k~rR~RT~ft~~Ql~~Le~~F   79 (274)
                      ..-.+||++|||+||||||+++++..++..          +......  ......+..+++||+||.|+..|+.+||..|
T Consensus        29 al~~l~g~~~Sqtti~rfe~l~ls~knm~kLkPlL~~wl~e~e~~~~--~~~~~~~~~~~~rr~Rt~ft~~Q~~~Le~~F  106 (146)
T 1au7_A           29 ALAAVHGSEFSQTTICRFENLQLSFKNACKLKAILSKWLEEAEQVGA--LYNEKVGANERKRKRRTTISIAAKDALERHF  106 (146)
T ss_dssp             HHHHTTSSCCCHHHHHHHHTTCSBHHHHHHHHHHHHHHHHHCCC------------------CCCCCCCHHHHHHHHHHH
T ss_pred             hcchhccCCCCcchHHHHhccCCChHHHHhcchHHHHHHHHhhcccC--ccCcccCCCCCCCCCCcCccHHHHHHHHHHH
Confidence            345789999999999999999999776621          1111111  1112223446778899999999999999999


Q ss_pred             hhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           80 NAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        80 ~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      ..++||+..+|++||..|||++++|+|||||||+|+||+
T Consensus       107 ~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A          107 GEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             HHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             HHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            999999999999999999999999999999999999984

>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=99.88  E-value=4.1e-24  Score=180.31  Aligned_cols=109  Identities=19%  Similarity=0.314  Sum_probs=79.8

Q ss_pred             HHHHHhCCCCCcccccCcccCCCCcCCCCC----------CCc------cCCCCCCCCC--CCCCCCCCCCCCCcCCHHH
Q psy526           10 YYKKINNNNITNNTMSYYGKKDIRDARDLP----------KPA------ALSNLPGLAQ--SQPPTGRKKRSRAAFSHAQ   71 (274)
Q Consensus        10 ~~~~~~g~~~sqttis~fe~~~ls~~~~~~----------~~~------~~~~~~~~~~--~~~~~~k~rR~RT~ft~~Q   71 (274)
                      ..-.+||++|+|+|||+||.++++..+++.          +..      .....+....  ......++||+||.|+..|
T Consensus        33 ~lg~l~g~~~sq~ti~rfE~l~lS~knm~klkPlL~~WL~e~e~~~~~~~~~~s~~~~~~~~~~~~~~~rr~Rt~ft~~Q  112 (160)
T 1e3o_C           33 AMGKLYGNDFSQTTISRFEALNLSFKNMSKLKPLLEKWLNDAEANLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNI  112 (160)
T ss_dssp             HHHHHHSCCCCHHHHHHHHHTCSCHHHHHHHHHHHHHHHHHHC----------------------------CCCCCCHHH
T ss_pred             hhccccCCCcCccccccccccCCChHHHHhcchhHHHHHHhhhcccccCCCCCCCCCcCCCCCCCCCCCCcCccccCHHH
Confidence            345689999999999999999998766521          000      0000000000  1112357888999999999


Q ss_pred             HHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           72 VYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        72 l~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      +.+||.+|..++||+..+|++||.+|||++++|+|||||||+|+||+
T Consensus       113 ~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C          113 RVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             HHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             HHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            99999999999999999999999999999999999999999999984

>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=99.88  E-value=1.7e-24  Score=180.96  Aligned_cols=106  Identities=21%  Similarity=0.340  Sum_probs=83.9

Q ss_pred             HHHhCCCCCcccccCcccCCCCcCCCCCCCc----------c--CCCCCCC-CCCCCCCCCCCCCCCcCCHHHHHHHHHH
Q psy526           12 KKINNNNITNNTMSYYGKKDIRDARDLPKPA----------A--LSNLPGL-AQSQPPTGRKKRSRAAFSHAQVYELEKR   78 (274)
Q Consensus        12 ~~~~g~~~sqttis~fe~~~ls~~~~~~~~~----------~--~~~~~~~-~~~~~~~~k~rR~RT~ft~~Ql~~Le~~   78 (274)
                      ..+||++|||+|||+|++++++..++....+          .  ....... .......+++||+||.|+..|+.+||.+
T Consensus        32 ~~l~g~~~Sqsti~rfe~l~ls~kn~~klkPll~~Wl~e~e~~~~~~~~~~~~~~~~~~~~~rr~Rt~ft~~q~~~Le~~  111 (151)
T 3d1n_I           32 TATEGPAYSQSAISRFEKLDITPKSAQKLKPVLEKWLNEAELRNQEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEALNAY  111 (151)
T ss_dssp             SCSSSCCCCHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHHHHHHHHCSTTHHHHHCSSCCCCCCCCCCCCHHHHHHHHHH
T ss_pred             ccccCCCCCccccccccCCCCChhHHHHhchhHHHHHHHHHhccccCcccccccCCCCCCCCCCCCcccCHHHHHHHHHH
Confidence            3578999999999999999998776631100          0  0000000 0011234577889999999999999999


Q ss_pred             HhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           79 FNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        79 F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      |..++||+..+|++||.+|||++++|+|||||||+|+||
T Consensus       112 F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I          112 FEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             HHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             HHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            999999999999999999999999999999999999987

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

Probab=99.84  E-value=6.7e-21  Score=142.76  Aligned_cols=68  Identities=29%  Similarity=0.524  Sum_probs=63.1

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHHHhc
Q psy526           58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQLLEG  125 (274)
Q Consensus        58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~~~~  125 (274)
                      .+.||.||.|+..|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||..+.....
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            46788899999999999999999999999999999999999999999999999999999987766543

>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=99.83  E-value=6.7e-21  Score=142.53  Aligned_cols=64  Identities=28%  Similarity=0.483  Sum_probs=60.5

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHH
Q psy526           58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQ  121 (274)
Q Consensus        58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~  121 (274)
                      .++||.||.|+.+|+.+||.+|..++||+..++++||.+|||++++|+|||||||+|+||+...
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (80)
T 2dmq_A            5 SSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLR   68 (80)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHH
Confidence            4678899999999999999999999999999999999999999999999999999999997654

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

Probab=99.83  E-value=4.3e-21  Score=143.78  Aligned_cols=64  Identities=34%  Similarity=0.569  Sum_probs=60.2

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526           57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL  120 (274)
Q Consensus        57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~  120 (274)
                      ..++||.||.|+.+|+.+||..|..++||+..+|++||..|||++++|+|||||||+|+||...
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~   67 (80)
T 2dms_A            4 GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQ   67 (80)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHH
Confidence            3567889999999999999999999999999999999999999999999999999999999643

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

Probab=99.83  E-value=9.7e-21  Score=141.89  Aligned_cols=63  Identities=51%  Similarity=0.810  Sum_probs=59.8

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           56 PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        56 ~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      ...+.||.||.|+..|+.+||..|..++||+..+|++||..|||++++|+|||||||+|+||.
T Consensus        13 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~   75 (80)
T 2dmt_A           13 KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKS   75 (80)
T ss_dssp             CCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcc
Confidence            456778899999999999999999999999999999999999999999999999999999984

>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=99.83  E-value=1.8e-20  Score=139.44  Aligned_cols=67  Identities=55%  Similarity=0.893  Sum_probs=62.0

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526           56 PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL  122 (274)
Q Consensus        56 ~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~  122 (274)
                      ...++||.||.|+..|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||.....
T Consensus         5 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~~   71 (77)
T 1nk2_P            5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEK   71 (77)
T ss_dssp             CSCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhccc
Confidence            3456788899999999999999999999999999999999999999999999999999999976543

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

Probab=99.82  E-value=1.3e-20  Score=134.97  Aligned_cols=60  Identities=52%  Similarity=0.836  Sum_probs=56.0

Q ss_pred             CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        59 k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      +.||.||.|+..|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||.
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            468899999999999999999999999999999999999999999999999999999985

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

Probab=99.82  E-value=4.2e-21  Score=136.99  Aligned_cols=61  Identities=46%  Similarity=0.702  Sum_probs=53.1

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      +++||.||.|+..|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||.
T Consensus         1 g~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A            1 GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             -------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            3578899999999999999999999999999999999999999999999999999999984

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

Probab=99.82  E-value=2e-20  Score=141.22  Aligned_cols=65  Identities=42%  Similarity=0.626  Sum_probs=60.8

Q ss_pred             CCCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           55 PPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        55 ~~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      ....++||.||.|+..|+.+||.+|..++||+..+|++||..|||++++|+|||||||+|+||.+
T Consensus        17 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   81 (84)
T 2kt0_A           17 KVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQ   81 (84)
T ss_dssp             CCCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHh
Confidence            34567888999999999999999999999999999999999999999999999999999999853

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

Probab=99.82  E-value=1.7e-20  Score=136.43  Aligned_cols=63  Identities=41%  Similarity=0.695  Sum_probs=59.8

Q ss_pred             CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526           60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL  122 (274)
Q Consensus        60 ~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~  122 (274)
                      +||.||.|+..|+.+||..|..++||+..++++||..|||++++|+|||||||+|+|+...+.
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            578999999999999999999999999999999999999999999999999999999976553

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

Probab=99.82  E-value=1.8e-20  Score=139.95  Aligned_cols=63  Identities=22%  Similarity=0.383  Sum_probs=59.8

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           56 PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        56 ~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      ...++||.||.|+.+|+.+||.+|..++||+..++++||.+|||++++|+|||||||+|+||.
T Consensus        13 ~~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   75 (80)
T 2da3_A           13 EPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKS   75 (80)
T ss_dssp             CCCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhh
Confidence            346778899999999999999999999999999999999999999999999999999999985

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

Probab=99.81  E-value=2.4e-20  Score=136.19  Aligned_cols=61  Identities=34%  Similarity=0.613  Sum_probs=58.5

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      .+.||.||.|+.+|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||.
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~   65 (70)
T 2dmu_A            5 SSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRS   65 (70)
T ss_dssp             TSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehcccccccccccc
Confidence            4578889999999999999999999999999999999999999999999999999999985

>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=99.81  E-value=1.4e-20  Score=137.57  Aligned_cols=62  Identities=34%  Similarity=0.673  Sum_probs=58.9

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      ..+.||+||.|+..|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||.
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            35678899999999999999999999999999999999999999999999999999999984

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

Probab=99.81  E-value=1.4e-20  Score=141.32  Aligned_cols=61  Identities=15%  Similarity=0.224  Sum_probs=58.1

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhh----CCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           57 TGRKKRSRAAFSHAQVYELEKRFNA----QKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        57 ~~k~rR~RT~ft~~Ql~~Le~~F~~----~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      .+++||+||.|+.+|+.+||..|+.    ++||+..+|++||..|||++++|+|||||||+|+|+
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           14 GGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            4578889999999999999999999    999999999999999999999999999999999875

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

Probab=99.81  E-value=1.6e-20  Score=133.61  Aligned_cols=59  Identities=42%  Similarity=0.769  Sum_probs=53.4

Q ss_pred             CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        59 k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      ++||.||.|+..|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            2 AEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             -----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            35788999999999999999999999999999999999999999999999999999997

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

Probab=99.81  E-value=6.2e-20  Score=136.54  Aligned_cols=66  Identities=42%  Similarity=0.645  Sum_probs=61.6

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526           57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL  122 (274)
Q Consensus        57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~  122 (274)
                      .++.||+||.|+..|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||..+..
T Consensus        10 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k~~   75 (77)
T 1puf_A           10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDR   75 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhhhc
Confidence            356788999999999999999999999999999999999999999999999999999999987653

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

Probab=99.81  E-value=2.9e-20  Score=135.64  Aligned_cols=62  Identities=23%  Similarity=0.395  Sum_probs=59.1

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      ..++||.||.|+.+|+.+||.+|..++||+..++++||..|||++++|+|||||||+|+||.
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            35678899999999999999999999999999999999999999999999999999999985

>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=99.81  E-value=1.2e-20  Score=137.06  Aligned_cols=63  Identities=33%  Similarity=0.646  Sum_probs=59.8

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526           58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL  120 (274)
Q Consensus        58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~  120 (274)
                      +++||.||.|+..|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||...
T Consensus         1 g~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~   63 (68)
T 1yz8_P            1 GSQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREE   63 (68)
T ss_dssp             CCSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhh
Confidence            467899999999999999999999999999999999999999999999999999999998653

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

Probab=99.81  E-value=3.4e-20  Score=142.94  Aligned_cols=66  Identities=50%  Similarity=0.817  Sum_probs=61.4

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHH
Q psy526           56 PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQ  121 (274)
Q Consensus        56 ~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~  121 (274)
                      ...++||+||.|+..|+.+||..|..++||+..+|++||..|||++++|+|||||||+|+||....
T Consensus        13 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~   78 (93)
T 3a01_A           13 TPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAE   78 (93)
T ss_dssp             CCCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHH
Confidence            345678899999999999999999999999999999999999999999999999999999997644

>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=99.81  E-value=2.7e-20  Score=135.84  Aligned_cols=62  Identities=27%  Similarity=0.478  Sum_probs=59.0

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      .+++||.||.|+..|+.+||..|..++||+..++++||..|||++.+|+|||||||+|+||.
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            35678899999999999999999999999999999999999999999999999999999984

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

Probab=99.81  E-value=3.9e-20  Score=130.12  Aligned_cols=57  Identities=56%  Similarity=0.894  Sum_probs=55.6

Q ss_pred             CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        61 rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      ||+||.|+..|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||
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            578999999999999999999999999999999999999999999999999999997

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

Probab=99.81  E-value=6e-20  Score=134.14  Aligned_cols=62  Identities=53%  Similarity=0.775  Sum_probs=58.5

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      .+.||+|+.|+.+|+.+||.+|..++||+..++++||..|||++++|+|||||||+|+||..
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            45677899999999999999999999999999999999999999999999999999999863

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

Probab=99.80  E-value=4.9e-20  Score=138.27  Aligned_cols=64  Identities=34%  Similarity=0.655  Sum_probs=59.7

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526           57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL  120 (274)
Q Consensus        57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~  120 (274)
                      .+++||.||.|+..|+.+||.+|..++||+..++++||..|||++++|+|||||||+|+||+..
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            4677889999999999999999999999999999999999999999999999999999999764

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

Probab=99.80  E-value=3e-20  Score=139.15  Aligned_cols=62  Identities=23%  Similarity=0.330  Sum_probs=59.2

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhhC----CCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           57 TGRKKRSRAAFSHAQVYELEKRFNAQ----KYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~----~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      ..++||.||.|+.+|+.+||.+|..+    +||+..+|++||.+|||++++|+|||||||+|+||.
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            45778899999999999999999999    999999999999999999999999999999999984

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

Probab=99.80  E-value=2.7e-20  Score=139.82  Aligned_cols=61  Identities=18%  Similarity=0.278  Sum_probs=57.4

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhh-----CCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           56 PTGRKKRSRAAFSHAQVYELEKRFNA-----QKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        56 ~~~k~rR~RT~ft~~Ql~~Le~~F~~-----~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      ...++||.||.|+.+|+.+|| .|..     ++||+..+|++||.+|||++++|+|||||||+|+|+
T Consensus        13 ~~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           13 SGGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            456788999999999999999 7999     999999999999999999999999999999999875

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

Probab=99.80  E-value=2.7e-20  Score=135.98  Aligned_cols=62  Identities=47%  Similarity=0.761  Sum_probs=58.8

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      ..+.||.||.|+..|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||.
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            35678899999999999999999999999999999999999999999999999999999984

>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=99.80  E-value=4.6e-20  Score=134.15  Aligned_cols=60  Identities=47%  Similarity=0.805  Sum_probs=57.8

Q ss_pred             CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        60 ~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      +||.||.|+..|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||..
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   61 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN   61 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhc
Confidence            578899999999999999999999999999999999999999999999999999999964

>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=99.80  E-value=3.6e-20  Score=133.75  Aligned_cols=60  Identities=22%  Similarity=0.450  Sum_probs=57.8

Q ss_pred             CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        59 k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      ++||.||.|+.+|+.+||..|..++||+..++++||..|||++.+|+|||||||+|+||.
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            568899999999999999999999999999999999999999999999999999999874

>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=99.80  E-value=4.4e-20  Score=138.72  Aligned_cols=63  Identities=44%  Similarity=0.784  Sum_probs=54.6

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      .+++||.||.|+..|+.+||..|..++||+..+|++||..|||++++|+|||||||+|+||..
T Consensus        17 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   79 (81)
T 1b8i_A           17 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEI   79 (81)
T ss_dssp             -------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhc
Confidence            456788999999999999999999999999999999999999999999999999999999853

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

Probab=99.80  E-value=6.9e-20  Score=134.99  Aligned_cols=61  Identities=33%  Similarity=0.648  Sum_probs=58.5

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      .+.||+||.|+..|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||.
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   65 (73)
T 2l7z_A            5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKV   65 (73)
T ss_dssp             SCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHH
Confidence            4678889999999999999999999999999999999999999999999999999999985

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

Probab=99.79  E-value=6.4e-20  Score=130.01  Aligned_cols=58  Identities=47%  Similarity=0.835  Sum_probs=55.6

Q ss_pred             CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        61 rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      ||.||.|+..|+.+||..|..++||+..++++||..|||++.+|+|||||||+|+||+
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            6789999999999999999999999999999999999999999999999999999984

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

Probab=99.79  E-value=1e-19  Score=132.19  Aligned_cols=60  Identities=62%  Similarity=1.009  Sum_probs=57.8

Q ss_pred             CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        60 ~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      +||.||.|+..|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||..
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~   61 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA   61 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhh
Confidence            678899999999999999999999999999999999999999999999999999999864

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

Probab=99.79  E-value=1.2e-19  Score=133.81  Aligned_cols=63  Identities=40%  Similarity=0.656  Sum_probs=59.8

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           56 PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        56 ~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      ..+++||.||.|+..|+.+||..|..++||+..++++||..|||++.+|+|||||||+|+||.
T Consensus         5 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   67 (75)
T 2m0c_A            5 NKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKR   67 (75)
T ss_dssp             CCSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHH
Confidence            356778899999999999999999999999999999999999999999999999999999985

>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=99.79  E-value=8.1e-20  Score=129.72  Aligned_cols=59  Identities=29%  Similarity=0.514  Sum_probs=48.6

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHH
Q psy526           58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK  116 (274)
Q Consensus        58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~K  116 (274)
                      .++||.||.|+..|+.+||.+|..++||+..++++||..|||++.+|+|||||||+|+|
T Consensus         3 ~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            3 EKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             ---------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            56788999999999999999999999999999999999999999999999999999975

>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=99.78  E-value=9.3e-20  Score=135.40  Aligned_cols=59  Identities=20%  Similarity=0.309  Sum_probs=54.9

Q ss_pred             CCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHH
Q psy526           63 SRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQ  121 (274)
Q Consensus        63 ~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~  121 (274)
                      +|+.||.+|+.+||++|..++||+..+|++||..|||++++|+|||||||+|+|+....
T Consensus         6 ~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~l~   64 (76)
T 2ecc_A            6 SGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLK   64 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCCS
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHHHH
Confidence            45679999999999999999999999999999999999999999999999999986433

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

Probab=99.78  E-value=1.4e-19  Score=126.80  Aligned_cols=57  Identities=67%  Similarity=1.094  Sum_probs=54.9

Q ss_pred             CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHH
Q psy526           60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK  116 (274)
Q Consensus        60 ~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~K  116 (274)
                      +||.||.|+..|+.+||..|..++||+..++++||..|||++.+|+|||||||+|+|
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            567899999999999999999999999999999999999999999999999999975

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

Probab=99.78  E-value=1.9e-19  Score=139.09  Aligned_cols=65  Identities=26%  Similarity=0.432  Sum_probs=61.2

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhC---------------CCcccchhhhhhhhhHHHHHHHH
Q psy526           57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLK---------------LTETQVKIWFQNRRYKTKRKQLQ  121 (274)
Q Consensus        57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~---------------L~~~~V~vWFqNrR~k~Kr~~~~  121 (274)
                      ..++||.||.|+..|+.+||.+|..++||+..+|++||..||               |++.+|+|||||||+|+||+..+
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               99999999999999999997654

>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=99.78  E-value=5.8e-19  Score=137.92  Aligned_cols=67  Identities=28%  Similarity=0.371  Sum_probs=62.3

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHh---------------------CCCcccchhhhhhhhhHH
Q psy526           57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSL---------------------KLTETQVKIWFQNRRYKT  115 (274)
Q Consensus        57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l---------------------~L~~~~V~vWFqNrR~k~  115 (274)
                      .+++||.||.|+..|+.+||+.|..++||+..+|++||..|                     .|++.+|+|||||||+|+
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            45788999999999999999999999999999999999999                     799999999999999999


Q ss_pred             HHHHHHHH
Q psy526          116 KRKQLQLL  123 (274)
Q Consensus       116 Kr~~~~~~  123 (274)
                      |++.....
T Consensus        83 kr~~~~~~   90 (102)
T 2da6_A           83 AFRQKLAM   90 (102)
T ss_dssp             HHHHHHHH
T ss_pred             HHhhHhhh
Confidence            99876653

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

Probab=99.78  E-value=2.6e-19  Score=136.45  Aligned_cols=62  Identities=47%  Similarity=0.807  Sum_probs=55.0

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      .++.||.||.|+..|+.+||..|..++||+..+|++||..|||++++|+|||||||+|+||.
T Consensus        25 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~   86 (88)
T 2r5y_A           25 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   86 (88)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhh
Confidence            45678899999999999999999999999999999999999999999999999999999985

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

Probab=99.78  E-value=2.2e-19  Score=129.92  Aligned_cols=60  Identities=38%  Similarity=0.584  Sum_probs=57.2

Q ss_pred             CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        60 ~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      .||+||.|+..|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||..
T Consensus         1 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~   60 (67)
T 2k40_A            1 GRRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSH   60 (67)
T ss_dssp             CCCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSC
T ss_pred             CcCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhc
Confidence            368899999999999999999999999999999999999999999999999999999853

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

Probab=99.77  E-value=2.1e-19  Score=139.33  Aligned_cols=63  Identities=49%  Similarity=0.781  Sum_probs=56.2

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526           58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL  120 (274)
Q Consensus        58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~  120 (274)
                      ++.||+||.|+..|+.+||..|..++||+..+|++||..|||++++|+|||||||+|+||..+
T Consensus        32 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   94 (97)
T 1b72_A           32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   94 (97)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhc
Confidence            567889999999999999999999999999999999999999999999999999999998753

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

Probab=99.77  E-value=3.9e-19  Score=130.91  Aligned_cols=59  Identities=27%  Similarity=0.313  Sum_probs=56.4

Q ss_pred             CCCCCcCCHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           61 KRSRAAFSHAQVYELEKRFNA-QKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        61 rR~RT~ft~~Ql~~Le~~F~~-~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      +++||.|+..|+.+||..|.. ++||+..++++||..|||++++|+|||||||+|+||..
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~   62 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   62 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhc
Confidence            567999999999999999995 99999999999999999999999999999999999965

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

Probab=99.77  E-value=4e-19  Score=130.42  Aligned_cols=59  Identities=29%  Similarity=0.350  Sum_probs=56.2

Q ss_pred             CCCCCcCCHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           61 KRSRAAFSHAQVYELEKRFNA-QKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        61 rR~RT~ft~~Ql~~Le~~F~~-~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      .++||.|+..|+.+||..|.. ++||+..+|++||..|||++++|+|||||||+|+||..
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 99999999999999999999999999999999999965

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

Probab=99.77  E-value=2e-19  Score=127.39  Aligned_cols=57  Identities=37%  Similarity=0.621  Sum_probs=50.7

Q ss_pred             CCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           63 SRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        63 ~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      .||.|+..|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||..
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            489999999999999999999999999999999999999999999999999999864

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

Probab=99.77  E-value=4.5e-19  Score=124.04  Aligned_cols=54  Identities=57%  Similarity=0.906  Sum_probs=51.1

Q ss_pred             CcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           65 AAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        65 T~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      |.|+..|+.+||..|..++||+..+|++||..+||++++|+|||||||+|+||+
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            689999999999999999999999999999999999999999999999999985

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

Probab=99.76  E-value=1.1e-18  Score=128.27  Aligned_cols=63  Identities=21%  Similarity=0.299  Sum_probs=58.6

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           57 TGRKKRSRAAFSHAQVYELEKRFNA---QKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        57 ~~k~rR~RT~ft~~Ql~~Le~~F~~---~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      .++.||+|+.|+..|+.+||.+|..   ++||+..++++||.++||++++|+|||||||+|+|+..
T Consensus         4 ~~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~   69 (73)
T 1x2n_A            4 GSSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSG   69 (73)
T ss_dssp             CSSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhccccc
Confidence            3467888999999999999999987   99999999999999999999999999999999999853

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

Probab=99.75  E-value=6.2e-19  Score=136.52  Aligned_cols=64  Identities=23%  Similarity=0.325  Sum_probs=56.4

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           56 PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        56 ~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      ...+.+|+||.|+..|+.+||..|..++||+..+|++||.+|||++++|+|||||||+|+||.+
T Consensus        21 ~~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   84 (96)
T 3nar_A           21 PKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGN   84 (96)
T ss_dssp             ------CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTC
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhc
Confidence            3456678899999999999999999999999999999999999999999999999999999864

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

Probab=99.75  E-value=9.2e-19  Score=126.40  Aligned_cols=60  Identities=23%  Similarity=0.302  Sum_probs=56.1

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHH
Q psy526           57 TGRKKRSRAAFSHAQVYELEKRFNA-QKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK  116 (274)
Q Consensus        57 ~~k~rR~RT~ft~~Ql~~Le~~F~~-~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~K  116 (274)
                      ..++||.||.|+.+||.+|+.+|+. ++||+...|+.||.+|||++++|+|||||||.-.|
T Consensus         4 ~~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~~~   64 (71)
T 1wi3_A            4 GSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVK   64 (71)
T ss_dssp             CCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceeeec
Confidence            3578899999999999999999999 99999999999999999999999999999997543

>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=99.75  E-value=1.3e-18  Score=131.30  Aligned_cols=62  Identities=19%  Similarity=0.292  Sum_probs=57.9

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           58 GRKKRSRAAFSHAQVYELEKRFNA---QKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        58 ~k~rR~RT~ft~~Ql~~Le~~F~~---~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      .++||+|+.|+.+|+.+|+.+|..   ++||+..+|++||.++||+++||+|||||||+|+|+..
T Consensus         5 ~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~   69 (83)
T 2dmn_A            5 SSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDM   69 (83)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHH
Confidence            467788999999999999999987   69999999999999999999999999999999998864

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

Probab=99.75  E-value=1e-18  Score=128.79  Aligned_cols=61  Identities=23%  Similarity=0.380  Sum_probs=57.6

Q ss_pred             CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        59 k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      ..++.||.|+.+|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||.+
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            3467899999999999999999999999999999999999999999999999999999853

>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=99.75  E-value=5e-19  Score=134.35  Aligned_cols=62  Identities=27%  Similarity=0.439  Sum_probs=57.1

Q ss_pred             CCCCCCcCCHHHHHHHHHHH---hhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHH
Q psy526           60 KKRSRAAFSHAQVYELEKRF---NAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQ  121 (274)
Q Consensus        60 ~rR~RT~ft~~Ql~~Le~~F---~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~  121 (274)
                      .||+|+.|+..|+.+||.+|   ..++||+..++++||.+|||++.+|+|||||||+|+||....
T Consensus         1 ~rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~   65 (87)
T 1b72_B            1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGK   65 (87)
T ss_dssp             --CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGG
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhcccc
Confidence            36889999999999999999   899999999999999999999999999999999999986543

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

Probab=99.75  E-value=1.1e-18  Score=129.34  Aligned_cols=59  Identities=24%  Similarity=0.425  Sum_probs=56.0

Q ss_pred             CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        60 ~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      ..+.||.|+.+|+.+||..|..++||+..+|++||.+|||++++|+|||||||+|+||.
T Consensus         8 ~~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~   66 (76)
T 2dn0_A            8 ASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNL   66 (76)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSC
T ss_pred             CCCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHh
Confidence            34568999999999999999999999999999999999999999999999999999985

>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=99.74  E-value=1.8e-18  Score=127.16  Aligned_cols=60  Identities=28%  Similarity=0.470  Sum_probs=57.0

Q ss_pred             CCCCCCcCCHHHHHHHHHHH---hhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           60 KKRSRAAFSHAQVYELEKRF---NAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        60 ~rR~RT~ft~~Ql~~Le~~F---~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      .||+|+.|+..|+.+||.+|   ..++||+..++++||..+||++.+|+|||||||+|+|+..
T Consensus         1 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~   63 (73)
T 1puf_B            1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccccc
Confidence            36889999999999999999   8999999999999999999999999999999999999854

>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=99.74  E-value=2.9e-18  Score=126.98  Aligned_cols=58  Identities=21%  Similarity=0.321  Sum_probs=54.5

Q ss_pred             CCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           62 RSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        62 R~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      ++|+.||.+|+.+||..|..++||+..+|++||..|||++++|+|||||||+|+||..
T Consensus         9 ~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~   66 (75)
T 2da5_A            9 TKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEE   66 (75)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSS
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhh
Confidence            3466799999999999999999999999999999999999999999999999999854

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

Probab=99.74  E-value=7.6e-19  Score=125.92  Aligned_cols=59  Identities=24%  Similarity=0.362  Sum_probs=56.1

Q ss_pred             CCCCCCCcCCHHHHHHHHHHH---hhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           59 RKKRSRAAFSHAQVYELEKRF---NAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        59 k~rR~RT~ft~~Ql~~Le~~F---~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      ..+|+|+.|+..|+.+||.+|   ..++||+..++++||..+||++.+|+|||||||+|+||
T Consensus         2 ~~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A            2 SGHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             CCCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            357889999999999999999   89999999999999999999999999999999999886

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

Probab=99.73  E-value=4.2e-18  Score=120.48  Aligned_cols=55  Identities=31%  Similarity=0.461  Sum_probs=53.3

Q ss_pred             CCCcCCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           63 SRAAFSHAQVYELEKRFNA---QKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        63 ~RT~ft~~Ql~~Le~~F~~---~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      +|+.|+.+|+.+||.+|..   ++||+..++++||.++||++.+|++||+|||+|+||
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            4789999999999999999   999999999999999999999999999999999987

>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=99.72  E-value=4.9e-18  Score=129.03  Aligned_cols=60  Identities=30%  Similarity=0.428  Sum_probs=56.3

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           58 GRKKRSRAAFSHAQVYELEKRFNA---QKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        58 ~k~rR~RT~ft~~Ql~~Le~~F~~---~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      .+++|+|+.|+.+|+.+||.+|..   ++||+..++++||..+||++++|+|||||||+|+|.
T Consensus        25 ~~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k~   87 (87)
T 1mnm_C           25 STKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   87 (87)
T ss_dssp             ESSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccC
Confidence            456677999999999999999999   999999999999999999999999999999999873

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

Probab=99.72  E-value=2.9e-18  Score=131.20  Aligned_cols=54  Identities=20%  Similarity=0.335  Sum_probs=52.1

Q ss_pred             cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      .||.+||.+||+.|..++||+..+|++||..|||++++|+|||||||+||||+.
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~   70 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE   70 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCC
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHH
Confidence            689999999999999999999999999999999999999999999999999854

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

Probab=99.71  E-value=2e-18  Score=134.67  Aligned_cols=65  Identities=31%  Similarity=0.429  Sum_probs=54.0

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHH------------------hC---CCcccchhhhhhhhhH
Q psy526           56 PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKS------------------LK---LTETQVKIWFQNRRYK  114 (274)
Q Consensus        56 ~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~------------------l~---L~~~~V~vWFqNrR~k  114 (274)
                      ..+++||.||.|+..|+.+||..|..++||+..+|++||..                  ||   |++.+|+|||||||+|
T Consensus         5 ~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k   84 (99)
T 1lfb_A            5 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE   84 (99)
T ss_dssp             --------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHH
Confidence            34678889999999999999999999999999999999999                  88   9999999999999999


Q ss_pred             HHHHHH
Q psy526          115 TKRKQL  120 (274)
Q Consensus       115 ~Kr~~~  120 (274)
                      +|++..
T Consensus        85 ~k~k~~   90 (99)
T 1lfb_A           85 EAFRHK   90 (99)
T ss_dssp             TSCCC-
T ss_pred             HHHhch
Confidence            887643

>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=99.71  E-value=1.1e-17  Score=127.77  Aligned_cols=53  Identities=23%  Similarity=0.354  Sum_probs=51.4

Q ss_pred             CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      ||.+|+.+||..|..++||+..+|++||.+|||++++|+|||||||+|+|+..
T Consensus        20 ~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~   72 (89)
T 2dmp_A           20 KTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSME   72 (89)
T ss_dssp             CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSC
T ss_pred             CCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHh
Confidence            89999999999999999999999999999999999999999999999998854

>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=99.70  E-value=9.8e-18  Score=126.42  Aligned_cols=58  Identities=28%  Similarity=0.383  Sum_probs=53.7

Q ss_pred             CCCCCcCCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           61 KRSRAAFSHAQVYELEKRFNA---QKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        61 rR~RT~ft~~Ql~~Le~~F~~---~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      +++|+.|+..|+.+||.+|..   ++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus         3 ~krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~   63 (83)
T 1le8_B            3 PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTI   63 (83)
T ss_dssp             --CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHcccccc
Confidence            445677999999999999999   9999999999999999999999999999999999985

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

Probab=99.70  E-value=1.3e-17  Score=120.25  Aligned_cols=52  Identities=21%  Similarity=0.464  Sum_probs=50.1

Q ss_pred             CHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           68 SHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        68 t~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      +.+|+.+||..|..++||+..+|++||..|||++++|++||||||+|+|+..
T Consensus        12 ~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg~   63 (66)
T 3nau_A           12 TKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGI   63 (66)
T ss_dssp             CHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhccC
Confidence            6899999999999999999999999999999999999999999999999753

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

Probab=99.70  E-value=3.2e-18  Score=125.99  Aligned_cols=58  Identities=22%  Similarity=0.368  Sum_probs=53.0

Q ss_pred             CCCCCcCCHHHHHHHHHHH-hhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           61 KRSRAAFSHAQVYELEKRF-NAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        61 rR~RT~ft~~Ql~~Le~~F-~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      .+.|+.++.+|+.+||..| ..++||+..+|++||.+|||++++|+|||||||+|+|+.
T Consensus         9 ~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~   67 (72)
T 2cqx_A            9 IKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPS   67 (72)
T ss_dssp             CCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCC
Confidence            3445667788999999999 999999999999999999999999999999999999973

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

Probab=99.67  E-value=2.3e-17  Score=118.66  Aligned_cols=54  Identities=19%  Similarity=0.188  Sum_probs=50.6

Q ss_pred             CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           64 RAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        64 RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      +..++..|+.+||..|..++||+..+|++||.+|||++++|+|||||||+|.++
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            445679999999999999999999999999999999999999999999999776

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

Probab=99.67  E-value=3.1e-17  Score=119.80  Aligned_cols=55  Identities=76%  Similarity=1.118  Sum_probs=52.0

Q ss_pred             CcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           65 AAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        65 T~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      ..++..|+.+||..|..++||+..+|++||.+|||++++|+|||||||+|+||.+
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            3578999999999999999999999999999999999999999999999999853

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

Probab=99.66  E-value=3.9e-17  Score=137.78  Aligned_cols=63  Identities=24%  Similarity=0.287  Sum_probs=55.0

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      ..++||+||.|+..|+.+||..|..++||+..+|++||.+|||++++|+|||||||+|+|+..
T Consensus        94 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~  156 (164)
T 2d5v_A           94 GNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKW  156 (164)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC-
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccC
Confidence            356788999999999999999999999999999999999999999999999999999999854

>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=99.65  E-value=4.1e-17  Score=117.33  Aligned_cols=48  Identities=25%  Similarity=0.340  Sum_probs=45.6

Q ss_pred             HHHHHHHHHH-hhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           70 AQVYELEKRF-NAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        70 ~Ql~~Le~~F-~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      .|+.+||+.| ..++||+..+|++||.+|||+++||+|||||||+|+|+
T Consensus        10 ~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~   58 (64)
T 1x2m_A           10 QPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   58 (64)
T ss_dssp             CHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             hHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCC
Confidence            4799999999 57999999999999999999999999999999999986

>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding, transcription, nucleus, phosphoprotein, DNA bindi protein; 1.95A {Homo sapiens} SCOP: a.4.1.1

Probab=99.58  E-value=1.4e-15  Score=110.20  Aligned_cols=56  Identities=21%  Similarity=0.329  Sum_probs=50.4

Q ss_pred             CcCCHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526           65 AAFSHAQVYELEKRFN---AQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL  120 (274)
Q Consensus        65 T~ft~~Ql~~Le~~F~---~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~  120 (274)
                      ..|+.+|+.+|+.+|.   .++||+..++++||..+||++++|++||||||+|+||...
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            3699999999999999   9999999999999999999999999999999999998543

>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=99.57  E-value=1.8e-15  Score=109.80  Aligned_cols=46  Identities=17%  Similarity=0.296  Sum_probs=43.9

Q ss_pred             HHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhH
Q psy526           69 HAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYK  114 (274)
Q Consensus        69 ~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k  114 (274)
                      .+|+.+||++|..+++|+.+++..||..+||++++|||||||||++
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~   59 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVY   59 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhcccc
Confidence            4689999999999999999999999999999999999999999974

>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=99.56  E-value=5.7e-16  Score=134.25  Aligned_cols=62  Identities=31%  Similarity=0.421  Sum_probs=53.9

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhC---------------------CCcccchhhhhhhhhH
Q psy526           56 PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLK---------------------LTETQVKIWFQNRRYK  114 (274)
Q Consensus        56 ~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~---------------------L~~~~V~vWFqNrR~k  114 (274)
                      ..+++||.||.|+..|+.+||+.|..++||+..+|++||..|+                     |++.+|+|||||||+|
T Consensus       111 ~~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~  190 (194)
T 1ic8_A          111 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE  190 (194)
T ss_dssp             ------CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHH
T ss_pred             ccccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhh
Confidence            4467889999999999999999999999999999999999999                     9999999999999999


Q ss_pred             HHH
Q psy526          115 TKR  117 (274)
Q Consensus       115 ~Kr  117 (274)
                      +|.
T Consensus       191 ~k~  193 (194)
T 1ic8_A          191 EAF  193 (194)
T ss_dssp             CC-
T ss_pred             hhc
Confidence            764

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

Probab=99.48  E-value=1.8e-14  Score=126.51  Aligned_cols=61  Identities=30%  Similarity=0.447  Sum_probs=53.6

Q ss_pred             CCCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhC---------------------CCcccchhhhhhhhh
Q psy526           55 PPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLK---------------------LTETQVKIWFQNRRY  113 (274)
Q Consensus        55 ~~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~---------------------L~~~~V~vWFqNrR~  113 (274)
                      ...+++||.||.|+..|+.+||++|..++||+..+|++||..+|                     |++.+|+|||+|||+
T Consensus       137 ~~~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~  216 (221)
T 2h8r_A          137 PTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRK  216 (221)
T ss_dssp             -----CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHT
T ss_pred             cccCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhh
Confidence            44577899999999999999999999999999999999999998                     899999999999998


Q ss_pred             HH
Q psy526          114 KT  115 (274)
Q Consensus       114 k~  115 (274)
                      +.
T Consensus       217 ~~  218 (221)
T 2h8r_A          217 EE  218 (221)
T ss_dssp             TC
T ss_pred             hh
Confidence            63

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

Probab=99.43  E-value=1.5e-13  Score=104.78  Aligned_cols=58  Identities=24%  Similarity=0.298  Sum_probs=53.5

Q ss_pred             CcCCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526           65 AAFSHAQVYELEKRFNA---QKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL  122 (274)
Q Consensus        65 T~ft~~Ql~~Le~~F~~---~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~  122 (274)
                      -.|+.+++.+|+.+|..   ++||+..++++||.++||++.||++||+|+|.|+|+.....
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   99999999999999999999999999999999998875543

>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=99.35  E-value=1.6e-13  Score=128.60  Aligned_cols=57  Identities=33%  Similarity=0.516  Sum_probs=53.9

Q ss_pred             CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHH
Q psy526           60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK  116 (274)
Q Consensus        60 ~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~K  116 (274)
                      .++.|+.|+..|+..||+.|+.++||+..+|++||.++||+++||+|||||||+|+|
T Consensus       365 ~~~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          365 QTAAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            356688999999999999999999999999999999999999999999999999875

>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=98.67  E-value=4e-09  Score=67.33  Aligned_cols=23  Identities=48%  Similarity=0.788  Sum_probs=19.7

Q ss_pred             ccchhhhhhhhhHHHHHHHHHHh
Q psy526          102 TQVKIWFQNRRYKTKRKQLQLLE  124 (274)
Q Consensus       102 ~~V~vWFqNrR~k~Kr~~~~~~~  124 (274)
                      +||+|||||||+||||.......
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~~~   23 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFNDAR   23 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHHTT
T ss_pred             CCceeccHHHHHHHHHHhHHHHH
Confidence            58999999999999998876533

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

Probab=95.40  E-value=0.014  Score=41.90  Aligned_cols=39  Identities=23%  Similarity=0.474  Sum_probs=36.8

Q ss_pred             HHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhh
Q psy526           72 VYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQN  110 (274)
Q Consensus        72 l~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqN  110 (274)
                      .+.|+.+|...+.+.......|+.+..|+..+|+-||-.
T Consensus        18 ~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~   56 (70)
T 2ys9_A           18 IQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDS   56 (70)
T ss_dssp             CHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             chHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHh
Confidence            368999999999999999999999999999999999954

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

Probab=85.24  E-value=1.3  Score=32.12  Aligned_cols=46  Identities=17%  Similarity=0.347  Sum_probs=33.0

Q ss_pred             CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhh
Q psy526           59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQ  109 (274)
Q Consensus        59 k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFq  109 (274)
                      ++|+.+..|+.++....-..+.. ..    -..+||..+|++...|..|.+
T Consensus        15 ~~~~~~~~ys~e~k~~~v~~~~~-g~----s~~~iA~~~gIs~sTl~rW~k   60 (87)
T 2elh_A           15 KGKRPLRSLTPRDKIHAIQRIHD-GE----SKASVARDIGVPESTLRGWCK   60 (87)
T ss_dssp             CCSSCCSSCCHHHHHHHHHHHHH-TC----CHHHHHHHHTCCHHHHHHHHH
T ss_pred             cCCCCCCCCCHHHHHHHHHHHHC-CC----CHHHHHHHHCcCHHHHHHHHH
Confidence            34456678898886555555542 22    356889999999999999974

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

Probab=83.83  E-value=1.5  Score=29.28  Aligned_cols=46  Identities=13%  Similarity=0.273  Sum_probs=32.2

Q ss_pred             CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhh
Q psy526           64 RAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQN  110 (274)
Q Consensus        64 RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqN  110 (274)
                      |..|+.+....+...+.. .........+||.++|++...|..|.+.
T Consensus         3 r~~ys~efK~~~~~~~~~-g~s~~~~~~~vA~~~gIs~~tl~~W~~~   48 (59)
T 2glo_A            3 RRIFTPHFKLQVLESYRN-DNDCKGNQRATARKYNIHRRQIQKWLQC   48 (59)
T ss_dssp             CCCCCHHHHHHHHHHHHH-CTTTTTCHHHHHHHTTSCHHHHHHHHTT
T ss_pred             CCcCCHHHHHHHHHHHHc-CCCcchHHHHHHHHHCcCHHHHHHHHHH
Confidence            446888887777554443 3322223678999999999999999753

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

Probab=83.68  E-value=2.1  Score=31.03  Aligned_cols=50  Identities=14%  Similarity=0.115  Sum_probs=38.2

Q ss_pred             cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526           66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL  120 (274)
Q Consensus        66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~  120 (274)
                      .++..++.+|.-.|...     ....+||..+|++...|+.+...-|.|.|+...
T Consensus        37 ~L~~~~r~vl~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~   86 (92)
T 3hug_A           37 QLSAEHRAVIQRSYYRG-----WSTAQIATDLGIAEGTVKSRLHYAVRALRLTLQ   86 (92)
T ss_dssp             TSCHHHHHHHHHHHTSC-----CCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            36777888887765332     246789999999999999999888888777543

>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=82.68  E-value=2.2  Score=32.72  Aligned_cols=49  Identities=10%  Similarity=0.273  Sum_probs=38.2

Q ss_pred             CCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhH
Q psy526           63 SRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYK  114 (274)
Q Consensus        63 ~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k  114 (274)
                      +|..||.++...+-..+..+....   ..+||..+|++...|..|.++++..
T Consensus         4 ~r~~~t~e~K~~iv~~~~~~g~~~---~~~~A~~~gvs~stl~~~~~~~~~~   52 (131)
T 1hlv_A            4 KRRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNKRAI   52 (131)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTHHHH
T ss_pred             cceeCCHHHHHHHHHHHHHCCCCc---HHHHHHHhCCCHHHHHHHHhchhhh
Confidence            577899999988877776555544   3368999999999999998776543

---

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	274
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	3e-24
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	6e-24
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	8e-24
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	2e-23
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	2e-22
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	3e-22
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	4e-22
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	5e-22
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	1e-21
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	1e-20
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	2e-20
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	3e-20
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	3e-20
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	4e-20
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	5e-20
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	8e-19
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	7e-18
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	7e-18
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	9e-18
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	1e-17
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	3e-17
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	3e-16
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	3e-16
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	6e-16
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	6e-16
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	1e-15
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	2e-15
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	3e-15
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	4e-15
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	1e-14
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	5e-14
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	3e-12

>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 = 90.6 bits (225), Expect = 3e-24
 Identities = 20/59 (33%), Positives = 34/59 (57%)

Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
           +R+R +F+  Q+  LEK F    Y     R  +A  + L E ++++WF NRR K +R++
Sbjct: 2   QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREE 60

>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 = 89.5 bits (222), Expect = 6e-24
 Identities = 13/64 (20%), Positives = 30/64 (46%)

Query: 59  RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
           +  R R   +  Q++ L   + A        +  + +   L+   +++WFQN+R K K++
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

Query: 119 QLQL 122
            + +
Sbjct: 62  SIMM 65

>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 = 89.5 bits (222), Expect = 8e-24
 Identities = 29/69 (42%), Positives = 38/69 (55%)

Query: 51  AQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQN 110
           A +       ++ R  ++  Q  ELEK F    YL+   R +VA+ L LTE QVKIWFQN
Sbjct: 4   AANWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQN 63

Query: 111 RRYKTKRKQ 119
           RR K K+  
Sbjct: 64  RRMKMKKIN 72

>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 = 88.0 bits (218), Expect = 2e-23
 Identities = 33/57 (57%), Positives = 40/57 (70%)

Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           K  +  FS+ Q  ELEK+F  QKYLS PER  +AK L+L+E QVK WFQNRR K +R
Sbjct: 1   KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 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 = 86.1 bits (213), Expect = 2e-22
 Identities = 22/61 (36%), Positives = 40/61 (65%)

Query: 59  RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
           +++RSR  FS +Q+ ELE+ F   +Y     R ++A+   LTE ++++WFQNRR + +++
Sbjct: 1   KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 60

Query: 119 Q 119
            
Sbjct: 61  H 61

>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 = 86.2 bits (213), Expect = 3e-22
 Identities = 33/69 (47%), Positives = 45/69 (65%)

Query: 53  SQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRR 112
           S+P  G     R  F+  Q+ ELEK F+  KYLS   R ++A +L+L ETQVKIWFQNRR
Sbjct: 20  SEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRR 79

Query: 113 YKTKRKQLQ 121
            K K+++ +
Sbjct: 80  MKQKKRERE 88

>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 = 84.4 bits (209), Expect = 4e-22
 Identities = 26/55 (47%), Positives = 37/55 (67%)

Query: 64  RAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
           R  ++  Q  ELEK F+  +YL+   R ++A +L LTE Q+KIWFQNRR K K++
Sbjct: 1   RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 55

>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 = 84.5 bits (209), Expect = 5e-22
 Identities = 21/57 (36%), Positives = 37/57 (64%)

Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           ++ R  +S  Q+ ELE+ + A K+++  +R  ++ +  L+E Q+ IWFQNRR K K+
Sbjct: 2   RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 58

>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 = 83.8 bits (207), Expect = 1e-21
 Identities = 37/62 (59%), Positives = 44/62 (70%)

Query: 60  KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
           +++ R  FS AQVYELE+RF  QKYLS PER  +A  + LT TQVKIWFQN RYK KR+ 
Sbjct: 2   RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61

Query: 120 LQ 121
             
Sbjct: 62  KD 63

>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 = 80.7 bits (199), Expect = 1e-20
 Identities = 24/53 (45%), Positives = 32/53 (60%)

Query: 62  RSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYK 114
           R R AFS  Q+  L++ FN  +YL+   R  ++  L L E Q+KIWFQN R K
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>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 = 80.4 bits (198), Expect = 2e-20
 Identities = 20/59 (33%), Positives = 35/59 (59%)

Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
           +R R  F+  Q+ +LE  F   +Y     R ++A    LTE +V++WF+NRR K ++++
Sbjct: 2   RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 60

>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 = 79.9 bits (197), Expect = 3e-20
 Identities = 27/57 (47%), Positives = 37/57 (64%)

Query: 62  RSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
           R R AF+  Q+  LEK F  + Y+S P R ++A  L L E+ +K+WFQNRR K KR+
Sbjct: 1   RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 57

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 58

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

 Score = 79.6 bits (196), Expect = 3e-20
 Identities = 32/57 (56%), Positives = 42/57 (73%)

Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           ++ R  F+ AQ+  LE++F  ++YLS  ERA+ + SL LTETQVKIWFQNRR K KR
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>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 = 79.6 bits (196), Expect = 4e-20
 Identities = 19/58 (32%), Positives = 28/58 (48%)

Query: 62  RSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
           + R   S A    LE+ F      S  E   +A+ L L +  V++WF NRR + KR +
Sbjct: 1   KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRVK 58

>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 = 79.6 bits (196), Expect = 5e-20
 Identities = 27/66 (40%), Positives = 41/66 (62%)

Query: 61  KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120
           +R+R  F+ +Q+ ELE+ F   +YL+ P  AD++  L L   QVKIWF+NRR + K +  
Sbjct: 2   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 61

Query: 121 QLLEGS 126
           Q  + S
Sbjct: 62  QHKDQS 67

>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 = 76.6 bits (188), Expect = 8e-19
 Identities = 38/69 (55%), Positives = 48/69 (69%)

Query: 53  SQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRR 112
           S     +K++ R  F+ AQ YELE+RF  Q+YLS PER  +A  ++LT TQVKIWFQN R
Sbjct: 2   SDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHR 61

Query: 113 YKTKRKQLQ 121
           YKTKR Q +
Sbjct: 62  YKTKRAQNE 70

>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 = 74.3 bits (182), Expect = 7e-18
 Identities = 17/73 (23%), Positives = 29/73 (39%), Gaps = 15/73 (20%)

Query: 62  RSRAAFSHAQVYELEKRFNAQKYLSGPERADVAK---------------SLKLTETQVKI 106
            SR  +    +  +E  FN  +Y    +R ++A                  ++T  +V  
Sbjct: 2   GSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYN 61

Query: 107 WFQNRRYKTKRKQ 119
           WF NRR + KR+ 
Sbjct: 62  WFANRRKEIKRRA 74

>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 = 73.0 bits (179), Expect = 7e-18
 Identities = 13/49 (26%), Positives = 20/49 (40%)

Query: 64  RAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRR 112
           R  F+  Q   L   F   K  S   +  +++ L L  + V  +F N R
Sbjct: 2   RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>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 = 73.5 bits (180), Expect = 9e-18
 Identities = 19/60 (31%), Positives = 28/60 (46%)

Query: 59  RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
            +KR R +  +   + LE  F      S  +   +A  L L +  V++WF NRR K KR 
Sbjct: 7   ARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS 66

>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 = 72.6 bits (178), Expect = 1e-17
 Identities = 17/53 (32%), Positives = 32/53 (60%)

Query: 64  RAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116
           +++ S      LE+ F  ++ L+  E+ +VAK   +T  QV++WF N+R ++K
Sbjct: 1   KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53

>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 = 71.7 bits (176), Expect = 3e-17
 Identities = 19/62 (30%), Positives = 25/62 (40%), Gaps = 7/62 (11%)

Query: 59  RKKRSRAAFSHAQVYELEKRFNAQK---YLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115
           R  R    F+   V  LE  F       YL      ++ K+  L+  Q+K W  NRR K 
Sbjct: 1   RGHR----FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKE 56

Query: 116 KR 117
           K 
Sbjct: 57  KT 58

>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 = 69.4 bits (170), Expect = 3e-16
 Identities = 17/68 (25%), Positives = 24/68 (35%), Gaps = 9/68 (13%)

Query: 57  TGRKKRSRAAFSHAQVYELEKRFNAQK---YLSGPERADVAKSLKLTETQVKIWFQNRRY 113
           +G+ KR            +           Y +  E+  +A    LT  QV  WF N R 
Sbjct: 1   SGKNKRGV--LPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINAR- 57

Query: 114 KTKRKQLQ 121
              R+ LQ
Sbjct: 58  ---RRILQ 62

>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 = 69.6 bits (170), Expect = 3e-16
 Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 1/60 (1%)

Query: 61  KRSRAAFSHAQVYELEKRFNA-QKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
               A  +  QV  LE  FN   K+        +A    LTE Q + WF+ R  + +R +
Sbjct: 2   SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 61

>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 = 69.0 bits (168), Expect = 6e-16
 Identities = 15/78 (19%), Positives = 29/78 (37%), Gaps = 2/78 (2%)

Query: 55  PPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYK 114
           P    +K      +  Q+  L+  F     L+  E   +    KLT  ++  WF  ++  
Sbjct: 1   PDFTPQKFKE--KTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKS 58

Query: 115 TKRKQLQLLEGSLNTPSA 132
              K+ ++     N  S+
Sbjct: 59  KALKEEKMEIDESNAGSS 76

>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 = 68.5 bits (167), Expect = 6e-16
 Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 3/64 (4%)

Query: 61  KRSRAAFSHAQVYELEKRFNA---QKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           +R R  F+      L + F +     Y S   + ++AK   +T +QV  WF N+R + K+
Sbjct: 2   RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61

Query: 118 KQLQ 121
              +
Sbjct: 62  NIGK 65

>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 = 67.8 bits (165), Expect = 1e-15
 Identities = 16/76 (21%), Positives = 31/76 (40%)

Query: 58  GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           G    S    +  Q+  L+  F   ++    +   + +   L   ++  WF + RY  K 
Sbjct: 1   GSSGSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH 60

Query: 118 KQLQLLEGSLNTPSAG 133
            QL+    + + PS+G
Sbjct: 61  GQLKWFRDNASGPSSG 76

>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 = 66.9 bits (163), Expect = 2e-15
 Identities = 15/54 (27%), Positives = 26/54 (48%)

Query: 64  RAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
           R +        LEK F   +  +  +   +A+ L + +  +++WF NRR K KR
Sbjct: 2   RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 55

>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 = 67.1 bits (163), Expect = 3e-15
 Identities = 16/77 (20%), Positives = 25/77 (32%), Gaps = 21/77 (27%)

Query: 64  RAAFSHAQVYELEKRFNAQKYLSGPERADVAKSL---------------------KLTET 102
           R  +  A    L + +  QK  S  ER  + +                        +TE 
Sbjct: 1   RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 103 QVKIWFQNRRYKTKRKQ 119
           +V  WF NRR +   + 
Sbjct: 61  RVYNWFANRRKEEAFRH 77

>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 = 66.3 bits (161), Expect = 4e-15
 Identities = 14/61 (22%), Positives = 23/61 (37%), Gaps = 1/61 (1%)

Query: 58  GRKKRSRAAFSHAQVYELEKRF-NAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116
               RSR   S   +  L+    +   Y        ++  L L +  +  +FQN+RY  K
Sbjct: 5   SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVK 64

Query: 117 R 117
            
Sbjct: 65  H 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 = 64.4 bits (157), Expect = 1e-14
 Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 1/48 (2%)

Query: 71  QVYELEKRFNAQ-KYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
               LEK F A  K+        ++K L      ++ WF+ RR + K 
Sbjct: 4   PNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 51

>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 = 63.2 bits (154), Expect = 5e-14
 Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 1/56 (1%)

Query: 62  RSRAAFSHAQVYELEKRFNAQ-KYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116
           +            LEK F +  KY        ++K L  +  +++ WF++RR + K
Sbjct: 3   KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

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

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

 Score = 58.9 bits (142), Expect = 3e-12
 Identities = 10/71 (14%), Positives = 19/71 (26%), Gaps = 4/71 (5%)

Query: 51  AQSQPPTGRKKRSRAAFSHAQVYELE----KRFNAQKYLSGPERADVAKSLKLTETQVKI 106
           +      G  KR R  F+  Q  ++     +     +               +    +KI
Sbjct: 8   SNPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKI 67

Query: 107 WFQNRRYKTKR 117
           W  N +     
Sbjct: 68  WMHNNKNSGPS 78

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	274
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.85
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.85
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.85
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.85
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.85
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.84
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.84
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.83
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.83
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.83
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.83
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.82
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.82
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.82
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.81
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.81
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.8
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.79
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.79
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.78
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.77
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.77
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.77
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.72
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.72
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.71
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.7
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.65
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.64
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.64
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.62
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.62
d1e3oc2	75	Oct-1 {Human (Homo sapiens) [TaxId: 9606]}	97.27
d1au7a2	72	Pit-1 {Rat (Rattus norvegicus) [TaxId: 10116]}	97.25
d1hlva1	66	DNA-binding domain of centromere binding protein B	92.33

>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=99.85  E-value=1.7e-22  Score=141.28  Aligned_cols=57  Identities=37%  Similarity=0.743  Sum_probs=55.2

Q ss_pred             CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        61 rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      ||+||.||.+|+.+||..|..++||+..+|++||..|||++++|+|||||||+|+||
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            677999999999999999999999999999999999999999999999999999885

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

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

Probab=99.85  E-value=4.1e-22  Score=139.29  Aligned_cols=57  Identities=56%  Similarity=0.894  Sum_probs=55.6

Q ss_pred             CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        61 rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      ||+||.|+.+|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||
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            578999999999999999999999999999999999999999999999999999997

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

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

Probab=99.85  E-value=4e-22  Score=143.25  Aligned_cols=61  Identities=43%  Similarity=0.732  Sum_probs=58.0

Q ss_pred             CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHH
Q psy526           61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQ  121 (274)
Q Consensus        61 rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~  121 (274)
                      ||+||.||.+|+.+||..|..++||+..++.+||..|||++++|+|||||||+|+||...+
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            6789999999999999999999999999999999999999999999999999999986544

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

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

Probab=99.85  E-value=9.6e-22  Score=140.45  Aligned_cols=63  Identities=35%  Similarity=0.672  Sum_probs=59.7

Q ss_pred             CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHH
Q psy526           59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQ  121 (274)
Q Consensus        59 k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~  121 (274)
                      |+||.||.|+.+|+.+||.+|..++||+..++++||..|||++.+|+|||||||+|+||....
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~~   63 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHTS   63 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhcccc
Confidence            578899999999999999999999999999999999999999999999999999999987643

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

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

Probab=99.85  E-value=1.5e-21  Score=143.88  Aligned_cols=65  Identities=43%  Similarity=0.652  Sum_probs=60.4

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526           58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL  122 (274)
Q Consensus        58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~  122 (274)
                      +.+||+||.|+.+|+.+||.+|..++||+..+|++||..|||++++|+|||||||+|+||..+..
T Consensus        11 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~~   75 (77)
T d1pufa_          11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDR   75 (77)
T ss_dssp             CTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHHh
Confidence            34577899999999999999999999999999999999999999999999999999999976543

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

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

Probab=99.84  E-value=1.1e-21  Score=136.65  Aligned_cols=56  Identities=48%  Similarity=0.840  Sum_probs=54.8

Q ss_pred             CCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           62 RSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        62 R~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      |.||.||..|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||
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            67999999999999999999999999999999999999999999999999999997

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

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

Probab=99.84  E-value=1.3e-21  Score=136.29  Aligned_cols=57  Identities=58%  Similarity=0.853  Sum_probs=55.3

Q ss_pred             CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        61 rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      |+.||.||..|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||
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            578999999999999999999999999999999999999999999999999999986

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

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

Probab=99.83  E-value=1.4e-21  Score=135.43  Aligned_cols=55  Identities=47%  Similarity=0.807  Sum_probs=53.7

Q ss_pred             CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           64 RAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        64 RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      ||.||.+|+.+||..|..++||+..+|++||..|||++++|+|||||||+|+||+
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            8999999999999999999999999999999999999999999999999999984

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

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

Probab=99.83  E-value=3.5e-21  Score=138.67  Aligned_cols=62  Identities=32%  Similarity=0.591  Sum_probs=58.5

Q ss_pred             CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526           61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL  122 (274)
Q Consensus        61 rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~  122 (274)
                      ||+||.||..|+.+||..|..++||+..+|++||..|||++++|+|||||+|+|+|+.....
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~~   63 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLR   63 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhhhh
Confidence            57799999999999999999999999999999999999999999999999999999876544

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

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

Probab=99.83  E-value=1.8e-21  Score=146.85  Aligned_cols=62  Identities=50%  Similarity=0.806  Sum_probs=55.8

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      +++||.||.||..|+.+||.+|..++||+..+|++||..|||++++|+|||||||+|+||..
T Consensus        25 ~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~   86 (88)
T d1b72a_          25 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRE   86 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhc
Confidence            45678899999999999999999999999999999999999999999999999999999865

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

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

Probab=99.83  E-value=1.1e-21  Score=144.54  Aligned_cols=64  Identities=56%  Similarity=0.930  Sum_probs=59.8

Q ss_pred             CCCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           55 PPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        55 ~~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      +...++||.||.||.+|+.+||.+|..++||+..++++||..|||++++|+|||||||+|+||.
T Consensus         4 g~p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   67 (77)
T d1vnda_           4 GLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRA   67 (77)
T ss_dssp             CCSSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSS
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHH
Confidence            3446778899999999999999999999999999999999999999999999999999999874

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

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

Probab=99.82  E-value=4.2e-21  Score=138.25  Aligned_cols=59  Identities=63%  Similarity=1.027  Sum_probs=57.1

Q ss_pred             CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        60 ~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      +||.||.||..|+.+||+.|..++||+..+|.+||..|||++.+|+|||||||+|+|+.
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~   60 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ   60 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhc
Confidence            57889999999999999999999999999999999999999999999999999999985

>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=99.82  E-value=2.9e-21  Score=132.58  Aligned_cols=53  Identities=45%  Similarity=0.786  Sum_probs=51.7

Q ss_pred             CCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhH
Q psy526           62 RSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYK  114 (274)
Q Consensus        62 R~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k  114 (274)
                      |+||.||.+|+.+||..|..++||+..+|++||..|||++++|+|||||||+|
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            67999999999999999999999999999999999999999999999999986

>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=99.82  E-value=1.9e-21  Score=136.78  Aligned_cols=59  Identities=34%  Similarity=0.660  Sum_probs=56.9

Q ss_pred             CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        60 ~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      +||.||.|+.+|+.+||.+|..++||+..++++||..|||++.+|++||+|||+|+||.
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            46889999999999999999999999999999999999999999999999999999985

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

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

Probab=99.81  E-value=1.2e-20  Score=137.10  Aligned_cols=59  Identities=29%  Similarity=0.350  Sum_probs=55.8

Q ss_pred             CCCCCcCCHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           61 KRSRAAFSHAQVYELEKRFNA-QKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        61 rR~RT~ft~~Ql~~Le~~F~~-~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      +|.|+.||.+|+.+||..|.+ ++||+..+|++||..|||++++|+|||||||+|+||..
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~   61 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhcc
Confidence            578999999999999999987 78999999999999999999999999999999999853

>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=99.81  E-value=5.8e-21  Score=137.11  Aligned_cols=60  Identities=32%  Similarity=0.449  Sum_probs=57.3

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      ..+||+||.|+.+|+.+|+.+|..++||+..++++||..|||++++|+|||||+|+|+||
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            456788999999999999999999999999999999999999999999999999999987

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

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

Probab=99.80  E-value=1.2e-20  Score=134.99  Aligned_cols=60  Identities=22%  Similarity=0.450  Sum_probs=57.7

Q ss_pred             CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        59 k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      |.+|.||.|+.+|+.+||.+|..|+||+..++++||.++||++++|++||||||+|.|+.
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            578899999999999999999999999999999999999999999999999999998874

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

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

Probab=99.79  E-value=2.3e-20  Score=130.29  Aligned_cols=57  Identities=33%  Similarity=0.509  Sum_probs=55.0

Q ss_pred             CCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           62 RSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        62 R~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      |+||.|+.+|+.+||.+|..++||+..++++||..|||++++|+|||||||+|+||.
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr~   57 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV   57 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHhc
Confidence            579999999999999999999999999999999999999999999999999999873

>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=99.79  E-value=5.1e-20  Score=137.18  Aligned_cols=60  Identities=28%  Similarity=0.490  Sum_probs=56.5

Q ss_pred             CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhC---------------CCcccchhhhhhhhhHHHHHHH
Q psy526           61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLK---------------LTETQVKIWFQNRRYKTKRKQL  120 (274)
Q Consensus        61 rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~---------------L~~~~V~vWFqNrR~k~Kr~~~  120 (274)
                      ||+||.|+.+|+.+||.+|..++||+..+|++||..+|               |++.+|+|||||||+|+||+..
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               9999999999999999999653

>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=99.78  E-value=7.6e-20  Score=135.58  Aligned_cols=62  Identities=16%  Similarity=0.210  Sum_probs=57.0

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhh----CCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           56 PTGRKKRSRAAFSHAQVYELEKRFNA----QKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        56 ~~~k~rR~RT~ft~~Ql~~Le~~F~~----~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      ...++||.||.||.+|+++|+.+|++    ++||+..++++||.+|||++++|+|||||+|++.|+
T Consensus        13 ~~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          13 SGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            34567889999999999999999997    899999999999999999999999999999988764

>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=99.77  E-value=1.1e-19  Score=126.34  Aligned_cols=55  Identities=27%  Similarity=0.488  Sum_probs=53.8

Q ss_pred             CCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           63 SRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        63 ~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      +||.|+.+|+.+||.+|..++||+..++++||.+|||++++|++||||||+|+||
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            5899999999999999999999999999999999999999999999999999987

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

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

Probab=99.77  E-value=1.1e-19  Score=124.64  Aligned_cols=53  Identities=32%  Similarity=0.546  Sum_probs=51.5

Q ss_pred             CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHH
Q psy526           64 RAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK  116 (274)
Q Consensus        64 RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~K  116 (274)
                      ||.|+.+|+.+||.+|..++||+..++.+||.++||++++|++||||||+|.|
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            79999999999999999999999999999999999999999999999999865

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

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

Probab=99.77  E-value=1.2e-19  Score=131.61  Aligned_cols=59  Identities=24%  Similarity=0.317  Sum_probs=55.4

Q ss_pred             CCCCCCCcCCHHHHHHHHHHHh-hCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           59 RKKRSRAAFSHAQVYELEKRFN-AQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        59 k~rR~RT~ft~~Ql~~Le~~F~-~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      ..||+||.|+.+|+.+||++|. .++||+..++++||.+|||++++|++||||||+|.||
T Consensus         6 ~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk   65 (71)
T d1wi3a_           6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             CCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             CCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhcc
Confidence            4567899999999999999997 4999999999999999999999999999999999886

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

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

Probab=99.72  E-value=8.6e-19  Score=118.58  Aligned_cols=50  Identities=26%  Similarity=0.329  Sum_probs=49.0

Q ss_pred             CCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhh
Q psy526           63 SRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRR  112 (274)
Q Consensus        63 ~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR  112 (274)
                      +||.||.+|+.+||+.|..++||+..++++||.+|||++++|++||||||
T Consensus         1 PRt~ft~~Q~~~Le~~F~~n~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1           1 PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             CCSCCCHHHHHHHHHHTTSSCSSTHHHHHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhhcCCcCc
Confidence            58999999999999999999999999999999999999999999999998

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=99.72  E-value=2.3e-18  Score=126.29  Aligned_cols=56  Identities=18%  Similarity=0.280  Sum_probs=52.4

Q ss_pred             CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526           64 RAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ  119 (274)
Q Consensus        64 RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~  119 (274)
                      ++.||.+|+.+||.+|..++||+..++++||..|||++++|++||+|||+|+|+..
T Consensus         7 ~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~~   62 (76)
T d2ecca1           7 GKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ   62 (76)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhch
Confidence            34579999999999999999999999999999999999999999999999999843

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

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

Probab=99.71  E-value=5.3e-18  Score=123.36  Aligned_cols=58  Identities=29%  Similarity=0.508  Sum_probs=54.5

Q ss_pred             CCCCCcCCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           61 KRSRAAFSHAQVYELEKRFNA---QKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        61 rR~RT~ft~~Ql~~Le~~F~~---~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      ||+|+.|+.+|+.+||.+|..   ++||+..++++||.++||++.+|++||+|+|+|.|+.
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~   62 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN   62 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhccc
Confidence            567999999999999999974   8899999999999999999999999999999998874

>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=99.70  E-value=2.3e-18  Score=126.27  Aligned_cols=52  Identities=21%  Similarity=0.337  Sum_probs=49.4

Q ss_pred             CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526           67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      +|.+|+.+||.+|..++||+..++++||..|||++++|+|||||||+|.|+.
T Consensus        11 ~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~   62 (76)
T d2ecba1          11 KTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALK   62 (76)
T ss_dssp             CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSC
T ss_pred             CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHH
Confidence            4899999999999999999999999999999999999999999999987764

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

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

Probab=99.65  E-value=1.5e-17  Score=113.23  Aligned_cols=50  Identities=26%  Similarity=0.358  Sum_probs=46.6

Q ss_pred             CHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           68 SHAQVYELEKRFNA-QKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        68 t~~Ql~~Le~~F~~-~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      |.+|+.+||.+|.. ++||+..++++||.+|||++++|+|||||||+|+|+
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            45799999999987 789999999999999999999999999999999875

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

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

Probab=99.64  E-value=1.6e-17  Score=122.21  Aligned_cols=55  Identities=29%  Similarity=0.376  Sum_probs=52.3

Q ss_pred             CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhC---------------------CCcccchhhhhhhhhHHHHH
Q psy526           64 RAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLK---------------------LTETQVKIWFQNRRYKTKRK  118 (274)
Q Consensus        64 RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~---------------------L~~~~V~vWFqNrR~k~Kr~  118 (274)
                      |+.|+.+|+.+||++|+.++||+..+|++||.+||                     |++.+|++||+|||+|.|++
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            78999999999999999999999999999999995                     89999999999999998874

>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=99.64  E-value=1.1e-16  Score=111.97  Aligned_cols=51  Identities=33%  Similarity=0.514  Sum_probs=48.3

Q ss_pred             CCHHHHHHHHHHHhhC---CCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526           67 FSHAQVYELEKRFNAQ---KYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR  117 (274)
Q Consensus        67 ft~~Ql~~Le~~F~~~---~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr  117 (274)
                      |+.+|+.+|+.+|..+   +||+..++++||.++||++++|++||+|+|+|.|+
T Consensus         5 ft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           5 FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             CCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            9999999999999764   79999999999999999999999999999998875

>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=99.62  E-value=3e-16  Score=110.53  Aligned_cols=56  Identities=23%  Similarity=0.344  Sum_probs=51.8

Q ss_pred             CCCCCcCCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHH
Q psy526           61 KRSRAAFSHAQVYELEKRFNA---QKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK  116 (274)
Q Consensus        61 rR~RT~ft~~Ql~~Le~~F~~---~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~K  116 (274)
                      ||+|+.|+.+++.+|+.+|..   +|||+..++.+||.++||+..||++||+|+|+|..
T Consensus         3 krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R~l   61 (62)
T d1x2na1           3 KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRIL   61 (62)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhc
Confidence            456889999999999999985   89999999999999999999999999999998754

>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=99.62  E-value=5.1e-17  Score=113.40  Aligned_cols=55  Identities=24%  Similarity=0.393  Sum_probs=50.9

Q ss_pred             CCCCcCCHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHH
Q psy526           62 RSRAAFSHAQVYELEKRFNA-QKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK  116 (274)
Q Consensus        62 R~RT~ft~~Ql~~Le~~F~~-~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~K  116 (274)
                      |.|+.++.++..+||.+|.. ++||+..++++||.+|||++++|++||||||+++|
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            55778888999999999986 68999999999999999999999999999999975

>d1e3oc2 a.35.1.1 (C:1-75) Oct-1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: POU-specific domain
domain: Oct-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.27  E-value=6.2e-06  Score=58.15  Aligned_cols=27  Identities=15%  Similarity=0.198  Sum_probs=24.0

Q ss_pred             HHHhCCCCCcccccCcccCCCCcCCCC
Q psy526           12 KKINNNNITNNTMSYYGKKDIRDARDL   38 (274)
Q Consensus        12 ~~~~g~~~sqttis~fe~~~ls~~~~~   38 (274)
                      -.+||++|||+||||||+++|+.+++.
T Consensus        35 ~~l~g~~~SQttIcRFE~l~LS~kn~~   61 (75)
T d1e3oc2          35 GKLYGNDFSQTTISRFEALNLSFKNMS   61 (75)
T ss_dssp             HHHHSCCCCHHHHHHHHHTCSCHHHHH
T ss_pred             HHHcCcchhHHHHHHHHHhccCHHHHH
Confidence            468999999999999999999987653

>d1au7a2 a.35.1.1 (A:5-76) Pit-1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: POU-specific domain
domain: Pit-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.25  E-value=6.9e-06  Score=57.39  Aligned_cols=27  Identities=4%  Similarity=0.160  Sum_probs=24.0

Q ss_pred             HHHhCCCCCcccccCcccCCCCcCCCC
Q psy526           12 KKINNNNITNNTMSYYGKKDIRDARDL   38 (274)
Q Consensus        12 ~~~~g~~~sqttis~fe~~~ls~~~~~   38 (274)
                      -.+||++|||+||||||+++|+.++++
T Consensus        31 ~~l~g~~~SQttIcRFE~l~LS~kn~~   57 (72)
T d1au7a2          31 AAVHGSEFSQTTICRFENLQLSFKNAC   57 (72)
T ss_dssp             HHTTSSCCCHHHHHHHHTTCSBHHHHH
T ss_pred             HHhcCcccchhHHHHHHhcccCHHHHH
Confidence            468999999999999999999987763

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

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

Probab=92.33  E-value=0.13  Score=34.74  Aligned_cols=46  Identities=11%  Similarity=0.321  Sum_probs=37.9

Q ss_pred             CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhh
Q psy526           64 RAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRR  112 (274)
Q Consensus        64 RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR  112 (274)
                      |..+|-.+...+-..|+..+...   ..+||..+|+.+..|..|.+|+.
T Consensus         5 Rk~LT~~eK~~ii~~~e~g~k~s---q~eIA~~fGv~~STvs~IlKnK~   50 (66)
T d1hlva1           5 RRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNKR   50 (66)
T ss_dssp             SCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTHH
T ss_pred             cccCCHHHHHHHHHHHHcCCcch---HHHHHHHhCCChhHHHHHHHHHH
Confidence            44589988888888888887544   56799999999999999998843