Psyllid ID: psy3281

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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-------280-------290-------300-------310-------
Protein Sequence
MSSYFANSYMPDIKNGGVLPPEHHQQHHYGATVLPQNNGVEDPSMYDPRQVHHYGQVPNNGQPVHGMPYPRFPPYDRMDIRNAAYYGAHEGGMEQYPRPDSPSMGHMGPQNGHQTPVVYASCKLQAAVGNGIIPGPESPNDLVDPTLNNHHHHQHHHMNHHPHPHPQQQQPQQPPPQHMMYAQQPPPQHHQVVVNHQQTPPNQPPSQPPNQPPNQQPNNTSASLPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGGSDAGSDITPATSPQ
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccHHHHHHHHHHHccccHHHHHHHccccHHHHHHccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccEEEcccccccccccccccccccccccccccccccccccccHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHcHcHHHHccccccccccccccccc
Coil and Loop (DISEMBL)
mssyfansympdiknggvlppehhqqhhygatvlpqnngvedpsmydprqvhhygqvpnngqpvhgmpyprfppydrmdirnaayygaheggmeqyprpdspsmghmgpqnghqtpVVYASCKLQAavgngiipgpespndlvdptlnnhhhhqhhhmnhhphphpqqqqpqqpppqhmmyaqqpppqhhqvvvnhqqtppnqppsqppnqppnqqpnntsaslpsplypwmrsqferkrgrqtytRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKkenkskdggsdagsditpatspq
Flexible Loop (DISEMBL)
MSSYFANSYMPDIKNGGVLPPEHHQQHHYGATVLPQNNGVEDPSMYDPRQVHHYgqvpnngqpvhGMPYPRFPPYDRMDIRNAAYYGAHEGGMEQYPRPDSPSMGHMGPQNGHQTPVVYASCKLQAAVGNGIIPGPESPNDLVDPTLNNHHHHQHHHMNHHPHPHPQQQQPQQPPPQHMMYAQQPPPQHHQVVVNHQQTPPNQPPSQPPNQPPNQQPNNTSASLPSPLYPWMRSQFERKRGRQTYtryqtlelekefhfnryltrRRRIEIAHalclterqikiwfqnrrMKWKkenkskdggsdagsditpatspq
Low Complexity Region (SEG)
MSSYFANSYMPDIKNGGVLPPEHHQQHHYGATVLPQNNGVEDPSMYDPRQVHHYGQVPNNGQPVHGMPYPRFPPYDRMDIRNAAYYGAHEGGMEQYPRPDSPSMGHMGPQNGHQTPVVYASCKLQAAVGNGIIPGPESPNDLVDPTLnnhhhhqhhhmnhhphphpqqqqpqqpppqhmmyaqqpppqhhqvvvnhqqtppnqppsqppnqppnqqpnnTSASLPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGGSDAGSDITPATSPQ
Disordered region (IsUnstruct)
***********************************************************************FPPYDRMDIRNAAYYG*****************************VVYASCKLQAAVGNGII************************************************************************************************************RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM**************************
Disordered Region (DISOPRED)
MSSYFANSYMP***************************************************************************************************************************************************************************************************************************************QTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR***************************
Disordered Region (DISEMBL)
MSSYFANSYMPDIKNGGVLPPEHHQQHHYGATVLPQNNGVEDPSMYDPRQVHHYGQVPNNGQPVHGMPYPRFPPYDRMDIRNAAYYGAHEGGMEQYPRPDSPSMGHMGPQNGHQTPVVYASCKLQAAVGNGIIPGPESPNDLVDPTLNN*******************************YAQQPPPQHHQVVV***************************ASLPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK*************************
Disordered Region (DISPRO)
*SSYFANSYMPDIKNGGVLPPEHHQQHHYGATVLPQNNGVEDPSMYDPRQVHHYGQVPNNGQPVHGMPYPRFPPYDRMDIRNAAYYGAHEGGMEQYPRPDSPSMGHMGPQNGHQTPVVYASCKLQAAVGNGIIPGPESPNDLVDPTLNNHHHHQHHHMNHHPHPHPQQQQPQQPPP**************************************************************KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE*********************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSSYFANSYMPDIKNGGVLPPEHHQQHHYGATVLPQNNGVEDPSMYDPRQVHHYGQVPNNGQPVHGMPYPRFPPYDRMDIRNAAYYGAHEGGMEQYPRPDSPSMGHMGPQNGHQTPVVYASCKLQAAVGNGIIPGPESPNDLVDPTLNNHHHHQHHHMNHHPHPHPQQQQPQQPPPQHMMYAQQPPPQHHQVVVNHQQTPPNQPPSQPPNQPPNQQPNNTSASLPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGGSDAGSDITPATSPQ
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	317	2.2.26 [Sep-21-2011]
Q24645	394	Homeotic protein antennap	N/A	N/A	0.599	0.482	0.554	2e-55
P02833	378	Homeotic protein antennap	yes	N/A	0.580	0.486	0.565	4e-53
Q8AWY9	227	Homeobox protein Hox-B7a	yes	N/A	0.261	0.365	0.833	2e-36
A1YFA5	217	Homeobox protein Hox-B7 O	N/A	N/A	0.318	0.465	0.696	4e-36
P18864	219	Homeobox protein Hox-B7 O	yes	N/A	0.268	0.388	0.802	7e-36
Q9TT89	217	Homeobox protein Hox-B7 O	yes	N/A	0.296	0.433	0.726	1e-35
P09629	217	Homeobox protein Hox-B7 O	yes	N/A	0.296	0.433	0.715	4e-35
Q91771	220	Homeobox protein Hox-B7-A	N/A	N/A	0.249	0.359	0.837	4e-35
P09071	209	Homeobox protein Hox-A7 O	N/A	N/A	0.277	0.421	0.8	4e-35
P04476	220	Homeobox protein Hox-B7-B	N/A	N/A	0.249	0.359	0.837	6e-35

>sp|Q24645|ANTP_DROSU Homeotic protein antennapedia OS=Drosophila subobscura GN=Antp PE=3 SV=1

 Score =  216 bits (549), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 144/238 (60%), Gaps = 48/238 (20%)

Query: 116 PVVYASCKLQAAVGNGIIPGPESPNDLVDPTLNNHH--------HHQHH----------- 156
           PVVYASCKLQAAVG G+   PE  +  +   +  HH        HH  H           
Sbjct: 169 PVVYASCKLQAAVGVGLGMVPEGGSPPLVDQMTGHHMNAQMSLPHHMGHPQAQLGYTDVG 228

Query: 157 -------HMNHHPHPHPQQQQ----PQQPPPQHMMYAQQPPPQHHQVVVNHQQTPPNQPP 205
                  H NHH      QQQ    P   PPQ MM+  Q PPQ HQ  +  Q TPP+Q  
Sbjct: 229 VPDVTEVHQNHHNMGMYGQQQTGVPPVGAPPQAMMHQGQGPPQMHQGHLPGQHTPPSQ-- 286

Query: 206 SQPPNQPPNQQPNNTSASLPSPLYPWMRSQF----ERKRGRQTYTRYQTLELEKEFHFNR 261
                      PN+ S+ +PSPLYPWMRSQF    ERKRGRQTYTRYQTLELEKEFHFNR
Sbjct: 287 ----------NPNSQSSGMPSPLYPWMRSQFGKCQERKRGRQTYTRYQTLELEKEFHFNR 336

Query: 262 YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD--GGSDAGSDITPATSPQ 317
           YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK+K   G    G +ITP  SPQ
Sbjct: 337 YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKTKGEPGSGGEGDEITPPNSPQ 394

Sequence-specific transcription factor which is part of a developmental regulatory system that regulates segmental identity in the mesothorax. Provides cells with specific positional identities on the anterior-posterior axis.
Drosophila subobscura (taxid: 7241)

>sp|P02833|ANTP_DROME Homeotic protein antennapedia OS=Drosophila melanogaster GN=Antp PE=1 SV=1

 Score =  208 bits (529), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 133/235 (56%), Positives = 145/235 (61%), Gaps = 51/235 (21%)

Query: 119 YASCKLQAAVGN-GIIPGPESPNDLVDPTLNNHH--------HHQHH------------- 156
           YASCKLQAAVG  G++P   SP  LVD  ++ HH        HH  H             
Sbjct: 159 YASCKLQAAVGGLGMVPEGGSP-PLVD-QMSGHHMNAQMTLPHHMGHPQAQLGYTDVGVP 216

Query: 157 -----HMNHHPHPHPQQQQ---PQQPPPQHMMYAQQPPPQHHQVVVNHQQTPPNQPPSQP 208
                H NHH     QQQ    P   PPQ MM+  Q PPQ HQ         P Q     
Sbjct: 217 DVTEVHQNHHNMGMYQQQSGVPPVGAPPQGMMHQGQGPPQMHQ-------GHPGQ----- 264

Query: 209 PNQPPNQQPNNTSASLPSPLYPWMRSQF----ERKRGRQTYTRYQTLELEKEFHFNRYLT 264
            + PP+Q PN+ S+ +PSPLYPWMRSQF    ERKRGRQTYTRYQTLELEKEFHFNRYLT
Sbjct: 265 -HTPPSQNPNSQSSGMPSPLYPWMRSQFGKCQERKRGRQTYTRYQTLELEKEFHFNRYLT 323

Query: 265 RRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD--GGSDAGSDITPATSPQ 317
           RRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK+K   G    G +ITP  SPQ
Sbjct: 324 RRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKTKGEPGSGGEGDEITPPNSPQ 378

Sequence-specific transcription factor which is part of a developmental regulatory system that regulates segmental identity in the mesothorax. Provides cells with specific positional identities on the anterior-posterior axis.

Drosophila melanogaster (taxid: 7227)

>sp|Q8AWY9|HXB7A_DANRE Homeobox protein Hox-B7a OS=Danio rerio GN=hoxb7a PE=2 SV=1

 Score =  153 bits (386), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 70/84 (83%), Positives = 74/84 (88%), Gaps = 1/84 (1%)

Query: 228 LYPWMRSQ-FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWF 286
           +YPWMRS   +RKRGRQTY+RYQTLELEKEFHFNRYL+RRRRIEIAHALCLTERQIKIWF
Sbjct: 134 IYPWMRSTGADRKRGRQTYSRYQTLELEKEFHFNRYLSRRRRIEIAHALCLTERQIKIWF 193

Query: 287 QNRRMKWKKENKSKDGGSDAGSDI 310
           QNRRMKWKKENKS D  S A   I
Sbjct: 194 QNRRMKWKKENKSTDRCSPAADQI 217

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

Danio rerio (taxid: 7955)

>sp|A1YFA5|HXB7_GORGO Homeobox protein Hox-B7 OS=Gorilla gorilla gorilla GN=HOXB7 PE=3 SV=1

 Score =  152 bits (383), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 71/102 (69%), Positives = 80/102 (78%), Gaps = 1/102 (0%)

Query: 206 SQPPNQPPNQQPNNTSASLPSPLYPWMRSQ-FERKRGRQTYTRYQTLELEKEFHFNRYLT 264
           S        Q+ ++ +A     +YPWMRS   +RKRGRQTYTRYQTLELEKEFH+NRYLT
Sbjct: 104 SAKAAGAKEQRDSDLAAESNFRIYPWMRSSGTDRKRGRQTYTRYQTLELEKEFHYNRYLT 163

Query: 265 RRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGGSDA 306
           RRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK+   G+ A
Sbjct: 164 RRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKTAGPGTTA 205

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

Gorilla gorilla gorilla (taxid: 9595)

>sp|P18864|HXB7_RAT Homeobox protein Hox-B7 OS=Rattus norvegicus GN=Hoxb7 PE=2 SV=2

 Score =  151 bits (381), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 69/86 (80%), Positives = 76/86 (88%), Gaps = 1/86 (1%)

Query: 215 QQPNNTSASLPSPLYPWMRSQ-FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAH 273
           Q+ ++ +A     +YPWMRS   ERKRGRQTYTRYQTLELEKEFH+NRYLTRRRRIEIAH
Sbjct: 113 QRDSDLAAESNFRIYPWMRSSGTERKRGRQTYTRYQTLELEKEFHYNRYLTRRRRIEIAH 172

Query: 274 ALCLTERQIKIWFQNRRMKWKKENKS 299
           ALCLTERQIKIWFQNRRMKWKKENK+
Sbjct: 173 ALCLTERQIKIWFQNRRMKWKKENKT 198

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

Rattus norvegicus (taxid: 10116)

>sp|Q9TT89|HXB7_BOVIN Homeobox protein Hox-B7 OS=Bos taurus GN=HOXB7 PE=2 SV=1

 Score =  150 bits (380), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 69/95 (72%), Positives = 77/95 (81%), Gaps = 1/95 (1%)

Query: 206 SQPPNQPPNQQPNNTSASLPSPLYPWMRSQ-FERKRGRQTYTRYQTLELEKEFHFNRYLT 264
           S        Q+ ++ +A     +YPWMRS   +RKRGRQTYTRYQTLELEKEFH+NRYLT
Sbjct: 104 SAKAAGAKEQRDSDLAAESNFRIYPWMRSSGTDRKRGRQTYTRYQTLELEKEFHYNRYLT 163

Query: 265 RRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS 299
           RRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK+
Sbjct: 164 RRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKT 198

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

Bos taurus (taxid: 9913)

>sp|P09629|HXB7_HUMAN Homeobox protein Hox-B7 OS=Homo sapiens GN=HOXB7 PE=1 SV=4

 Score =  149 bits (375), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 68/95 (71%), Positives = 76/95 (80%), Gaps = 1/95 (1%)

Query: 206 SQPPNQPPNQQPNNTSASLPSPLYPWMRSQ-FERKRGRQTYTRYQTLELEKEFHFNRYLT 264
           S        Q+ ++ +A     +YPWMRS   +RKRGRQTYTRYQTLELEKEFH+NRYLT
Sbjct: 104 SAKAAGAKEQRDSDLAAESNFRIYPWMRSSGTDRKRGRQTYTRYQTLELEKEFHYNRYLT 163

Query: 265 RRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS 299
           RRRRIEIAH LCLTERQIKIWFQNRRMKWKKENK+
Sbjct: 164 RRRRIEIAHTLCLTERQIKIWFQNRRMKWKKENKT 198

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

Homo sapiens (taxid: 9606)

>sp|Q91771|HXB7A_XENLA Homeobox protein Hox-B7-A OS=Xenopus laevis GN=hoxb7-a PE=2 SV=1

 Score =  149 bits (375), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 67/80 (83%), Positives = 72/80 (90%), Gaps = 1/80 (1%)

Query: 228 LYPWMRSQ-FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWF 286
           +YPWMRS   +RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAH LCLTERQIKIWF
Sbjct: 129 IYPWMRSAGADRKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHVLCLTERQIKIWF 188

Query: 287 QNRRMKWKKENKSKDGGSDA 306
           QNRRMKWKKENK+    S++
Sbjct: 189 QNRRMKWKKENKASSPSSNS 208

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

Xenopus laevis (taxid: 8355)

>sp|P09071|HXA7_XENLA Homeobox protein Hox-A7 OS=Xenopus laevis GN=hoxa7 PE=2 SV=1

 Score =  148 bits (374), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 72/90 (80%), Positives = 78/90 (86%), Gaps = 2/90 (2%)

Query: 228 LYPWMRSQF-ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWF 286
           +YPWMRS   +RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWF
Sbjct: 111 IYPWMRSSGPDRKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWF 170

Query: 287 QNRRMKWKKENKSK-DGGSDAGSDITPATS 315
           QNRRMKWKKE+K + D   DAG + T  T+
Sbjct: 171 QNRRMKWKKEHKEESDQTPDAGEESTAPTT 200

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

Xenopus laevis (taxid: 8355)

>sp|P04476|HXB7B_XENLA Homeobox protein Hox-B7-B OS=Xenopus laevis GN=hoxb7-b PE=2 SV=1

 Score =  148 bits (373), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 67/80 (83%), Positives = 72/80 (90%), Gaps = 1/80 (1%)

Query: 228 LYPWMRSQ-FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWF 286
           +YPWMRS   +RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAH LCLTERQIKIWF
Sbjct: 127 IYPWMRSAGSDRKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHTLCLTERQIKIWF 186

Query: 287 QNRRMKWKKENKSKDGGSDA 306
           QNRRMKWKKENK+    S++
Sbjct: 187 QNRRMKWKKENKASSPSSNS 206

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

Xenopus laevis (taxid: 8355)

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	317
15450324	323	homeodomain transcription factor Prothor	0.962	0.944	0.608	3e-75
86515364	325	prothoraxless [Tribolium castaneum] gi|7	0.962	0.938	0.560	2e-69
58585092	352	homeobox protein H90 [Apis mellifera] gi	0.974	0.877	0.526	5e-69
195446505	374	GK10824 [Drosophila willistoni] gi|19416	0.889	0.754	0.458	1e-63
357626567	303	antennapedia-like proteinue protein [Dan	0.880	0.920	0.536	6e-63
194742008	378	GF17789 [Drosophila ananassae] gi|190626	0.861	0.722	0.451	2e-59
112983708	259	antennapedia homologue protein [Bombyx m	0.728	0.891	0.576	3e-59
195389692	376	antennapedia [Drosophila virilis] gi|194	0.883	0.744	0.451	7e-56
198453463	392	antp, isoform A [Drosophila pseudoobscur	0.599	0.484	0.564	8e-56
195152057	395	GL22036 [Drosophila persimilis] gi|19411	0.599	0.481	0.564	8e-56

>gi|15450324|gb|AAK96031.1| homeodomain transcription factor Prothoraxless [Tribolium castaneum] gi|270002803|gb|EEZ99250.1| antennapedia [Tribolium castaneum]

 Score =  288 bits (736), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 204/335 (60%), Positives = 219/335 (65%), Gaps = 30/335 (8%)

Query: 1   MSSYFANSYMPDIKNGGVLPPEH-HQQHHYGATV-LPQNNGVE--DPSMYDP----RQV- 51
           MSSYFANSYMPD++NGGV+  EH HQ  HYGA V +PQ  G    DP   DP    RQ  
Sbjct: 1   MSSYFANSYMPDMRNGGVVSAEHPHQHQHYGAAVQVPQGGGAVQPDPGSCDPSVGLRQGI 60

Query: 52  --HHYGQVPNNGQPVHGMPYPRFPPYDRMDIRNAAYYGAHEGGMEQYPRPDSPSMGHMGP 109
             HHYG  P+ GQP  GMPYPRFPPYDRMDIR A YYG  +    Q  RPDSPS  HM  
Sbjct: 61  PPHHYGGPPSGGQPPQGMPYPRFPPYDRMDIRAAGYYGPQQQMDGQEYRPDSPSSMHMAN 120

Query: 110 Q---NGHQTPVVYASCKLQAAVG--NGIIPGPESPNDLVDPTLNNHHHHQHHHMNHHPHP 164
               NGHQT VVYASCKLQAA    NG++ GP     L   ++NNHH      M HH   
Sbjct: 121 TAAPNGHQTQVVYASCKLQAAAVTQNGVL-GPTGSPPLTTQSMNNHH------MGHHMQE 173

Query: 165 HPQQQQPQQPPPQHMMYAQQPPPQHHQVVVNHQQTPPNQPPSQPPNQPPNQQPNNTSASL 224
              Q        QHMMY  Q     HQ    HQQ P  Q P+Q       Q P NT+A+L
Sbjct: 174 QHPQHHQPHHQQQHMMYGGQQGANMHQQGPPHQQPPIQQQPNQG-----QQPPGNTAAAL 228

Query: 225 PSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKI 284
           PSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKI
Sbjct: 229 PSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKI 288

Query: 285 WFQNRRMKWKKENKSK--DGGSDAGSDITPATSPQ 317
           WFQNRRMKWKKENK+K   G    G DI+P  SPQ
Sbjct: 289 WFQNRRMKWKKENKTKGEGGSEGGGDDISPQGSPQ 323

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|86515364|ref|NP_001034505.1| prothoraxless [Tribolium castaneum] gi|7767519|gb|AAF69136.1|AF228509_1 prothoraxless [Tribolium castaneum]

 Score =  269 bits (687), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 189/337 (56%), Positives = 210/337 (62%), Gaps = 32/337 (9%)

Query: 1   MSSYFANSYMPDIKNGGVLPPEH-HQQHHYGATV-LPQNN-------GVEDPSMYDPRQV 51
           MSSYFANSYMPD++NGGV+  EH HQ  HYGA V +PQ         GV     +   + 
Sbjct: 1   MSSYFANSYMPDMRNGGVVSAEHPHQHQHYGAAVQVPQGGRRRAARPGVVTTPRWGCARA 60

Query: 52  HHYGQV--PNNGQPV-HGMPYPRFPPYDRMDIRNA-AYYGAHEGGMEQYPRPDSPSMGHM 107
                +  P  G+    GMPYPRFPPYDRMDIR+  + +G  +    Q  RPDSPS  HM
Sbjct: 61  SSATTMGGPRYGRAAAQGMPYPRFPPYDRMDIRDRRSLHGPQQQMDGQEYRPDSPSSMHM 120

Query: 108 GPQ---NGHQTPVVYASCKLQAAVG--NGIIPGPESPNDLVDPTLNNHHHHQHHHMNHHP 162
                 NGHQT VVY SCKLQAA    NG++ GP     L   ++NNHH      M HH 
Sbjct: 121 ANTAAPNGHQTQVVYDSCKLQAAAVTQNGVL-GPTGSPPLTTQSMNNHH------MGHHM 173

Query: 163 HPHPQQQQPQQPPPQHMMYAQQPPPQHHQVVVNHQQTPPNQPPSQPPNQPPNQQPNNTSA 222
                Q        QHMMY  Q     HQ    HQQ P  Q P+Q       Q P NT+A
Sbjct: 174 QEQHPQHHQPHHQQQHMMYGGQQGANMHQQGPPHQQPPIQQQPNQG-----QQPPGNTAA 228

Query: 223 SLPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQI 282
           +LPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQI
Sbjct: 229 ALPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQI 288

Query: 283 KIWFQNRRMKWKKENKSK--DGGSDAGSDITPATSPQ 317
           KIWFQNRRMKWKKENK+K   G    G DI+P  SPQ
Sbjct: 289 KIWFQNRRMKWKKENKTKGEGGSEGGGDDISPQGSPQ 325

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|58585092|ref|NP_001011571.1| homeobox protein H90 [Apis mellifera] gi|9967824|emb|CAC06383.1| Antennapedia protein [Apis mellifera]

 Score =  267 bits (682), Expect = 5e-69,   Method: Compositional matrix adjust.
 Identities = 189/359 (52%), Positives = 211/359 (58%), Gaps = 50/359 (13%)

Query: 1   MSSYFANSYMPDIKNGGVLPPEHHQQHHYGATVLPQNNGVE------------DPSMYDP 48
           MSSYFANSY+PD++NGGV  P  HQQH YGA V                    DPS+   
Sbjct: 1   MSSYFANSYIPDLRNGGVEHPHQHQQH-YGAAVQVPQQTQSVQQQSQQAGDPCDPSLL-- 57

Query: 49  RQV---HHYGQVPNNGQPVHGMPYPRFPPYDRMDIRNAAYY------GAHEGGMEQYPRP 99
           RQ    HHYG   +       MPYPRFPPY+RMD+RNA YY      G+   GM  Y   
Sbjct: 58  RQGVPGHHYGAAGSQ----QDMPYPRFPPYNRMDMRNATYYQHQQDHGSGMDGMGGYRSA 113

Query: 100 D-SPSMGHMGPQ---NGH-QTPVVYASCKLQAAVGN---GIIPGPESPNDLVDPTLNNHH 151
             SP MGHMG     NGH  TP+VYASCKLQAA  +    ++ GP+SP  LV+  +++  
Sbjct: 114 SPSPGMGHMGHTPTPNGHPSTPIVYASCKLQAAAVDHQGSVLDGPDSP-PLVESQMHHQM 172

Query: 152 HHQHHHMNHHPHPHPQQQQPQQPPP--QHMMYAQQPP---------PQHHQVVVNHQQTP 200
           H QH HM      H  Q Q Q      QHMMY QQ           P  H       Q  
Sbjct: 173 HTQHPHMQPQQGQHQSQAQQQHLQAHEQHMMYQQQQQSQAASQQSQPGMHPRQQQQAQQH 232

Query: 201 PNQPPSQPPNQPPNQQPNNTSASLPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFN 260
                S    Q         SA+LPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFH+N
Sbjct: 233 QGVVTSPLSQQQQAAPQGAASANLPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHYN 292

Query: 261 RYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD--GGSDAGSDITPATSPQ 317
           RYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSK   G  D  ++I+P TSPQ
Sbjct: 293 RYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKGTPGSGDGDTEISPQTSPQ 351

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195446505|ref|XP_002070809.1| GK10824 [Drosophila willistoni] gi|194166894|gb|EDW81795.1| GK10824 [Drosophila willistoni]

 Score =  249 bits (636), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 183/399 (45%), Positives = 205/399 (51%), Gaps = 117/399 (29%)

Query: 1   MSSYFANSYMPDIKNGGVLPPEHHQQHHYGATVLPQNNGVEDPSMYDPRQVHHYGQVPNN 60
           M+SYF NSYM           + H  H+ G       NGV D    D +Q+HHY Q PN+
Sbjct: 11  MTSYFTNSYMG---------ADMHHGHYPG-------NGVTD---LDAQQMHHYSQNPNH 51

Query: 61  GQPVHGMPYPRFPPYDRMDIRNAAYYGAHEGGMEQYPRPDSPS--MGHMGPQ---NG--- 112
                 MPYPRFPPYDRM   N       +   + Y RPDSPS  +G + PQ   NG   
Sbjct: 52  ---QGNMPYPRFPPYDRMPYYNGQGMDQQQQQHQGYSRPDSPSSQVGGVMPQTQTNGGQL 108

Query: 113 ----------------------------------------HQTPVVYASCKLQAAVGNGI 132
                                                    Q PVVYASCKLQAAVG G+
Sbjct: 109 VNQQQQQQSQNQQQQSQQAPQQLQQQQQQQQQQQQHPQQQQQQPVVYASCKLQAAVGGGL 168

Query: 133 IPGPESPNDLVDPTLNNHH--------HHQHH------------------HMNHHPHPHP 166
              PE  +  +   +  HH        HH  H                  H NHH     
Sbjct: 169 GLVPEGGSPPLVDQMGGHHMNAQMTLPHHLGHPQSQLGYTDVGVPDVTEVHQNHHNMGMY 228

Query: 167 QQQQPQQPP------PQHMMYAQQPPPQHHQVVVNHQQTPPNQPPSQPPNQPPNQQPNNT 220
            QQQ   PP      PQ MM+A Q PPQ HQ    H        P Q  + PP+Q PN+ 
Sbjct: 229 GQQQTGVPPGVGAPGPQGMMHAGQGPPQMHQ---GH--------PGQ--HTPPSQNPNSQ 275

Query: 221 SASLPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTER 280
           S+ +PSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTER
Sbjct: 276 SSGMPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTER 335

Query: 281 QIKIWFQNRRMKWKKENKSKD--GGSDAGSDITPATSPQ 317
           QIKIWFQNRRMKWKKENK+K   G    G +ITP  SPQ
Sbjct: 336 QIKIWFQNRRMKWKKENKTKGEPGSGGEGDEITPPNSPQ 374

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357626567|gb|EHJ76618.1| antennapedia-like proteinue protein [Danaus plexippus]

 Score =  247 bits (630), Expect = 6e-63,   Method: Compositional matrix adjust.
 Identities = 177/330 (53%), Positives = 199/330 (60%), Gaps = 51/330 (15%)

Query: 3   SYFANSYMPDIKNGGVLPPEHHQQH-HYGATVLPQNNGVEDPSMYDPRQV-HHYGQVPNN 60
           +YF+N+Y+PD++NGG    +H Q H HYGA  +PQ     D      R   HHY     +
Sbjct: 10  TYFSNAYVPDMRNGGH---DHQQAHAHYGA--VPQQGHEMDGCDQQLRPAQHHY-----S 59

Query: 61  GQPVHGMPYPRFPPYDRMDIRNAAYYGAHEGGMEQYPRPDSPS-MGHMGPQ------NGH 113
            Q   GMPYPRFPPYDR+      YY   E   +   RPDSPS MGHMGP+      NGH
Sbjct: 60  AQTAPGMPYPRFPPYDRL-----GYYQQME---QNGYRPDSPSQMGHMGPKSDGYGPNGH 111

Query: 114 Q--TPVVY-ASCKLQAAVG-NGIIPGPESPNDLVDPTLNNHHHHQHHHMNHHPHPHPQQQ 169
           Q   P VY +SCK+QAA    G +PG  SP  L       HH H   HM  H  P    Q
Sbjct: 112 QPPAPAVYPSSCKVQAAAAMAGGVPG--SP-PLEQAQQMPHHMHPQQHMAQHGMP--SHQ 166

Query: 170 QPQQPPPQHMMYAQQPPPQHHQVVVNHQQTPPNQPPSQPPNQPPNQQPNNTSASLPSPLY 229
           Q    P   M +  Q PP H Q +   Q  P              Q P NT+ASLPSPLY
Sbjct: 167 QHLMYPVDDMQHQTQMPPMHQQSMHAQQAPP-------------QQPPPNTNASLPSPLY 213

Query: 230 PWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 289
           PWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR
Sbjct: 214 PWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 273

Query: 290 RMKWKKENKSKD--GGSDAGSDITPATSPQ 317
           RMKWKKENK+K   G  D   +++P TSPQ
Sbjct: 274 RMKWKKENKTKGEPGSGDEPDNMSPPTSPQ 303

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194742008|ref|XP_001953501.1| GF17789 [Drosophila ananassae] gi|190626538|gb|EDV42062.1| GF17789 [Drosophila ananassae]

 Score =  235 bits (599), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 186/412 (45%), Positives = 206/412 (50%), Gaps = 139/412 (33%)

Query: 1   MSSYFANSYMPDIKNGGVLPPEHHQQHHYGATVLPQNNGVEDPSMYDPRQVHHYGQVPNN 60
           M+SYF NSYM           + H  H+ G       NGV D    D +Q+H Y Q PN+
Sbjct: 11  MTSYFTNSYMG---------ADMHHGHYPG-------NGVTD---LDAQQMHPYSQNPNH 51

Query: 61  GQPVHGMPYPRFPPYDRMDIRNAAYYGAHEGGMEQ------------YPRPDSPS--MGH 106
                 MPYPRFPPYDRM   N         GM+Q            Y RPDSPS  +G 
Sbjct: 52  ---QGNMPYPRFPPYDRMPYYNGQ-------GMDQQQQQQQHQQHQVYSRPDSPSSQVGG 101

Query: 107 MGPQ---NGHQT---------------------------------------------PVV 118
           + PQ   NG                                                PVV
Sbjct: 102 VMPQAQTNGQLVAQQQQQPSQNQQQQQQAQGPQHQQQIPQVTQQGTHPQQQQQQQQQPVV 161

Query: 119 YASCKLQAAVGN-GIIPGPESPNDLVDPTLNNHH--------HHQHH------------- 156
           YASCKLQAAVG  G++P   SP  LVD  +  HH        HH  H             
Sbjct: 162 YASCKLQAAVGGLGMVPEGGSP-PLVD-QMTGHHMNAQMSLTHHMGHPQAQLGYTDVGVP 219

Query: 157 -----HMNHHPHPHPQQQQ----PQQPPPQHMMYAQQPPPQHHQVVVNHQQTPPNQPPSQ 207
                H NHH      QQQ    P   PPQ MM+  Q P Q HQ    H        P Q
Sbjct: 220 DVTEVHQNHHNMGMYGQQQTGVPPVGAPPQGMMHQGQGPSQMHQ---GH--------PGQ 268

Query: 208 PPNQPPNQQPNNTSASLPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRR 267
             + PP+Q PN+ S+ +PSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRR
Sbjct: 269 --HTPPSQNPNSQSSGMPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRR 326

Query: 268 RIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD--GGSDAGSDITPATSPQ 317
           RIEIAHALCLTERQIKIWFQNRRMKWKKENK+K   G    G +ITP  SPQ
Sbjct: 327 RIEIAHALCLTERQIKIWFQNRRMKWKKENKTKGEPGSGGEGDEITPPNSPQ 378

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|112983708|ref|NP_001037319.1| antennapedia homologue protein [Bombyx mori] gi|391615|dbj|BAA04087.1| Antennapedia homologue protein [Bombyx mori] gi|426204115|gb|AFY12623.1| antennapedia-like protein [Bombyx mori]

 Score =  234 bits (598), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 155/269 (57%), Positives = 168/269 (62%), Gaps = 38/269 (14%)

Query: 61  GQPVHGMPYPRFPPYDRMDIRNAAYYGAHEGGMEQYPRPDSPS-MGHMGPQ------NGH 113
            QP  GMPYPRFPPYDR+      YY   E   +   RPDSPS MGHMGP+      NGH
Sbjct: 17  AQPAPGMPYPRFPPYDRL-----GYYQQME---QNGYRPDSPSQMGHMGPKTDGYGPNGH 68

Query: 114 Q--TPVVYASCKLQAAVGNG-IIPGPESPNDLVDPTLNNHHHHQHHHMNHHPHPHPQQQQ 170
           Q  TP VY SCKLQAA   G  +PG  SP       + +H H Q H + H   PH   QQ
Sbjct: 69  QPATPAVYTSCKLQAAAATGGAVPG--SPPLEQAQQMPHHMHPQQHMVQHGVPPH---QQ 123

Query: 171 PQQPPPQHMMYAQQPPPQHHQVVVNHQQTPPNQPPSQPPNQPPNQQPNNTSASLPSPLYP 230
               P   M +  Q PP H Q +   Q  P              Q P NT  SLPSPLYP
Sbjct: 124 HLMYPVDDMQHQTQMPPMHQQSMHAQQPPP-------------QQPPPNTKPSLPSPLYP 170

Query: 231 WMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR 290
           WMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR
Sbjct: 171 WMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR 230

Query: 291 MKWKKENKSKD--GGSDAGSDITPATSPQ 317
           MKWKKENK+K   G  D   +++P TSPQ
Sbjct: 231 MKWKKENKTKGEPGSGDEPDNMSPPTSPQ 259

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195389692|ref|XP_002053510.1| antennapedia [Drosophila virilis] gi|194151596|gb|EDW67030.1| antennapedia [Drosophila virilis]

 Score =  223 bits (569), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 182/403 (45%), Positives = 203/403 (50%), Gaps = 123/403 (30%)

Query: 1   MSSYFANSYMPDIKNGGVLPPEHHQQHHYGATVLPQNNGVEDPSMYDPRQVHHYGQVPNN 60
           M+SYF NSYM           + H  H+ G       NGV D    D +Q+HHY Q PN 
Sbjct: 11  MTSYFTNSYMG---------ADMHHGHYPG-------NGVTD---LDAQQMHHYSQNPNQ 51

Query: 61  GQPVHGMPYPRFPPYDRMDIRNAAYYGAHEGGMEQYPRPDSPS--MGHMGPQ---NGHQT 115
                 MPYPRFPPYDRM   N       +   + Y RPDSPS  +G + PQ   NG   
Sbjct: 52  ---QGNMPYPRFPPYDRMPYYNGQGMDQQQQQHQGYSRPDSPSSQVGGVMPQAQTNGQLV 108

Query: 116 PV----------------------------------------------VYASCKLQAAVG 129
            V                                              VYASCKLQAAVG
Sbjct: 109 SVAQQQQQTQQQQQAQTQQQQAQQAPLQQQQHPQVTQQVTHPQQQQPVVYASCKLQAAVG 168

Query: 130 N-GIIPGPESPNDLVDPTLNNHH--------HHQHH------------------HMNHHP 162
             G++    SP  LVD  +  HH        HH  H                  H NHH 
Sbjct: 169 GLGMVQEGGSP-PLVD-QMGGHHMNAQMTLPHHMGHPQAQLGYTDVGVPDVTEVHQNHHN 226

Query: 163 HPHPQQQQ----PQQPPPQHMMY--AQQPPPQHHQVVVNHQQTPPNQPPSQPPNQPPNQQ 216
                QQQ    P   PPQ MM+  A Q PPQ HQ         P Q      + PP+Q 
Sbjct: 227 MGMYGQQQTGVPPVVAPPQAMMHPGAGQGPPQMHQ-------GHPGQ------HTPPSQN 273

Query: 217 PNNTSASLPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC 276
           P++ S+ +PSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC
Sbjct: 274 PSSQSSGMPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC 333

Query: 277 LTERQIKIWFQNRRMKWKKENKSKD--GGSDAGSDITPATSPQ 317
           LTERQIKIWFQNRRMKWKKENK+K   G    G +ITP  SPQ
Sbjct: 334 LTERQIKIWFQNRRMKWKKENKTKGEPGSGGEGDEITPPNSPQ 376

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198453463|ref|XP_002137673.1| antp, isoform A [Drosophila pseudoobscura pseudoobscura] gi|198132367|gb|EDY68231.1| antp, isoform A [Drosophila pseudoobscura pseudoobscura]

 Score =  223 bits (569), Expect = 8e-56,   Method: Compositional matrix adjust.
 Identities = 132/234 (56%), Positives = 145/234 (61%), Gaps = 44/234 (18%)

Query: 116 PVVYASCKLQAAVGNGIIPGPESPNDLVDPTLNNHH--------HHQHH----------- 156
           PVVYASCKLQAAVG G+   PE  +  +   +  HH        HH  H           
Sbjct: 171 PVVYASCKLQAAVGVGLGLVPEGGSPPLVDQMTGHHMNAQMSLPHHMGHPQAQLGYTDVG 230

Query: 157 -------HMNHHPHPHPQQQQ----PQQPPPQHMMYAQQPPPQHHQVVVNHQQTPPNQPP 205
                  H NHH      QQQ    P   PPQ MM+  Q PPQ HQ  ++ Q TPP+Q  
Sbjct: 231 VPDVTEVHQNHHNMGMYGQQQTGVPPVGAPPQAMMHQGQGPPQMHQGHLSGQHTPPSQ-- 288

Query: 206 SQPPNQPPNQQPNNTSASLPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTR 265
                      PN+ S+ +PSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTR
Sbjct: 289 ----------NPNSQSSGMPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTR 338

Query: 266 RRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD--GGSDAGSDITPATSPQ 317
           RRRIEIAHALCLTERQIKIWFQNRRMKWKKENK+K   G    G +ITP  SPQ
Sbjct: 339 RRRIEIAHALCLTERQIKIWFQNRRMKWKKENKTKGEPGSGGEGDEITPPNSPQ 392

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195152057|ref|XP_002016955.1| GL22036 [Drosophila persimilis] gi|194112012|gb|EDW34055.1| GL22036 [Drosophila persimilis]

 Score =  223 bits (569), Expect = 8e-56,   Method: Compositional matrix adjust.
 Identities = 132/234 (56%), Positives = 145/234 (61%), Gaps = 44/234 (18%)

Query: 116 PVVYASCKLQAAVGNGIIPGPESPNDLVDPTLNNHH--------HHQHH----------- 156
           PVVYASCKLQAAVG G+   PE  +  +   +  HH        HH  H           
Sbjct: 174 PVVYASCKLQAAVGVGLGLVPEGGSPPLVDQMTGHHMNAQMSLPHHMGHPQAQLGYTDVG 233

Query: 157 -------HMNHHPHPHPQQQQ----PQQPPPQHMMYAQQPPPQHHQVVVNHQQTPPNQPP 205
                  H NHH      QQQ    P   PPQ MM+  Q PPQ HQ  ++ Q TPP+Q  
Sbjct: 234 VPDVTEVHQNHHNMGMYGQQQTGVPPVGAPPQAMMHQGQGPPQMHQGHLSGQHTPPSQ-- 291

Query: 206 SQPPNQPPNQQPNNTSASLPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTR 265
                      PN+ S+ +PSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTR
Sbjct: 292 ----------NPNSQSSGMPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTR 341

Query: 266 RRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD--GGSDAGSDITPATSPQ 317
           RRRIEIAHALCLTERQIKIWFQNRRMKWKKENK+K   G    G +ITP  SPQ
Sbjct: 342 RRRIEIAHALCLTERQIKIWFQNRRMKWKKENKTKGEPGSGGEGDEITPPNSPQ 395

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

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	317
FB|FBgn0260642	378	Antp "Antennapedia" [Drosophil	0.305	0.256	0.815	2.6e-63
UNIPROTKB|Q24645	394	Antp "Homeotic protein antenna	0.305	0.246	0.815	3.4e-63
UNIPROTKB|E2QT43	269	HOXB5 "Uncharacterized protein	0.293	0.345	0.641	5e-35
UNIPROTKB|P09067	269	HOXB5 "Homeobox protein Hox-B5	0.293	0.345	0.641	5e-35
UNIPROTKB|F1RWG0	269	HOXB5 "Uncharacterized protein	0.293	0.345	0.641	5e-35
MGI|MGI:96186	269	Hoxb5 "homeobox B5" [Mus muscu	0.293	0.345	0.641	5e-35
RGD|1562292	269	Hoxb5 "homeo box B5" [Rattus n	0.293	0.345	0.641	5e-35
UNIPROTKB|E2QT33	237	HOXB7 "Uncharacterized protein	0.255	0.341	0.853	2.8e-34
UNIPROTKB|E2RQ19	242	HOXB8 "Uncharacterized protein	0.252	0.330	0.75	3.4e-34
UNIPROTKB|I3L3R1	242	HOXB8 "Homeobox B8, isoform CR	0.252	0.330	0.75	3.4e-34

FB|FBgn0260642 Antp "Antennapedia" [Drosophila melanogaster (taxid:7227)]

 Score = 435 (158.2 bits), Expect = 2.6e-63, Sum P(3) = 2.6e-63
 Identities = 84/103 (81%), Positives = 88/103 (85%)

Query:   221 SASLPSPLYPWMRSQF----ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC 276
             S+ +PSPLYPWMRSQF    ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC
Sbjct:   276 SSGMPSPLYPWMRSQFGKCQERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC 335

Query:   277 LTERQIKIWFQNRRMKWKKENKSKD--GGSDAGSDITPATSPQ 317
             LTERQIKIWFQNRRMKWKKENK+K   G    G +ITP  SPQ
Sbjct:   336 LTERQIKIWFQNRRMKWKKENKTKGEPGSGGEGDEITPPNSPQ 378

GO:0005634 "nucleus" evidence=NAS;IDA

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

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

GO:0003677 "DNA binding" evidence=IDA

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

GO:0007494 "midgut development" evidence=TAS

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

GO:0007379 "segment specification" evidence=NAS

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

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

GO:0005737 "cytoplasm" evidence=IDA

GO:0007507 "heart development" evidence=IEP

GO:0007383 "specification of segmental identity, antennal segment" evidence=IMP

GO:0048542 "lymph gland development" evidence=IMP

GO:0014019 "neuroblast development" evidence=IMP

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

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

UNIPROTKB|Q24645 Antp "Homeotic protein antennapedia" [Drosophila subobscura (taxid:7241)]

 Score = 435 (158.2 bits), Expect = 3.4e-63, Sum P(3) = 3.4e-63
 Identities = 84/103 (81%), Positives = 88/103 (85%)

Query:   221 SASLPSPLYPWMRSQF----ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC 276
             S+ +PSPLYPWMRSQF    ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC
Sbjct:   292 SSGMPSPLYPWMRSQFGKCQERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC 351

Query:   277 LTERQIKIWFQNRRMKWKKENKSKD--GGSDAGSDITPATSPQ 317
             LTERQIKIWFQNRRMKWKKENK+K   G    G +ITP  SPQ
Sbjct:   352 LTERQIKIWFQNRRMKWKKENKTKGEPGSGGEGDEITPPNSPQ 394

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0007384 "specification of segmental identity, thorax" evidence=ISS

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

UNIPROTKB|E2QT43 HOXB5 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 318 (117.0 bits), Expect = 5.0e-35, Sum P(3) = 5.0e-35
 Identities = 68/106 (64%), Positives = 76/106 (71%)

Query:   220 TSASLP---SP-LYPWMRSQF--------ERKRGRQTYTRYQTLELEKEFHFNRYLTRRR 267
             TS + P   +P ++PWMR           + KR R  YTRYQTLELEKEFHFNRYLTRRR
Sbjct:   164 TSTAAPEGQTPQIFPWMRKLHISHDMTGPDGKRARTAYTRYQTLELEKEFHFNRYLTRRR 223

Query:   268 RIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGG-SDAGSDITP 312
             RIEIAHALCL+ERQIKIWFQNRRMKWKK+NK K    + AGS   P
Sbjct:   224 RIEIAHALCLSERQIKIWFQNRRMKWKKDNKLKSMSLATAGSAFQP 269

GO:0005634 "nucleus" evidence=IEA

GO:0048704 "embryonic skeletal system morphogenesis" evidence=IEA

GO:0045446 "endothelial cell differentiation" evidence=IEA

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

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

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

UNIPROTKB|P09067 HOXB5 "Homeobox protein Hox-B5" [Homo sapiens (taxid:9606)]

 Score = 318 (117.0 bits), Expect = 5.0e-35, Sum P(3) = 5.0e-35
 Identities = 68/106 (64%), Positives = 76/106 (71%)

Query:   220 TSASLP---SP-LYPWMRSQF--------ERKRGRQTYTRYQTLELEKEFHFNRYLTRRR 267
             TS + P   +P ++PWMR           + KR R  YTRYQTLELEKEFHFNRYLTRRR
Sbjct:   164 TSTAAPEGQTPQIFPWMRKLHISHDMTGPDGKRARTAYTRYQTLELEKEFHFNRYLTRRR 223

Query:   268 RIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGG-SDAGSDITP 312
             RIEIAHALCL+ERQIKIWFQNRRMKWKK+NK K    + AGS   P
Sbjct:   224 RIEIAHALCLSERQIKIWFQNRRMKWKKDNKLKSMSLATAGSAFQP 269

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

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

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

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

GO:0045446 "endothelial cell differentiation" evidence=IEA

GO:0048704 "embryonic skeletal system morphogenesis" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0009653 "anatomical structure morphogenesis" evidence=TAS

UNIPROTKB|F1RWG0 HOXB5 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 318 (117.0 bits), Expect = 5.0e-35, Sum P(3) = 5.0e-35
 Identities = 68/106 (64%), Positives = 76/106 (71%)

Query:   220 TSASLP---SP-LYPWMRSQF--------ERKRGRQTYTRYQTLELEKEFHFNRYLTRRR 267
             TS + P   +P ++PWMR           + KR R  YTRYQTLELEKEFHFNRYLTRRR
Sbjct:   164 TSTAAPEGQTPQIFPWMRKLHISHDMTGPDGKRARTAYTRYQTLELEKEFHFNRYLTRRR 223

Query:   268 RIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGG-SDAGSDITP 312
             RIEIAHALCL+ERQIKIWFQNRRMKWKK+NK K    + AGS   P
Sbjct:   224 RIEIAHALCLSERQIKIWFQNRRMKWKKDNKLKSMSLATAGSAFQP 269

GO:0005634 "nucleus" evidence=IEA

GO:0048704 "embryonic skeletal system morphogenesis" evidence=IEA

GO:0045446 "endothelial cell differentiation" evidence=IEA

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

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

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

MGI|MGI:96186 Hoxb5 "homeobox B5" [Mus musculus (taxid:10090)]

 Score = 318 (117.0 bits), Expect = 5.0e-35, Sum P(3) = 5.0e-35
 Identities = 68/106 (64%), Positives = 76/106 (71%)

Query:   220 TSASLP---SP-LYPWMRSQF--------ERKRGRQTYTRYQTLELEKEFHFNRYLTRRR 267
             TS + P   +P ++PWMR           + KR R  YTRYQTLELEKEFHFNRYLTRRR
Sbjct:   164 TSTAAPEGQTPQIFPWMRKLHISHDMTGPDGKRARTAYTRYQTLELEKEFHFNRYLTRRR 223

Query:   268 RIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGG-SDAGSDITP 312
             RIEIAHALCL+ERQIKIWFQNRRMKWKK+NK K    + AGS   P
Sbjct:   224 RIEIAHALCLSERQIKIWFQNRRMKWKKDNKLKSMSLATAGSAFQP 269

GO:0003677 "DNA binding" evidence=IDA

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

GO:0005634 "nucleus" evidence=IDA

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

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

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

GO:0045446 "endothelial cell differentiation" evidence=IDA

GO:0048704 "embryonic skeletal system morphogenesis" evidence=IGI;IMP

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

RGD|1562292 Hoxb5 "homeo box B5" [Rattus norvegicus (taxid:10116)]

 Score = 318 (117.0 bits), Expect = 5.0e-35, Sum P(3) = 5.0e-35
 Identities = 68/106 (64%), Positives = 76/106 (71%)

Query:   220 TSASLP---SP-LYPWMRSQF--------ERKRGRQTYTRYQTLELEKEFHFNRYLTRRR 267
             TS + P   +P ++PWMR           + KR R  YTRYQTLELEKEFHFNRYLTRRR
Sbjct:   164 TSTAAPEGQTPQIFPWMRKLHISHDMTGPDGKRARTAYTRYQTLELEKEFHFNRYLTRRR 223

Query:   268 RIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGG-SDAGSDITP 312
             RIEIAHALCL+ERQIKIWFQNRRMKWKK+NK K    + AGS   P
Sbjct:   224 RIEIAHALCLSERQIKIWFQNRRMKWKKDNKLKSMSLATAGSAFQP 269

GO:0003677 "DNA binding" evidence=ISO

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

GO:0005634 "nucleus" evidence=IEA;ISO

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

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

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

GO:0045446 "endothelial cell differentiation" evidence=IEA;ISO

GO:0048704 "embryonic skeletal system morphogenesis" evidence=IEA;ISO

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

UNIPROTKB|E2QT33 HOXB7 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 372 (136.0 bits), Expect = 2.8e-34, P = 2.8e-34
 Identities = 70/82 (85%), Positives = 74/82 (90%)

Query:   228 LYPWMRSQ-FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWF 286
             +YPWMRS   +RKRGRQTYTRYQTLELEKEFH+NRYLTRRRRIEIAHALCLTERQIKIWF
Sbjct:   126 IYPWMRSSGTDRKRGRQTYTRYQTLELEKEFHYNRYLTRRRRIEIAHALCLTERQIKIWF 185

Query:   287 QNRRMKWKKENKSKDGGSDAGS 308
             QNRRMKWKKENKS   G+ A S
Sbjct:   186 QNRRMKWKKENKSTGPGATASS 207

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

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

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

UNIPROTKB|E2RQ19 HOXB8 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 317 (116.6 bits), Expect = 3.4e-34, Sum P(2) = 3.4e-34
 Identities = 63/84 (75%), Positives = 71/84 (84%)

Query:   221 SASLPSP--LYPWMRSQFE-RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCL 277
             S   PSP  L+PWMR Q   R+RGRQTY+RYQTLELEKEF FN YLTR+RRIE++HAL L
Sbjct:   125 SQQSPSPTQLFPWMRPQAAGRRRGRQTYSRYQTLELEKEFLFNPYLTRKRRIEVSHALGL 184

Query:   278 TERQIKIWFQNRRMKWKKENKSKD 301
             TERQ+KIWFQNRRMKWKKEN +KD
Sbjct:   185 TERQVKIWFQNRRMKWKKEN-NKD 207

GO:0005634 "nucleus" evidence=IEA

GO:0048704 "embryonic skeletal system morphogenesis" evidence=IEA

GO:0021516 "dorsal spinal cord development" evidence=IEA

GO:0019233 "sensory perception of pain" evidence=IEA

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

GO:0008344 "adult locomotory behavior" evidence=IEA

GO:0007625 "grooming behavior" evidence=IEA

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

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

UNIPROTKB|I3L3R1 HOXB8 "Homeobox B8, isoform CRA_a" [Homo sapiens (taxid:9606)]

 Score = 317 (116.6 bits), Expect = 3.4e-34, Sum P(2) = 3.4e-34
 Identities = 63/84 (75%), Positives = 71/84 (84%)

Query:   221 SASLPSP--LYPWMRSQFE-RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCL 277
             S   PSP  L+PWMR Q   R+RGRQTY+RYQTLELEKEF FN YLTR+RRIE++HAL L
Sbjct:   125 SEQSPSPTQLFPWMRPQAAGRRRGRQTYSRYQTLELEKEFLFNPYLTRKRRIEVSHALGL 184

Query:   278 TERQIKIWFQNRRMKWKKENKSKD 301
             TERQ+KIWFQNRRMKWKKEN +KD
Sbjct:   185 TERQVKIWFQNRRMKWKKEN-NKD 207

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P09629	HXB7_HUMAN	No assigned EC number	0.7157	0.2965	0.4331	yes	N/A
P09024	HXB7_MOUSE	No assigned EC number	0.7472	0.2839	0.4147	yes	N/A
P02833	ANTP_DROME	No assigned EC number	0.5659	0.5804	0.4867	yes	N/A
Q9TT89	HXB7_BOVIN	No assigned EC number	0.7263	0.2965	0.4331	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	317
pfam00046	57	pfam00046, Homeobox, Homeobox domain	3e-29
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	3e-24
smart00389	57	smart00389, HOX, Homeodomain	5e-24
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	3e-09
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	1e-07
pfam13388	422	pfam13388, DUF4106, Protein of unknown function (D	7e-07
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	1e-06
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	8e-04
PRK10263	1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	0.001
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	0.002
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	0.002
PRK03427	333	PRK03427, PRK03427, cell division protein ZipA; Pr	0.002

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

 Score =  106 bits (266), Expect = 3e-29
 Identities = 33/57 (57%), Positives = 40/57 (70%)

Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           +R R T+T  Q  ELEKEF  NRY +   R E+A  L LTERQ+K+WFQNRR KWK+
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 = 93.1 bits (232), Expect = 3e-24
 Identities = 32/59 (54%), Positives = 38/59 (64%)

Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
           +R R  +T  Q  ELEKEF  N Y +R  R E+A  L LTERQ+KIWFQNRR K K+  
Sbjct: 1   RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59

Length = 59

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 92.3 bits (230), Expect = 5e-24
 Identities = 31/57 (54%), Positives = 40/57 (70%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294
           ++R R ++T  Q  ELEKEF  N Y +R  R E+A  L L+ERQ+K+WFQNRR KWK
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 = 54.8 bits (132), Expect = 3e-09
 Identities = 23/63 (36%), Positives = 36/63 (57%)

Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
           K  R+  T  Q + LE+EF  N Y +   RI+++  L +  + ++IWFQN+R K KK+  
Sbjct: 52  KSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRS 111

Query: 299 SKD 301
            K 
Sbjct: 112 GKV 114

Length = 156

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 52.8 bits (127), Expect = 1e-07
 Identities = 37/188 (19%), Positives = 45/188 (23%), Gaps = 35/188 (18%)

Query: 48  PRQVHHYGQVPNNGQPVHGMPYPRFPPYDRMDIRNAAYYGAHEGGMEQYPRPDSPSMGHM 107
             Q+    Q P   QP   +     PP      R AA+         Q   P+ P     
Sbjct: 160 EAQLQQRQQAPQLPQPPQQVLPQGMPP------RQAAFP--------QQGPPEQPPGYPQ 205

Query: 108 GPQNGHQTPVVYASCKLQAAVGNGIIPGPESPNDLVDPTLNNHHHHQHHHMNHHPHPHPQ 167
            PQ   +           +         P+ P              Q   +     P   
Sbjct: 206 PPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQ-------------QPPPLQQPQFPGLS 252

Query: 168 QQQPQQPPPQHMMYAQQPPPQHHQVVVN--------HQQTPPNQPPSQPPNQPPNQQPNN 219
           QQ P  PP       Q P PQ      N         Q      PP Q P   P  Q   
Sbjct: 253 QQMPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLLPLVQQPQ 312

Query: 220 TSASLPSP 227
                P  
Sbjct: 313 GQQRGPQF 320

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|222095 pfam13388, DUF4106, Protein of unknown function (DUF4106)

 Score = 50.1 bits (119), Expect = 7e-07
 Identities = 32/99 (32%), Positives = 36/99 (36%), Gaps = 8/99 (8%)

Query: 127 AVGNGIIPGP--ESPNDLVDPTLNNHHHHQHHHMNHHPHPHPQQQQPQQPPPQHMMYAQQ 184
           A G  I P P  E+P   +  T  + H H+H H      P P QQ   Q P Q     Q 
Sbjct: 167 ASGTYIPPNPPREAPAPGLPKTFTSSHGHRHRHA-----PKPTQQPTVQNPAQQPT-VQN 220

Query: 185 PPPQHHQVVVNHQQTPPNQPPSQPPNQPPNQQPNNTSAS 223
           P  Q  Q        P  QP  Q P Q P Q       S
Sbjct: 221 PAQQPQQQPQQQPVQPAQQPTPQNPAQQPPQTEQGHKRS 259

This family of proteins are found in large numbers in the Trichomonas vaginalis proteome. The function of this protein is unknown. Length = 422

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 49.8 bits (119), Expect = 1e-06
 Identities = 39/182 (21%), Positives = 52/182 (28%), Gaps = 7/182 (3%)

Query: 98  RPDSPSMGHMGPQNGHQTPVVYASCKLQAAVGNGIIPGPESPNDLVDPTLNNHHHHQHHH 157
            P  P         G          +       G    P+   + V P        Q   
Sbjct: 169 APQLPQPPQQVLPQGMPPRQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPA 228

Query: 158 MNHHPHPHPQQQQP-QQPP----PQHMMYAQQPPPQHHQVVVNHQQTPPNQPPSQPPNQP 212
               P   PQQ  P QQP      Q M      PPQ  Q     Q  PP Q    P    
Sbjct: 229 QPPLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGL 288

Query: 213 PNQQPNNTSASLPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIA 272
           P  Q           L P ++    ++RG Q   R Q ++L ++          +R +  
Sbjct: 289 PQGQNAPLPPPQQPQLLPLVQQPQGQQRGPQ--FREQLVQLSQQQREALSQEEAKRAKRR 346

Query: 273 HA 274
           H 
Sbjct: 347 HK 348

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 41.1 bits (96), Expect = 8e-04
 Identities = 19/69 (27%), Positives = 22/69 (31%), Gaps = 5/69 (7%)

Query: 162  PHPHPQQQQPQQPPPQHMMYAQQPPPQHHQVVVNHQQTPPNQPPSQPPNQPPNQQPNNTS 221
                P  Q  + P PQ    A  PP    Q     Q  PP  PP +P         +   
Sbjct: 2897 SFALPPDQPERPPQPQ----APPPPQPQPQPPPPPQPQPPPPPPPRPQPPLA-PTTDPAG 2951

Query: 222  ASLPSPLYP 230
            A  PS   P
Sbjct: 2952 AGEPSGAVP 2960

Length = 3151

>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional

 Score = 40.8 bits (95), Expect = 0.001
 Identities = 27/88 (30%), Positives = 28/88 (31%), Gaps = 6/88 (6%)

Query: 144 DPTLNNHHHHQHHHMNHHPHPHPQQQQPQQP--PPQHMMYAQQPPPQHHQVVVNHQQTPP 201
            P        Q+        P PQ QQPQQP  P       QQP     Q     Q   P
Sbjct: 754 QPQQPVAPQQQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAP 813

Query: 202 NQPPSQPPN----QPPNQQPNNTSASLP 225
                QP      QP  QQP    A  P
Sbjct: 814 QPQYQQPQQPVAPQPQYQQPQQPVAPQP 841

Length = 1355

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 39.9 bits (93), Expect = 0.002
 Identities = 18/71 (25%), Positives = 22/71 (30%), Gaps = 5/71 (7%)

Query: 162  PHPHPQQQQPQQPPPQHMMYAQQPPPQHHQVVVNHQQTPPNQPPSQPPNQPPNQQPNNTS 221
              P  Q ++P QP          P PQ         Q PP  PP   P   P   P    
Sbjct: 2899 ALPPDQPERPPQPQAP-----PPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAG 2953

Query: 222  ASLPSPLYPWM 232
                +   PW+
Sbjct: 2954 EPSGAVPQPWL 2964

Length = 3151

>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 17/74 (22%), Positives = 19/74 (25%), Gaps = 2/74 (2%)

Query: 162 PHPHPQQQQPQQPPPQHMMYAQQPPPQHHQVVVNHQQTPPNQPPSQPP--NQPPNQQPNN 219
           P P       Q P P       Q              TP   P + PP     P      
Sbjct: 51  PSPQAPPPVAQLPQPLPQPPPTQALQALPAGDQQQHNTPTGSPAANPPATFALPAGPAGP 110

Query: 220 TSASLPSPLYPWMR 233
           T  + P  LYP   
Sbjct: 111 TIQTEPGQLYPVQV 124

Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription. Length = 332

>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional

 Score = 39.2 bits (92), Expect = 0.002
 Identities = 18/69 (26%), Positives = 25/69 (36%), Gaps = 5/69 (7%)

Query: 157 HMNHHPHPHPQQQQPQQPPPQHMMYAQQPPPQHHQVVVNHQQTPPNQPPSQPPNQPPNQQ 216
           H    P+   Q +QP Q PP+  +    P              P  QP  QP  + P QQ
Sbjct: 90  HQYQPPYASAQPRQPVQQPPEAQV---PPQHAPRPAQP--APQPVQQPAYQPQPEQPLQQ 144

Query: 217 PNNTSASLP 225
           P +   +  
Sbjct: 145 PVSPQVAPA 153

Length = 333

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	317
KOG0489|consensus	261		99.82
KOG0487|consensus	308		99.73
KOG0850|consensus	245		99.73
KOG0488|consensus	309		99.71
KOG0843|consensus	197		99.68
KOG2251|consensus	228		99.68
KOG0484|consensus	125		99.67
KOG0494|consensus	332		99.67
KOG0842|consensus	307		99.67
KOG0848|consensus	317		99.66
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.62
KOG0485|consensus	268		99.61
KOG0492|consensus	246		99.6
KOG3802|consensus	398		99.53
KOG0491|consensus	194		99.52
KOG0493|consensus	342		99.52
KOG0486|consensus	351		99.5
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.49
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.49
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.49
KOG0844|consensus	408		99.47
COG5576	156	Homeodomain-containing transcription factor [Trans	99.46
KOG0483|consensus	198		99.41
KOG0847|consensus	288		99.29
KOG4577|consensus	383		99.28
KOG0490|consensus	235		99.25
KOG1168|consensus	385		99.1
KOG0849|consensus	354		99.05
KOG0775|consensus	304		98.91
KOG0774|consensus	334		98.6
KOG2252|consensus	558		98.39
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.37
KOG1146|consensus	1406		98.0
KOG0490|consensus	235		97.98
KOG0773|consensus	342		96.83
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	96.83
KOG3623|consensus	1007		96.14
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	95.2
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	88.92
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	83.57
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	83.11
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	81.07

>KOG0489|consensus

Probab=99.82  E-value=6.5e-21  Score=179.20  Aligned_cols=79  Identities=73%  Similarity=1.201  Sum_probs=73.2

Q ss_pred             CCCCCcchhccc----------ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhh
Q psy3281         225 PSPLYPWMRSQF----------ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK  294 (317)
Q Consensus       225 ~s~~~P~~~s~~----------krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~K  294 (317)
                      +..+++||+...          +.||.||.||..||.+||++|..|+|+++..|.|||..|+|+|++|||||||||+|||
T Consensus       136 ~~~~~p~~~~~~~~~~~~~~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~K  215 (261)
T KOG0489|consen  136 SNQIYPWMKSTANYLSSSETGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWK  215 (261)
T ss_pred             ccccccchhhhhcccccccccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHH
Confidence            347899999864          5789999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhcccCCC
Q psy3281         295 KENKSKDGG  303 (317)
Q Consensus       295 K~~k~k~~~  303 (317)
                      |.++.+...
T Consensus       216 k~~k~~~~~  224 (261)
T KOG0489|consen  216 KENKAKSSQ  224 (261)
T ss_pred             Hhhcccccc
Confidence            998877754

>KOG0487|consensus

Probab=99.73  E-value=2.5e-18  Score=164.52  Aligned_cols=74  Identities=53%  Similarity=0.790  Sum_probs=67.1

Q ss_pred             CCcchhcccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         228 LYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       228 ~~P~~~s~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      ..+|...-++.||||.-+|+.|+.+||++|..|.|++++.|.||++.|+|+++||||||||||.|+||.++...
T Consensus       225 ~~~~~~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r  298 (308)
T KOG0487|consen  225 HLPNASSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR  298 (308)
T ss_pred             CCcccccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence            44566666677889999999999999999999999999999999999999999999999999999999987444

>KOG0850|consensus

Probab=99.73  E-value=8.1e-18  Score=154.33  Aligned_cols=67  Identities=39%  Similarity=0.611  Sum_probs=62.9

Q ss_pred             ccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         235 QFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       235 ~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      .+|.||.||.|+..||..|.+.|+++.|+...||.+||..|||+.++|||||||||.|.||..|.+.
T Consensus       119 ~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~  185 (245)
T KOG0850|consen  119 GKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGS  185 (245)
T ss_pred             cccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCC
Confidence            3466788999999999999999999999999999999999999999999999999999999999555

>KOG0488|consensus

Probab=99.71  E-value=6.8e-18  Score=162.42  Aligned_cols=66  Identities=42%  Similarity=0.765  Sum_probs=61.7

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      +|+||.||.||..||..||+.|++.+|++..+|++||..|||+..|||+||||||+||||......
T Consensus       170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~  235 (309)
T KOG0488|consen  170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGG  235 (309)
T ss_pred             cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhh
Confidence            577788999999999999999999999999999999999999999999999999999999766533

>KOG0843|consensus

Probab=99.68  E-value=8e-17  Score=143.23  Aligned_cols=64  Identities=41%  Similarity=0.654  Sum_probs=60.9

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhccc
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSK  300 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k  300 (317)
                      +.||.||.||.+||..||..|+.+.|....||+.||..|+|++.+|||||||||.|.||+...+
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            6688999999999999999999999999999999999999999999999999999999987763

>KOG2251|consensus

Probab=99.68  E-value=5.3e-17  Score=148.23  Aligned_cols=68  Identities=32%  Similarity=0.510  Sum_probs=63.7

Q ss_pred             hcccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhccc
Q psy3281         233 RSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSK  300 (317)
Q Consensus       233 ~s~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k  300 (317)
                      ...+|.||+||+|+..||++||..|.++.||++..|++||.+|+|.+.+|+|||+|||+|+|+..+..
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            44567789999999999999999999999999999999999999999999999999999999988764

>KOG0484|consensus

Probab=99.67  E-value=8.3e-18  Score=137.96  Aligned_cols=66  Identities=38%  Similarity=0.579  Sum_probs=62.4

Q ss_pred             hcccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281         233 RSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK  298 (317)
Q Consensus       233 ~s~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k  298 (317)
                      .+++|.||.||.||..||.+||+.|..+.||++-.|++||.++.|++.+|+|||||||+|.||.++
T Consensus        12 ~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr   77 (125)
T KOG0484|consen   12 TEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER   77 (125)
T ss_pred             hHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence            456678899999999999999999999999999999999999999999999999999999999765

>KOG0494|consensus

Probab=99.67  E-value=5.9e-17  Score=150.95  Aligned_cols=71  Identities=38%  Similarity=0.601  Sum_probs=64.2

Q ss_pred             hcccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCCC
Q psy3281         233 RSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGG  303 (317)
Q Consensus       233 ~s~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~~  303 (317)
                      ++++|+|+.||.||..|+++||+.|++..||+...|+.||.++.|.|.+|+|||||||+||||++|....+
T Consensus       136 kkk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~s  206 (332)
T KOG0494|consen  136 KKKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGS  206 (332)
T ss_pred             ccccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcc
Confidence            33445555699999999999999999999999999999999999999999999999999999999987654

>KOG0842|consensus

Probab=99.67  E-value=4.8e-17  Score=155.70  Aligned_cols=69  Identities=39%  Similarity=0.624  Sum_probs=63.9

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCCCC
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGGS  304 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~~~  304 (317)
                      .+|||.|..||..|+.+||+.|+..+|++..||+.||..|.||++||||||||||-|.||..+.+...+
T Consensus       151 ~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~  219 (307)
T KOG0842|consen  151 RKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA  219 (307)
T ss_pred             ccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence            466778889999999999999999999999999999999999999999999999999999988887433

>KOG0848|consensus

Probab=99.66  E-value=2.1e-17  Score=154.44  Aligned_cols=76  Identities=54%  Similarity=0.838  Sum_probs=66.9

Q ss_pred             CCCCCcchhccc-----------ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhh
Q psy3281         225 PSPLYPWMRSQF-----------ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW  293 (317)
Q Consensus       225 ~s~~~P~~~s~~-----------krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~  293 (317)
                      ....+.||++.-           .+.|-|.++|+.|..+||++|..++|+++..+.|||..|||+|++|||||||||+|+
T Consensus       175 R~s~~dwmrkpa~~~~g~~~KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKE  254 (317)
T KOG0848|consen  175 RRSPYDWMRKPAQPGTGQNVKTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKE  254 (317)
T ss_pred             CCChhhhhhcccccCCCCCceeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHH
Confidence            345678887631           223568899999999999999999999999999999999999999999999999999


Q ss_pred             hhhhccc
Q psy3281         294 KKENKSK  300 (317)
Q Consensus       294 KK~~k~k  300 (317)
                      ||.+|++
T Consensus       255 RK~nKKk  261 (317)
T KOG0848|consen  255 RKDNKKK  261 (317)
T ss_pred             HHHHHHH
Confidence            9998887

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.62  E-value=2.9e-16  Score=114.11  Aligned_cols=57  Identities=51%  Similarity=0.674  Sum_probs=55.4

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281         239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  295 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK  295 (317)
                      ||+|+.||.+|+.+|+.+|..+.||+..++++||..|||+..+|++||+|||.++||
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence            578999999999999999999999999999999999999999999999999999986

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

>KOG0485|consensus

Probab=99.61  E-value=1.9e-16  Score=144.53  Aligned_cols=67  Identities=42%  Similarity=0.740  Sum_probs=62.2

Q ss_pred             ccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         235 QFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       235 ~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      ..+|||.||+|+..|+..||..|+..+|++..||..||++|.|+|.||||||||||.||||......
T Consensus       101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~  167 (268)
T KOG0485|consen  101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADL  167 (268)
T ss_pred             ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhh
Confidence            3477899999999999999999999999999999999999999999999999999999999765444

>KOG0492|consensus

Probab=99.60  E-value=4.1e-16  Score=141.44  Aligned_cols=72  Identities=38%  Similarity=0.558  Sum_probs=65.4

Q ss_pred             cchhcccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         230 PWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       230 P~~~s~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      ..+++.+..|+.||-||..||..||+.|....|++++||.+++..|.|++.+|||||||||+|.||.+..+.
T Consensus       136 C~LrKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~  207 (246)
T KOG0492|consen  136 CTLRKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAEL  207 (246)
T ss_pred             chhcccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHH
Confidence            345666777889999999999999999999999999999999999999999999999999999999766544

>KOG3802|consensus

Probab=99.53  E-value=5.5e-15  Score=144.75  Aligned_cols=70  Identities=27%  Similarity=0.333  Sum_probs=64.5

Q ss_pred             CcchhcccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281         229 YPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK  298 (317)
Q Consensus       229 ~P~~~s~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k  298 (317)
                      ...+....+|||+||.|....+..||++|.+|+.|+..|+..||++|+|.+++|+|||+|||.|+||...
T Consensus       285 ~e~i~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  285 IEKIGAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             HHHhhccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            3344445588899999999999999999999999999999999999999999999999999999999888

>KOG0491|consensus

Probab=99.52  E-value=3.1e-15  Score=131.62  Aligned_cols=71  Identities=42%  Similarity=0.706  Sum_probs=65.0

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCCCCCCC
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGGSDAG  307 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~~~s~~  307 (317)
                      +++|.|++|+..|+..||+.|++.+|++..||.|||..|+|++++||.||||||+|.||..++....++.+
T Consensus        99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p~nS~~  169 (194)
T KOG0491|consen   99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQPKNSNG  169 (194)
T ss_pred             HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCCCCCCc
Confidence            56778999999999999999999999999999999999999999999999999999999988887554443

>KOG0493|consensus

Probab=99.52  E-value=7e-15  Score=137.33  Aligned_cols=63  Identities=54%  Similarity=0.763  Sum_probs=58.6

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      ||.||.||.+||..|+.+|..|+|+++..|.+||.+|+|.|.+|||||||+|+|.||.--.+.
T Consensus       247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn  309 (342)
T KOG0493|consen  247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKN  309 (342)
T ss_pred             cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCC
Confidence            578999999999999999999999999999999999999999999999999999998654443

>KOG0486|consensus

Probab=99.50  E-value=1.3e-14  Score=138.39  Aligned_cols=72  Identities=38%  Similarity=0.631  Sum_probs=65.9

Q ss_pred             cchhcccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         230 PWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       230 P~~~s~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      +.+++.+|+||.||.|+..||.+||..|.+|+||+-+.|+|||..++|+|.+|++||+|||+||||+++...
T Consensus       104 ~~~kki~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~  175 (351)
T KOG0486|consen  104 PNKKKISKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ  175 (351)
T ss_pred             cccchhhhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence            344555578899999999999999999999999999999999999999999999999999999999887665

>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=99.49  E-value=2.3e-14  Score=103.67  Aligned_cols=58  Identities=55%  Similarity=0.788  Sum_probs=54.8

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      ++.|+.|+.+++.+||.+|..++||+..++++||..|||++++|++||+|||.+.|+.
T Consensus         1 ~~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~   58 (59)
T cd00086           1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS   58 (59)
T ss_pred             CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence            3667899999999999999999999999999999999999999999999999998874

>smart00389 HOX Homeodomain

Probab=99.49  E-value=2.2e-14  Score=103.27  Aligned_cols=56  Identities=55%  Similarity=0.880  Sum_probs=52.8

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhh
Q psy3281         239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK  294 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~K  294 (317)
                      ++.|+.|+.+++.+|+.+|..+.||+..++++||..|||+.++|++||+|||.+.|
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            35678899999999999999999999999999999999999999999999999864

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

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.49  E-value=2.8e-14  Score=106.14  Aligned_cols=53  Identities=21%  Similarity=0.358  Sum_probs=51.0

Q ss_pred             cCCCCcccCHHHHHHHHHHhhhCCC----CCHHHHHHHHHHcCCCcccchhhcccch
Q psy3281         238 RKRGRQTYTRYQTLELEKEFHFNRY----LTRRRRIEIAHALCLTERQIKIWFQNRR  290 (317)
Q Consensus       238 rRR~Rt~fT~~Ql~~LE~~F~~n~y----Ps~~er~eLA~~LgLse~qVkiWFQNRR  290 (317)
                      +||.||.||.+|+..||++|+.+.|    |+..++++||..|||++++|+|||+|.+
T Consensus         1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            4789999999999999999999999    9999999999999999999999999965

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

>KOG0844|consensus

Probab=99.47  E-value=1.2e-14  Score=138.21  Aligned_cols=65  Identities=48%  Similarity=0.671  Sum_probs=60.7

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhccc
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSK  300 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k  300 (317)
                      ..-||-||.||.|||..||++|-+..|.++..|.|||..|+|.|..||+||||||+|+||.+..-
T Consensus       179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlam  243 (408)
T KOG0844|consen  179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAM  243 (408)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhc
Confidence            35579999999999999999999999999999999999999999999999999999999976643

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.46  E-value=7e-14  Score=122.86  Aligned_cols=66  Identities=35%  Similarity=0.515  Sum_probs=61.0

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      ...+++|++.|.+|+.+|++.|++++||+..+|.+|+..|+|+++.|+|||||||++.|+....+.
T Consensus        49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~  114 (156)
T COG5576          49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKV  114 (156)
T ss_pred             CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccch
Confidence            355778889999999999999999999999999999999999999999999999999999877644

>KOG0483|consensus

Probab=99.41  E-value=8.7e-14  Score=126.43  Aligned_cols=63  Identities=37%  Similarity=0.592  Sum_probs=58.1

Q ss_pred             cCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhccc
Q psy3281         238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSK  300 (317)
Q Consensus       238 rRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k  300 (317)
                      .++++.+|+.+|+..||+.|+.+.++..+++..||+.|||.+++|+|||||||+|||.++...
T Consensus        50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~  112 (198)
T KOG0483|consen   50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEK  112 (198)
T ss_pred             cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhh
Confidence            456677899999999999999999999999999999999999999999999999999876543

>KOG0847|consensus

Probab=99.29  E-value=1.2e-12  Score=119.90  Aligned_cols=64  Identities=42%  Similarity=0.776  Sum_probs=59.8

Q ss_pred             ccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281         235 QFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK  298 (317)
Q Consensus       235 ~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k  298 (317)
                      ..+++..|.+|+..||..||+.|+..+|+-.++|.+||..+|+++.+|+|||||||.||||+..
T Consensus       164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA  227 (288)
T KOG0847|consen  164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA  227 (288)
T ss_pred             CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence            4467778999999999999999999999999999999999999999999999999999999744

>KOG4577|consensus

Probab=99.28  E-value=2.4e-12  Score=121.89  Aligned_cols=65  Identities=31%  Similarity=0.419  Sum_probs=61.2

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      ..||.||+||+.||+.|+.+|+..+.|.+-.|+.|+.++||..++|+|||||||+|+||.+|...
T Consensus       166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAG  230 (383)
T KOG4577|consen  166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAG  230 (383)
T ss_pred             ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcc
Confidence            45899999999999999999999999999999999999999999999999999999999887543

>KOG0490|consensus

Probab=99.25  E-value=5.3e-12  Score=113.99  Aligned_cols=64  Identities=33%  Similarity=0.420  Sum_probs=60.9

Q ss_pred             ccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281         235 QFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK  298 (317)
Q Consensus       235 ~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k  298 (317)
                      ..++||.|+.|+..++++||+.|+++.||+...|+.||..++|++..|++||+|||+||++.++
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            4577899999999999999999999999999999999999999999999999999999999874

>KOG1168|consensus

Probab=99.10  E-value=3.4e-11  Score=114.22  Aligned_cols=65  Identities=28%  Similarity=0.384  Sum_probs=60.6

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhccc
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSK  300 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k  300 (317)
                      ..|||+||.+..-+.+.||.+|...+.|+.+.+..||++|+|.+.+|++||+|.|.|.||++...
T Consensus       307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa  371 (385)
T KOG1168|consen  307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSA  371 (385)
T ss_pred             cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhh
Confidence            36789999999999999999999999999999999999999999999999999999999966544

>KOG0849|consensus

Probab=99.05  E-value=1.4e-10  Score=113.84  Aligned_cols=71  Identities=30%  Similarity=0.507  Sum_probs=63.5

Q ss_pred             CcchhcccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281         229 YPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS  299 (317)
Q Consensus       229 ~P~~~s~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~  299 (317)
                      .+.....++.+|+||+|+.+|++.||+.|+++.||++..|++||.+++|++..|.+||+|||+|+||....
T Consensus       167 ~p~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~  237 (354)
T KOG0849|consen  167 PPGYALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD  237 (354)
T ss_pred             cccccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence            33344455677889999999999999999999999999999999999999999999999999999998843

>KOG0775|consensus

Probab=98.91  E-value=1.6e-09  Score=102.22  Aligned_cols=55  Identities=27%  Similarity=0.386  Sum_probs=49.7

Q ss_pred             ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281         244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK  298 (317)
Q Consensus       244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k  298 (317)
                      .|...-..+|.++|..++||+.+++.+||+++||+..||-+||+|||.|+|-...
T Consensus       182 CFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~a  236 (304)
T KOG0775|consen  182 CFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAAA  236 (304)
T ss_pred             ehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhccc
Confidence            4666678899999999999999999999999999999999999999999994433

>KOG0774|consensus

Probab=98.60  E-value=2.3e-08  Score=94.01  Aligned_cols=59  Identities=29%  Similarity=0.523  Sum_probs=55.3

Q ss_pred             cCCCCcccCHHHHHHHHHHhh---hCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         238 RKRGRQTYTRYQTLELEKEFH---FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       238 rRR~Rt~fT~~Ql~~LE~~F~---~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      .||+|+.|++...++|..+|-   .|+||+.+++++||++++++..+|..||.|+|-+.||.
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~  249 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN  249 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence            478899999999999999995   57899999999999999999999999999999999985

>KOG2252|consensus

Probab=98.39  E-value=4.1e-07  Score=92.91  Aligned_cols=58  Identities=24%  Similarity=0.282  Sum_probs=54.2

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhh
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK  294 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~K  294 (317)
                      ..||.|.+||..|++.|..+|+.+++|+.+..+.|+..|+|....|.+||-|-|+|.+
T Consensus       419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl  476 (558)
T KOG2252|consen  419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSL  476 (558)
T ss_pred             cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence            3477899999999999999999999999999999999999999999999999988853

>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=98.37  E-value=1.2e-07  Score=65.55  Aligned_cols=34  Identities=32%  Similarity=0.589  Sum_probs=29.1

Q ss_pred             hCCCCCHHHHHHHHHHcCCCcccchhhcccchhh
Q psy3281         259 FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK  292 (317)
Q Consensus       259 ~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK  292 (317)
                      .++||+.+|+++||+++||+.++|..||-|.|.|
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            4789999999999999999999999999999875

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

>KOG1146|consensus

Probab=98.00  E-value=5.4e-06  Score=91.59  Aligned_cols=77  Identities=25%  Similarity=0.339  Sum_probs=66.9

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCCCCCCCCCCCCC
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGGSDAGSDITPA  313 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~~~s~~s~~sp~  313 (317)
                      .+|+.|+.++..+|++|..+|..-.++..++.|.|.+.++|..+.|.+||+|.|.|.||........++.+...++-
T Consensus       902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~~~~ss~~~s~sp~  978 (1406)
T KOG1146|consen  902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNGTAASSTGGSSSPL  978 (1406)
T ss_pred             hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhccccccccccccCcc
Confidence            56789999999999999999999999999999999999999999999999999999999888664444444444443

>KOG0490|consensus

Probab=97.98  E-value=8.1e-06  Score=73.70  Aligned_cols=64  Identities=34%  Similarity=0.494  Sum_probs=59.4

Q ss_pred             ccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281         235 QFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK  298 (317)
Q Consensus       235 ~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k  298 (317)
                      ..+.++.|+.|+..++..|+..|..+.+|+...++.|+..+|++++.|.+||+|+|.+.|+...
T Consensus       150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            3466788999999999999999999999999999999999999999999999999999998655

>KOG0773|consensus

Probab=96.83  E-value=0.00074  Score=65.62  Aligned_cols=60  Identities=18%  Similarity=0.270  Sum_probs=50.8

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~---n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      .++|.+..|.+....+|+.++..   .+||+..++..||+++||+..+|.+||-|.|.|..+.
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            34566678999999999988432   4699999999999999999999999999999876653

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

Probab=96.83  E-value=0.00058  Score=50.72  Aligned_cols=43  Identities=19%  Similarity=0.302  Sum_probs=31.5

Q ss_pred             HHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhh
Q psy3281         250 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK  292 (317)
Q Consensus       250 l~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK  292 (317)
                      +..|+++|...+++...+...|..+.+|+..+|+.||-.|+.+
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            4569999999999999999999999999999999999766543

>KOG3623|consensus

Probab=96.14  E-value=0.0062  Score=64.87  Aligned_cols=52  Identities=19%  Similarity=0.270  Sum_probs=47.6

Q ss_pred             HHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         250 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       250 l~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      +.+|+.+|..|.+|+.+|...||..+||+.+.|+.||.+++++++..++.-.
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps  619 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPS  619 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCcc
Confidence            7889999999999999999999999999999999999999999888765433

>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=95.20  E-value=0.028  Score=40.89  Aligned_cols=47  Identities=21%  Similarity=0.344  Sum_probs=35.5

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccch
Q psy3281         239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR  290 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRR  290 (317)
                      ||+|..+|-++...+-..++...     ...+||.++|++..+|..|..|+.
T Consensus         1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~   47 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD   47 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred             CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence            57889999999887777777666     477899999999999999998853

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=88.92  E-value=0.42  Score=33.51  Aligned_cols=47  Identities=13%  Similarity=0.146  Sum_probs=35.6

Q ss_pred             ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281         244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  295 (317)
Q Consensus       244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK  295 (317)
                      .+++.+..+|...|     .......++|+.+|++...|+.+...-..|.|+
T Consensus         4 ~L~~~er~vi~~~y-----~~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~   50 (50)
T PF04545_consen    4 QLPPREREVIRLRY-----FEGLTLEEIAERLGISRSTVRRILKRALKKLRK   50 (50)
T ss_dssp             TS-HHHHHHHHHHH-----TST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHh-----cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence            46788999999888     233457889999999999999998766666553

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 ....

>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella

Probab=83.57  E-value=2  Score=25.72  Aligned_cols=38  Identities=18%  Similarity=0.117  Sum_probs=27.1

Q ss_pred             ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhc
Q psy3281         244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWF  286 (317)
Q Consensus       244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWF  286 (317)
                      .++.+....+...|.. ..    ...++|+.++++...|..|+
T Consensus         5 ~~~~~~~~~i~~~~~~-~~----s~~~ia~~~~is~~tv~~~~   42 (42)
T cd00569           5 KLTPEQIEEARRLLAA-GE----SVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             cCCHHHHHHHHHHHHc-CC----CHHHHHHHHCCCHHHHHHhC
Confidence            4566666666666653 22    46688999999999998884

The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D

>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=83.11  E-value=0.85  Score=30.53  Aligned_cols=44  Identities=14%  Similarity=0.096  Sum_probs=32.4

Q ss_pred             ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhh
Q psy3281         244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK  292 (317)
Q Consensus       244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK  292 (317)
                      .++..+..+|+..|.     ......++|+.+|++...|+.|...-+.+
T Consensus        10 ~l~~~~~~~~~~~~~-----~~~~~~~ia~~~~~s~~~i~~~~~~~~~~   53 (55)
T cd06171          10 KLPEREREVILLRFG-----EGLSYEEIAEILGISRSTVRQRLHRALKK   53 (55)
T ss_pred             hCCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            456777777776653     22456788999999999999998665544

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

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

Probab=81.07  E-value=0.85  Score=34.16  Aligned_cols=44  Identities=18%  Similarity=0.310  Sum_probs=28.9

Q ss_pred             CCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcc
Q psy3281         240 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ  287 (317)
Q Consensus       240 R~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQ  287 (317)
                      ++|+.||.++...+-..+.    .......+||+++||+...|..|-.
T Consensus         2 ~~r~~ys~e~K~~~v~~~~----~~g~sv~~va~~~gi~~~~l~~W~~   45 (76)
T PF01527_consen    2 RKRRRYSPEFKLQAVREYL----ESGESVSEVAREYGISPSTLYNWRK   45 (76)
T ss_dssp             -SS----HHHHHHHHHHHH----HHHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHH----HCCCceEeeecccccccccccHHHH
Confidence            4677899998776666552    2235678899999999999999964

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	317
1hom_A	68	Determination Of The Three-Dimensional Structure Of		2e-31
9ant_A	62	Antennapedia Homeodomain-Dna Complex Length = 62		5e-30
1ahd_P	68	Determination Of The Nmr Solution Structure Of An A		1e-29
2r5y_A	88	Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO		5e-28
1san_A	62	The Des(1-6)antennapedia Homeodomain: Comparison Of		1e-26
1b8i_A	81	Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX		1e-25
1ftz_A	70	Nuclear Magnetic Resonance Solution Structure Of Th		5e-23
2h1k_A	63	Crystal Structure Of The Pdx1 Homeodomain In Comple		3e-19
1puf_A	77	Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo		7e-19
2lp0_A	60	The Solution Structure Of Homeodomain-Protein Compl		2e-18
2m34_A	71	Nmr Structure Of The Homeodomain Transcription Fact		2e-14
1b72_A	97	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		7e-14
2l7z_A	73	Nmr Structure Of A13 Homedomain Length = 73		2e-10
1hdd_C	61	Crystal Structure Of An Engrailed Homeodomain-Dna C		3e-10
3a01_A	93	Crystal Structure Of Aristaless And Clawless Homeod		4e-10
2dmt_A	80	Solution Structure Of The Homeobox Domain Of Homeob		4e-10
3hdd_A	60	Engrailed Homeodomain Dna Complex Length = 60		5e-10
2hdd_A	61	Engrailed Homeodomain Q50k Variant Dna Complex Leng		1e-09
1p7j_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		1e-09
2ld5_A	67	Solution Nmr-Derived Complex Structure Of Hoxa13 Dn		1e-09
1p7i_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		1e-09
3a03_A	56	Crystal Structure Of Hox11l1 Homeodomain Length = 5		1e-09
1jgg_A	60	Even-Skipped Homeodomain Complexed To At-Rich Dna L		3e-09
2cra_A	70	Solution Structure Of The Homeobox Domain Of Human		4e-09
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		6e-09
1du0_A	57	Engrailed Homeodomain Q50a Variant Dna Complex Leng		6e-09
1enh_A	54	Structural Studies Of The Engrailed Homeodomain Len		1e-08
1ztr_A	61	Solution Structure Of Engrailed Homeodomain L16a Mu		1e-08
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		2e-08
3a02_A	60	Crystal Structure Of Aristaless Homeodomain Length		3e-08
2e1o_A	70	Solution Structure Of Rsgi Ruh-028, A Homeobox Doma		3e-08
2hos_A	63	Phage-selected Homeodomain Bound To Unmodified Dna		4e-08
1ig7_A	58	Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58		4e-08
2p81_A	44	Engrailed Homeodomain Helix-Turn-Helix Motif Length		5e-08
2l9r_A	69	Solution Nmr Structure Of Homeobox Domain Of Homeob		9e-08
2l7f_P	68	Solution Structure Of The Pitx2 Homeodomain Length		2e-07
3rkq_A	58	Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Lengt		3e-07
2djn_A	70	The Solution Structure Of The Homeobox Domain Of Hu		5e-07
2l7m_P	68	Solution Structure Of The Pitx2 Homeodomain R24h Mu		9e-07
3cmy_A	61	Structure Of A Homeodomain In Complex With Dna Leng		2e-06
1fjl_A	81	Homeodomain From The Drosophila Paired Protein Boun		3e-06
1zq3_P	68	Nmr Solution Structure Of The Bicoid Homeodomain Bo		3e-06
2m0c_A	75	Solution Nmr Structure Of Homeobox Domain Of Human		3e-06
1nk2_P	77	VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES		1e-05
2vi6_A	62	Crystal Structure Of The Nanog Homeodomain Length =		2e-05
2cue_A	80	Solution Structure Of The Homeobox Domain Of The Hu		2e-05
1qry_A	80	Homeobox Protein Vnd (Ventral Nervous System Defect		3e-05
2kt0_A	84	Solution Structure Of Human Stem Cell Transcription		4e-05
1ftt_A	68	Thyroid Transcription Factor 1 Homeodomain (Rattus		6e-05
2dms_A	80	Solution Structure Of The Homeobox Domain Of Homeob		1e-04
2nzz_A	37	Nmr Structure Analysis Of The Penetratin Conjugated		3e-04
2dmu_A	70	Solution Structure Of The Homeobox Domain Of Homeob		4e-04
1kz0_A	16	Solution Structure Of The Third Helix Of Antennaped		8e-04

>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 =  132 bits (333), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 62/63 (98%), Positives = 63/63 (100%)
Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
           RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN
Sbjct: 2   RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 61
Query: 298 KSK 300
           K+K
Sbjct: 62  KTK 64

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

Iteration: 1
 Score =  128 bits (321), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 60/61 (98%), Positives = 60/61 (98%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
           ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKE
Sbjct: 2   ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61
Query: 297 N 297
           N
Sbjct: 62  N 62

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

Iteration: 1
 Score =  127 bits (318), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 61/63 (96%), Positives = 62/63 (98%)
Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
           RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKEN
Sbjct: 2   RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61
Query: 298 KSK 300
           K+K
Sbjct: 62  KTK 64

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

Iteration: 1
 Score =  121 bits (303), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 61/84 (72%), Positives = 66/84 (78%), Gaps = 10/84 (11%)
Query: 225 PSPLYPWMR----------SQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHA 274
           P  +YPWM+          +  E KR R +YTRYQTLELEKEFHFNRYLTRRRRIEIAHA
Sbjct: 5   PPQIYPWMKRVHLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHA 64
Query: 275 LCLTERQIKIWFQNRRMKWKKENK 298
           L LTERQIKIWFQNRRMKWKKE+K
Sbjct: 65  LSLTERQIKIWFQNRRMKWKKEHK 88

>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 =  117 bits (292), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 55/57 (96%), Positives = 56/57 (98%)
Query: 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSK 300
           TYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKENK+K
Sbjct: 2   TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTK 58

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

Iteration: 1
 Score =  114 bits (284), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 57/72 (79%), Positives = 60/72 (83%), Gaps = 3/72 (4%)
Query: 228 LYPWMR---SQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKI 284
            YPWM    +   R+RGRQTYTRYQTLELEKEFH N YLTRRRRIE+AHAL LTERQIKI
Sbjct: 7   FYPWMAIAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKI 66
Query: 285 WFQNRRMKWKKE 296
           WFQNRRMK KKE
Sbjct: 67  WFQNRRMKLKKE 78

>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 =  105 bits (261), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 50/60 (83%), Positives = 56/60 (93%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
           + KR RQTYTRYQTLELEKEFHFNRY+TRRRRI+IA+AL L+ERQIKIWFQNRRMK KK+
Sbjct: 2   DSKRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKD 61

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

Iteration: 1
 Score = 92.0 bits (227), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 42/58 (72%), Positives = 47/58 (81%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
           KR R  YTR Q LELEKEF FN+Y++R RR+E+A  L LTER IKIWFQNRRMKWKKE
Sbjct: 4   KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61

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

Iteration: 1
 Score = 91.3 bits (225), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 46/75 (61%), Positives = 56/75 (74%), Gaps = 1/75 (1%)
Query: 226 SPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIW 285
           +P   W+ ++  RK+ R  YT++QTLELEKEF FN YLTR RR E+A  L LTERQ+KIW
Sbjct: 2   NPAANWLHARSTRKK-RCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIW 60
Query: 286 FQNRRMKWKKENKSK 300
           FQNRRMK KK NK +
Sbjct: 61  FQNRRMKMKKINKDR 75

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

Iteration: 1
 Score = 89.4 bits (220), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 42/59 (71%), Positives = 47/59 (79%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
           ++ R  YT+YQTLELEKEF FN YLTR RR E+A  L LTERQ+KIWFQNRRMK KK N
Sbjct: 2   RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKMN 60

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

Iteration: 1
 Score = 76.6 bits (187), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 34/57 (59%), Positives = 42/57 (73%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           +R R  +T  Q LELEKEFH  +YL+   R +IAHAL L+E Q+KIWFQNRR KWK+
Sbjct: 8   RRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKR 64

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

Iteration: 1
 Score = 74.3 bits (181), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 38/62 (61%), Positives = 46/62 (74%), Gaps = 2/62 (3%)
Query: 242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301
           R  +T  Q  ELEKEFHFN+YL+R RR+EIA  L L E Q+KIWFQNRRMK KK  + ++
Sbjct: 38  RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK--RERE 95
Query: 302 GG 303
           GG
Sbjct: 96  GG 97

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

Iteration: 1
 Score = 62.8 bits (151), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 28/64 (43%), Positives = 42/64 (65%)
Query: 232 MRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 291
           M    E ++ R  YT+ Q  ELE+E+  N+++T+ +R  I+    L+ERQ+ IWFQNRR+
Sbjct: 1   MSHMLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRV 60
Query: 292 KWKK 295
           K KK
Sbjct: 61  KEKK 64

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

Iteration: 1
 Score = 62.4 bits (150), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 30/59 (50%), Positives = 40/59 (67%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           + KR R  ++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWFQN+R K KK
Sbjct: 2   DEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60

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

Iteration: 1
 Score = 62.4 bits (150), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 28/61 (45%), Positives = 40/61 (65%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
           +RK+ R ++TR Q  ELEK FH  +YL    R  +A  L +T+ Q+K WFQNRR KW+++
Sbjct: 16  KRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQ 75
Query: 297 N 297
Sbjct: 76  T 76

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

Iteration: 1
 Score = 62.0 bits (149), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 28/61 (45%), Positives = 40/61 (65%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
           +R R  +T  Q + LEK F   +YL+   RI++A +L L++ Q+K W+QNRRMKWKK   
Sbjct: 18  RRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGP 77
Query: 299 S 299
           S
Sbjct: 78  S 78

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

Iteration: 1
 Score = 61.6 bits (148), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 30/57 (52%), Positives = 39/57 (68%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           KR R  ++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWFQN+R K KK
Sbjct: 2   KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58

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

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 29/57 (50%), Positives = 39/57 (68%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           KR R  ++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWF+N+R K KK
Sbjct: 4   KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

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

Iteration: 1
 Score = 60.5 bits (145), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 30/57 (52%), Positives = 38/57 (66%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           KR R  ++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWFQN R K KK
Sbjct: 2   KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58

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

Iteration: 1
 Score = 60.5 bits (145), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 26/57 (45%), Positives = 40/57 (70%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           ++ R  YT+ Q  ELE+E+  N+++T+ +R  I+    L+ERQ+ IWFQNRR+K KK
Sbjct: 2   RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58

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

Iteration: 1
 Score = 60.5 bits (145), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 30/57 (52%), Positives = 38/57 (66%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           KR R  ++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWFQN R K KK
Sbjct: 2   KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58

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

Iteration: 1
 Score = 60.1 bits (144), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 24/53 (45%), Positives = 36/53 (67%)
Query: 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
           +++R Q LELE+ F   +YL    R  +A AL +T+ Q+K WFQNRR KW+++
Sbjct: 3   SFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

>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 = 30/58 (51%), Positives = 39/58 (67%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
           +R R  +TR Q   LEKEF+   Y++R RR E+A  L L E  IK+WFQNRRMK K++
Sbjct: 2   RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 28/61 (45%), Positives = 43/61 (70%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
           ++ R  Y++ Q  ELE+E+  N+++T+ +R +I+ A  L+ERQI IWFQNRR+K KK   
Sbjct: 8   RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGP 67
Query: 299 S 299
           S
Sbjct: 68  S 68

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 28/62 (45%), Positives = 40/62 (64%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
           +++R R T+T +Q  ELEK F    Y     R E+A  + LTE +I++WFQNRR KW+K+
Sbjct: 5   KQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 64
Query: 297 NK 298
            K
Sbjct: 65  EK 66

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 28/56 (50%), Positives = 37/56 (66%)
Query: 240 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           R R  ++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWF N+R K KK
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 27/53 (50%), Positives = 36/53 (67%)
Query: 240 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 292
           R R  ++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWFQN+R K
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 27/59 (45%), Positives = 39/59 (66%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           + KR R  ++  Q    ++EF+ NRYLT RRR +++  L L E QIKIWFQN+R K ++
Sbjct: 2   DEKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 27/57 (47%), Positives = 36/57 (63%)
Query: 240 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
           R R T+T +Q  ELEK F    Y     R E+A  + LTE +I++WFQNRR KW+K+
Sbjct: 1   RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 26/55 (47%), Positives = 35/55 (63%)
Query: 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
           T+T +Q  ELEK F    Y     R E+A  + LTE +I++WFQNRR KW+K+ K
Sbjct: 5   TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 59

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 26/55 (47%), Positives = 37/55 (67%)
Query: 245 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS 299
           ++  QT+ELEK+F   +YL+   R  +A  L L+ERQ+K WFQNRR KW++   S
Sbjct: 14  FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGPS 68

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 27/59 (45%), Positives = 38/59 (64%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           + KR R  ++  Q   L++EF+ NRYLT RRR +++  L L E Q+K WF+N R K KK
Sbjct: 3   DEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 26/57 (45%), Positives = 37/57 (64%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           ++ R  +T  Q L LE++F   +YL+   R E + +L LTE Q+KIWFQNRR K K+
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 25/42 (59%), Positives = 32/42 (76%)
Query: 254 EKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           ++EF+ NRYLT RRR +++  L L E QIKIWFQN+R K KK
Sbjct: 2   KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43

>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 = 54.3 bits (129), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 26/55 (47%), Positives = 36/55 (65%)
Query: 249 QTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGG 303
           Q +ELE++F   +YL+   R  +A  L LTE Q+KIWFQNRR K K++  S + G
Sbjct: 15  QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSELG 69

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 26/61 (42%), Positives = 36/61 (59%)
Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
           ++R R  +T  Q  ELE  F  NRY     R EIA    LTE ++++WF+NRR KW+K  
Sbjct: 3   QRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
Query: 298 K 298
           +
Sbjct: 63  E 63

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 26/57 (45%), Positives = 36/57 (63%)
Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294
           R++ R  +++ Q  ELE+ F   RYL+   R ++A  L LT  Q+KIWFQNRR K K
Sbjct: 2   RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 25/61 (40%), Positives = 37/61 (60%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
           ++ R  Y+ +Q   L++ F   +YL    R E+A +L LT+ Q+KIWFQN+R K KK   
Sbjct: 8   RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGP 67
Query: 299 S 299
           S
Sbjct: 68  S 68

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 25/61 (40%), Positives = 35/61 (57%)
Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
           ++R R  +T  Q  ELE  F  N Y     R EIA    LTE ++++WF+NRR KW+K  
Sbjct: 3   QRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
Query: 298 K 298
           +
Sbjct: 63  E 63

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 23/59 (38%), Positives = 35/59 (59%)
Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
           ++R R T+T  Q  ELE+ F    Y     R E+A    LTE ++++WF NRR +W+K+
Sbjct: 2   QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 25/70 (35%), Positives = 42/70 (60%)
Query: 230 PWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 289
           P +  + +++R R T++  Q  ELE+ F   +Y     R E+A    LTE +I++WFQNR
Sbjct: 10  PGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNR 69
Query: 290 RMKWKKENKS 299
           R + +K++ S
Sbjct: 70  RARLRKQHTS 79

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 27/64 (42%), Positives = 39/64 (60%), Gaps = 1/64 (1%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK-KEN 297
           +R R T+T  Q  ELE+ F   RYLT  R  +++  L L   Q+KIWF+NRR + K + +
Sbjct: 3   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 62
Query: 298 KSKD 301
           + KD
Sbjct: 63  QHKD 66

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/62 (41%), Positives = 38/62 (61%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
           +++R R T+T YQ  ELEK F    Y     R ++A    LTE ++++WFQNRR KW+K 
Sbjct: 8   KKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKR 67
Query: 297 NK 298
            +
Sbjct: 68  ER 69

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/64 (40%), Positives = 38/64 (59%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
           ++++ R  +T+ QT ELE+ F   RYL+   R  +A  + LT  Q+KIWFQN R K K+ 
Sbjct: 8   KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRA 67
Query: 297 NKSK 300
              K
Sbjct: 68  QNEK 71

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 19/58 (32%), Positives = 37/58 (63%)
Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           +++ R  +++ Q   L+  F   +YL+ ++  E++  L L+ +Q+K WFQN+RMK K+
Sbjct: 3   KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 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 = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 39/69 (56%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
           +R R ++T+ Q   LEKEF    Y     R  +A  + L E +I++WF NRR KW++E K
Sbjct: 8   QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 67
Query: 299 SKDGGSDAG 307
            ++    +G
Sbjct: 68  LRNQRRQSG 76

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/64 (39%), Positives = 37/64 (57%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
           ++++ R  +T+ QT ELE+ F   RYL+   R  +   + LT  Q+KIWFQN R K K+ 
Sbjct: 11  KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRA 70
Query: 297 NKSK 300
              K
Sbjct: 71  QNEK 74

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 21/64 (32%), Positives = 39/64 (60%), Gaps = 3/64 (4%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK---W 293
           ++++ R  ++  Q   L   F   +YL+ ++  E+++ L L+ +Q+K WFQN+RMK   W
Sbjct: 21  KKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRW 80
Query: 294 KKEN 297
           +K N
Sbjct: 81  QKNN 84

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 38/65 (58%)
Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
           R++ R  +++ Q  ELE+ F   +YL+   R  +A  + LT  Q+KIWFQN R K K++ 
Sbjct: 2   RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61
Query: 298 KSKDG 302
           K K  
Sbjct: 62  KDKAA 66

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/69 (34%), Positives = 39/69 (56%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
           +R R T+TR Q   LE  F   RY     R E+A  + L E ++++WF+NRR K +++ +
Sbjct: 8   RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQ 67
Query: 299 SKDGGSDAG 307
            +  G  +G
Sbjct: 68  QQQNGGQSG 76

>pdb|2NZZ|A Chain A, Nmr Structure Analysis Of The Penetratin Conjugated Gas (374-394) Peptide Length = 37

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 18/24 (75%), Positives = 20/24 (83%), Gaps = 2/24 (8%)
Query: 280 RQIKIWFQNRRMKWKKE--NKSKD 301
           RQIKIWFQNRRMKWKK   N ++D
Sbjct: 1   RQIKIWFQNRRMKWKKRVFNDARD 24

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 20/61 (32%), Positives = 33/61 (54%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
           +R R  +T  Q   LE  F   +Y     R ++A  + L E ++++WF+NRR KW++   
Sbjct: 8   RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP 67
Query: 299 S 299
           S
Sbjct: 68  S 68

>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia Homeodomain Length = 16

Iteration: 1
 Score = 41.2 bits (95), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 16/16 (100%), Positives = 16/16 (100%)
Query: 280 RQIKIWFQNRRMKWKK 295
           RQIKIWFQNRRMKWKK
Sbjct: 1   RQIKIWFQNRRMKWKK 16

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	317
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	6e-51
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	6e-48
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	1e-47
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	4e-47
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	2e-45
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	3e-45
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	6e-45
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	8e-45
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	1e-44
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	1e-44
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	5e-43
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	5e-43
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	3e-40
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	1e-39
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	2e-35
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	6e-34
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	1e-32
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	3e-31
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	1e-30
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	7e-29
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	6e-28
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	1e-27
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	1e-27
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	4e-27
1e3o_C	160	Octamer-binding transcription factor 1; transcript	3e-24
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	2e-19
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	1e-18
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	1e-18
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	3e-18
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	2e-17
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	8e-17
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	4e-16
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	4e-16
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	2e-15
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	3e-15
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	6e-15
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	7e-15
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	8e-15
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	8e-15
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	9e-15
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	1e-14
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	1e-14
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	6e-14
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	6e-13
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	1e-12
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	1e-12
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	2e-12
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	4e-12
1uhs_A	72	HOP, homeodomain only protein; structural genomics	8e-12
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	3e-11
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	6e-11
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	5e-08
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	1e-06
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-06
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	4e-05
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	6e-05
1lfb_A	99	Liver transcription factor (LFB1); transcription r	2e-06
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	3e-06
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	5e-06
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	1e-05
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	3e-05
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	5e-05
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	8e-04

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

 Score =  162 bits (411), Expect = 6e-51
 Identities = 57/80 (71%), Positives = 62/80 (77%), Gaps = 3/80 (3%)

Query: 223 SLPSPLYPWMRSQ---FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTE 279
           +     YPWM        R+RGRQTYTRYQTLELEKEFH N YLTRRRRIE+AHAL LTE
Sbjct: 2   ASNHTFYPWMAIAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTE 61

Query: 280 RQIKIWFQNRRMKWKKENKS 299
           RQIKIWFQNRRMK KKE ++
Sbjct: 62  RQIKIWFQNRRMKLKKEIQA 81

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

 Score =  155 bits (392), Expect = 6e-48
 Identities = 61/84 (72%), Positives = 66/84 (78%), Gaps = 10/84 (11%)

Query: 225 PSPLYPWMR----------SQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHA 274
           P  +YPWM+          +  E KR R +YTRYQTLELEKEFHFNRYLTRRRRIEIAHA
Sbjct: 5   PPQIYPWMKRVHLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHA 64

Query: 275 LCLTERQIKIWFQNRRMKWKKENK 298
           L LTERQIKIWFQNRRMKWKKE+K
Sbjct: 65  LSLTERQIKIWFQNRRMKWKKEHK 88

>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 =  153 bits (388), Expect = 1e-47
 Identities = 61/63 (96%), Positives = 62/63 (98%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
           RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKEN
Sbjct: 2   RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61

Query: 298 KSK 300
           K+K
Sbjct: 62  KTK 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 =  152 bits (386), Expect = 4e-47
 Identities = 44/75 (58%), Positives = 55/75 (73%), Gaps = 1/75 (1%)

Query: 226 SPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIW 285
           +P   W+ ++   ++ R  YT++QTLELEKEF FN YLTR RR E+A  L LTERQ+KIW
Sbjct: 2   NPAANWLHAR-STRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIW 60

Query: 286 FQNRRMKWKKENKSK 300
           FQNRRMK KK NK +
Sbjct: 61  FQNRRMKMKKINKDR 75

>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 =  148 bits (376), Expect = 2e-45
 Identities = 38/92 (41%), Positives = 49/92 (53%), Gaps = 14/92 (15%)

Query: 223 SLPSPLYPWMRSQF--------------ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRR 268
           +  +  + WM+ +                    R  +T  Q  ELEKEFHFN+YL+R RR
Sbjct: 5   TPTARTFDWMKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARR 64

Query: 269 IEIAHALCLTERQIKIWFQNRRMKWKKENKSK 300
           +EIA  L L E Q+KIWFQNRRMK KK  +  
Sbjct: 65  VEIAATLELNETQVKIWFQNRRMKQKKREREG 96

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

 Score =  147 bits (372), Expect = 3e-45
 Identities = 42/61 (68%), Positives = 47/61 (77%)

Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
             KR R  YTR Q LELEKEF FN+Y++R RR+E+A  L LTER IKIWFQNRRMKWKKE
Sbjct: 2   SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61

Query: 297 N 297
            
Sbjct: 62  E 62

>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 =  146 bits (370), Expect = 6e-45
 Identities = 28/64 (43%), Positives = 40/64 (62%)

Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
             K G+  ++  QT+ELEK+F   +YL+   R  +A  L L+ERQ+K WFQNRR KW++ 
Sbjct: 6   SGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRS 65

Query: 297 NKSK 300
             S 
Sbjct: 66  GPSS 69

>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 =  146 bits (369), Expect = 8e-45
 Identities = 26/67 (38%), Positives = 37/67 (55%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
            +R R T+T  Q  ELE+ F   RYLT  R  +++  L L   Q+KIWF+NRR + K ++
Sbjct: 2   PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQS 61

Query: 298 KSKDGGS 304
                 S
Sbjct: 62  DQHKDQS 68

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

 Score =  145 bits (368), Expect = 1e-44
 Identities = 29/73 (39%), Positives = 43/73 (58%)

Query: 232 MRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 291
           M    E ++ R  YT+ Q  ELE+E+  N+++T+ +R  I+    L+ERQ+ IWFQNRR+
Sbjct: 1   MSHMLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRV 60

Query: 292 KWKKENKSKDGGS 304
           K KK        S
Sbjct: 61  KEKKVINKLKTTS 73

>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 =  145 bits (368), Expect = 1e-44
 Identities = 28/64 (43%), Positives = 43/64 (67%)

Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
             ++ R  Y++ Q  ELE+E+  N+++T+ +R +I+ A  L+ERQI IWFQNRR+K KK 
Sbjct: 6   SGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKS 65

Query: 297 NKSK 300
             S 
Sbjct: 66  GPSS 69

>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 =  141 bits (357), Expect = 5e-43
 Identities = 29/57 (50%), Positives = 39/57 (68%)

Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           KR R  ++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWF+N+R K KK
Sbjct: 4   KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

>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 =  141 bits (357), Expect = 5e-43
 Identities = 30/58 (51%), Positives = 39/58 (67%)

Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
           +R R  +TR Q   LEKEF+   Y++R RR E+A  L L E  IK+WFQNRRMK K++
Sbjct: 2   RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59

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

 Score =  134 bits (340), Expect = 3e-40
 Identities = 28/64 (43%), Positives = 41/64 (64%)

Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
           + +R R  +T  Q + LEK F   +YL+   RI++A +L L++ Q+K W+QNRRMKWKK 
Sbjct: 16  KGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKS 75

Query: 297 NKSK 300
             S 
Sbjct: 76  GPSS 79

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

 Score =  133 bits (336), Expect = 1e-39
 Identities = 31/87 (35%), Positives = 51/87 (58%), Gaps = 2/87 (2%)

Query: 229 YPWM-RSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 287
           +P+  R+  +RK+ R ++TR Q  ELEK FH  +YL    R  +A  L +T+ Q+K WFQ
Sbjct: 7   HPYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQ 66

Query: 288 NRRMKWKKENKSK-DGGSDAGSDITPA 313
           NRR KW+++   + +    A + +  +
Sbjct: 67  NRRTKWRRQTAEEREAERQAANRLMLS 93

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

 Score =  122 bits (307), Expect = 2e-35
 Identities = 25/64 (39%), Positives = 37/64 (57%)

Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
             ++ R  Y+ +Q   L++ F   +YL    R E+A +L LT+ Q+KIWFQN+R K KK 
Sbjct: 6   SGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKS 65

Query: 297 NKSK 300
             S 
Sbjct: 66  GPSS 69

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

 Score =  117 bits (296), Expect = 6e-34
 Identities = 26/67 (38%), Positives = 37/67 (55%)

Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
                    +  Q +ELE++F   +YL+   R  +A  L LTE Q+KIWFQNRR K K++
Sbjct: 3   HHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRK 62

Query: 297 NKSKDGG 303
             S + G
Sbjct: 63  QLSSELG 69

>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 =  114 bits (287), Expect = 1e-32
 Identities = 15/58 (25%), Positives = 31/58 (53%)

Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294
           +  +G+ + +      LE+ F   + L  + + E+A    +T  Q+++WF N+RM+ K
Sbjct: 4   KSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61

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

 Score =  110 bits (278), Expect = 3e-31
 Identities = 26/57 (45%), Positives = 37/57 (64%)

Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           ++ R  +T  Q L LE++F   +YL+   R E + +L LTE Q+KIWFQNRR K K+
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

 Score =  108 bits (273), Expect = 1e-30
 Identities = 19/59 (32%), Positives = 37/59 (62%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
           +++ R  +++ Q   L+  F   +YL+ ++  E++  L L+ +Q+K WFQN+RMK K+ 
Sbjct: 3   KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW 61

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

 Score =  105 bits (263), Expect = 7e-29
 Identities = 23/94 (24%), Positives = 43/94 (45%), Gaps = 11/94 (11%)

Query: 206 SQPPNQPPNQQPNNTSASLPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTR 265
           S+ P    N                      ++++ R  ++  Q   L   F   +YL+ 
Sbjct: 1   SKQPTSAENSVAKKEDKVPV-----------KKQKTRTVFSSTQLCVLNDRFQRQKYLSL 49

Query: 266 RRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS 299
           ++  E+++ L L+ +Q+K WFQN+RMK K+  K+
Sbjct: 50  QQMQELSNILNLSYKQVKTWFQNQRMKSKRWQKN 83

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

 Score =  102 bits (255), Expect = 6e-28
 Identities = 24/53 (45%), Positives = 36/53 (67%)

Query: 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
           +++R Q LELE+ F   +YL    R  +A AL +T+ Q+K WFQNRR KW+++
Sbjct: 3   SFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

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

 Score =  101 bits (253), Expect = 1e-27
 Identities = 26/57 (45%), Positives = 36/57 (63%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294
           R++ R  +++ Q  ELE+ F   RYL+   R ++A  L LT  Q+KIWFQNRR K K
Sbjct: 2   RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

>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 =  101 bits (254), Expect = 1e-27
 Identities = 26/64 (40%), Positives = 37/64 (57%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
           +++ R  +T+ QT ELE+ F   RYL+   R  +A  + LT  Q+KIWFQN R K K+  
Sbjct: 9   KRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ 68

Query: 298 KSKD 301
             K 
Sbjct: 69  NEKG 72

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

 Score =  100 bits (250), Expect = 4e-27
 Identities = 25/63 (39%), Positives = 38/63 (60%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
           R++ R  +++ Q  ELE+ F   +YL+   R  +A  + LT  Q+KIWFQN R K K++ 
Sbjct: 2   RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61

Query: 298 KSK 300
           K K
Sbjct: 62  KDK 64

>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 = 95.4 bits (237), Expect = 3e-24
 Identities = 25/109 (22%), Positives = 40/109 (36%), Gaps = 6/109 (5%)

Query: 195 NHQQTPPNQPPSQPPNQPPNQQPNNTSASLPSPLYP------WMRSQFERKRGRQTYTRY 248
               +  N    +P  +          +S  S   P       +     R++ R +    
Sbjct: 52  ALNLSFKNMSKLKPLLEKWLNDAEANLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETN 111

Query: 249 QTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
             + LEK F  N+  T      IA  L + +  I++WF NRR K K+ N
Sbjct: 112 IRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRIN 160

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

 Score = 82.8 bits (204), Expect = 2e-19
 Identities = 16/70 (22%), Positives = 30/70 (42%)

Query: 234 SQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 293
           +Q  +++ R +        LE  F      +      +A +L L +  +++WF NRR K 
Sbjct: 95  AQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKE 154

Query: 294 KKENKSKDGG 303
           K+   +   G
Sbjct: 155 KRMTPAAGAG 164

>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 = 77.8 bits (192), Expect = 1e-18
 Identities = 20/62 (32%), Positives = 29/62 (46%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
            +  R  +T YQ   L+  F  N Y       ++++ L L  R I +WFQN R K +K  
Sbjct: 7   GRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSG 66

Query: 298 KS 299
            S
Sbjct: 67  PS 68

>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 = 80.0 bits (197), Expect = 1e-18
 Identities = 19/101 (18%), Positives = 40/101 (39%), Gaps = 4/101 (3%)

Query: 195 NHQQTPPNQPPSQPPNQPPNQQPNNTSASLPSPLYPWMRSQFERKRGRQTYTRYQTLELE 254
           N Q +  N    +       ++     A     +    R    +++ R T +      LE
Sbjct: 48  NLQLSFKNACKLKAILSKWLEEAEQVGALYNEKVGANER----KRKRRTTISIAAKDALE 103

Query: 255 KEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           + F  +   + +  + +A  L L +  +++WF NRR + K+
Sbjct: 104 RHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 144

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

 Score = 76.7 bits (189), Expect = 3e-18
 Identities = 12/64 (18%), Positives = 26/64 (40%)

Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
              +   +  Q   L+  F  N++  +     +     L+ R+++ WF +RR   +    
Sbjct: 9   SIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKG 68

Query: 299 SKDG 302
           S+ G
Sbjct: 69  SRSG 72

>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 = 74.8 bits (184), Expect = 2e-17
 Identities = 21/62 (33%), Positives = 33/62 (53%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
            KR R T T  Q   L +++  +   TR+    IAH + L +R +++WFQN R + +K  
Sbjct: 17  DKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSG 76

Query: 298 KS 299
            S
Sbjct: 77  PS 78

>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 = 75.1 bits (184), Expect = 8e-17
 Identities = 22/101 (21%), Positives = 40/101 (39%), Gaps = 2/101 (1%)

Query: 197 QQTPPNQPPSQPPNQPPNQQPNNTSASLPSPLYPWMRSQFERKRGRQTYTRYQTLELEKE 256
           Q +  N    +P  +   ++ +N                  RKR R +        LE  
Sbjct: 57  QLSLKNMSKLRPLLEKWVEEADNNENLQEISKS--ETLVQARKRKRTSIENRVRWSLETM 114

Query: 257 FHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
           F  +   + ++   IA+ L L +  +++WF NRR K K+ +
Sbjct: 115 FLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRSS 155

>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 = 70.8 bits (174), Expect = 4e-16
 Identities = 18/62 (29%), Positives = 27/62 (43%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
            KR R   T  Q   L + F  N   +  +  E+A    L ++ IK WF+N   K ++  
Sbjct: 7   GKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSG 66

Query: 298 KS 299
            S
Sbjct: 67  PS 68

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

 Score = 70.9 bits (174), Expect = 4e-16
 Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 1/61 (1%)

Query: 239 KRGRQTYTRYQTLELEKEFH-FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
            +     T  Q   LE  F+  N++        IA    LTE Q + WF+ R  +W++  
Sbjct: 3   AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 62

Query: 298 K 298
            
Sbjct: 63  G 63

>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 = 69.4 bits (170), Expect = 2e-15
 Identities = 24/71 (33%), Positives = 39/71 (54%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
            +R R T+TR Q   LE  F   RY     R E+A  + L E ++++WF+NRR K +++ 
Sbjct: 7   GRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQ 66

Query: 298 KSKDGGSDAGS 308
           + +  G  +G 
Sbjct: 67  QQQQNGGQSGP 77

>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 = 68.6 bits (168), Expect = 3e-15
 Identities = 18/71 (25%), Positives = 36/71 (50%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
            KR R ++  +Q   ++  F  N     +   ++A    LT+R +++WFQN R K+++  
Sbjct: 7   GKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNL 66

Query: 298 KSKDGGSDAGS 308
             ++ G  +G 
Sbjct: 67  LRQENGGVSGP 77

>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 = 67.7 bits (166), Expect = 6e-15
 Identities = 25/62 (40%), Positives = 36/62 (58%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
           ++R R  +T  Q  +LE  F  NRY     R EIA    LTE ++++WF+NRR KW+K  
Sbjct: 3   QRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62

Query: 298 KS 299
           + 
Sbjct: 63  EF 64

>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 = 70.1 bits (171), Expect = 7e-15
 Identities = 18/103 (17%), Positives = 32/103 (31%), Gaps = 2/103 (1%)

Query: 195 NHQQTPPNQPPSQPPNQPP--NQQPNNTSASLPSPLYPWMRSQFERKRGRQTYTRYQTLE 252
                 P       P      N+          + +        ++++ R ++T      
Sbjct: 48  EKLDITPKSAQKLKPVLEKWLNEAELRNQEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEA 107

Query: 253 LEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           L   F  N   T +   E+A  L      +++WF NRR   K 
Sbjct: 108 LNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN 150

>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 = 67.8 bits (166), Expect = 8e-15
 Identities = 24/62 (38%), Positives = 38/62 (61%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
           ++R R T++  Q  ELE+ F   +Y     R E+A    LTE +I++WFQNRR + +K++
Sbjct: 18  QRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH 77

Query: 298 KS 299
            S
Sbjct: 78  TS 79

>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 = 67.3 bits (165), Expect = 8e-15
 Identities = 22/62 (35%), Positives = 32/62 (51%)

Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
           +R R  +T+ Q   LE  F  N Y       ++A  L L   +I+IWFQNRR K K+ ++
Sbjct: 2   RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61

Query: 299 SK 300
             
Sbjct: 62  ES 63

>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 = 67.4 bits (165), Expect = 9e-15
 Identities = 20/62 (32%), Positives = 33/62 (53%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
            +R R  +T  Q   LE  F   +Y     R ++A  + L E ++++WF+NRR KW++  
Sbjct: 7   GRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSG 66

Query: 298 KS 299
            S
Sbjct: 67  PS 68

>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 = 67.0 bits (164), Expect = 1e-14
 Identities = 16/62 (25%), Positives = 25/62 (40%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
             R R      Q   L   +  N       + ++     L+ R I++WFQN+R K KK +
Sbjct: 3   TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS 62

Query: 298 KS 299
             
Sbjct: 63  IM 64

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

 Score = 67.0 bits (164), Expect = 1e-14
 Identities = 25/71 (35%), Positives = 39/71 (54%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
            +R R ++T+ Q   LEKEF    Y     R  +A  + L E +I++WF NRR KW++E 
Sbjct: 7   GQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREE 66

Query: 298 KSKDGGSDAGS 308
           K ++    +G 
Sbjct: 67  KLRNQRRQSGP 77

>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 = 64.6 bits (158), Expect = 6e-14
 Identities = 26/57 (45%), Positives = 35/57 (61%)

Query: 242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
             T+T +Q  ELEK F    Y     R E+A  + LTE +I++WFQNRR KW+K+ K
Sbjct: 3   HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 59

>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 = 62.1 bits (151), Expect = 6e-13
 Identities = 10/59 (16%), Positives = 22/59 (37%)

Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
                 +  T+ Q   L+  F  +++        +     L   +IK WF + R + ++
Sbjct: 3   HHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR 61

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

 Score = 61.4 bits (149), Expect = 1e-12
 Identities = 14/64 (21%), Positives = 22/64 (34%), Gaps = 1/64 (1%)

Query: 237 ERKRGRQTYTRYQTLELEKEFH-FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
              R R   +      L+   H    Y  +     ++  L L +  I  +FQN+R   K 
Sbjct: 6   SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH 65

Query: 296 ENKS 299
              S
Sbjct: 66  SGPS 69

>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 = 61.9 bits (150), Expect = 1e-12
 Identities = 14/72 (19%), Positives = 26/72 (36%)

Query: 242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301
            +  T+ Q   LE  F  + + T+     +     L+ R+I  WF  RR       ++  
Sbjct: 17  FKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAVL 76

Query: 302 GGSDAGSDITPA 313
               +G     +
Sbjct: 77  DSMGSGKSGPSS 88

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

 Score = 63.4 bits (153), Expect = 2e-12
 Identities = 15/92 (16%), Positives = 28/92 (30%)

Query: 210 NQPPNQQPNNTSASLPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRI 269
            +         +A                K+ R  +T  Q   L   F  N+  ++  +I
Sbjct: 69  PEFQRMSALRLAACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQI 128

Query: 270 EIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301
            I+  L L    +  +F N R +   +     
Sbjct: 129 TISQQLGLELSTVSNFFMNARRRSLDKWLEHH 160

>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 = 4e-12
 Identities = 17/71 (23%), Positives = 23/71 (32%), Gaps = 1/71 (1%)

Query: 234 SQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 293
                 + ++     Q   LE  F  N          +     +T R+I  WF  RR K 
Sbjct: 4   GSSGPTKYKER-APEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKV 62

Query: 294 KKENKSKDGGS 304
             E   K G S
Sbjct: 63  NAEETKKSGPS 73

>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 = 58.9 bits (143), Expect = 8e-12
 Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 240 RGRQTYTRYQTLELEKEFH-FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
            G  T T  Q   LE  F+  N++        IA    LTE Q + WF+ R  +W++   
Sbjct: 3   EGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG 62

>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 = 58.1 bits (140), Expect = 3e-11
 Identities = 18/76 (23%), Positives = 31/76 (40%), Gaps = 15/76 (19%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC---------------LTERQI 282
            +  R T+ +     +E  F+ N+Y    +R EIA+A                 +T  ++
Sbjct: 7   GRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKV 66

Query: 283 KIWFQNRRMKWKKENK 298
             WF NRR + K+   
Sbjct: 67  YNWFANRRKEIKRRAN 82

>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 = 56.9 bits (137), Expect = 6e-11
 Identities = 13/74 (17%), Positives = 25/74 (33%)

Query: 242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301
            +  T  Q   L+  F  +  LT      +     LT R+I  WF  ++     + +  +
Sbjct: 15  FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKME 74

Query: 302 GGSDAGSDITPATS 315
                    +  +S
Sbjct: 75  IDESNAGSSSGPSS 88

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

 Score = 48.6 bits (116), Expect = 5e-08
 Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 3/63 (4%)

Query: 238 RKRGRQTYTRYQTLELEKEF-HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
           +              LEK F    +Y   +R   ++  L  + R+I+ WF++RR + K  
Sbjct: 10  KDSPVNKVE--PNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPS 67

Query: 297 NKS 299
             S
Sbjct: 68  GPS 70

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 49.1 bits (116), Expect = 1e-06
 Identities = 24/156 (15%), Positives = 35/156 (22%), Gaps = 8/156 (5%)

Query: 86  YGAHEGGMEQYPRPDSPSMGHMGPQNGHQTPVVYASCKLQAAVGNGIIPGPESPNDLVDP 145
           Y   +    Q   P       M PQ+     + Y           G+ P    P+     
Sbjct: 9   YPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYG--------QMGMPPQGAVPSMGQQQ 60

Query: 146 TLNNHHHHQHHHMNHHPHPHPQQQQPQQPPPQHMMYAQQPPPQHHQVVVNHQQTPPNQPP 205
            L       H  ++              P      Y Q   P      +  QQ P   P 
Sbjct: 61  FLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPA 120

Query: 206 SQPPNQPPNQQPNNTSASLPSPLYPWMRSQFERKRG 241
              P+    Q     +   P  L   +         
Sbjct: 121 YGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTL 156

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 48.3 bits (114), Expect = 2e-06
 Identities = 23/141 (16%), Positives = 35/141 (24%), Gaps = 1/141 (0%)

Query: 95  QYPRPDSPSMGHMGPQNGHQTPVVYASCKLQAAVGNGIIPGPESPNDLVDPTLNNHHHHQ 154
           Q+  P  P+   M        P        Q               D    ++N+ H H 
Sbjct: 28  QFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHN 87

Query: 155 HHHMNHHPHPHPQQQQPQQPPPQHMMYAQQPPPQHHQVVVNHQQTPPNQPPSQPPNQPPN 214
              ++ + +  PQ       P Q        P          Q   P      P +    
Sbjct: 88  VPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLY-PIDLLTE 146

Query: 215 QQPNNTSASLPSPLYPWMRSQ 235
             P  T  +LP P       +
Sbjct: 147 LPPPITDLTLPPPPLVIPPER 167

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 44.0 bits (103), Expect = 4e-05
 Identities = 31/218 (14%), Positives = 59/218 (27%), Gaps = 22/218 (10%)

Query: 23  HHQQHHYGATVLPQNNGVEDPSMYDPRQVHHYGQVPNNGQPVHGMPYPRFPPYDRMDIRN 82
           HH++  Y    L          +  P Q      +P       GM Y +     +  + +
Sbjct: 3   HHKKRVYPQAQLQYGQNA--TPLQQPAQ-----FMPPQDPAAAGMSYGQMGMPPQGAVPS 55

Query: 83  AAYYGAHEGGMEQYPRPDSPSMGHMGPQNGHQTPVVYASCKLQAAVGNGIIPGPESPNDL 142
                      EQ  +    +   M   + H  P+V  +  +Q  V              
Sbjct: 56  MGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVP------------- 102

Query: 143 VDPTLNNHHHHQHHHMNHHPHPHPQQQQPQQPPPQHMMYAQQPPPQHHQVVVNHQQTPPN 202
               +      Q   M    +  P     Q   P + +Y      +    + +    PP 
Sbjct: 103 --VQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPP 160

Query: 203 QPPSQPPNQPPNQQPNNTSASLPSPLYPWMRSQFERKR 240
                     P++  N +   + S L    ++    K+
Sbjct: 161 LVIPPERMLVPSELSNASPDYIRSTLNAVPKNSSLLKK 198

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 43.7 bits (102), Expect = 6e-05
 Identities = 19/148 (12%), Positives = 26/148 (17%), Gaps = 2/148 (1%)

Query: 104 MGHMGPQNGHQTPVVYASCKLQAAVGNGIIP--GPESPNDLVDPTLNNHHHHQHHHMNHH 161
           M H   +   Q  + Y             +P   P +                       
Sbjct: 1   MSHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQ 60

Query: 162 PHPHPQQQQPQQPPPQHMMYAQQPPPQHHQVVVNHQQTPPNQPPSQPPNQPPNQQPNNTS 221
                Q+Q  QQ                  V  N    P        P Q   Q     +
Sbjct: 61  FLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPA 120

Query: 222 ASLPSPLYPWMRSQFERKRGRQTYTRYQ 249
              PS           +       T   
Sbjct: 121 YGQPSAAMGQNMRPMNQLYPIDLLTELP 148

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

 Score = 44.8 bits (105), Expect = 2e-06
 Identities = 12/82 (14%), Positives = 25/82 (30%), Gaps = 21/82 (25%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC--------------------- 276
            +R R  +       L + +   +  ++  R  +                          
Sbjct: 9   GRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNL 68

Query: 277 LTERQIKIWFQNRRMKWKKENK 298
           +TE ++  WF NRR +    +K
Sbjct: 69  VTEVRVYNWFANRRKEEAFRHK 90

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

 Score = 46.5 bits (109), Expect = 3e-06
 Identities = 18/139 (12%), Positives = 36/139 (25%), Gaps = 27/139 (19%)

Query: 177 QHMMYAQQPPPQHHQVVVNHQQTPPNQPPSQPPNQPPNQQPNNTSASLPSPLYPWMRSQF 236
           Q  +  Q          +  + +        P     +  P  +  +   P    MR   
Sbjct: 87  QREILRQFNQTVQSSGNMTDKSSQDQLLFLFPEFSQQSHGPGQSDDACSEPTNKKMR--- 143

Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC-------------------- 276
              R R  +       L + +   +  ++  R  +                         
Sbjct: 144 ---RNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSN 200

Query: 277 -LTERQIKIWFQNRRMKWK 294
            +TE ++  WF NRR +  
Sbjct: 201 LVTEVRVYNWFANRRKEEA 219

>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 = 14/48 (29%), Positives = 22/48 (45%), Gaps = 1/48 (2%)

Query: 253 LEKEF-HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS 299
           LEK F    ++   +R   ++  L    R I+ WF+ RR + K    S
Sbjct: 15  LEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPSGPS 62

>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 = 42.5 bits (99), Expect = 1e-05
 Identities = 15/89 (16%), Positives = 26/89 (29%), Gaps = 7/89 (7%)

Query: 209 PNQPPNQQPNNTSASLPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRR 268
            +   +          P+P       +          T  Q   L+  F   ++ +    
Sbjct: 3   HHHHHHSSGLEVLFQGPAP-------KSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEY 55

Query: 269 IEIAHALCLTERQIKIWFQNRRMKWKKEN 297
            ++A    L    I  WF + R  WK  N
Sbjct: 56  DKLAKESGLARTDIVSWFGDTRYAWKNGN 84

>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 Length = 37

 Score = 39.6 bits (92), Expect = 3e-05
 Identities = 18/24 (75%), Positives = 20/24 (83%), Gaps = 2/24 (8%)

Query: 280 RQIKIWFQNRRMKWKKE--NKSKD 301
           RQIKIWFQNRRMKWKK   N ++D
Sbjct: 1   RQIKIWFQNRRMKWKKRVFNDARD 24

>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 = 42.6 bits (99), Expect = 5e-05
 Identities = 13/111 (11%), Positives = 29/111 (26%), Gaps = 21/111 (18%)

Query: 205 PSQPPNQPPNQQPNNTSASLPSPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLT 264
             +   +   Q  +     L            + +R R  +       L + +   +  +
Sbjct: 82  YVRKQREVAQQFTHAGQGGLIEEPTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPS 141

Query: 265 RRRRIEIAHALC---------------------LTERQIKIWFQNRRMKWK 294
           +  R  +                          +TE ++  WF NRR +  
Sbjct: 142 KEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEA 192

>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 = 36.9 bits (84), Expect = 8e-04
 Identities = 11/66 (16%), Positives = 24/66 (36%), Gaps = 4/66 (6%)

Query: 238 RKRGRQTYTRYQTLELEKEFH----FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 293
             + R  ++      L+K +         + R +   +A  L +    ++ W  NRR K+
Sbjct: 8   ALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKY 67

Query: 294 KKENKS 299
           +     
Sbjct: 68  RLMGIE 73

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	317
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.8
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.79
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.79
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.78
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.78
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.78
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.77
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.77
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.77
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.77
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.76
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.76
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.76
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.76
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.76
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.75
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.75
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.75
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.75
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.75
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.75
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.75
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.75
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.75
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.75
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.74
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.74
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.74
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.74
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.74
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.74
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.74
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.74
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.74
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.74
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.73
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.73
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.73
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.73
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.73
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.72
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.72
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.72
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.72
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.72
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.71
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.71
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.7
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.7
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.7
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.7
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.69
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.69
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.68
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.68
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.68
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.67
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.67
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.66
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.65
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.65
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.64
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.64
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.64
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.63
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.62
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.61
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.61
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.59
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.58
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.58
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.54
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.46
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.43
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.35
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.31
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.26
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.46
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	95.4
3oka_C	21	N-terminal His-affinity TAG; GT-B fold, alpha-mann	90.55
2l4h_A	214	Calcium and integrin-binding protein 1; metal bind	90.49
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	89.37
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	88.58
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	86.57
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	86.24
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	84.54
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	83.68
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	81.97
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	80.93
3c57_A	95	Two component transcriptional regulatory protein;	80.88
3tla_A	371	MCCF; serine protease, hydrolase; 1.20A {Escherich	80.58
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	80.32

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

Probab=99.80  E-value=8.4e-20  Score=141.17  Aligned_cols=71  Identities=32%  Similarity=0.520  Sum_probs=64.6

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCCCCCC
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGGSDA  306 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~~~s~  306 (317)
                      .+.||.|++|+.+|+.+||.+|..++||+..++++||.+|+|++++|++||+|||+|+||..+........
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~~~~~~~~   75 (80)
T 2dms_A            5 SSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQQNGGQS   75 (80)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCSCCCCCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHccCCCCCC
Confidence            45688999999999999999999999999999999999999999999999999999999988776654433

>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=99.79  E-value=1.1e-19  Score=140.24  Aligned_cols=69  Identities=25%  Similarity=0.434  Sum_probs=63.7

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCCCC
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGGS  304 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~~~  304 (317)
                      .+.||.|+.|+.+|+.+||.+|..++||+..++++||.+|||++++|++||+|||+|+||..+.....+
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~~~~   73 (80)
T 2dmq_A            5 SSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQENGG   73 (80)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHSSCCCS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHHHhcCC
Confidence            356889999999999999999999999999999999999999999999999999999999887766543

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

Probab=99.79  E-value=1.1e-19  Score=143.09  Aligned_cols=63  Identities=89%  Similarity=1.328  Sum_probs=56.2

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK  298 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k  298 (317)
                      .+.||.|+.||.+|+.+||.+|..+.||+..+|++||..|||++++|++||+|||+|+||..|
T Consensus        26 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k   88 (88)
T 2r5y_A           26 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEHK   88 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTCC
T ss_pred             CCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhhcC
Confidence            356889999999999999999999999999999999999999999999999999999998754

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

Probab=99.78  E-value=1.3e-19  Score=140.99  Aligned_cols=64  Identities=31%  Similarity=0.561  Sum_probs=60.5

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS  299 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~  299 (317)
                      .++||.|+.|+.+|+.+||.+|..+.||+..++++||..|||++++|++||+|||+|+||..+.
T Consensus        20 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k~   83 (84)
T 2kt0_A           20 VKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQKN   83 (84)
T ss_dssp             SCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhhc
Confidence            4668899999999999999999999999999999999999999999999999999999997654

>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=99.78  E-value=1.8e-19  Score=139.39  Aligned_cols=65  Identities=43%  Similarity=0.770  Sum_probs=60.5

Q ss_pred             ccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281         235 QFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS  299 (317)
Q Consensus       235 ~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~  299 (317)
                      ..+.||.|+.|+.+|+.+||.+|..+.||+..++++||..|||++++|++||+|||+|+||..+.
T Consensus        14 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~~s   78 (80)
T 2dmt_A           14 AKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGPS   78 (80)
T ss_dssp             CCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCCSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcccCC
Confidence            34667899999999999999999999999999999999999999999999999999999987653

>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=99.78  E-value=1.1e-19  Score=141.17  Aligned_cols=71  Identities=80%  Similarity=1.216  Sum_probs=57.8

Q ss_pred             CCcchhc---ccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281         228 LYPWMRS---QFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK  298 (317)
Q Consensus       228 ~~P~~~s---~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k  298 (317)
                      .+||+..   ..++||.|+.||.+|+.+||.+|..+.||+..++++||.+|||++++|++||+|||+|+||..+
T Consensus         7 ~~p~~~~~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   80 (81)
T 1b8i_A            7 FYPWMAIAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEIQ   80 (81)
T ss_dssp             CCTTCC-----------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC-
T ss_pred             CCCccccCCCCCCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhcc
Confidence            4555543   2456789999999999999999999999999999999999999999999999999999998654

>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=99.77  E-value=2.2e-19  Score=135.10  Aligned_cols=65  Identities=94%  Similarity=1.412  Sum_probs=61.3

Q ss_pred             cCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCC
Q psy3281         238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDG  302 (317)
Q Consensus       238 rRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~  302 (317)
                      +||.|+.||.+|+.+||..|..+.||+..++++||..|||++++|++||+|||+|+||..+.+..
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~~~~~   66 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTKGE   66 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSCCCSS
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhccccCC
Confidence            47899999999999999999999999999999999999999999999999999999998876654

>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=99.77  E-value=2.3e-19  Score=135.39  Aligned_cols=63  Identities=43%  Similarity=0.688  Sum_probs=59.5

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK  298 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k  298 (317)
                      .+.||+|+.||.+|+.+||.+|..++||+..++++||.+|||++++|++||+|||+|+||..+
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (70)
T 2cra_A            5 SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGP   67 (70)
T ss_dssp             CCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSCT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccCC
Confidence            356789999999999999999999999999999999999999999999999999999998664

>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=99.77  E-value=2.2e-19  Score=138.25  Aligned_cols=64  Identities=33%  Similarity=0.412  Sum_probs=60.2

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS  299 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~  299 (317)
                      .++||.|+.||.+|+.+||.+|..++||+..++++||.+|||++++|++||+|||+|+||..+.
T Consensus        15 ~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~   78 (80)
T 2da3_A           15 QRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSGPS   78 (80)
T ss_dssp             CCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhccC
Confidence            4668899999999999999999999999999999999999999999999999999999986643

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

Probab=99.77  E-value=3e-19  Score=134.65  Aligned_cols=63  Identities=32%  Similarity=0.606  Sum_probs=59.7

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS  299 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~  299 (317)
                      +.||.|+.|+.+|+.+||.+|..++||+..++++||.+|||++++|++||+|||+|+||..+.
T Consensus         6 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~~   68 (70)
T 2dmu_A            6 SGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGPS   68 (70)
T ss_dssp             SSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTSTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccCCC
Confidence            567899999999999999999999999999999999999999999999999999999997653

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

Probab=99.76  E-value=1.7e-19  Score=139.53  Aligned_cols=66  Identities=36%  Similarity=0.630  Sum_probs=62.0

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      .+.||.|+.|+.+|+.+||.+|..++||+..++++||..|||++++|++||+|||+|+||..+...
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~~   70 (80)
T 2cue_A            5 SSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRN   70 (80)
T ss_dssp             CSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhhh
Confidence            356789999999999999999999999999999999999999999999999999999999887655

>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=99.76  E-value=2.5e-19  Score=134.96  Aligned_cols=64  Identities=28%  Similarity=0.321  Sum_probs=60.3

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS  299 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~  299 (317)
                      .+.||.|+.||.+|+.+||.+|..+.||+..++++||..|||++++|++||+|||+|+||..+.
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (70)
T 2da1_A            5 SSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGPS   68 (70)
T ss_dssp             CCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhccc
Confidence            3568899999999999999999999999999999999999999999999999999999997654

>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=99.76  E-value=3.1e-19  Score=134.46  Aligned_cols=64  Identities=31%  Similarity=0.445  Sum_probs=60.1

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS  299 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~  299 (317)
                      .+.||.|++|+.+|+.+||.+|..++||+..++++||..|||++++|++||+|||+|+||..+.
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (70)
T 2da2_A            5 SSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGPS   68 (70)
T ss_dssp             CCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCSSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhcccc
Confidence            3568899999999999999999999999999999999999999999999999999999986654

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

Probab=99.76  E-value=5e-19  Score=134.86  Aligned_cols=66  Identities=41%  Similarity=0.666  Sum_probs=61.1

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      .+.||.|+.|+.+|+.+||.+|..++||+..++++||..|||++++|++||+|||+|+||..+...
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~~   70 (73)
T 2l7z_A            5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINKLK   70 (73)
T ss_dssp             SCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSSSSSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHhcccC
Confidence            356889999999999999999999999999999999999999999999999999999999765543

>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=99.76  E-value=6.6e-19  Score=135.35  Aligned_cols=67  Identities=39%  Similarity=0.609  Sum_probs=62.4

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCC
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDG  302 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~  302 (317)
                      .++||.|+.||.+|+.+||.+|..+.||+..++++||..|||++++|++||+|||+|+|+..+.+..
T Consensus         7 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~~~~   73 (77)
T 1nk2_P            7 NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGY   73 (77)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhccccC
Confidence            3567889999999999999999999999999999999999999999999999999999998776654

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

Probab=99.75  E-value=4.2e-19  Score=133.98  Aligned_cols=63  Identities=38%  Similarity=0.644  Sum_probs=59.4

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK  298 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k  298 (317)
                      .+.||.|+.||.+|+.+||.+|..++||+..++++||.+|||++++|++||+|||+|+||..+
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2djn_A            5 SSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGP   67 (70)
T ss_dssp             CCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccCC
Confidence            356889999999999999999999999999999999999999999999999999999998654

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

Probab=99.75  E-value=6.8e-19  Score=132.26  Aligned_cols=65  Identities=38%  Similarity=0.621  Sum_probs=61.2

Q ss_pred             cCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCC
Q psy3281         238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDG  302 (317)
Q Consensus       238 rRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~  302 (317)
                      .||.|+.||.+|+.+||..|..+.||+..++++||..|||++++|++||+|||+|+|+..+....
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~~~~   66 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQHKD   66 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhccccc
Confidence            47899999999999999999999999999999999999999999999999999999998776553

>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=99.75  E-value=7.1e-19  Score=132.71  Aligned_cols=63  Identities=44%  Similarity=0.790  Sum_probs=59.5

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS  299 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~  299 (317)
                      +.+|.|++|+.+|+.+||.+|..++||+..++++||..|||++++|++||+|||+|+|+..+.
T Consensus         6 ~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~~~   68 (70)
T 2e1o_A            6 SGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGPS   68 (70)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHSCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCCCC
Confidence            457889999999999999999999999999999999999999999999999999999997653

>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=99.75  E-value=6.4e-19  Score=141.10  Aligned_cols=63  Identities=57%  Similarity=0.865  Sum_probs=57.2

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS  299 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~  299 (317)
                      +.+|.|+.||.+|+.+||.+|..+.||+..++++||..|||++++|++||+|||+|+||..+.
T Consensus        33 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~   95 (97)
T 1b72_A           33 SPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE   95 (97)
T ss_dssp             ----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhcc
Confidence            457889999999999999999999999999999999999999999999999999999998764

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

Probab=99.75  E-value=7.2e-19  Score=132.13  Aligned_cols=64  Identities=39%  Similarity=0.679  Sum_probs=60.4

Q ss_pred             cCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       238 rRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      +||.|+.||.+|+.+||.+|..+.||+..++++||..|||++++|++||+|||+|+|+..+.+.
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~~~~   65 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDKA   65 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSCCS
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhhHhh
Confidence            5789999999999999999999999999999999999999999999999999999999876543

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

Probab=99.75  E-value=6.2e-19  Score=130.47  Aligned_cols=61  Identities=69%  Similarity=1.097  Sum_probs=56.5

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN  297 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~  297 (317)
                      +.||.|+.||.+|+.+||..|..++||+..++++||..|||++++|++||+|||+|+||.+
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   62 (63)
T 2h1k_A            2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE   62 (63)
T ss_dssp             ---CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhhc
Confidence            3578999999999999999999999999999999999999999999999999999999864

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

Probab=99.75  E-value=6.2e-19  Score=133.95  Aligned_cols=65  Identities=40%  Similarity=0.670  Sum_probs=60.9

Q ss_pred             ccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281         235 QFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS  299 (317)
Q Consensus       235 ~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~  299 (317)
                      ..+++|.|+.|+.+|+.+||.+|..+.||+..++++||..|||++++|++||+|||+|+||..+.
T Consensus         6 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r~   70 (75)
T 2m0c_A            6 KGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRERF   70 (75)
T ss_dssp             CSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHhh
Confidence            34668899999999999999999999999999999999999999999999999999999997665

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

Probab=99.75  E-value=5.5e-19  Score=130.23  Aligned_cols=60  Identities=32%  Similarity=0.574  Sum_probs=53.2

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      +++|.|+.||.+|+.+||.+|..+.||+..++++||..|||++++|++||+|||+|+||.
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            457899999999999999999999999999999999999999999999999999999985

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

Probab=99.75  E-value=1.8e-18  Score=137.63  Aligned_cols=58  Identities=21%  Similarity=0.248  Sum_probs=55.3

Q ss_pred             ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      +||.+||.+||+.|..++||+..+|++||..|||++++|+|||+|||+|||++++...
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~~~~   74 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKME   74 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCCC
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHHHhh
Confidence            7899999999999999999999999999999999999999999999999998776655

>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=99.75  E-value=6.2e-19  Score=129.57  Aligned_cols=60  Identities=48%  Similarity=0.764  Sum_probs=53.8

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      +.||.|+.||.+|+.+||..|..++||+..++++||..|||++++|++||+|||+|+||.
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   61 (61)
T 2hdd_A            2 AEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKKS   61 (61)
T ss_dssp             -----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhccccccC
Confidence            357899999999999999999999999999999999999999999999999999999973

>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=99.74  E-value=8.3e-19  Score=134.79  Aligned_cols=65  Identities=65%  Similarity=0.918  Sum_probs=61.1

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhccc
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSK  300 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k  300 (317)
                      .+.+|.|+.||.+|+.+||.+|..+.||+..++++||..|||++++|++||+|||+|+|+..+.+
T Consensus        11 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k~~   75 (77)
T 1puf_A           11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDR   75 (77)
T ss_dssp             CTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhhhc
Confidence            35678999999999999999999999999999999999999999999999999999999987754

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

Probab=99.74  E-value=9.2e-19  Score=139.53  Aligned_cols=69  Identities=41%  Similarity=0.748  Sum_probs=61.6

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCCCC
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGGS  304 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~~~  304 (317)
                      .++||.|+.||.+|+.+||.+|..+.||+..++++||..|||++++|++||+|||+|+||..+......
T Consensus        15 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~~~~   83 (93)
T 3a01_A           15 PKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEEREAE   83 (93)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC----
T ss_pred             CCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHHHHHH
Confidence            356789999999999999999999999999999999999999999999999999999999877665433

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

Probab=99.74  E-value=1.8e-18  Score=131.69  Aligned_cols=66  Identities=24%  Similarity=0.266  Sum_probs=60.6

Q ss_pred             CCCCcccCHHHHHHHHHHhhh-CCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCCCC
Q psy3281         239 KRGRQTYTRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGGS  304 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~-n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~~~  304 (317)
                      +++|+.||.+|+.+||.+|.. ++||+..++++||..|||++++|++||+|||+|+||..+.....+
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~~~~~~~~   69 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLPSECR   69 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHTCCSSSC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhccCCCcCC
Confidence            578999999999999999995 999999999999999999999999999999999999886655433

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

Probab=99.74  E-value=1.3e-18  Score=126.41  Aligned_cols=58  Identities=45%  Similarity=0.720  Sum_probs=55.9

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      ||.|+.||.+|+.+||..|..++||+..++++||..|||++++|++||+|||+|+||.
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   58 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL   58 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhccC
Confidence            5789999999999999999999999999999999999999999999999999999973

>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=99.74  E-value=1.8e-18  Score=131.11  Aligned_cols=66  Identities=27%  Similarity=0.340  Sum_probs=60.4

Q ss_pred             CCCCcccCHHHHHHHHHHhhh-CCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCCCC
Q psy3281         239 KRGRQTYTRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGGS  304 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~-n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~~~  304 (317)
                      .++|+.|+.+|+.+||.+|.. ++||+..++++||.+|||++++|++||+|||+|+||..+.....+
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~~~~~~~~   68 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLPSECR   68 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhccCCCcCC
Confidence            468899999999999999996 999999999999999999999999999999999999886655433

>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=99.74  E-value=1.3e-18  Score=135.44  Aligned_cols=60  Identities=15%  Similarity=0.131  Sum_probs=57.4

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhh----CCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  295 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~----n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK  295 (317)
                      .++||.||.||.+|+.+||.+|+.    ++||+..+|++||.+|||++++|+|||||||+|+|+
T Consensus        15 ~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           15 GIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            467889999999999999999999    999999999999999999999999999999999886

>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=99.74  E-value=9.1e-19  Score=130.57  Aligned_cols=62  Identities=26%  Similarity=0.324  Sum_probs=58.8

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK  298 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k  298 (317)
                      ++||.|+.||.+|+.+||.+|..++||+..++++||..|||++++|++||+|||+|+|+...
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   63 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI   63 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHHhh
Confidence            46789999999999999999999999999999999999999999999999999999998653

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

Probab=99.74  E-value=9.9e-19  Score=135.14  Aligned_cols=63  Identities=17%  Similarity=0.270  Sum_probs=59.2

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhC----CCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFN----RYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK  298 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n----~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k  298 (317)
                      .++||.|+.||.+|+.+||.+|+.+    +||+..++++||.+|||++++|++||+|||+|+|+...
T Consensus         6 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~~~   72 (80)
T 2da4_A            6 SGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMGI   72 (80)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhccC
Confidence            4568899999999999999999999    99999999999999999999999999999999998543

>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=99.74  E-value=1.4e-18  Score=134.65  Aligned_cols=64  Identities=36%  Similarity=0.594  Sum_probs=59.6

Q ss_pred             ccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281         235 QFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK  298 (317)
Q Consensus       235 ~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k  298 (317)
                      ..++||.|+.|+.+|+.+||.+|..++||+..++++||..|||++++|++||+|||+|+||..+
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            4567889999999999999999999999999999999999999999999999999999999764

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

Probab=99.74  E-value=2e-18  Score=137.72  Aligned_cols=69  Identities=26%  Similarity=0.309  Sum_probs=63.7

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcC---------------CCcccchhhcccchhhhhhhhccc
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC---------------LTERQIKIWFQNRRMKWKKENKSK  300 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~Lg---------------Lse~qVkiWFQNRRaK~KK~~k~k  300 (317)
                      .++||.|+.|+.+|+.+||.+|+.++||+..+|++||.+|+               |++.+|++||+|||+|+|++.+..
T Consensus         5 ~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~~~   84 (95)
T 2cuf_A            5 SSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANIA   84 (95)
T ss_dssp             SCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhhcc
Confidence            46688999999999999999999999999999999999999               999999999999999999988875


Q ss_pred             CCCC
Q psy3281         301 DGGS  304 (317)
Q Consensus       301 ~~~~  304 (317)
                      ....
T Consensus        85 ~~~~   88 (95)
T 2cuf_A           85 AILE   88 (95)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            5433

>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=99.73  E-value=8.2e-19  Score=131.67  Aligned_cols=64  Identities=39%  Similarity=0.641  Sum_probs=60.3

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhccc
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSK  300 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k  300 (317)
                      ++||.|+.||.+|+.+||.+|..++||+..++++||..|||++++|++||+|||+|+||..+..
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~~~   65 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEFI   65 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhhcc
Confidence            4578999999999999999999999999999999999999999999999999999999977653

>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=99.73  E-value=2.9e-18  Score=131.37  Aligned_cols=64  Identities=25%  Similarity=0.297  Sum_probs=58.9

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCC
Q psy3281         239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDG  302 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~  302 (317)
                      .++|++||.+|+.+||..|..+.||+..++++||..|||++++|++||+|||+|+|+..+...+
T Consensus         8 ~~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~~~~~   71 (75)
T 2da5_A            8 PTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETKKSG   71 (75)
T ss_dssp             SCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSCSSCC
T ss_pred             CCCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhhcccC
Confidence            3567789999999999999999999999999999999999999999999999999998766554

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

Probab=99.73  E-value=2e-18  Score=126.44  Aligned_cols=58  Identities=52%  Similarity=0.751  Sum_probs=55.6

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      ||.|+.||.+|+.+||..|..++||+..++++||..|||++++|++||+|||+|+||.
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            6889999999999999999999999999999999999999999999999999999984

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

Probab=99.73  E-value=2.2e-18  Score=128.86  Aligned_cols=61  Identities=36%  Similarity=0.537  Sum_probs=58.3

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281         239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS  299 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~  299 (317)
                      ||.|+.||.+|+.+||.+|..++||+..++++||..|||++++|++||+|||+|+|+..+.
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~~   62 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRE   62 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCCT
T ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhchh
Confidence            6889999999999999999999999999999999999999999999999999999987654

>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=99.73  E-value=4.4e-18  Score=131.83  Aligned_cols=64  Identities=17%  Similarity=0.161  Sum_probs=58.8

Q ss_pred             CCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCCC
Q psy3281         240 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGG  303 (317)
Q Consensus       240 R~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~~  303 (317)
                      .+|++||.+|+.+||++|..++||+..+|++||+.|||++++|++||+|||+|+|+........
T Consensus         5 ~~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~l~w~~~   68 (76)
T 2ecc_A            5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLKWFRD   68 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCCSSTTC
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHHHHHHHH
Confidence            4567799999999999999999999999999999999999999999999999999987766543

>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=99.72  E-value=2.7e-18  Score=133.84  Aligned_cols=60  Identities=17%  Similarity=0.137  Sum_probs=56.6

Q ss_pred             ccccCCCCcccCHHHHHHHHHHhhh-----CCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281         235 QFERKRGRQTYTRYQTLELEKEFHF-----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  295 (317)
Q Consensus       235 ~~krRR~Rt~fT~~Ql~~LE~~F~~-----n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK  295 (317)
                      ..++||.||.||.+|+.+|| .|..     ++||+..+|++||.+|+|++++|+|||||||+|+|+
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           14 GGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            34678899999999999999 7999     999999999999999999999999999999999986

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

Probab=99.72  E-value=2.8e-18  Score=131.54  Aligned_cols=63  Identities=17%  Similarity=0.316  Sum_probs=58.6

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      ++.|++||.+|+.+||.+|..++||+..++++||.+|||++++|++||+|||+|+||..+...
T Consensus         9 ~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~~~~   71 (76)
T 2dn0_A            9 SIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGSRS   71 (76)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCSSSC
T ss_pred             CCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhcccCC
Confidence            456899999999999999999999999999999999999999999999999999999766544

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

Probab=99.72  E-value=2.7e-18  Score=124.05  Aligned_cols=57  Identities=46%  Similarity=0.727  Sum_probs=55.0

Q ss_pred             cCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhh
Q psy3281         238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK  294 (317)
Q Consensus       238 rRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~K  294 (317)
                      +||.|+.|+.+|+.+||..|..+.||+..++++||..|||++++|++||+|||+|+|
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            578899999999999999999999999999999999999999999999999999986

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

Probab=99.72  E-value=5.4e-18  Score=128.87  Aligned_cols=65  Identities=22%  Similarity=0.297  Sum_probs=60.4

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      ..++.|+.||.+|+.+||..|..+.||+..++++||.+|||++++|++||+|||+|+||.+....
T Consensus         5 ~~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~   69 (74)
T 2ly9_A            5 DSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKSNQC   69 (74)
T ss_dssp             CCCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTTCSCC
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhCcCCC
Confidence            34688999999999999999999999999999999999999999999999999999999766544

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

Probab=99.72  E-value=2.6e-18  Score=125.83  Aligned_cols=58  Identities=45%  Similarity=0.735  Sum_probs=50.7

Q ss_pred             CCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281         241 GRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK  298 (317)
Q Consensus       241 ~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k  298 (317)
                      .|+.||.+|+.+||..|..++||+..++++||..|||++++|++||+|||+|+||..+
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~k   59 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK   59 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC----
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhcc
Confidence            5899999999999999999999999999999999999999999999999999998764

>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=99.71  E-value=2.8e-18  Score=125.75  Aligned_cols=59  Identities=25%  Similarity=0.450  Sum_probs=48.6

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhh
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK  294 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~K  294 (317)
                      .+.+|.|+.|+.+|+.+||.+|..++||+..++++||..|||++.+|++||+|||+|+|
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            45678899999999999999999999999999999999999999999999999999976

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

Probab=99.71  E-value=5.1e-18  Score=135.74  Aligned_cols=63  Identities=21%  Similarity=0.240  Sum_probs=56.9

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK  298 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k  298 (317)
                      ...+|+|++|+.+|+.+||..|..+.||+..++++||.+|||++++|++||+|||+|+||...
T Consensus        23 ~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~l   85 (96)
T 3nar_A           23 SGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNL   85 (96)
T ss_dssp             ----CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTCC
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhcc
Confidence            455688999999999999999999999999999999999999999999999999999998654

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

Probab=99.70  E-value=2.4e-17  Score=130.44  Aligned_cols=61  Identities=21%  Similarity=0.220  Sum_probs=56.1

Q ss_pred             CcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCC
Q psy3281         242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDG  302 (317)
Q Consensus       242 Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~  302 (317)
                      +..||.+||.+||.+|..++||+..+|++||.+|||++++|++||+|||+|+|++++....
T Consensus        17 ~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~~~~~   77 (89)
T 2dmp_A           17 FKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAVLD   77 (89)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCSCCCC
T ss_pred             cccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhHhhhc
Confidence            3448999999999999999999999999999999999999999999999999987776653

>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=99.70  E-value=1.6e-17  Score=129.82  Aligned_cols=67  Identities=15%  Similarity=0.138  Sum_probs=61.1

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCC
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDG  302 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~---n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~  302 (317)
                      .++||.|+.|+.+++.+||.+|..   ++||+..+|++||..+||++++|++||+|||+|+|+....+..
T Consensus         5 ~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~~~~~   74 (83)
T 2dmn_A            5 SSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQRR   74 (83)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHTCCCC
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHHHhcc
Confidence            356788999999999999999987   5999999999999999999999999999999999987766554

>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=99.70  E-value=1.1e-17  Score=127.09  Aligned_cols=64  Identities=23%  Similarity=0.239  Sum_probs=59.4

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS  299 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~---n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~  299 (317)
                      .+.||.|+.|+.+++.+||.+|..   ++||+..++++||..+||++++|++||+|||+|+|+....
T Consensus         5 ~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~   71 (73)
T 1x2n_A            5 SSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSGPS   71 (73)
T ss_dssp             SSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhccccccc
Confidence            356788999999999999999987   9999999999999999999999999999999999987654

>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=99.70  E-value=2.3e-18  Score=134.78  Aligned_cols=63  Identities=27%  Similarity=0.455  Sum_probs=58.6

Q ss_pred             CCCCcccCHHHHHHHHHHh---hhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         239 KRGRQTYTRYQTLELEKEF---HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F---~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      ||+|++|+.+++.+||.+|   ..++||+..++++||..|||++++|++||+|||+|+|+..+...
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~~   67 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQ   67 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGGGH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhcccccc
Confidence            6889999999999999999   89999999999999999999999999999999999999766554

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

Probab=99.69  E-value=9.8e-18  Score=121.40  Aligned_cols=54  Identities=44%  Similarity=0.863  Sum_probs=51.1

Q ss_pred             cccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         243 QTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       243 t~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      |.||.+|+.+||+.|..++||+..+|++||..|||++++|++||+|||+|+||.
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            679999999999999999999999999999999999999999999999999985

>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=99.69  E-value=1.3e-17  Score=126.56  Aligned_cols=63  Identities=27%  Similarity=0.455  Sum_probs=59.1

Q ss_pred             CCCCcccCHHHHHHHHHHh---hhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         239 KRGRQTYTRYQTLELEKEF---HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F---~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      ||+|++|+.+++.+||.+|   ..++||+..++++||..|||++++|++||+|||+|+|+..+...
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~~~   67 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQ   67 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTTTT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccccccccc
Confidence            6889999999999999999   89999999999999999999999999999999999998766544

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

Probab=99.68  E-value=9.8e-18  Score=146.52  Aligned_cols=68  Identities=22%  Similarity=0.277  Sum_probs=53.0

Q ss_pred             cccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         234 SQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       234 s~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      ...++||+|++|+.+|+.+||++|..++||+..+|++||..|||++++|++||+|||+|+||..+...
T Consensus        95 ~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~  162 (164)
T 2xsd_C           95 AQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTPAAG  162 (164)
T ss_dssp             -----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC---
T ss_pred             ccccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhccCCCC
Confidence            44577889999999999999999999999999999999999999999999999999999999776543

>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=99.68  E-value=2.2e-17  Score=134.47  Aligned_cols=71  Identities=17%  Similarity=0.184  Sum_probs=64.3

Q ss_pred             ccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHc---------------------CCCcccchhhcccchhhh
Q psy3281         235 QFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL---------------------CLTERQIKIWFQNRRMKW  293 (317)
Q Consensus       235 ~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~L---------------------gLse~qVkiWFQNRRaK~  293 (317)
                      ..++||.|+.|+..++.+||++|+.++||+..+|++||++|                     +|++.+|++||+|||+|+
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            34678999999999999999999999999999999999999                     799999999999999999


Q ss_pred             hhhhcccCCCCC
Q psy3281         294 KKENKSKDGGSD  305 (317)
Q Consensus       294 KK~~k~k~~~~s  305 (317)
                      |++.+......+
T Consensus        83 kr~~~~~~~~~~   94 (102)
T 2da6_A           83 AFRQKLAMDAYS   94 (102)
T ss_dssp             HHHHHHHHSSSS
T ss_pred             HHhhHhhhcccc
Confidence            998877665444

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

Probab=99.68  E-value=1e-17  Score=123.95  Aligned_cols=59  Identities=25%  Similarity=0.394  Sum_probs=56.2

Q ss_pred             ccCCCCcccCHHHHHHHHHHh---hhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281         237 ERKRGRQTYTRYQTLELEKEF---HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  295 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F---~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK  295 (317)
                      ..+|.|+.|+.+++.+||.+|   ..++||+..++++||..|||++++|++||+|||+|+||
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            347889999999999999999   89999999999999999999999999999999999987

>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=99.67  E-value=2e-17  Score=143.63  Aligned_cols=62  Identities=31%  Similarity=0.409  Sum_probs=55.1

Q ss_pred             ccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         235 QFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       235 ~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      ..++||+|+.|+.+|+.+||++|..++||+..+|++||.+|||++++|++||+|||+|+||.
T Consensus        98 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C           98 LSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            34678899999999999999999999999999999999999999999999999999999985

>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=99.67  E-value=1.9e-17  Score=129.90  Aligned_cols=61  Identities=28%  Similarity=0.328  Sum_probs=57.3

Q ss_pred             ccccCCCCcccCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281         235 QFERKRGRQTYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  295 (317)
Q Consensus       235 ~~krRR~Rt~fT~~Ql~~LE~~F~~---n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK  295 (317)
                      ..+++|+|++|+.+|+.+||.+|..   ++||+..++++||..+||++++|++||+|||+|+|.
T Consensus        24 ~~~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k~   87 (87)
T 1mnm_C           24 KSTKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   87 (87)
T ss_dssp             EESSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTC
T ss_pred             cCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccC
Confidence            4566778999999999999999999   999999999999999999999999999999999883

>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=99.66  E-value=5e-17  Score=118.83  Aligned_cols=56  Identities=30%  Similarity=0.348  Sum_probs=53.6

Q ss_pred             CCcccCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         241 GRQTYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       241 ~Rt~fT~~Ql~~LE~~F~~---n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      +|++|+.+|+.+||.+|..   ++||+..++++||.++||++++|++||+|||+|+||.
T Consensus         1 rr~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A            1 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CCCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             CcCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            4689999999999999999   9999999999999999999999999999999999974

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

Probab=99.65  E-value=3.5e-17  Score=132.41  Aligned_cols=69  Identities=19%  Similarity=0.241  Sum_probs=54.3

Q ss_pred             hcccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHH------------------cC---CCcccchhhcccchh
Q psy3281         233 RSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHA------------------LC---LTERQIKIWFQNRRM  291 (317)
Q Consensus       233 ~s~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~------------------Lg---Lse~qVkiWFQNRRa  291 (317)
                      +..+++||.|+.|+.+|+.+||.+|+.++||+..+|++||..                  ||   |++.+|++||+|||+
T Consensus         4 ~~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~   83 (99)
T 1lfb_A            4 DPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRK   83 (99)
T ss_dssp             ---------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHH
Confidence            345677899999999999999999999999999999999999                  88   999999999999999


Q ss_pred             hhhhhhcccC
Q psy3281         292 KWKKENKSKD  301 (317)
Q Consensus       292 K~KK~~k~k~  301 (317)
                      |+|++.+...
T Consensus        84 k~k~k~~~~~   93 (99)
T 1lfb_A           84 EEAFRHKLAM   93 (99)
T ss_dssp             TTSCCC----
T ss_pred             HHHHhchhhh
Confidence            9987665544

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

Probab=99.65  E-value=2.3e-17  Score=125.91  Aligned_cols=59  Identities=24%  Similarity=0.357  Sum_probs=54.9

Q ss_pred             CCCCcccCHHHHHHHHHHh-hhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281         239 KRGRQTYTRYQTLELEKEF-HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN  297 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F-~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~  297 (317)
                      .+.|++++.+|+.+||+.| ..+.||+..+|++||.+|||++++|++||||||+|+|+..
T Consensus         9 ~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~~   68 (72)
T 2cqx_A            9 IKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSG   68 (72)
T ss_dssp             CCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCCC
Confidence            4566778899999999999 9999999999999999999999999999999999999754

>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=99.64  E-value=7.1e-17  Score=138.43  Aligned_cols=62  Identities=23%  Similarity=0.378  Sum_probs=55.9

Q ss_pred             ccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         235 QFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       235 ~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      ..++||.|++|+.+|+.+||.+|..++||+..+|++||..|||++++|++||+|||+|+||.
T Consensus        84 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           84 NERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            34667889999999999999999999999999999999999999999999999999999985

>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=99.64  E-value=5.7e-17  Score=126.40  Aligned_cols=61  Identities=26%  Similarity=0.285  Sum_probs=55.4

Q ss_pred             CCCCcccCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281         239 KRGRQTYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS  299 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~---n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~  299 (317)
                      +++|++|+.+|+.+||.+|..   ++||+..++++||..+||++++|++||+|||+|+|+....
T Consensus         3 ~krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~~~   66 (83)
T 1le8_B            3 PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITIA   66 (83)
T ss_dssp             --CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSCCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHccccccccC
Confidence            456677999999999999999   9999999999999999999999999999999999986543

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

Probab=99.64  E-value=9e-17  Score=122.08  Aligned_cols=59  Identities=42%  Similarity=0.701  Sum_probs=54.4

Q ss_pred             cccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         243 QTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       243 t~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      ..+|..|+.+||+.|..++||+..+|++||.+|||++++|++||+|||+|+||..+..+
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~~~~~   67 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSE   67 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSSSSCC
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhhhhhh
Confidence            35789999999999999999999999999999999999999999999999998765543

>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=99.63  E-value=1.3e-16  Score=121.13  Aligned_cols=60  Identities=22%  Similarity=0.180  Sum_probs=56.5

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhh-CCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  295 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~-n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK  295 (317)
                      +++||.||.|+.+||.+|+.+|+. +.||+.++|+.||.+|||++++|++||||||--.|.
T Consensus         5 ~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~~~~   65 (71)
T 1wi3_A            5 SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             CCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceeeecC
Confidence            467899999999999999999999 999999999999999999999999999999987654

>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=99.62  E-value=1.8e-16  Score=136.25  Aligned_cols=60  Identities=25%  Similarity=0.426  Sum_probs=57.5

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  295 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK  295 (317)
                      .++||+|++|+.+|+.+||++|..++||+..+|++||.+|||++++|++||+|||+|+||
T Consensus        91 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           91 SKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            356788999999999999999999999999999999999999999999999999999997

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

Probab=99.61  E-value=2.5e-16  Score=118.81  Aligned_cols=51  Identities=20%  Similarity=0.382  Sum_probs=49.6

Q ss_pred             CHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         246 TRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       246 T~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      |.+||.+||+.|..++||+..++++||..|||++++|++||+|||+|+|+.
T Consensus        12 ~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg   62 (66)
T 3nau_A           12 TKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRG   62 (66)
T ss_dssp             CHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhcc
Confidence            789999999999999999999999999999999999999999999999974

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

Probab=99.61  E-value=2.8e-16  Score=117.43  Aligned_cols=55  Identities=16%  Similarity=0.148  Sum_probs=51.1

Q ss_pred             CcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       242 Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      +..++.+|+.+||++|..++||+..+|++||++|||++++|++||+|||+|.++.
T Consensus         7 ~~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~~   61 (64)
T 2e19_A            7 GQPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISV   61 (64)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSCS
T ss_pred             CCCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCCC
Confidence            4456799999999999999999999999999999999999999999999998763

>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=99.59  E-value=4.8e-16  Score=134.38  Aligned_cols=60  Identities=30%  Similarity=0.426  Sum_probs=57.2

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      ++||+|+.|+.+|+.+||.+|..++||+..+|++||..|||++++|++||+|||+|+||.
T Consensus        95 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A           95 ARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             CSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            567889999999999999999999999999999999999999999999999999999984

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

Probab=99.58  E-value=5e-16  Score=134.77  Aligned_cols=66  Identities=21%  Similarity=0.227  Sum_probs=55.0

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      .+.||.|+.|+.+|+.+||.+|..++||+..+|++||..|||++++|++||+|||+|+|+......
T Consensus        95 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~~~~  160 (164)
T 2d5v_A           95 NTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWLEHH  160 (164)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC-----
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccCCCCC
Confidence            356889999999999999999999999999999999999999999999999999999998655433

>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=99.58  E-value=3.4e-16  Score=117.48  Aligned_cols=50  Identities=26%  Similarity=0.349  Sum_probs=46.7

Q ss_pred             HHHHHHHHHHh-hhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         247 RYQTLELEKEF-HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       247 ~~Ql~~LE~~F-~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      .+++.+||++| ..++||+..+|++||++|||++++|++||||||+|+|+.
T Consensus         9 ~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~~   59 (64)
T 1x2m_A            9 AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPS   59 (64)
T ss_dssp             SCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCCS
T ss_pred             chHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCCC
Confidence            45799999999 579999999999999999999999999999999999873

>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=99.54  E-value=2.3e-15  Score=113.15  Aligned_cols=59  Identities=17%  Similarity=0.250  Sum_probs=50.8

Q ss_pred             cccCHHHHHHHHHHhh---hCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         243 QTYTRYQTLELEKEFH---FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       243 t~fT~~Ql~~LE~~F~---~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      .+|+.+++.+|+.+|.   .++||+..++++||..+||++++|++||+|||+|+||....+.
T Consensus         3 g~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~~   64 (67)
T 3k2a_A            3 GIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQS   64 (67)
T ss_dssp             ---CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC----
T ss_pred             CcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHHHHh
Confidence            3799999999999999   9999999999999999999999999999999999998766554

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

Probab=99.46  E-value=4e-14  Score=112.60  Aligned_cols=74  Identities=18%  Similarity=0.209  Sum_probs=62.3

Q ss_pred             cccCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCCCCCCCCCCCCCCCC
Q psy3281         243 QTYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGGSDAGSDITPATSP  316 (317)
Q Consensus       243 t~fT~~Ql~~LE~~F~~---n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~~~s~~s~~sp~tSP  316 (317)
                      ..|+.+++.+|+.+|..   ++||+.++|++||+++||++++|++||+|+|.|+|+....+.+.....-+++-..||
T Consensus        10 ~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~~~~~~~p~~~~i~r~~~~   86 (89)
T 2lk2_A           10 HMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRKDGKDPNQFTISRRGAK   86 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHHHHCSSCCSCCCCSSCCC
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHHHhcCCCcccccccCCCCC
Confidence            35889999999999987   899999999999999999999999999999999999877666554444455544444

>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=99.43  E-value=2.1e-14  Score=128.83  Aligned_cols=61  Identities=18%  Similarity=0.247  Sum_probs=54.0

Q ss_pred             ccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcC---------------------CCcccchhhcccchhhh
Q psy3281         235 QFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC---------------------LTERQIKIWFQNRRMKW  293 (317)
Q Consensus       235 ~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~Lg---------------------Lse~qVkiWFQNRRaK~  293 (317)
                      ..++||.|+.|+..|+.+||++|..++||+..+|++||..|+                     |++.+|++||+|||+|+
T Consensus       112 ~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~~  191 (194)
T 1ic8_A          112 TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEE  191 (194)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHHC
T ss_pred             cccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhhh
Confidence            356788999999999999999999999999999999999999                     99999999999999998


Q ss_pred             hh
Q psy3281         294 KK  295 (317)
Q Consensus       294 KK  295 (317)
                      |.
T Consensus       192 k~  193 (194)
T 1ic8_A          192 AF  193 (194)
T ss_dssp             C-
T ss_pred             hc
Confidence            75

>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=99.35  E-value=4.1e-13  Score=102.28  Aligned_cols=48  Identities=19%  Similarity=0.292  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhh
Q psy3281         247 RYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK  294 (317)
Q Consensus       247 ~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~K  294 (317)
                      ++|+.+||.+|..|.+|+.+++..||..+||++++|++||+|||++..
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~~~   61 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVYQY   61 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhcccccc
Confidence            678999999999999999999999999999999999999999998533

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

Probab=99.31  E-value=6.2e-13  Score=121.35  Aligned_cols=60  Identities=18%  Similarity=0.276  Sum_probs=54.0

Q ss_pred             ccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcC---------------------CCcccchhhcccchhhh
Q psy3281         235 QFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC---------------------LTERQIKIWFQNRRMKW  293 (317)
Q Consensus       235 ~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~Lg---------------------Lse~qVkiWFQNRRaK~  293 (317)
                      .+++||.|+.|+..++.+||++|..++||+..+|++||..|+                     |++.+|++||+|||+++
T Consensus       139 ~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~~~  218 (221)
T 2h8r_A          139 NKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEE  218 (221)
T ss_dssp             ---CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHTTC
T ss_pred             cCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhhhh
Confidence            456788999999999999999999999999999999999988                     89999999999999875


Q ss_pred             h
Q psy3281         294 K  294 (317)
Q Consensus       294 K  294 (317)
                      .
T Consensus       219 ~  219 (221)
T 2h8r_A          219 A  219 (221)
T ss_dssp             C
T ss_pred             h
Confidence            3

>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=99.26  E-value=8.6e-13  Score=125.68  Aligned_cols=56  Identities=25%  Similarity=0.414  Sum_probs=53.4

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhh
Q psy3281         239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK  294 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~K  294 (317)
                      ++.|+.|+.+++.+||+.|..++||++.+|++||++|||++++|++||+|||+|+|
T Consensus       366 ~~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          366 TAAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            46678899999999999999999999999999999999999999999999999986

>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=98.46  E-value=2.4e-08  Score=67.09  Aligned_cols=23  Identities=70%  Similarity=1.141  Sum_probs=20.1

Q ss_pred             ccchhhcccchhhhhhhhcccCC
Q psy3281         280 RQIKIWFQNRRMKWKKENKSKDG  302 (317)
Q Consensus       280 ~qVkiWFQNRRaK~KK~~k~k~~  302 (317)
                      ++|+|||||||+||||..+....
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~~~   23 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFNDAR   23 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHHTT
T ss_pred             CCceeccHHHHHHHHHHhHHHHH
Confidence            58999999999999998887553

>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=0.0077  Score=45.58  Aligned_cols=39  Identities=21%  Similarity=0.342  Sum_probs=36.6

Q ss_pred             HHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhccc
Q psy3281         250 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQN  288 (317)
Q Consensus       250 l~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQN  288 (317)
                      .++|+.+|...+.+..++...|+.+..|+..+|+.||-.
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            467999999999999999999999999999999999954

>3oka_C N-terminal His-affinity TAG; GT-B fold, alpha-mannosyltransferase, GDP-MAN binding, trans; HET: GDD; 2.20A {Escherichia coli}

Probab=90.55  E-value=0.083  Score=30.32  Aligned_cols=6  Identities=67%  Similarity=1.420  Sum_probs=2.3

Q ss_pred             CCCCCC
Q psy3281         148 NNHHHH  153 (317)
Q Consensus       148 ~hHhhh  153 (317)
                      +|||||
T Consensus         2 ghhhhh    7 (21)
T 3oka_C            2 GHHHHH    7 (26)
T ss_pred             Cccccc
Confidence            343333

>2l4h_A Calcium and integrin-binding protein 1; metal binding protei; NMR {Homo sapiens} PDB: 2l4i_A 2lm5_A

Probab=90.49  E-value=0.067  Score=46.42  Aligned_cols=31  Identities=10%  Similarity=0.076  Sum_probs=24.0

Q ss_pred             CCCcccCHHHHHHHHHHhhh-----------C--CCCCHHHHHH
Q psy3281         240 RGRQTYTRYQTLELEKEFHF-----------N--RYLTRRRRIE  270 (317)
Q Consensus       240 R~Rt~fT~~Ql~~LE~~F~~-----------n--~yPs~~er~e  270 (317)
                      +..|.|+.+++..|.+.|..           +  .+++..|...
T Consensus        40 ~~~t~~s~~ei~~l~~~F~~~D~~~~~~d~~~~dG~I~~~E~~~   83 (214)
T 2l4h_A           40 QDLTFLTKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILS   83 (214)
T ss_dssp             HSCCSCCHHHHHHHHHHHHHHSCGGGCCHHHHTTSEECHHHHTT
T ss_pred             HHhCCCCHHHHHHHHHHHHHhCcccccccccccCCcCCHHHHHH
Confidence            45678999999999999976           4  6777766655

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

Probab=89.37  E-value=0.52  Score=35.65  Aligned_cols=45  Identities=18%  Similarity=0.331  Sum_probs=32.8

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhccc
Q psy3281         239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQN  288 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQN  288 (317)
                      |+.+..|+.++...+...+.. .    ....+||+++||+...|..|...
T Consensus        17 ~~~~~~ys~e~k~~~v~~~~~-g----~s~~~iA~~~gIs~sTl~rW~k~   61 (87)
T 2elh_A           17 KRPLRSLTPRDKIHAIQRIHD-G----ESKASVARDIGVPESTLRGWCKN   61 (87)
T ss_dssp             SSCCSSCCHHHHHHHHHHHHH-T----CCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHC-C----CCHHHHHHHHCcCHHHHHHHHHH
Confidence            456678899886555555542 2    23568899999999999999853

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

Probab=88.58  E-value=0.35  Score=33.90  Aligned_cols=46  Identities=20%  Similarity=0.325  Sum_probs=32.6

Q ss_pred             CcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhccc
Q psy3281         242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQN  288 (317)
Q Consensus       242 Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQN  288 (317)
                      |..|+.+....+...+... ........++|+++||+...|..|...
T Consensus         3 r~~ys~efK~~~~~~~~~g-~s~~~~~~~vA~~~gIs~~tl~~W~~~   48 (59)
T 2glo_A            3 RRIFTPHFKLQVLESYRND-NDCKGNQRATARKYNIHRRQIQKWLQC   48 (59)
T ss_dssp             CCCCCHHHHHHHHHHHHHC-TTTTTCHHHHHHHTTSCHHHHHHHHTT
T ss_pred             CCcCCHHHHHHHHHHHHcC-CCcchHHHHHHHHHCcCHHHHHHHHHH
Confidence            4578888876665555433 322233678999999999999999754

>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=86.57  E-value=0.68  Score=36.81  Aligned_cols=50  Identities=20%  Similarity=0.205  Sum_probs=38.6

Q ss_pred             CCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhh
Q psy3281         240 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK  292 (317)
Q Consensus       240 R~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK  292 (317)
                      ++|+.||.++...+...+..+...+   ..+||+.+|++...|..|..+++..
T Consensus         3 ~~r~~~t~e~K~~iv~~~~~~g~~~---~~~~A~~~gvs~stl~~~~~~~~~~   52 (131)
T 1hlv_A            3 PKRRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNKRAI   52 (131)
T ss_dssp             CSSCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTHHHH
T ss_pred             CcceeCCHHHHHHHHHHHHHCCCCc---HHHHHHHhCCCHHHHHHHHhchhhh
Confidence            3577899999877777775555444   3368999999999999999877654

>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C

Probab=86.24  E-value=0.37  Score=31.52  Aligned_cols=43  Identities=7%  Similarity=0.164  Sum_probs=28.7

Q ss_pred             ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchh
Q psy3281         244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM  291 (317)
Q Consensus       244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRa  291 (317)
                      .++.+++..+...+...     ....+||+.||++...|..|+.....
T Consensus         5 ~~~~~~~~~i~~l~~~g-----~s~~~ia~~lgvs~~Tv~r~l~~~~~   47 (52)
T 1jko_C            5 AINKHEQEQISRLLEKG-----HPRQQLAIIFGIGVSTLYRYFPASSI   47 (52)
T ss_dssp             SSCTTHHHHHHHHHHTT-----CCHHHHHHTTSCCHHHHHHHSCTTC-
T ss_pred             CCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHccc
Confidence            34555555554445432     23568899999999999999975443

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

Probab=84.54  E-value=0.42  Score=36.21  Aligned_cols=51  Identities=10%  Similarity=0.099  Sum_probs=39.3

Q ss_pred             ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281         244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS  299 (317)
Q Consensus       244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~  299 (317)
                      .++..+..+|...|-..     ....+||+.||++...|+.+...-|.|.|+..+.
T Consensus        37 ~L~~~~r~vl~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~   87 (92)
T 3hug_A           37 QLSAEHRAVIQRSYYRG-----WSTAQIATDLGIAEGTVKSRLHYAVRALRLTLQE   87 (92)
T ss_dssp             TSCHHHHHHHHHHHTSC-----CCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence            46788888887654322     3467899999999999999998888888876544

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

Probab=83.68  E-value=1.1  Score=28.62  Aligned_cols=40  Identities=8%  Similarity=0.203  Sum_probs=28.1

Q ss_pred             ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhccc
Q psy3281         244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQN  288 (317)
Q Consensus       244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQN  288 (317)
                      .++.++...+...+.. ..    ...+||+.||++...|..|+..
T Consensus         5 ~l~~~~~~~i~~~~~~-g~----s~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C            5 ALSDTERAQLDVMKLL-NV----SLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             CCCHHHHHHHHHHHHT-TC----CHHHHHHHHTCCHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHc-CC----CHHHHHHHHCcCHHHHHHHHhh
Confidence            4667766555455532 22    3668899999999999999853

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=81.97  E-value=0.66  Score=32.56  Aligned_cols=49  Identities=12%  Similarity=-0.063  Sum_probs=36.8

Q ss_pred             ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281         244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN  297 (317)
Q Consensus       244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~  297 (317)
                      .++..+..+|...|...     ....+||..+|++...|+.|...-|.|.|+..
T Consensus        15 ~L~~~~r~il~l~~~~g-----~s~~eIA~~lgis~~tv~~~~~ra~~~l~~~l   63 (70)
T 2o8x_A           15 DLTTDQREALLLTQLLG-----LSYADAAAVCGCPVGTIRSRVARARDALLADA   63 (70)
T ss_dssp             SSCHHHHHHHHHHHTSC-----CCHHHHHHHHTSCHHHHHHHHHHHHHHHHC--
T ss_pred             hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            47888888888765322     34678999999999999999887777766543

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=80.93  E-value=0.89  Score=32.36  Aligned_cols=53  Identities=15%  Similarity=0.103  Sum_probs=38.8

Q ss_pred             ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281         244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN  297 (317)
Q Consensus       244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~  297 (317)
                      .++..+..+|...|-.+.+ .....++||+.+|++...|+.+...-+.|.|+..
T Consensus         5 ~L~~~er~il~l~~~l~~~-~g~s~~eIA~~lgis~~tV~~~~~ra~~kLr~~~   57 (68)
T 2p7v_B            5 GLTAREAKVLRMRFGIDMN-TDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPS   57 (68)
T ss_dssp             CCCHHHHHHHHHHTTTTSS-SCCCHHHHHHHHTCCHHHHHHHHHHHHHGGGSCC
T ss_pred             cCCHHHHHHHHHHHccCCC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            4688888888888743222 1234578999999999999999887777766543

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=80.88  E-value=0.93  Score=34.77  Aligned_cols=51  Identities=18%  Similarity=0.131  Sum_probs=38.6

Q ss_pred             cccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281         243 QTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS  299 (317)
Q Consensus       243 t~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~  299 (317)
                      ..++..+..+|...++  .    ....+||..||+++..|+.+..+-|.|.+...+.
T Consensus        26 ~~Lt~~e~~vl~l~~~--g----~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~~   76 (95)
T 3c57_A           26 SGLTDQERTLLGLLSE--G----LTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRT   76 (95)
T ss_dssp             -CCCHHHHHHHHHHHT--T----CCHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCCC
T ss_pred             hcCCHHHHHHHHHHHc--C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCHH
Confidence            3588999999887533  2    2347899999999999999998777777665443

>3tla_A MCCF; serine protease, hydrolase; 1.20A {Escherichia coli} PDB: 3tle_A* 3tlg_A 3tlb_A* 3tlc_A* 3tlz_A* 3tly_A

Probab=80.58  E-value=0.33  Score=46.97  Aligned_cols=10  Identities=10%  Similarity=0.112  Sum_probs=5.5

Q ss_pred             HHHHHHHHhh
Q psy3281         249 QTLELEKEFH  258 (317)
Q Consensus       249 Ql~~LE~~F~  258 (317)
                      ..+.|.+.|.
T Consensus        97 Ra~dL~~af~  106 (371)
T 3tla_A           97 RAQEFNELVY  106 (371)
T ss_dssp             HHHHHHHHHT
T ss_pred             HHHHHHHHhh
Confidence            4555666654

>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A

Probab=80.32  E-value=1  Score=33.58  Aligned_cols=49  Identities=20%  Similarity=0.078  Sum_probs=37.4

Q ss_pred             CcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       242 Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      -..++..+..+|..+++  .    ....+||+.||+++..|+.+..+-+.|.+..
T Consensus        19 ~~~Lt~~e~~vl~l~~~--g----~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~   67 (82)
T 1je8_A           19 VNQLTPRERDILKLIAQ--G----LPNKMIARRLDITESTVKVHVKHMLKKMKLK   67 (82)
T ss_dssp             GGGSCHHHHHHHHHHTT--T----CCHHHHHHHHTSCHHHHHHHHHHHHHHTTCS
T ss_pred             HccCCHHHHHHHHHHHc--C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHcCC
Confidence            34688999999887432  2    3567899999999999999988766666543

---

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	317
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	5e-29
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	1e-27
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	1e-27
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	3e-27
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	1e-24
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	6e-24
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	1e-23
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	4e-23
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	2e-22
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	2e-22
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	4e-22
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	1e-21
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	2e-21
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	4e-21
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	7e-21
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	1e-20
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	2e-20
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	4e-20
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	2e-19
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	5e-19
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	1e-18
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	2e-18
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	3e-18
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	4e-18
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	9e-18
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	1e-17
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	1e-17
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	3e-16
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	5e-16
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	2e-14
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	6e-12
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	7e-12

>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 =  104 bits (261), Expect = 5e-29
 Identities = 44/75 (58%), Positives = 55/75 (73%), Gaps = 1/75 (1%)

Query: 226 SPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIW 285
           +P   W+ ++   ++ R  YT++QTLELEKEF FN YLTR RR E+A  L LTERQ+KIW
Sbjct: 2   NPAANWLHAR-STRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIW 60

Query: 286 FQNRRMKWKKENKSK 300
           FQNRRMK KK NK +
Sbjct: 61  FQNRRMKMKKINKDR 75

>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 =  100 bits (250), Expect = 1e-27
 Identities = 24/63 (38%), Positives = 37/63 (58%)

Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
           +R R ++T+ Q   LEKEF    Y     R  +A  + L E +I++WF NRR KW++E K
Sbjct: 2   QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 61

Query: 299 SKD 301
            ++
Sbjct: 62  LRN 64

>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 = 99.9 bits (249), Expect = 1e-27
 Identities = 55/56 (98%), Positives = 55/56 (98%)

Query: 242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
           RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKEN
Sbjct: 1   RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 56

>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 = 99.1 bits (247), Expect = 3e-27
 Identities = 27/57 (47%), Positives = 39/57 (68%)

Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           K G+  ++  QT+ELEK+F   +YL+   R  +A  L L+ERQ+K WFQNRR KW++
Sbjct: 1   KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 57

>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 = 92.6 bits (230), Expect = 1e-24
 Identities = 27/57 (47%), Positives = 42/57 (73%)

Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           ++ R  Y++ Q  ELE+E+  N+++T+ +R +I+ A  L+ERQI IWFQNRR+K KK
Sbjct: 2   RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 58

>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 = 90.7 bits (225), Expect = 6e-24
 Identities = 24/62 (38%), Positives = 38/62 (61%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
           ++R R T++  Q  ELE+ F   +Y     R E+A    LTE +I++WFQNRR + +K++
Sbjct: 2   QRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH 61

Query: 298 KS 299
            S
Sbjct: 62  TS 63

>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 = 89.9 bits (223), Expect = 1e-23
 Identities = 16/62 (25%), Positives = 25/62 (40%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
             R R      Q   L   +  N       + ++     L+ R I++WFQN+R K KK +
Sbjct: 3   TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS 62

Query: 298 KS 299
             
Sbjct: 63  IM 64

>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 = 88.4 bits (219), Expect = 4e-23
 Identities = 25/63 (39%), Positives = 38/63 (60%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
           R++ R  +++ Q  ELE+ F   +YL+   R  +A  + LT  Q+KIWFQN R K K++ 
Sbjct: 2   RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61

Query: 298 KSK 300
           K K
Sbjct: 62  KDK 64

>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 = 87.4 bits (216), Expect = 2e-22
 Identities = 38/87 (43%), Positives = 47/87 (54%), Gaps = 14/87 (16%)

Query: 226 SPLYPWMRS--------------QFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEI 271
           +  + WM+                      R  +T  Q  ELEKEFHFN+YL+R RR+EI
Sbjct: 1   ARTFDWMKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEI 60

Query: 272 AHALCLTERQIKIWFQNRRMKWKKENK 298
           A  L L E Q+KIWFQNRRMK KK  +
Sbjct: 61  AATLELNETQVKIWFQNRRMKQKKRER 87

>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 = 86.1 bits (213), Expect = 2e-22
 Identities = 26/57 (45%), Positives = 37/57 (64%)

Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           ++ R  +T  Q L LE++F   +YL+   R E + +L LTE Q+KIWFQNRR K K+
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 = 85.7 bits (212), Expect = 4e-22
 Identities = 14/56 (25%), Positives = 28/56 (50%)

Query: 240 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           + R T +      LE+ F  +   + +  + +A  L L +  +++WF NRR + K+
Sbjct: 1   KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 56

>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 = 84.1 bits (208), Expect = 1e-21
 Identities = 27/53 (50%), Positives = 35/53 (66%)

Query: 240 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 292
           R R  ++  Q   L++EF+ NRYLT RRR +++  L L E QIKIWFQN R K
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57

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

 Score = 83.8 bits (207), Expect = 2e-21
 Identities = 30/57 (52%), Positives = 38/57 (66%)

Query: 240 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
           R R  +TR Q   LEKEF+   Y++R RR E+A  L L E  IK+WFQNRRMK K++
Sbjct: 1   RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 57

>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 = 83.6 bits (206), Expect = 4e-21
 Identities = 17/74 (22%), Positives = 28/74 (37%), Gaps = 15/74 (20%)

Query: 240 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIA---------------HALCLTERQIKI 284
             R T+ +     +E  F+ N+Y    +R EIA                   +T  ++  
Sbjct: 2   GSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYN 61

Query: 285 WFQNRRMKWKKENK 298
           WF NRR + K+   
Sbjct: 62  WFANRRKEIKRRAN 75

>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 = 82.3 bits (203), Expect = 7e-21
 Identities = 25/58 (43%), Positives = 34/58 (58%)

Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
           +R R  +T  Q  +LE  F  NRY     R EIA    LTE ++++WF+NRR KW+K 
Sbjct: 2   RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 59

>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 = 81.6 bits (201), Expect = 1e-20
 Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 2/68 (2%)

Query: 239 KRGRQTYTRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK-E 296
             G  T T  Q   LE  F+  N++        IA    LTE Q + WF+ R  +W++ E
Sbjct: 2   SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 61

Query: 297 NKSKDGGS 304
               +  S
Sbjct: 62  GLPSECRS 69

>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 = 81.2 bits (200), Expect = 2e-20
 Identities = 18/60 (30%), Positives = 29/60 (48%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
           RKR R +        LE  F      + ++   IA+ L L +  +++WF NRR K K+ +
Sbjct: 8   RKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRSS 67

>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 = 80.4 bits (198), Expect = 4e-20
 Identities = 26/66 (39%), Positives = 37/66 (56%)

Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
           +R R T+T  Q  ELE+ F   RYLT  R  +++  L L   Q+KIWF+NRR + K ++ 
Sbjct: 2   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 61

Query: 299 SKDGGS 304
                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 = 78.9 bits (194), Expect = 2e-19
 Identities = 26/64 (40%), Positives = 37/64 (57%)

Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
           +++ R  +T+ QT ELE+ F   RYL+   R  +A  + LT  Q+KIWFQN R K K+  
Sbjct: 9   KRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ 68

Query: 298 KSKD 301
             K 
Sbjct: 69  NEKG 72

>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 = 77.1 bits (190), Expect = 5e-19
 Identities = 18/60 (30%), Positives = 24/60 (40%), Gaps = 5/60 (8%)

Query: 239 KRGRQTYTRYQTLELEKEFHFNR---YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           +  R  +T+     LE  F  N    YL  +    +     L+  QIK W  NRR K K 
Sbjct: 1   RGHR--FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

>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 = 75.9 bits (187), Expect = 1e-18
 Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 1/51 (1%)

Query: 246 TRYQTLELEKEF-HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           T      LEK F    ++   +R   ++  L    R I+ WF+ RR + K 
Sbjct: 1   TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 51

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

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

 Score = 75.3 bits (185), Expect = 2e-18
 Identities = 14/53 (26%), Positives = 28/53 (52%)

Query: 242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294
           + + +      LE+ F   + L  + + E+A    +T  Q+++WF N+RM+ K
Sbjct: 1   KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53

>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 = 74.9 bits (184), Expect = 3e-18
 Identities = 13/49 (26%), Positives = 21/49 (42%)

Query: 242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR 290
           R  +T  Q   L   F  N+  ++  +I I+  L L    +  +F N R
Sbjct: 2   RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

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

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

 Score = 74.8 bits (184), Expect = 4e-18
 Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 3/60 (5%)

Query: 239 KRGRQTYTRYQTLELEKEF---HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           K  R    ++ T  +         + Y T   + +IA    LT  Q+  WF N R +  +
Sbjct: 3   KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQ 62

>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 = 73.8 bits (181), Expect = 9e-18
 Identities = 19/56 (33%), Positives = 27/56 (48%)

Query: 242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
           R +      + LEK F  N+  T      IA  L + +  I++WF NRR K K+ N
Sbjct: 2   RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRIN 57

>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 = 74.0 bits (181), Expect = 1e-17
 Identities = 15/67 (22%), Positives = 23/67 (34%), Gaps = 1/67 (1%)

Query: 234 SQFERKRGRQTYTRYQTLELEKEFH-FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 292
           S     R R   +      L+   H    Y  +     ++  L L +  I  +FQN+R  
Sbjct: 3   SGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYH 62

Query: 293 WKKENKS 299
            K    S
Sbjct: 63  VKHSGPS 69

>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 = 73.8 bits (181), Expect = 1e-17
 Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 3/63 (4%)

Query: 239 KRGRQTYTRYQTLELEK---EFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
           +R R+ + +  T  L +       N Y +   + E+A    +T  Q+  WF N+R+++KK
Sbjct: 2   RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61

Query: 296 ENK 298
              
Sbjct: 62  NIG 64

>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 = 70.5 bits (172), Expect = 3e-16
 Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 1/71 (1%)

Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
            +  +  T  Q   L+  F  +  LT      +     LT R+I  WF  ++     + +
Sbjct: 5   PQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEE 64

Query: 299 SKDGG-SDAGS 308
             +   S+AGS
Sbjct: 65  KMEIDESNAGS 75

>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 = 69.0 bits (169), Expect = 5e-16
 Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 4/58 (6%)

Query: 241 GRQTYTRY---QTLELEKEF-HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294
           G +            LEK F    +Y   +R   ++  L  + R+I+ WF++RR + K
Sbjct: 1   GIKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

>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 = 65.2 bits (158), Expect = 2e-14
 Identities = 11/78 (14%), Positives = 23/78 (29%), Gaps = 21/78 (26%)

Query: 242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL---------------------CLTER 280
           R  +       L + +   +  ++  R  +                          +TE 
Sbjct: 1   RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 281 QIKIWFQNRRMKWKKENK 298
           ++  WF NRR +    +K
Sbjct: 61  RVYNWFANRRKEEAFRHK 78

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]} Length = 76

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

 Score = 58.2 bits (140), Expect = 6e-12
 Identities = 12/69 (17%), Positives = 23/69 (33%)

Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
               +  T+ Q   L+  F   ++  R    ++     L   +I  WF + R   K    
Sbjct: 4   GSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQL 63

Query: 299 SKDGGSDAG 307
                + +G
Sbjct: 64  KWFRDNASG 72

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

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

 Score = 58.5 bits (141), Expect = 7e-12
 Identities = 9/64 (14%), Positives = 18/64 (28%), Gaps = 4/64 (6%)

Query: 237 ERKRGRQTYTRYQTLELEKEFH----FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 292
             KR R  +T  Q  ++           +        +      +  + +KIW  N +  
Sbjct: 16  TTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNS 75

Query: 293 WKKE 296
               
Sbjct: 76  GPSS 79

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	317
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.8
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.79
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.79
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.78
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.78
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.78
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.78
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.78
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.78
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.78
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.77
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.76
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.76
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.75
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.75
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.74
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.73
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.72
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.72
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.71
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.71
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.7
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.7
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.67
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.67
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.64
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.63
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.59
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.58
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.55
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.54
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.52
d1hlva1	66	DNA-binding domain of centromere binding protein B	93.07
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	85.69

>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=99.80  E-value=1.3e-20  Score=137.23  Aligned_cols=57  Identities=47%  Similarity=0.781  Sum_probs=55.4

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281         239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  295 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK  295 (317)
                      ||.|+.||.+|+.+||.+|..++||+.+++++||..|||++++|++||||||+|+||
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            678999999999999999999999999999999999999999999999999999986

>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=99.79  E-value=2.2e-20  Score=139.48  Aligned_cols=63  Identities=40%  Similarity=0.645  Sum_probs=59.3

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      ||.|++||.+|+.+||.+|+.++||+..++++||..|||++++|+|||+|||+|+|+..+...
T Consensus         2 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~~~~   64 (67)
T d1zq3p1           2 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQHK   64 (67)
T ss_dssp             SCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhhhcc
Confidence            678999999999999999999999999999999999999999999999999999998766544

>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=99.79  E-value=2.3e-20  Score=135.54  Aligned_cols=58  Identities=45%  Similarity=0.720  Sum_probs=56.0

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      ||.|+.||.+|+.+||++|+.++||+..++++||..|||++++|++||+|||+|+||.
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   58 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL   58 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhccC
Confidence            5789999999999999999999999999999999999999999999999999999983

>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=99.78  E-value=3.2e-20  Score=142.25  Aligned_cols=64  Identities=66%  Similarity=0.949  Sum_probs=60.3

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhccc
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSK  300 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k  300 (317)
                      .+||+|++||.+|+.+||.+|+.++||+..++++||..|||++++|+|||||||+|+|+..+.+
T Consensus        12 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~~   75 (77)
T d1pufa_          12 STRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDR   75 (77)
T ss_dssp             TTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHHh
Confidence            4568899999999999999999999999999999999999999999999999999999987654

>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=99.78  E-value=4.2e-20  Score=133.81  Aligned_cols=57  Identities=47%  Similarity=0.865  Sum_probs=55.3

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281         239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  295 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK  295 (317)
                      |+.|++||.+|+.+||.+|+.|+||+.+++++||..|||++++|++||+|||+|+||
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

>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=99.78  E-value=4.3e-20  Score=133.73  Aligned_cols=57  Identities=53%  Similarity=0.749  Sum_probs=55.2

Q ss_pred             CCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         240 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       240 R~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      |.|+.||.+|+.+||..|+.++||+..++++||.+|||++++|++||+|||+|+||.
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk~   57 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   57 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhcC
Confidence            679999999999999999999999999999999999999999999999999999973

>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=99.78  E-value=3.9e-20  Score=133.77  Aligned_cols=55  Identities=98%  Similarity=1.485  Sum_probs=53.8

Q ss_pred             CcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       242 Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      ||.||.+|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||+
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            7899999999999999999999999999999999999999999999999999985

>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=99.78  E-value=5.6e-20  Score=144.18  Aligned_cols=62  Identities=58%  Similarity=0.878  Sum_probs=56.4

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK  298 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k  298 (317)
                      +.+|.|++||.+|+.+||.+|..|.||+.++|++||.+|||++++|+|||||||+|+||..+
T Consensus        26 ~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~~   87 (88)
T d1b72a_          26 SPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   87 (88)
T ss_dssp             ----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhcc
Confidence            44788999999999999999999999999999999999999999999999999999999765

>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=99.78  E-value=3.5e-20  Score=141.89  Aligned_cols=65  Identities=40%  Similarity=0.664  Sum_probs=60.1

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      ++||.|++||.+|+.+||.+|+.++||+..++++||..|||++++|++||+|||+|+|+....+.
T Consensus         8 k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~   72 (77)
T d1vnda_           8 KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKG   72 (77)
T ss_dssp             SSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSCCCSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHhhccC
Confidence            56788999999999999999999999999999999999999999999999999999998655443

>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=99.78  E-value=6.2e-20  Score=136.19  Aligned_cols=62  Identities=37%  Similarity=0.622  Sum_probs=58.9

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK  298 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k  298 (317)
                      ++||.|++||.+|+.+||.+|..++||+..++++||..|||++++|++||+|||+|+|+...
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~   62 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   62 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhccc
Confidence            46789999999999999999999999999999999999999999999999999999998754

>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=99.77  E-value=9e-20  Score=136.53  Aligned_cols=64  Identities=39%  Similarity=0.679  Sum_probs=59.8

Q ss_pred             cCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       238 rRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      +||.|++||.+|+.+||.+|..++||+..++++||..|||++++|++||+|||+|+|+..+...
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~~~~~   65 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDKA   65 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSCCS
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhcccchh
Confidence            4789999999999999999999999999999999999999999999999999999998765443

>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=99.76  E-value=2.1e-19  Score=136.08  Aligned_cols=63  Identities=29%  Similarity=0.372  Sum_probs=58.1

Q ss_pred             CCCCcccCHHHHHHHHHHhhh-CCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         239 KRGRQTYTRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~-n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      ++.|++||.+|+.+||..|.. ++||+..+|++||.+|||++++|++||||||+|+||......
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~~~p~   65 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLPS   65 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHCCCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhccCCcc
Confidence            578999999999999999986 789999999999999999999999999999999999765443

>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=99.76  E-value=1.4e-19  Score=129.11  Aligned_cols=53  Identities=51%  Similarity=0.799  Sum_probs=51.6

Q ss_pred             CCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhh
Q psy3281         240 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK  292 (317)
Q Consensus       240 R~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK  292 (317)
                      |.|+.||.+|+.+||..|+.++||+..+|++||.+|||++++|++||||||+|
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            57999999999999999999999999999999999999999999999999987

>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=99.75  E-value=1.2e-19  Score=132.48  Aligned_cols=58  Identities=43%  Similarity=0.713  Sum_probs=56.3

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      ||.|++||.+|+.+||.+|..|+||+..++++||.+|||++++|++||+|||+|+||.
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            6789999999999999999999999999999999999999999999999999999985

>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=99.75  E-value=2.5e-19  Score=134.04  Aligned_cols=61  Identities=39%  Similarity=0.675  Sum_probs=58.1

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281         239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS  299 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~  299 (317)
                      ||.||+||.+|+.+||..|+.|+||+..++++||.+|||++++|++||+|+|+|+|+..+.
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~   62 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL   62 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhhh
Confidence            6789999999999999999999999999999999999999999999999999999987654

>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=99.74  E-value=3.6e-19  Score=132.46  Aligned_cols=62  Identities=26%  Similarity=0.324  Sum_probs=58.8

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK  298 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k  298 (317)
                      +.+|.|++||.+|+.+||.+|..|+||+.+++++||.+|||++++|++||+|||+|+|+...
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~~~   63 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI   63 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCCC
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHHHH
Confidence            46889999999999999999999999999999999999999999999999999999988654

>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=99.73  E-value=3.9e-19  Score=132.70  Aligned_cols=60  Identities=30%  Similarity=0.397  Sum_probs=57.2

Q ss_pred             ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      .+||+|++|+.+|+.+||.+|..++||+.+++++||.+|||++++|++||+|||+|+||.
T Consensus         7 ~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_           7 ARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             CSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             ccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            457889999999999999999999999999999999999999999999999999999874

>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=99.72  E-value=9.4e-19  Score=126.99  Aligned_cols=57  Identities=25%  Similarity=0.396  Sum_probs=55.2

Q ss_pred             CCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         240 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       240 R~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      |+||.|+.+|+++||..|..|+||+..++++||.+|||++++|++||+|||+|+|+.
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            578999999999999999999999999999999999999999999999999999975

>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=99.72  E-value=1.3e-18  Score=134.40  Aligned_cols=63  Identities=29%  Similarity=0.403  Sum_probs=58.7

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcC---------------CCcccchhhcccchhhhhhhhcccC
Q psy3281         239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC---------------LTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~Lg---------------Lse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      ||+|++|+.+||.+||++|+.|+||+..+|++||.+||               |++.+|++||+|||+|+||+.+...
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~~a~   78 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANIAA   78 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhhHHH
Confidence            68899999999999999999999999999999999875               9999999999999999999776654

>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=99.71  E-value=1.8e-18  Score=123.40  Aligned_cols=53  Identities=26%  Similarity=0.466  Sum_probs=51.7

Q ss_pred             CcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhh
Q psy3281         242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK  294 (317)
Q Consensus       242 Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~K  294 (317)
                      |++||++|+.+||..|..++||+..++++||++|||++++|++||+|||+|+|
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            78999999999999999999999999999999999999999999999999976

>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=99.71  E-value=1.8e-18  Score=130.12  Aligned_cols=59  Identities=22%  Similarity=0.224  Sum_probs=55.6

Q ss_pred             ccCCCCcccCHHHHHHHHHHhh-hCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281         237 ERKRGRQTYTRYQTLELEKEFH-FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  295 (317)
Q Consensus       237 krRR~Rt~fT~~Ql~~LE~~F~-~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK  295 (317)
                      ..+|.|++|+.+|+.+||++|. .++||+.+++++||.+|||++++|++||+|||+|+|+
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            4478899999999999999997 5899999999999999999999999999999999887

>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=99.70  E-value=3.5e-18  Score=123.57  Aligned_cols=56  Identities=32%  Similarity=0.417  Sum_probs=54.4

Q ss_pred             CCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         241 GRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       241 ~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      +||.|+.+++.+||.+|..++||+.+++++||.+|||++++|++||+|||+|+||.
T Consensus         1 kRT~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk~   56 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI   56 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHcc
Confidence            58999999999999999999999999999999999999999999999999999985

>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=8.6e-18  Score=127.92  Aligned_cols=59  Identities=20%  Similarity=0.252  Sum_probs=53.6

Q ss_pred             cccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281         243 QTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD  301 (317)
Q Consensus       243 t~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~  301 (317)
                      .++|.+|+.+||.+|..|.||+..++++||..|||++++|++||+|||+|.|+..+...
T Consensus         9 k~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~~~~   67 (76)
T d2ecba1           9 KEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKME   67 (76)
T ss_dssp             CCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCCC
T ss_pred             CCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhHhhh
Confidence            34589999999999999999999999999999999999999999999999887665544

>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=99.67  E-value=1.3e-17  Score=128.12  Aligned_cols=60  Identities=15%  Similarity=0.077  Sum_probs=55.6

Q ss_pred             cccCCCCcccCHHHHHHHHHHhhh----CCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281         236 FERKRGRQTYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  295 (317)
Q Consensus       236 ~krRR~Rt~fT~~Ql~~LE~~F~~----n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK  295 (317)
                      .++||.||+||.+|+++|+.+|++    +.||+.+++++||++|||++++|+|||+|+|.+.|+
T Consensus        15 ~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          15 GTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             cCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            356789999999999999999986    789999999999999999999999999999998775

>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=99.67  E-value=3.8e-17  Score=124.21  Aligned_cols=60  Identities=18%  Similarity=0.221  Sum_probs=54.9

Q ss_pred             CCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281         240 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS  299 (317)
Q Consensus       240 R~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~  299 (317)
                      ..+++||.+|+.+||.+|..|+||+.+++++||..|||++++|++||+|||+|+|+....
T Consensus         5 s~~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~~~~   64 (76)
T d2ecca1           5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLK   64 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCCS
T ss_pred             CCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhchHH
Confidence            344568999999999999999999999999999999999999999999999999986543

>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=99.64  E-value=3.1e-17  Score=115.25  Aligned_cols=50  Identities=26%  Similarity=0.335  Sum_probs=48.8

Q ss_pred             CCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccch
Q psy3281         241 GRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR  290 (317)
Q Consensus       241 ~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRR  290 (317)
                      .|++||.+|+.+||+.|+.++||+.+++++||.+|||++++|++||+|||
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            48999999999999999999999999999999999999999999999998

>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=99.63  E-value=8.7e-17  Score=121.33  Aligned_cols=60  Identities=28%  Similarity=0.489  Sum_probs=55.6

Q ss_pred             CCCCcccCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281         239 KRGRQTYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK  298 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~---n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k  298 (317)
                      ||+|+.|+.+++.+||.+|..   ++||+.+++++||.++||++++|++||+|+|+|+|+...
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~~   64 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG   64 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccch
Confidence            678999999999999999974   789999999999999999999999999999999987543

>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=99.59  E-value=1.8e-16  Score=121.44  Aligned_cols=56  Identities=18%  Similarity=0.250  Sum_probs=53.0

Q ss_pred             CcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcC---------------------CCcccchhhcccchhhhhhhh
Q psy3281         242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALC---------------------LTERQIKIWFQNRRMKWKKEN  297 (317)
Q Consensus       242 Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~Lg---------------------Lse~qVkiWFQNRRaK~KK~~  297 (317)
                      |++||.+|+.+||++|+.++||+..+|++||++|+                     |++.+|++||+|||+|+|++.
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr~~   77 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFRH   77 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCCC
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHHhc
Confidence            68999999999999999999999999999999994                     899999999999999999864

>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=99.58  E-value=1.5e-16  Score=112.98  Aligned_cols=50  Identities=28%  Similarity=0.345  Sum_probs=47.0

Q ss_pred             CHHHHHHHHHHhhh-CCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281         246 TRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK  295 (317)
Q Consensus       246 T~~Ql~~LE~~F~~-n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK  295 (317)
                      |.+++.+||.+|.. ++||+..++++||++|||++++|++||+|||+|+|+
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            46789999999986 789999999999999999999999999999999986

>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=99.55  E-value=3.2e-16  Score=113.94  Aligned_cols=55  Identities=25%  Similarity=0.367  Sum_probs=51.5

Q ss_pred             CCCcccCHHHHHHHHHHhhh-CCCCCHHHHHHHHHHcCCCcccchhhcccchhhhh
Q psy3281         240 RGRQTYTRYQTLELEKEFHF-NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK  294 (317)
Q Consensus       240 R~Rt~fT~~Ql~~LE~~F~~-n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~K  294 (317)
                      |.+++++.++..+||++|.. ++||+..++++||++|||++++|++||+|||+|+|
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            56788899999999999986 68999999999999999999999999999999987

>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=99.54  E-value=1.6e-15  Score=110.31  Aligned_cols=54  Identities=31%  Similarity=0.373  Sum_probs=49.6

Q ss_pred             cccCHHHHHHHHHHhhhC---CCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281         243 QTYTRYQTLELEKEFHFN---RYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE  296 (317)
Q Consensus       243 t~fT~~Ql~~LE~~F~~n---~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~  296 (317)
                      .+|+.+++.+|+.+|..+   +||+.+++++||.++||++++|++||+|+|+|.|+.
T Consensus         3 ~Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~~   59 (60)
T d1k61a_           3 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhccccccC
Confidence            349999999999999765   699999999999999999999999999999998763

>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=99.52  E-value=4e-15  Score=108.99  Aligned_cols=56  Identities=25%  Similarity=0.272  Sum_probs=52.0

Q ss_pred             CCCCcccCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHcCCCcccchhhcccchhhhh
Q psy3281         239 KRGRQTYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK  294 (317)
Q Consensus       239 RR~Rt~fT~~Ql~~LE~~F~~---n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~K  294 (317)
                      ||+|+.|+.+++.+|+.+|..   ++||+.+++++||.++||+.++|++||+|+|+|..
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            567789999999999999985   78999999999999999999999999999998865

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

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

Probab=93.07  E-value=0.045  Score=39.10  Aligned_cols=48  Identities=21%  Similarity=0.234  Sum_probs=39.1

Q ss_pred             CCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchh
Q psy3281         241 GRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM  291 (317)
Q Consensus       241 ~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRa  291 (317)
                      +|..+|-++...+...|+.+...+   ..+||+.+||....|..|.+|+..
T Consensus         4 kRk~LT~~eK~~ii~~~e~g~k~s---q~eIA~~fGv~~STvs~IlKnK~k   51 (66)
T d1hlva1           4 KRRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNKRA   51 (66)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTHHH
T ss_pred             ccccCCHHHHHHHHHHHHcCCcch---HHHHHHHhCCChhHHHHHHHHHHH
Confidence            355689998888888888877555   567999999999999999998543

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=85.69  E-value=0.44  Score=31.37  Aligned_cols=41  Identities=7%  Similarity=0.139  Sum_probs=34.4

Q ss_pred             CcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcc
Q psy3281         242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ  287 (317)
Q Consensus       242 Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQ  287 (317)
                      +..+|++|++.+.+.+... .    .+.+||+.||++...|-.||-
T Consensus         3 ~~~lt~~q~~~a~~l~~~G-~----s~~~iA~~~gVSr~TiYry~p   43 (47)
T d1ijwc_           3 PRAINKHEQEQISRLLEKG-H----PRQQLAIIFGIGVSTLYRYFP   43 (47)
T ss_dssp             CCSSCHHHHHHHHHHHHTT-C----CHHHHHHHHTCCHHHHHHHSC
T ss_pred             CCcCCHHHHHHHHHHHHCC-C----CHHHHHHHHCcCHHHHHhhCC
Confidence            4578999999999988743 2    377899999999999999983