Psyllid ID: psy1901

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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-----
Protein Sequence
MDQDYQDDLWVVGRPSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLNAFNSMSLHHQYADSAANFSHQSHPTSWAQQAASYATAGAALTAGYNSHAYSSATPEFPVSGPGYHQTNQHCADSTAAWSRHHSSSTKSPVDVPSPWTSTTADNYR
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHcccccccHHHHHccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccHHHccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHcHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mdqdyqddlwvvgrpssgdesdtesepgiplkrkqrrsrttftgDQLEELERAFQrtqypdvytrEELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLNAFNSMSLHHqyadsaanfshqshptswAQQAASYATAGAALTagynshayssatpefpvsgpgyhqtnqhcadstaawsrhhssstkspvdvpspwtsttadnyr
Flexible Loop (DISEMBL)
mdqdyqddlwvvgrpssgdesdtesepgiplkrkqrrsrttftgdqleelerafqrtqypdvyTREELaqktkltearvQVWFSNRRARLRKQLNSQQLNAFNSMSLHHQYADSAANFSHQSHPTSWAQQAASYATAGAALTAGYNSHAYSSATPEFPVSGPGYHQTNQHCADSTAAWSRHHssstkspvdvpspwtsttadnyr
Low Complexity Region (SEG)
MDQDYQDDLWVVGRPSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLNAFNSMSLHHQYADSAANFSHQSHPTSWaqqaasyatagaaltagyNSHAYSSATPEFPVSGPGYHQTNQHCADSTAAWSRHHSSSTKSPVDVPSPWTSTTADNYR
Disordered region (IsUnstruct)
*********************************************************QYPDVYTREELAQKTKLTEARVQVWFSNRR**********************************************YATAGAALTAGYN***********************************************************
Disordered Region (DISOPRED)
****************************************TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR********************************************************************************************************************
Disordered Region (DISEMBL)
MDQDYQDDLWVVGR****************LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLNAFNSMSLHHQYADSA*****************SYATAGAALTAGYNSHAYSSATPEFPVSGPGY*****************************************
Disordered Region (DISPRO)
*************************************SRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ******SMSLHHQYADSAANFSHQSHPTSWAQQAASYATAGAALTAGYNSHAYSSATPEFPVSGPGYHQTNQHCADSTAAWSRHHSSSTKSPV***************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDQDYQDDLWVVGRPSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLNAFNSMSLHHQYADSAANFSHQSHPTSWAQQAASYATAGAALTAGYNSHAYSSATPEFPVSGPGYHQTNQHCADSTAAWSRHHSSSTKSPVDVPSPWTSTTADNYR
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	205	2.2.26 [Sep-21-2011]
Q28DP6	461	Paired box protein Pax-3	no	N/A	0.443	0.197	0.747	5e-34
P23759	520	Paired box protein Pax-7	no	N/A	0.424	0.167	0.770	5e-34
Q645N4	484	Paired box protein Pax-3-	N/A	N/A	0.443	0.188	0.747	5e-34
Q0IH87	483	Paired box protein Pax-3-	N/A	N/A	0.443	0.188	0.747	6e-34
P24610	479	Paired box protein Pax-3	yes	N/A	0.443	0.189	0.747	6e-34
P23760	479	Paired box protein Pax-3	yes	N/A	0.443	0.189	0.747	7e-34
P09083	449	Protein gooseberry-neuro	no	N/A	0.751	0.342	0.5	7e-34
P06601	613	Segmentation protein pair	yes	N/A	0.395	0.132	0.802	7e-34
P47239	503	Paired box protein Pax-7	no	N/A	0.414	0.168	0.788	8e-34
P09082	427	Protein gooseberry OS=Dro	no	N/A	0.439	0.210	0.733	9e-33

>sp|Q28DP6|PAX3_XENTR Paired box protein Pax-3 OS=Xenopus tropicalis GN=pax3 PE=2 SV=2

 Score =  144 bits (362), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 68/91 (74%), Positives = 77/91 (84%)

Query: 15  PSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKL 74
           P S + SD +SEP +PLKRKQRRSRTTFT +QLEELERAF+RT YPD+YTREELAQ+ KL
Sbjct: 176 PESEEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKL 235

Query: 75  TEARVQVWFSNRRARLRKQLNSQQLNAFNSM 105
           TEARVQVWFSNRRAR RKQ  + QL AFN +
Sbjct: 236 TEARVQVWFSNRRARWRKQAGANQLMAFNHL 266

Probable transcription factor. Promotes both hatching gland and neural crest cell fates, two of the cell populations that arise from the neural plate border. Acts downstream of msx1 to induce the neural crest, cooperating with zic1 and mediating signals from both the wnt and fgf8 signaling pathways. Induction of hatching gland cell fate is independent of zic1.
Xenopus tropicalis (taxid: 8364)

>sp|P23759|PAX7_HUMAN Paired box protein Pax-7 OS=Homo sapiens GN=PAX7 PE=2 SV=3

 Score =  144 bits (362), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 67/87 (77%), Positives = 76/87 (87%)

Query: 19  DESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEAR 78
           + SD ESEP +PLKRKQRRSRTTFT +QLEELE+AF+RT YPD+YTREELAQ+TKLTEAR
Sbjct: 201 EGSDVESEPDLPLKRKQRRSRTTFTAEQLEELEKAFERTHYPDIYTREELAQRTKLTEAR 260

Query: 79  VQVWFSNRRARLRKQLNSQQLNAFNSM 105
           VQVWFSNRRAR RKQ  + QL AFN +
Sbjct: 261 VQVWFSNRRARWRKQAGANQLAAFNHL 287

Probable transcription factor. May have a role in myogenesis.

Homo sapiens (taxid: 9606)

>sp|Q645N4|PAX3A_XENLA Paired box protein Pax-3-A OS=Xenopus laevis GN=pax3-a PE=2 SV=1

 Score =  144 bits (362), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 68/91 (74%), Positives = 77/91 (84%)

Query: 15  PSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKL 74
           P S + SD +SEP +PLKRKQRRSRTTFT +QLEELERAF+RT YPD+YTREELAQ+ KL
Sbjct: 200 PESEEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKL 259

Query: 75  TEARVQVWFSNRRARLRKQLNSQQLNAFNSM 105
           TEARVQVWFSNRRAR RKQ  + QL AFN +
Sbjct: 260 TEARVQVWFSNRRARWRKQAGANQLMAFNHL 290

Probable transcription factor. Promotes both hatching gland and neural crest cell fates, two of the cell populations that arise from the neural plate border. Acts downstream of msx1 to induce the neural crest, cooperating with zic1 and mediating signals from both the wnt and fgf8 signaling pathways. Induction of hatching gland cell fate is independent of zic1.

Xenopus laevis (taxid: 8355)

>sp|Q0IH87|PAX3B_XENLA Paired box protein Pax-3-B OS=Xenopus laevis GN=pax3-b PE=2 SV=2

 Score =  144 bits (362), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 68/91 (74%), Positives = 77/91 (84%)

Query: 15  PSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKL 74
           P S + SD +SEP +PLKRKQRRSRTTFT +QLEELERAF+RT YPD+YTREELAQ+ KL
Sbjct: 199 PESEEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKL 258

Query: 75  TEARVQVWFSNRRARLRKQLNSQQLNAFNSM 105
           TEARVQVWFSNRRAR RKQ  + QL AFN +
Sbjct: 259 TEARVQVWFSNRRARWRKQAGANQLMAFNHL 289

Probable transcription factor. Promotes both hatching gland and neural crest cell fates, two of the cell populations that arise from the neural plate border. Acts downstream of msx1 to induce the neural crest, cooperating with zic1 and mediating signals from both the wnt and fgf8 signaling pathways. Induction of hatching gland cell fate is independent of zic1.

Xenopus laevis (taxid: 8355)

>sp|P24610|PAX3_MOUSE Paired box protein Pax-3 OS=Mus musculus GN=Pax3 PE=1 SV=2

 Score =  144 bits (362), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 68/91 (74%), Positives = 77/91 (84%)

Query: 15  PSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKL 74
           P S + SD +SEP +PLKRKQRRSRTTFT +QLEELERAF+RT YPD+YTREELAQ+ KL
Sbjct: 199 PQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKL 258

Query: 75  TEARVQVWFSNRRARLRKQLNSQQLNAFNSM 105
           TEARVQVWFSNRRAR RKQ  + QL AFN +
Sbjct: 259 TEARVQVWFSNRRARWRKQAGANQLMAFNHL 289

Probable transcription factor associated with development of alveolar rhabdomyosarcoma.

Mus musculus (taxid: 10090)

>sp|P23760|PAX3_HUMAN Paired box protein Pax-3 OS=Homo sapiens GN=PAX3 PE=1 SV=2

 Score =  143 bits (361), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 68/91 (74%), Positives = 77/91 (84%)

Query: 15  PSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKL 74
           P S + SD +SEP +PLKRKQRRSRTTFT +QLEELERAF+RT YPD+YTREELAQ+ KL
Sbjct: 199 PQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKL 258

Query: 75  TEARVQVWFSNRRARLRKQLNSQQLNAFNSM 105
           TEARVQVWFSNRRAR RKQ  + QL AFN +
Sbjct: 259 TEARVQVWFSNRRARWRKQAGANQLMAFNHL 289

Probable transcription factor associated with development of alveolar rhabdomyosarcoma.

Homo sapiens (taxid: 9606)

>sp|P09083|GSBN_DROME Protein gooseberry-neuro OS=Drosophila melanogaster GN=gsb-n PE=1 SV=2

 Score =  143 bits (361), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 85/170 (50%), Positives = 96/170 (56%), Gaps = 16/170 (9%)

Query: 3   QDYQDDLWVVGRPSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDV 62
           +DY  +  + GR S  D SDTESEPGIPLKRKQRRSRTTFT +QLE LERAF RTQYPDV
Sbjct: 152 KDYTINGILGGRDS--DISDTESEPGIPLKRKQRRSRTTFTAEQLEALERAFSRTQYPDV 209

Query: 63  YTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLNAFNSMSLHHQYADSAANFSHQS 122
           YTREELAQ T LTEAR+QVWFSNRRARLRK       +  + M+            S  +
Sbjct: 210 YTREELAQTTALTEARIQVWFSNRRARLRKHSGGSN-SGLSPMNSGSSNVGVGVGLSGAT 268

Query: 123 HPTSWAQQAASYATAGAALTAGYNSHAYSSATPEFPVSGPGYHQTNQHCA 172
            P         Y   G    AGY      S  P    +G G +    H A
Sbjct: 269 APL-------GYGPLGVGSMAGY------SPAPGTTATGAGMNDGVHHAA 305

Expressed in a segmentally repeating pattern to define the polarity of embryonic segments.

Drosophila melanogaster (taxid: 7227)

>sp|P06601|PRD_DROME Segmentation protein paired OS=Drosophila melanogaster GN=prd PE=1 SV=1

 Score =  143 bits (361), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 65/81 (80%), Positives = 72/81 (88%)

Query: 13  GRPSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKT 72
           G+PS  D SD ESEPGI LKRKQRR RTTF+  QL+ELERAF+RTQYPD+YTREELAQ+T
Sbjct: 191 GKPSDEDISDCESEPGIALKRKQRRCRTTFSASQLDELERAFERTQYPDIYTREELAQRT 250

Query: 73  KLTEARVQVWFSNRRARLRKQ 93
            LTEAR+QVWFSNRRARLRKQ
Sbjct: 251 NLTEARIQVWFSNRRARLRKQ 271

Pair-rule protein expressed in a segmentally repeating pattern to define the polarity of embryonic segments. Capable of sequence-specific DNA-binding.

Drosophila melanogaster (taxid: 7227)

>sp|P47239|PAX7_MOUSE Paired box protein Pax-7 OS=Mus musculus GN=Pax7 PE=2 SV=2

 Score =  143 bits (360), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 67/85 (78%), Positives = 75/85 (88%)

Query: 21  SDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQ 80
           SD ESEP +PLKRKQRRSRTTFT +QLEELE+AF+RT YPD+YTREELAQ+TKLTEARVQ
Sbjct: 201 SDVESEPDLPLKRKQRRSRTTFTAEQLEELEKAFERTHYPDIYTREELAQRTKLTEARVQ 260

Query: 81  VWFSNRRARLRKQLNSQQLNAFNSM 105
           VWFSNRRAR RKQ  + QL AFN +
Sbjct: 261 VWFSNRRARWRKQAGANQLAAFNHL 285

Probable transcription factor. May have a role in myogenesis.

Mus musculus (taxid: 10090)

>sp|P09082|GSB_DROME Protein gooseberry OS=Drosophila melanogaster GN=gsb PE=2 SV=1

 Score =  140 bits (352), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 66/90 (73%), Positives = 76/90 (84%)

Query: 13  GRPSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKT 72
           G   S DES+ ++EP + LKRKQRRSRTTF+ DQ++ LER F RTQYPDVYTREELAQ T
Sbjct: 163 GSVGSEDESEDDAEPSVQLKRKQRRSRTTFSNDQIDALERIFARTQYPDVYTREELAQST 222

Query: 73  KLTEARVQVWFSNRRARLRKQLNSQQLNAF 102
            LTEARVQVWFSNRRARLRKQLN+QQ+ +F
Sbjct: 223 GLTEARVQVWFSNRRARLRKQLNTQQVPSF 252

Expressed in segmentally repeating pattern to define the polarity of embryonic segments.

Drosophila melanogaster (taxid: 7227)

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	205
270012821	406	gooseberry [Tribolium castaneum]	0.668	0.337	0.704	5e-49
189240573	410	PREDICTED: similar to AGAP010358-PA [Tri	0.643	0.321	0.720	3e-48
242015336	390	protein gooseberry, putative [Pediculus	0.809	0.425	0.564	8e-47
357608260	471	gooseberry [Danaus plexippus]	0.614	0.267	0.714	2e-42
307212050	438	Protein gooseberry-neuro [Harpegnathos s	0.448	0.210	0.923	3e-42
328778292	426	PREDICTED: protein gooseberry-like [Apis	0.502	0.241	0.813	8e-42
350420704	404	PREDICTED: protein gooseberry-like [Bomb	0.502	0.254	0.813	9e-42
380027472	405	PREDICTED: protein gooseberry-like [Apis	0.502	0.254	0.813	9e-42
307189638	574	Protein gooseberry [Camponotus floridanu	0.453	0.162	0.903	1e-41
383852872	398	PREDICTED: protein gooseberry-neuro-like	0.502	0.258	0.803	4e-41

>gi|270012821|gb|EFA09269.1| gooseberry [Tribolium castaneum]

 Score =  199 bits (506), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 112/159 (70%), Positives = 121/159 (76%), Gaps = 22/159 (13%)

Query: 11  VVGRPSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQ 70
           ++G  SS DESDTESEPGIPLKRKQRRSRTTFTG+QLE LERAF RTQYPDVYTREELAQ
Sbjct: 160 ILGPNSSCDESDTESEPGIPLKRKQRRSRTTFTGEQLEALERAFGRTQYPDVYTREELAQ 219

Query: 71  KTKLTEARVQVWFSNRRARLRKQLNSQQLNAFNSMSL------HHQYADSAANFSHQSHP 124
           KTKLTEARVQVWFSNRRARLRKQLNSQQLNAFNSMSL       HQY D A N S     
Sbjct: 220 KTKLTEARVQVWFSNRRARLRKQLNSQQLNAFNSMSLPSAFPVQHQYGDPAFNQS----- 274

Query: 125 TSWAQQAASYATAG--------AALTAGYNSHAYSSATP 155
            +WAQQ  SYA+A         +ALT G  S + +S+TP
Sbjct: 275 -TWAQQ--SYASAALSSGALPHSALTTGGASTSVASSTP 310

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189240573|ref|XP_974212.2| PREDICTED: similar to AGAP010358-PA [Tribolium castaneum]

 Score =  197 bits (500), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 111/154 (72%), Positives = 118/154 (76%), Gaps = 22/154 (14%)

Query: 16  SSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLT 75
           SS DESDTESEPGIPLKRKQRRSRTTFTG+QLE LERAF RTQYPDVYTREELAQKTKLT
Sbjct: 169 SSCDESDTESEPGIPLKRKQRRSRTTFTGEQLEALERAFGRTQYPDVYTREELAQKTKLT 228

Query: 76  EARVQVWFSNRRARLRKQLNSQQLNAFNSMSL------HHQYADSAANFSHQSHPTSWAQ 129
           EARVQVWFSNRRARLRKQLNSQQLNAFNSMSL       HQY D A N S      +WAQ
Sbjct: 229 EARVQVWFSNRRARLRKQLNSQQLNAFNSMSLPSAFPVQHQYGDPAFNQS------TWAQ 282

Query: 130 QAASYATAG--------AALTAGYNSHAYSSATP 155
           Q  SYA+A         +ALT G  S + +S+TP
Sbjct: 283 Q--SYASAALSSGALPHSALTTGGASTSVASSTP 314

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242015336|ref|XP_002428315.1| protein gooseberry, putative [Pediculus humanus corporis] gi|212512911|gb|EEB15577.1| protein gooseberry, putative [Pediculus humanus corporis]

 Score =  192 bits (487), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 122/216 (56%), Positives = 135/216 (62%), Gaps = 50/216 (23%)

Query: 29  IPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRA 88
           IPLKRKQRRSRTTFTG+QLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRA
Sbjct: 180 IPLKRKQRRSRTTFTGEQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRA 239

Query: 89  RLRKQLNSQQLNAFNSMSLH----HQYA--DSAANFSHQSHPTSWAQQAASYATAGAALT 142
           RLRKQ+NSQQLNAFNSMSL      QY+  D  ANF+ Q+   SWAQQ+A  A   A   
Sbjct: 240 RLRKQMNSQQLNAFNSMSLQTSFPSQYSVPDPTANFTSQT--PSWAQQSAVAAGYAAGAL 297

Query: 143 AGYNSHAYSSAT---------------------PEFPVSGPGYHQT------NQHCADST 175
             YN   YS+ T                     P+FPV    YHQT      +  CA   
Sbjct: 298 GNYNGSPYSTTTVTSGDPNSSLPANAPSPSSSHPQFPV----YHQTAATMMGSNPCAVGV 353

Query: 176 AA------WSRHHSSS-TKSPVDVPSPWTSTTADNY 204
            A      W+RHH+++ T S  DV S WT    DNY
Sbjct: 354 GAHHQGTPWTRHHTAAPTASTKDVTSAWT----DNY 385

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357608260|gb|EHJ65894.1| gooseberry [Danaus plexippus]

 Score =  177 bits (450), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 95/133 (71%), Positives = 108/133 (81%), Gaps = 7/133 (5%)

Query: 11  VVGRPSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQ 70
           ++G  SS ++SDTESEPGI LKRKQRRSRTTF+GDQLE LERAF RTQYPDVYTREELAQ
Sbjct: 161 ILGPSSSCEDSDTESEPGITLKRKQRRSRTTFSGDQLEALERAFTRTQYPDVYTREELAQ 220

Query: 71  KTKLTEARVQVWFSNRRARLRKQLNSQQLNAFNSMSLHHQYADSAANFSHQSH--PTSWA 128
           KTKLTEARVQVWFSNRRARLRKQLNSQQL+AFN+MSL      SA    HQ +  PT++ 
Sbjct: 221 KTKLTEARVQVWFSNRRARLRKQLNSQQLSAFNTMSLQ-----SAFPSVHQQYEPPTTFN 275

Query: 129 QQAASYATAGAAL 141
            Q AS+  + +AL
Sbjct: 276 AQCASWQQSYSAL 288

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307212050|gb|EFN87933.1| Protein gooseberry-neuro [Harpegnathos saltator]

 Score =  177 bits (448), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 85/92 (92%), Positives = 89/92 (96%)

Query: 16  SSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLT 75
           SSGD+SDTESEPGI LKRKQRRSRTTFTG+QLE+LE AF RTQYPDVYTREELAQKTKLT
Sbjct: 146 SSGDDSDTESEPGIALKRKQRRSRTTFTGEQLEQLEAAFHRTQYPDVYTREELAQKTKLT 205

Query: 76  EARVQVWFSNRRARLRKQLNSQQLNAFNSMSL 107
           EARVQVWFSNRRARLRKQLNSQQLNAFN+MSL
Sbjct: 206 EARVQVWFSNRRARLRKQLNSQQLNAFNTMSL 237

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328778292|ref|XP_394847.4| PREDICTED: protein gooseberry-like [Apis mellifera]

 Score =  175 bits (444), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 87/107 (81%), Positives = 93/107 (86%), Gaps = 4/107 (3%)

Query: 16  SSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLT 75
           SSGD+SDTESEPGI LKRKQRRSRTTFTG+QLE+LE AF RTQYPDVYTREELAQKT LT
Sbjct: 190 SSGDDSDTESEPGIALKRKQRRSRTTFTGEQLEQLEAAFHRTQYPDVYTREELAQKTNLT 249

Query: 76  EARVQVWFSNRRARLRKQLNSQQLNAFNSMSLH----HQYADSAANF 118
           EARVQVWFSNRRARLRKQLNSQQLNAFN+MSL       Y  SA ++
Sbjct: 250 EARVQVWFSNRRARLRKQLNSQQLNAFNTMSLQSFQTQHYGSSAESY 296

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350420704|ref|XP_003492596.1| PREDICTED: protein gooseberry-like [Bombus impatiens]

 Score =  175 bits (444), Expect = 9e-42,   Method: Compositional matrix adjust.
 Identities = 87/107 (81%), Positives = 93/107 (86%), Gaps = 4/107 (3%)

Query: 16  SSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLT 75
           SSGD+SDTESEPGI LKRKQRRSRTTFTG+QLE+LE AF RTQYPDVYTREELAQKT LT
Sbjct: 168 SSGDDSDTESEPGIALKRKQRRSRTTFTGEQLEQLEAAFHRTQYPDVYTREELAQKTNLT 227

Query: 76  EARVQVWFSNRRARLRKQLNSQQLNAFNSMSLH----HQYADSAANF 118
           EARVQVWFSNRRARLRKQLNSQQLNAFN+MSL       Y  SA ++
Sbjct: 228 EARVQVWFSNRRARLRKQLNSQQLNAFNTMSLQSFQTQHYGSSAESY 274

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380027472|ref|XP_003697447.1| PREDICTED: protein gooseberry-like [Apis florea]

 Score =  175 bits (444), Expect = 9e-42,   Method: Compositional matrix adjust.
 Identities = 87/107 (81%), Positives = 93/107 (86%), Gaps = 4/107 (3%)

Query: 16  SSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLT 75
           SSGD+SDTESEPGI LKRKQRRSRTTFTG+QLE+LE AF RTQYPDVYTREELAQKT LT
Sbjct: 169 SSGDDSDTESEPGIALKRKQRRSRTTFTGEQLEQLEAAFHRTQYPDVYTREELAQKTNLT 228

Query: 76  EARVQVWFSNRRARLRKQLNSQQLNAFNSMSLH----HQYADSAANF 118
           EARVQVWFSNRRARLRKQLNSQQLNAFN+MSL       Y  SA ++
Sbjct: 229 EARVQVWFSNRRARLRKQLNSQQLNAFNTMSLQSFQTQHYGSSAESY 275

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307189638|gb|EFN73976.1| Protein gooseberry [Camponotus floridanus]

 Score =  175 bits (443), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 84/93 (90%), Positives = 88/93 (94%)

Query: 16  SSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLT 75
           SSGD+SDTESEPGI LKRKQRRSRTTFTG+QLE+LE AF RTQYPDVYTREELAQKTKLT
Sbjct: 169 SSGDDSDTESEPGIALKRKQRRSRTTFTGEQLEQLEAAFHRTQYPDVYTREELAQKTKLT 228

Query: 76  EARVQVWFSNRRARLRKQLNSQQLNAFNSMSLH 108
           EARVQVWFSNRRARLRKQLNSQQLNAFN+M L 
Sbjct: 229 EARVQVWFSNRRARLRKQLNSQQLNAFNAMGLQ 261

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383852872|ref|XP_003701949.1| PREDICTED: protein gooseberry-neuro-like, partial [Megachile rotundata]

 Score =  173 bits (438), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 86/107 (80%), Positives = 93/107 (86%), Gaps = 4/107 (3%)

Query: 16  SSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLT 75
           SSGD+SDTESEPGI LKRKQRRSRTTFTG+QLE+LE AF RTQYPDVYTREELAQKT LT
Sbjct: 162 SSGDDSDTESEPGIALKRKQRRSRTTFTGEQLEQLEAAFHRTQYPDVYTREELAQKTNLT 221

Query: 76  EARVQVWFSNRRARLRKQLNSQQLNAFNSMSLH----HQYADSAANF 118
           EARVQVWFSNRRARLRKQLNSQQL+AFN+MSL       Y  SA ++
Sbjct: 222 EARVQVWFSNRRARLRKQLNSQQLSAFNTMSLQSFQTQHYGSSAESY 268

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	205
RGD|1564360	503	Pax7 "paired box 7" [Rattus no	0.424	0.172	0.784	1.3e-34
UNIPROTKB|P23759	520	PAX7 "Paired box protein Pax-7	0.424	0.167	0.784	1.5e-34
UNIPROTKB|F1PNX6	505	PAX7 "Uncharacterized protein"	0.424	0.172	0.784	2.7e-34
UNIPROTKB|E9PFV9	505	PAX7 "Paired box protein Pax-7	0.424	0.172	0.784	2.7e-34
MGI|MGI:97491	503	Pax7 "paired box gene 7" [Mus	0.424	0.172	0.784	2.7e-34
FB|FBgn0001147	449	gsb-n "gooseberry-neuro" [Dros	0.497	0.227	0.707	9e-34
ZFIN|ZDB-GENE-980526-52	509	pax3a "paired box gene 3a" [Da	0.463	0.186	0.742	2.5e-33
ZFIN|ZDB-GENE-080917-54	510	pax7b "paired box gene 7b" [Da	0.463	0.186	0.729	1.4e-32
UNIPROTKB|F1MTX0	484	PAX3 "Uncharacterized protein"	0.443	0.188	0.747	1.8e-32
UNIPROTKB|E2QX72	485	PAX3 "Uncharacterized protein"	0.443	0.187	0.747	1.8e-32

RGD|1564360 Pax7 "paired box 7" [Rattus norvegicus (taxid:10116)]

 Score = 353 (129.3 bits), Expect = 1.3e-34, Sum P(2) = 1.3e-34
 Identities = 69/88 (78%), Positives = 77/88 (87%)

Query:    19 DE-SDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEA 77
             DE SD ESEP +PLKRKQRRSRTTFT +QLEELE+AF+RT YPD+YTREELAQ+TKLTEA
Sbjct:   198 DEGSDVESEPDLPLKRKQRRSRTTFTAEQLEELEKAFERTHYPDIYTREELAQRTKLTEA 257

Query:    78 RVQVWFSNRRARLRKQLNSQQLNAFNSM 105
             RVQVWFSNRRAR RKQ  + QL AFN +
Sbjct:   258 RVQVWFSNRRARWRKQAGANQLAAFNHL 285

GO:0000983 "RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity" evidence=ISO

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

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0006338 "chromatin remodeling" evidence=ISO

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

GO:0007519 "skeletal muscle tissue development" evidence=ISO

GO:0010453 "regulation of cell fate commitment" evidence=ISO

GO:0010468 "regulation of gene expression" evidence=ISO

GO:0014813 "satellite cell commitment" evidence=IEA;ISO

GO:0021527 "spinal cord association neuron differentiation" evidence=IEA;ISO

GO:0021904 "dorsal/ventral neural tube patterning" evidence=IEA;ISO

GO:0031062 "positive regulation of histone methylation" evidence=ISO

GO:0043393 "regulation of protein binding" evidence=ISO

GO:0043403 "skeletal muscle tissue regeneration" evidence=IEA;ISO

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

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

GO:0048663 "neuron fate commitment" evidence=IEA;ISO

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

GO:0051216 "cartilage development" evidence=IEA;ISO

GO:0060415 "muscle tissue morphogenesis" evidence=IEA;ISO

GO:2000288 "positive regulation of myoblast proliferation" evidence=ISO

UNIPROTKB|P23759 PAX7 "Paired box protein Pax-7" [Homo sapiens (taxid:9606)]

 Score = 353 (129.3 bits), Expect = 1.5e-34, Sum P(2) = 1.5e-34
 Identities = 69/88 (78%), Positives = 77/88 (87%)

Query:    19 DE-SDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEA 77
             DE SD ESEP +PLKRKQRRSRTTFT +QLEELE+AF+RT YPD+YTREELAQ+TKLTEA
Sbjct:   200 DEGSDVESEPDLPLKRKQRRSRTTFTAEQLEELEKAFERTHYPDIYTREELAQRTKLTEA 259

Query:    78 RVQVWFSNRRARLRKQLNSQQLNAFNSM 105
             RVQVWFSNRRAR RKQ  + QL AFN +
Sbjct:   260 RVQVWFSNRRARWRKQAGANQLAAFNHL 287

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

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

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

GO:0014813 "satellite cell commitment" evidence=IEA

GO:0021527 "spinal cord association neuron differentiation" evidence=IEA

GO:0021904 "dorsal/ventral neural tube patterning" evidence=IEA

GO:0043403 "skeletal muscle tissue regeneration" evidence=IEA

GO:0048663 "neuron fate commitment" evidence=IEA

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

GO:0051216 "cartilage development" evidence=IEA

GO:0060415 "muscle tissue morphogenesis" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0009653 "anatomical structure morphogenesis" evidence=TAS

UNIPROTKB|F1PNX6 PAX7 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 353 (129.3 bits), Expect = 2.7e-34, Sum P(2) = 2.7e-34
 Identities = 69/88 (78%), Positives = 77/88 (87%)

Query:    19 DE-SDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEA 77
             DE SD ESEP +PLKRKQRRSRTTFT +QLEELE+AF+RT YPD+YTREELAQ+TKLTEA
Sbjct:   200 DEGSDVESEPDLPLKRKQRRSRTTFTAEQLEELEKAFERTHYPDIYTREELAQRTKLTEA 259

Query:    78 RVQVWFSNRRARLRKQLNSQQLNAFNSM 105
             RVQVWFSNRRAR RKQ  + QL AFN +
Sbjct:   260 RVQVWFSNRRARWRKQAGANQLAAFNHL 287

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

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

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

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

UNIPROTKB|E9PFV9 PAX7 "Paired box protein Pax-7" [Homo sapiens (taxid:9606)]

 Score = 353 (129.3 bits), Expect = 2.7e-34, Sum P(2) = 2.7e-34
 Identities = 69/88 (78%), Positives = 77/88 (87%)

Query:    19 DE-SDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEA 77
             DE SD ESEP +PLKRKQRRSRTTFT +QLEELE+AF+RT YPD+YTREELAQ+TKLTEA
Sbjct:   200 DEGSDVESEPDLPLKRKQRRSRTTFTAEQLEELEKAFERTHYPDIYTREELAQRTKLTEA 259

Query:    78 RVQVWFSNRRARLRKQLNSQQLNAFNSM 105
             RVQVWFSNRRAR RKQ  + QL AFN +
Sbjct:   260 RVQVWFSNRRARWRKQAGANQLAAFNHL 287

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

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

MGI|MGI:97491 Pax7 "paired box gene 7" [Mus musculus (taxid:10090)]

 Score = 353 (129.3 bits), Expect = 2.7e-34, Sum P(2) = 2.7e-34
 Identities = 69/88 (78%), Positives = 77/88 (87%)

Query:    19 DE-SDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEA 77
             DE SD ESEP +PLKRKQRRSRTTFT +QLEELE+AF+RT YPD+YTREELAQ+TKLTEA
Sbjct:   198 DEGSDVESEPDLPLKRKQRRSRTTFTAEQLEELEKAFERTHYPDIYTREELAQRTKLTEA 257

Query:    78 RVQVWFSNRRARLRKQLNSQQLNAFNSM 105
             RVQVWFSNRRAR RKQ  + QL AFN +
Sbjct:   258 RVQVWFSNRRARWRKQAGANQLAAFNHL 285

GO:0000983 "RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity" evidence=IDA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005667 "transcription factor complex" evidence=TAS

GO:0006338 "chromatin remodeling" evidence=IMP

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007519 "skeletal muscle tissue development" evidence=IMP

GO:0009887 "organ morphogenesis" evidence=TAS

GO:0010453 "regulation of cell fate commitment" evidence=IMP

GO:0010468 "regulation of gene expression" evidence=IMP

GO:0014813 "satellite cell commitment" evidence=IMP

GO:0021527 "spinal cord association neuron differentiation" evidence=IGI

GO:0021904 "dorsal/ventral neural tube patterning" evidence=IDA

GO:0031062 "positive regulation of histone methylation" evidence=IGI;IDA

GO:0043393 "regulation of protein binding" evidence=IMP

GO:0043403 "skeletal muscle tissue regeneration" evidence=IMP

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

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

GO:0048663 "neuron fate commitment" evidence=IGI

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

GO:0051216 "cartilage development" evidence=IMP

GO:0060415 "muscle tissue morphogenesis" evidence=IGI

GO:2000288 "positive regulation of myoblast proliferation" evidence=IMP

FB|FBgn0001147 gsb-n "gooseberry-neuro" [Drosophila melanogaster (taxid:7227)]

 Score = 343 (125.8 bits), Expect = 9.0e-34, Sum P(2) = 9.0e-34
 Identities = 75/106 (70%), Positives = 81/106 (76%)

Query:     3 QDYQDDLWVVGRPSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDV 62
             +DY  +  + GR S  D SDTESEPGIPLKRKQRRSRTTFT +QLE LERAF RTQYPDV
Sbjct:   152 KDYTINGILGGRDS--DISDTESEPGIPLKRKQRRSRTTFTAEQLEALERAFSRTQYPDV 209

Query:    63 YTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQ--LNAFNSMS 106
             YTREELAQ T LTEAR+QVWFSNRRARLRK        L+  NS S
Sbjct:   210 YTREELAQTTALTEARIQVWFSNRRARLRKHSGGSNSGLSPMNSGS 255

GO:0003677 "DNA binding" evidence=NAS

GO:0007367 "segment polarity determination" evidence=IEP;NAS

GO:0000977 "RNA polymerase II regulatory region sequence-specific DNA binding" evidence=IDA

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

GO:0005667 "transcription factor complex" evidence=ISS

GO:0005634 "nucleus" evidence=NAS

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

ZFIN|ZDB-GENE-980526-52 pax3a "paired box gene 3a" [Danio rerio (taxid:7955)]

 Score = 363 (132.8 bits), Expect = 2.5e-33, P = 2.5e-33
 Identities = 72/97 (74%), Positives = 82/97 (84%)

Query:    11 VVG-RPSSGDE-SDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREEL 68
             ++G R S  DE SD +SEPG+PLKRKQRRSRTTFT +QLEELERAF+RT YPD+YTREEL
Sbjct:   194 ILGDRSSHSDEGSDVDSEPGLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREEL 253

Query:    69 AQKTKLTEARVQVWFSNRRARLRKQLNSQQLNAFNSM 105
             AQ+ KLTEARVQVWFSNRRAR RKQ  + QL AFN +
Sbjct:   254 AQRAKLTEARVQVWFSNRRARWRKQAGANQLMAFNHL 290

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

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

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

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;IDA

GO:0001755 "neural crest cell migration" evidence=IMP

GO:0048066 "developmental pigmentation" evidence=IMP

GO:0050936 "xanthophore differentiation" evidence=IMP

GO:0048484 "enteric nervous system development" evidence=IMP

GO:0007275 "multicellular organismal development" evidence=IEA

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

ZFIN|ZDB-GENE-080917-54 pax7b "paired box gene 7b" [Danio rerio (taxid:7955)]

 Score = 356 (130.4 bits), Expect = 1.4e-32, P = 1.4e-32
 Identities = 70/96 (72%), Positives = 80/96 (83%)

Query:    11 VVGRPSSGDE-SDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELA 69
             ++G     DE SD ESEP +PLKRKQRRSRTTFT +QLEELE+AF+RT YPD+YTREELA
Sbjct:   198 ILGDKGRMDEVSDVESEPDLPLKRKQRRSRTTFTAEQLEELEKAFERTHYPDIYTREELA 257

Query:    70 QKTKLTEARVQVWFSNRRARLRKQLNSQQLNAFNSM 105
             Q+TKLTEARVQVWFSNRRAR RKQ  + QL AFN +
Sbjct:   258 QRTKLTEARVQVWFSNRRARWRKQAGANQLAAFNHL 293

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

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA;IDA

GO:0007275 "multicellular organismal development" evidence=IEA

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

UNIPROTKB|F1MTX0 PAX3 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 355 (130.0 bits), Expect = 1.8e-32, P = 1.8e-32
 Identities = 68/91 (74%), Positives = 77/91 (84%)

Query:    15 PSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKL 74
             P S + SD +SEP +PLKRKQRRSRTTFT +QLEELERAF+RT YPD+YTREELAQ+ KL
Sbjct:   199 PQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKL 258

Query:    75 TEARVQVWFSNRRARLRKQLNSQQLNAFNSM 105
             TEARVQVWFSNRRAR RKQ  + QL AFN +
Sbjct:   259 TEARVQVWFSNRRARWRKQAGANQLMAFNHL 289

GO:0005634 "nucleus" evidence=IEA

GO:0060594 "mammary gland specification" evidence=IEA

GO:0048663 "neuron fate commitment" evidence=IEA

GO:0048066 "developmental pigmentation" evidence=IEA

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

GO:0021527 "spinal cord association neuron differentiation" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0008283 "cell proliferation" evidence=IEA

GO:0007517 "muscle organ development" evidence=IEA

GO:0007507 "heart development" evidence=IEA

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

GO:0003682 "chromatin binding" evidence=IEA

GO:0001843 "neural tube closure" evidence=IEA

GO:0001755 "neural crest cell migration" evidence=IEA

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

UNIPROTKB|E2QX72 PAX3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 355 (130.0 bits), Expect = 1.8e-32, P = 1.8e-32
 Identities = 68/91 (74%), Positives = 77/91 (84%)

Query:    15 PSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKL 74
             P S + SD +SEP +PLKRKQRRSRTTFT +QLEELERAF+RT YPD+YTREELAQ+ KL
Sbjct:   200 PQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKL 259

Query:    75 TEARVQVWFSNRRARLRKQLNSQQLNAFNSM 105
             TEARVQVWFSNRRAR RKQ  + QL AFN +
Sbjct:   260 TEARVQVWFSNRRARWRKQAGANQLMAFNHL 290

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

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

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

GO:0003700 "sequence-specific DNA binding transcription factor activity" 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)
P24610	PAX3_MOUSE	No assigned EC number	0.7472	0.4439	0.1899	yes	N/A
P23760	PAX3_HUMAN	No assigned EC number	0.7472	0.4439	0.1899	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	205
pfam00046	57	pfam00046, Homeobox, Homeobox domain	5e-28
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	1e-24
smart00389	57	smart00389, HOX, Homeodomain	3e-24
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	8e-13
pfam05920	40	pfam05920, Homeobox_KN, Homeobox KN domain	0.001

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

 Score = 99.5 bits (249), Expect = 5e-28
 Identities = 33/57 (57%), Positives = 44/57 (77%)

Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          RR RTTFT +QLEELE+ F++ +YP    REELA+K  LTE +V+VWF NRRA+ ++
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 = 91.2 bits (227), Expect = 1e-24
 Identities = 31/58 (53%), Positives = 43/58 (74%)

Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          RR RT FT +QLEELE+ F++  YP    REELA++  LTE +V++WF NRRA+L++ 
Sbjct: 1  RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58

Length = 59

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 90.0 bits (224), Expect = 3e-24
 Identities = 32/57 (56%), Positives = 43/57 (75%)

Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91
          +RR RT+FT +QLEELE+ FQ+  YP    REELA+K  L+E +V+VWF NRRA+ +
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 = 63.2 bits (154), Expect = 8e-13
 Identities = 21/61 (34%), Positives = 32/61 (52%)

Query: 33  RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
              +  R   T +QL  LER F+   YP   TR +L+    +    VQ+WF N+RA+ +K
Sbjct: 49  SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKK 108

Query: 93  Q 93
           +
Sbjct: 109 K 109

Length = 156

>gnl|CDD|203350 pfam05920, Homeobox_KN, Homeobox KN domain

 Score = 35.2 bits (82), Expect = 0.001
 Identities = 12/31 (38%), Positives = 18/31 (58%)

Query: 59 YPDVYTREELAQKTKLTEARVQVWFSNRRAR 89
          YP    + ELA++T L+  ++  WF N R R
Sbjct: 10 YPSEEEKSELARQTGLSRKQIDNWFINARRR 40

This is a homeobox transcription factor KN domain conserved from fungi to human and plants. Length = 40

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	205
KOG0487|consensus	308		99.83
KOG0842|consensus	307		99.83
KOG0489|consensus	261		99.81
KOG0485|consensus	268		99.79
KOG0488|consensus	309		99.78
KOG0484|consensus	125		99.75
KOG0850|consensus	245		99.73
KOG3802|consensus	398		99.73
KOG0844|consensus	408		99.73
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.72
KOG0843|consensus	197		99.71
KOG2251|consensus	228		99.71
KOG0494|consensus	332		99.69
KOG0848|consensus	317		99.68
KOG0492|consensus	246		99.67
KOG0493|consensus	342		99.67
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.62
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.61
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.61
KOG0491|consensus	194		99.6
COG5576	156	Homeodomain-containing transcription factor [Trans	99.55
KOG0483|consensus	198		99.53
KOG0486|consensus	351		99.5
KOG4577|consensus	383		99.39
KOG0847|consensus	288		99.34
KOG1168|consensus	385		99.31
KOG0849|consensus	354		99.26
KOG0490|consensus	235		99.24
KOG0774|consensus	334		99.23
KOG0775|consensus	304		99.18
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.74
KOG2252|consensus	558		98.59
KOG0490|consensus	235		98.23
KOG1146|consensus	1406		97.76
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	97.43
KOG0773|consensus	342		97.42
KOG3623|consensus	1007		96.09
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	95.37
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	90.6
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	87.28
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	85.99
PRK03975	141	tfx putative transcriptional regulator; Provisiona	83.93
KOG1146|consensus	1406		83.82
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	83.6
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	81.76
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	80.46
PLN03162	526	golden-2 like transcription factor; Provisional	80.25

>KOG0487|consensus

Probab=99.83  E-value=5.6e-21  Score=164.89  Aligned_cols=70  Identities=34%  Similarity=0.530  Sum_probs=64.7

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHHhh
Q psy1901          31 LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLN  100 (205)
Q Consensus        31 ~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~~~  100 (205)
                      .-++.||||..+|+.|+.+||+.|..|.|++++.|.+|++.|+|+++||+|||||||+|+||..++....
T Consensus       231 ~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r~~  300 (308)
T KOG0487|consen  231 SARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENRLK  300 (308)
T ss_pred             cccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhhcc
Confidence            3478899999999999999999999999999999999999999999999999999999999998655443

>KOG0842|consensus

Probab=99.83  E-value=4e-20  Score=159.56  Aligned_cols=74  Identities=38%  Similarity=0.620  Sum_probs=67.4

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHHhhhhcc
Q psy1901          31 LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLNAFNS  104 (205)
Q Consensus        31 ~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~~~~~~s  104 (205)
                      .+++|||.|..|+..|+-+||+.|.+++|++..+|++||..|+||+.||||||||||-|.||+.++.......-
T Consensus       149 ~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~~  222 (307)
T KOG0842|consen  149 GKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALLL  222 (307)
T ss_pred             ccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcccC
Confidence            36778888999999999999999999999999999999999999999999999999999999988876655443

>KOG0489|consensus

Probab=99.81  E-value=1.2e-20  Score=161.43  Aligned_cols=67  Identities=37%  Similarity=0.603  Sum_probs=62.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHHh
Q psy1901          33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQL   99 (205)
Q Consensus        33 ~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~~   99 (205)
                      .+.||.|+.||.+|+.+||+.|+.|+|.++..|.|||..|+|+|+||+|||||||||+||..+....
T Consensus       157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~  223 (261)
T KOG0489|consen  157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSS  223 (261)
T ss_pred             CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccccc
Confidence            4578999999999999999999999999999999999999999999999999999999998766543

>KOG0485|consensus

Probab=99.79  E-value=6.6e-19  Score=143.86  Aligned_cols=70  Identities=31%  Similarity=0.578  Sum_probs=64.5

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHHhhh
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLNA  101 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~~~~  101 (205)
                      ..+|||.||+|+..|+..||..|+...|.+..+|..||++|.|++.||+|||||||.||||+-......+
T Consensus       101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ea~  170 (268)
T KOG0485|consen  101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLEAA  170 (268)
T ss_pred             ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhhhh
Confidence            4678889999999999999999999999999999999999999999999999999999999976654443

>KOG0488|consensus

Probab=99.78  E-value=1.6e-18  Score=151.11  Aligned_cols=66  Identities=42%  Similarity=0.706  Sum_probs=62.9

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ   97 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~   97 (205)
                      .||+||.||.||..|+..||+.|++..|.+..+|.+||+.|||+..||++||||||+||||.....
T Consensus       169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g  234 (309)
T KOG0488|consen  169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEG  234 (309)
T ss_pred             CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhh
Confidence            488899999999999999999999999999999999999999999999999999999999987663

>KOG0484|consensus

Probab=99.75  E-value=8.2e-19  Score=128.09  Aligned_cols=68  Identities=68%  Similarity=0.981  Sum_probs=63.7

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHH
Q psy1901          31 LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQ   98 (205)
Q Consensus        31 ~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~   98 (205)
                      .++|.||-|+.|+..|+..||+.|...+||++..|++||.++.|++..|+|||||||+|.||+++...
T Consensus        13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~   80 (125)
T KOG0484|consen   13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAI   80 (125)
T ss_pred             HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHH
Confidence            46788999999999999999999999999999999999999999999999999999999999876543

>KOG0850|consensus

Probab=99.73  E-value=5.8e-18  Score=139.44  Aligned_cols=66  Identities=39%  Similarity=0.658  Sum_probs=62.3

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901          31 LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS   96 (205)
Q Consensus        31 ~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   96 (205)
                      ..||.||.||.++.-||..|.+.|++++|+-..+|.+||..|||+..||+|||||||.|.||..+.
T Consensus       118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~  183 (245)
T KOG0850|consen  118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQ  183 (245)
T ss_pred             CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhc
Confidence            357778899999999999999999999999999999999999999999999999999999999773

>KOG3802|consensus

Probab=99.73  E-value=8.4e-19  Score=154.49  Aligned_cols=64  Identities=25%  Similarity=0.468  Sum_probs=60.7

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN   95 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   95 (205)
                      ..|||||||+|+..++..||++|.+|++|+.+++.+||++|+|++.+|+|||||||+|.||...
T Consensus       291 ~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  291 QSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             cccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            3488999999999999999999999999999999999999999999999999999999999743

>KOG0844|consensus

Probab=99.73  E-value=6.6e-18  Score=143.99  Aligned_cols=64  Identities=39%  Similarity=0.611  Sum_probs=60.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901          34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ   97 (205)
Q Consensus        34 k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~   97 (205)
                      .-||-||.|+++|+.+||+.|.+..|-++..|.|||..|+|.+..|+|||||||+|+||++..+
T Consensus       180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlam  243 (408)
T KOG0844|consen  180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAM  243 (408)
T ss_pred             HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhc
Confidence            4478899999999999999999999999999999999999999999999999999999987654

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.72  E-value=1e-17  Score=110.94  Aligned_cols=57  Identities=49%  Similarity=0.768  Sum_probs=55.3

Q ss_pred             CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901          36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK   92 (205)
Q Consensus        36 rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   92 (205)
                      ||+|+.|+.+|+.+|+++|..++||+..+++.||..|||+..+|++||+|+|.+.||
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 ....

>KOG0843|consensus

Probab=99.71  E-value=8.9e-18  Score=133.74  Aligned_cols=64  Identities=41%  Similarity=0.658  Sum_probs=61.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901          34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ   97 (205)
Q Consensus        34 k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~   97 (205)
                      |.||.||.|+.+|+..||..|..|+|..-.+|+.||..|+|++.||+|||||||.|.||+..+.
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            7789999999999999999999999999999999999999999999999999999999987664

>KOG2251|consensus

Probab=99.71  E-value=6.7e-18  Score=138.42  Aligned_cols=68  Identities=63%  Similarity=0.900  Sum_probs=64.6

Q ss_pred             CccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901          30 PLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ   97 (205)
Q Consensus        30 ~~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~   97 (205)
                      ...+|.||.||+|+.+|+.+||.+|.+.+||+...|++||.+|+|.+.+|+|||+|||+|+|++++.+
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            34689999999999999999999999999999999999999999999999999999999999987765

>KOG0494|consensus

Probab=99.69  E-value=5.6e-17  Score=135.64  Aligned_cols=65  Identities=58%  Similarity=0.886  Sum_probs=59.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHH
Q psy1901          34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQ   98 (205)
Q Consensus        34 k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~   98 (205)
                      |+|+-||.|+..|+..||+.|....||+...|+.||.+++|.+++|+|||||||+||||.++...
T Consensus       140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg  204 (332)
T KOG0494|consen  140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWG  204 (332)
T ss_pred             ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcC
Confidence            33444899999999999999999999999999999999999999999999999999999877643

>KOG0848|consensus

Probab=99.68  E-value=3.1e-17  Score=137.65  Aligned_cols=65  Identities=35%  Similarity=0.626  Sum_probs=59.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901          33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ   97 (205)
Q Consensus        33 ~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~   97 (205)
                      |.+-|-|.+++..|+.+||+.|.-++|+++..+.|||..|||+||||+|||||||+|+||..++.
T Consensus       197 RTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk  261 (317)
T KOG0848|consen  197 RTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK  261 (317)
T ss_pred             ecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence            33445688999999999999999999999999999999999999999999999999999987665

>KOG0492|consensus

Probab=99.67  E-value=5.7e-17  Score=131.74  Aligned_cols=68  Identities=37%  Similarity=0.658  Sum_probs=62.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHHhh
Q psy1901          33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLN  100 (205)
Q Consensus        33 ~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~~~  100 (205)
                      +-.|+.|+.|+.+|+..||+.|.+.+|.++.+|.+++..|.|++.||+|||||||+|.||.+..+.+.
T Consensus       142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~Ek  209 (246)
T KOG0492|consen  142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELEK  209 (246)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHHH
Confidence            44577899999999999999999999999999999999999999999999999999999986655443

>KOG0493|consensus

Probab=99.67  E-value=8.6e-17  Score=134.66  Aligned_cols=58  Identities=41%  Similarity=0.795  Sum_probs=56.4

Q ss_pred             CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        36 rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      ||.||.|+.+|+.+|...|+.|.|.+++.|.+||.+|+|.+.||+|||||+|+|.||.
T Consensus       247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs  304 (342)
T KOG0493|consen  247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS  304 (342)
T ss_pred             cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence            6789999999999999999999999999999999999999999999999999999986

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.62  E-value=4e-16  Score=103.84  Aligned_cols=53  Identities=23%  Similarity=0.431  Sum_probs=51.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhcCCC----CCHHHHHHHHHhhCCchhhhhhhhhchH
Q psy1901          35 QRRSRTTFTGDQLEELERAFQRTQY----PDVYTREELAQKTKLTEARVQVWFSNRR   87 (205)
Q Consensus        35 ~rr~R~~~s~~q~~~Le~~F~~~~~----ps~~~r~~LA~~l~l~~~qV~~WFqNrR   87 (205)
                      +||.||.|+.+|+..|+++|..++|    |+..+|.+||..|||++++|+|||||.+
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    9999999999999999999999999975

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

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

Probab=99.61  E-value=1.2e-15  Score=101.03  Aligned_cols=58  Identities=53%  Similarity=0.925  Sum_probs=54.7

Q ss_pred             CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        36 rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      ++.|..++.+|+.+|+++|..++||+..++..||.++||++.+|++||+|+|.+.++.
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            3567889999999999999999999999999999999999999999999999998864

>smart00389 HOX Homeodomain

Probab=99.61  E-value=1.2e-15  Score=100.27  Aligned_cols=56  Identities=57%  Similarity=0.926  Sum_probs=52.5

Q ss_pred             CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901          36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR   91 (205)
Q Consensus        36 rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~k   91 (205)
                      ++.|+.|+.+|+.+|+.+|..|+||+..++.+||..+||+..+|++||+|+|.+.|
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            35678899999999999999999999999999999999999999999999998754

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

>KOG0491|consensus

Probab=99.60  E-value=4.8e-16  Score=122.24  Aligned_cols=65  Identities=40%  Similarity=0.714  Sum_probs=60.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHH
Q psy1901          34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQ   98 (205)
Q Consensus        34 k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~   98 (205)
                      +++|-|++|+..|+..||+.|+.+.|.+..+|.|||..|+|+++||+.||||||+|.||..+..+
T Consensus        99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~  163 (194)
T KOG0491|consen   99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ  163 (194)
T ss_pred             HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence            45678999999999999999999999999999999999999999999999999999999876644

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.55  E-value=5.4e-15  Score=117.21  Aligned_cols=65  Identities=32%  Similarity=0.541  Sum_probs=59.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901          33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ   97 (205)
Q Consensus        33 ~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~   97 (205)
                      ...+++|++.+.+|+.+|++.|..|+||+...|..|+..|+|+++-|+|||||||++.|+.....
T Consensus        49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~  113 (156)
T COG5576          49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGK  113 (156)
T ss_pred             CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccc
Confidence            45577788899999999999999999999999999999999999999999999999999986543

>KOG0483|consensus

Probab=99.53  E-value=6.6e-15  Score=120.61  Aligned_cols=64  Identities=27%  Similarity=0.488  Sum_probs=57.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHH
Q psy1901          35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQ   98 (205)
Q Consensus        35 ~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~   98 (205)
                      .++++.+|+.+|+..||+.|..+.+....++..||+.|||..+||.|||||||+|||.++....
T Consensus        50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d  113 (198)
T KOG0483|consen   50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKD  113 (198)
T ss_pred             cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhh
Confidence            3444556999999999999999999999999999999999999999999999999998765544

>KOG0486|consensus

Probab=99.50  E-value=2.4e-14  Score=122.74  Aligned_cols=65  Identities=65%  Similarity=0.946  Sum_probs=62.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHH
Q psy1901          34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQ   98 (205)
Q Consensus        34 k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~   98 (205)
                      |+||.|+-|+.+|+..||.+|.+|.||+...|++||--++|++.+|+|||.|||+||||+++.++
T Consensus       111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~  175 (351)
T KOG0486|consen  111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ  175 (351)
T ss_pred             hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence            67888999999999999999999999999999999999999999999999999999999988776

>KOG4577|consensus

Probab=99.39  E-value=3.1e-13  Score=114.89  Aligned_cols=65  Identities=38%  Similarity=0.593  Sum_probs=60.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHH
Q psy1901          34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQ   98 (205)
Q Consensus        34 k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~   98 (205)
                      ..||.||+|+..|++.|...|+..++|-+..|++|+.++||.-++|||||||||+|+||-+++..
T Consensus       166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAG  230 (383)
T KOG4577|consen  166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAG  230 (383)
T ss_pred             ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcc
Confidence            45889999999999999999999999999999999999999999999999999999999876643

>KOG0847|consensus

Probab=99.34  E-value=5.5e-13  Score=109.49  Aligned_cols=69  Identities=41%  Similarity=0.702  Sum_probs=62.5

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHHhh
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLN  100 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~~~  100 (205)
                      ..++|-.|.+|+-.|+..||+.|.+.+|+--.+|.+||..+||++.||+|||||||.||||+...+...
T Consensus       164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmas  232 (288)
T KOG0847|consen  164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMAS  232 (288)
T ss_pred             CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhh
Confidence            356666788999999999999999999999999999999999999999999999999999997665443

>KOG1168|consensus

Probab=99.31  E-value=7.2e-13  Score=112.72  Aligned_cols=63  Identities=25%  Similarity=0.429  Sum_probs=59.2

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      ..-+|||||.+-.-++..||.+|..++.|+-+.+..||++|.|.+.+|+|||||+|+|.||++
T Consensus       306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~  368 (385)
T KOG1168|consen  306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK  368 (385)
T ss_pred             ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence            456688999999999999999999999999999999999999999999999999999999964

>KOG0849|consensus

Probab=99.26  E-value=3.5e-11  Score=107.11  Aligned_cols=78  Identities=54%  Similarity=0.850  Sum_probs=69.4

Q ss_pred             CCCCCCCCCCCCccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901          19 DESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS   96 (205)
Q Consensus        19 ~~~~~~~~~~~~~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   96 (205)
                      .+.+....++...+++.+|+|++|+..|+..||+.|..++||+...|++||.+++|++..|++||+|||++++|....
T Consensus       160 ~~~~~~~~p~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~  237 (354)
T KOG0849|consen  160 LSADDEEPPGYALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD  237 (354)
T ss_pred             ccCCccccccccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence            334444555666788889999999999999999999999999999999999999999999999999999999998744

>KOG0490|consensus

Probab=99.24  E-value=5.8e-12  Score=104.79  Aligned_cols=64  Identities=48%  Similarity=0.614  Sum_probs=61.3

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN   95 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   95 (205)
                      +.++|+.|+.|+..|+.+||+.|...+||+...|+.||..++|++..|+|||||||+|+++.++
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            5788899999999999999999999999999999999999999999999999999999999865

>KOG0774|consensus

Probab=99.23  E-value=1.9e-11  Score=102.80  Aligned_cols=62  Identities=34%  Similarity=0.629  Sum_probs=57.1

Q ss_pred             CCCCCCCCHHHHHHHHHHhh---cCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901          36 RRSRTTFTGDQLEELERAFQ---RTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ   97 (205)
Q Consensus        36 rr~R~~~s~~q~~~Le~~F~---~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~   97 (205)
                      ||||..|++....+|.++|.   .|+||+.+.+++||+++|++..||..||.|+|.+.||.....
T Consensus       189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~  253 (334)
T KOG0774|consen  189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKN  253 (334)
T ss_pred             HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhh
Confidence            67888999999999999994   689999999999999999999999999999999999975443

>KOG0775|consensus

Probab=99.18  E-value=6.6e-11  Score=100.09  Aligned_cols=61  Identities=36%  Similarity=0.547  Sum_probs=52.3

Q ss_pred             CCCCCCCCCCCHHH---------HHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          33 RKQRRSRTTFTGDQ---------LEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        33 ~k~rr~R~~~s~~q---------~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      ||.--.||.+..||         +.+|.++|.+|+||+..++.+||+++||+..||-+||.|||+|+|-.
T Consensus       165 rKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~  234 (304)
T KOG0775|consen  165 RKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAA  234 (304)
T ss_pred             ccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhc
Confidence            33334577655554         77999999999999999999999999999999999999999999944

>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=98.74  E-value=7.8e-09  Score=63.85  Aligned_cols=35  Identities=37%  Similarity=0.675  Sum_probs=29.7

Q ss_pred             hcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHH
Q psy1901          55 QRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR   89 (205)
Q Consensus        55 ~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k   89 (205)
                      ..++||+.+++.+||.++||+.+||..||-|.|.|
T Consensus         6 ~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR   40 (40)
T PF05920_consen    6 LHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR   40 (40)
T ss_dssp             TTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence            35799999999999999999999999999999975

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

>KOG2252|consensus

Probab=98.59  E-value=9.9e-08  Score=87.77  Aligned_cols=63  Identities=24%  Similarity=0.323  Sum_probs=57.1

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          31 LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        31 ~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      ..-+.||.|.+|+..|+..|..+|..+++|+.++.+.|+.+|+|....|.+||-|-|.|.+-+
T Consensus       416 ~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl~~  478 (558)
T KOG2252|consen  416 KMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSLDK  478 (558)
T ss_pred             ccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcccc
Confidence            345567789999999999999999999999999999999999999999999999999886444

>KOG0490|consensus

Probab=98.23  E-value=1.4e-06  Score=72.36  Aligned_cols=65  Identities=54%  Similarity=0.799  Sum_probs=60.8

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901          31 LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN   95 (205)
Q Consensus        31 ~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   95 (205)
                      ...+.++.|+.+...|+..|+..|..+.+|+...++.|+..+|+....|++||+|+|.+.++...
T Consensus       149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            35677889999999999999999999999999999999999999999999999999999998754

>KOG1146|consensus

Probab=97.76  E-value=3.7e-05  Score=77.12  Aligned_cols=63  Identities=27%  Similarity=0.381  Sum_probs=58.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901          33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN   95 (205)
Q Consensus        33 ~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   95 (205)
                      -.+|++|+.++..|+++|..+|....||..++.+.|-+.+++.+++|++||||-|.|.|+...
T Consensus       901 ~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~  963 (1406)
T KOG1146|consen  901 MGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL  963 (1406)
T ss_pred             hhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence            345778999999999999999999999999999999999999999999999999999998755

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

Probab=97.43  E-value=0.00011  Score=48.43  Aligned_cols=41  Identities=22%  Similarity=0.463  Sum_probs=31.1

Q ss_pred             HHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchH
Q psy1901          47 LEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRR   87 (205)
Q Consensus        47 ~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR   87 (205)
                      +..|+++|...+++.......|..+.+|+..||+.||-.|+
T Consensus        10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~   50 (56)
T PF11569_consen   10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM   50 (56)
T ss_dssp             -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred             hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence            45699999999999999999999999999999999996554

>KOG0773|consensus

Probab=97.42  E-value=0.0002  Score=63.47  Aligned_cols=64  Identities=25%  Similarity=0.386  Sum_probs=53.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhc---CCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHH
Q psy1901          35 QRRSRTTFTGDQLEELERAFQR---TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQ   98 (205)
Q Consensus        35 ~rr~R~~~s~~q~~~Le~~F~~---~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~   98 (205)
                      ++|.+..+......+|+.+...   .+||+..++..||+++||+..||.+||.|.|-|..+-.....
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~~  305 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIEEM  305 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchHHHH
Confidence            4455668999999999988543   589999999999999999999999999999998887655443

>KOG3623|consensus

Probab=96.09  E-value=0.0078  Score=57.83  Aligned_cols=48  Identities=21%  Similarity=0.250  Sum_probs=44.9

Q ss_pred             HHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          47 LEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        47 ~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      +.+|..+|..|..|+.++...||.++||..+.|+.||++++.......
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~  615 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE  615 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence            778999999999999999999999999999999999999998877754

>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=95.37  E-value=0.035  Score=36.03  Aligned_cols=47  Identities=15%  Similarity=0.360  Sum_probs=36.4

Q ss_pred             CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchH
Q psy1901          36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRR   87 (205)
Q Consensus        36 rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR   87 (205)
                      ||+|..++-++...+-+.++...     ...+||..+|+...+|..|..|+.
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            57888999999888888887776     578999999999999999998753

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=90.60  E-value=0.84  Score=28.61  Aligned_cols=46  Identities=17%  Similarity=0.260  Sum_probs=34.7

Q ss_pred             CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901          41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR   91 (205)
Q Consensus        41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~k   91 (205)
                      .+++.+..+|...|..+     ..-.++|+.+|++...|+.+...-..|.|
T Consensus         4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~kLR   49 (50)
T PF04545_consen    4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKKLR   49 (50)
T ss_dssp             TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence            47889999999998332     34678999999999999988765555544

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 ....

>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=87.28  E-value=0.86  Score=27.71  Aligned_cols=44  Identities=14%  Similarity=0.177  Sum_probs=33.3

Q ss_pred             CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHH
Q psy1901          41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR   89 (205)
Q Consensus        41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k   89 (205)
                      .++..+..+++..|...     ....++|+.+|++...|..|...-+.+
T Consensus        10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~   53 (55)
T cd06171          10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK   53 (55)
T ss_pred             hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            46778888888887433     346788999999999999998654443

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=85.99  E-value=0.67  Score=31.40  Aligned_cols=44  Identities=14%  Similarity=0.268  Sum_probs=30.5

Q ss_pred             CCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhh
Q psy1901          37 RSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFS   84 (205)
Q Consensus        37 r~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFq   84 (205)
                      ++|..|+.++...+-..+....    ....+||.++||....|..|-.
T Consensus         2 ~~r~~ys~e~K~~~v~~~~~~g----~sv~~va~~~gi~~~~l~~W~~   45 (76)
T PF01527_consen    2 RKRRRYSPEFKLQAVREYLESG----ESVSEVAREYGISPSTLYNWRK   45 (76)
T ss_dssp             -SS----HHHHHHHHHHHHHHH----CHHHHHHHHHTS-HHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCC----CceEeeecccccccccccHHHH
Confidence            4667899999888777763332    5688999999999999999985

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.

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=83.93  E-value=4  Score=31.94  Aligned_cols=52  Identities=21%  Similarity=0.188  Sum_probs=40.0

Q ss_pred             CCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901          39 RTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS   96 (205)
Q Consensus        39 R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   96 (205)
                      ...+++.|+.+|...+  ..    ....+||+.||++...|..|..+.+.+.|+....
T Consensus         4 ~~~Lt~rqreVL~lr~--~G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t   55 (141)
T PRK03975          4 ESFLTERQIEVLRLRE--RG----LTQQEIADILGTSRANVSSIEKRARENIEKARET   55 (141)
T ss_pred             ccCCCHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            3568999999997743  22    2356899999999999999999777777665443

>KOG1146|consensus

Probab=83.82  E-value=1.9  Score=44.49  Aligned_cols=63  Identities=24%  Similarity=0.321  Sum_probs=57.5

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      .-+-++-|..+-.++..+|-.+|-.+.-|+.+.+..|......+.+++.+||+|-|.|.++..
T Consensus       702 ~~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~  764 (1406)
T KOG1146|consen  702 SPRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ  764 (1406)
T ss_pred             CcccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence            345567778888999999999999999999999999999999999999999999999998875

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

Probab=83.60  E-value=3.5  Score=25.98  Aligned_cols=41  Identities=17%  Similarity=0.193  Sum_probs=28.8

Q ss_pred             CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchH
Q psy1901          42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRR   87 (205)
Q Consensus        42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR   87 (205)
                      +++.+..++.-.|..+     ....++|+.+|+++..|+.|.+.-|
T Consensus        11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~   51 (54)
T PF08281_consen   11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRAR   51 (54)
T ss_dssp             S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            5677777777765443     3578899999999999999997443

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

>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=81.76  E-value=5  Score=21.62  Aligned_cols=37  Identities=19%  Similarity=0.338  Sum_probs=26.8

Q ss_pred             CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhh
Q psy1901          42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWF   83 (205)
Q Consensus        42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WF   83 (205)
                      ++.++...+...|.. .+    ...++|+.+|++...|..|.
T Consensus         6 ~~~~~~~~i~~~~~~-~~----s~~~ia~~~~is~~tv~~~~   42 (42)
T cd00569           6 LTPEQIEEARRLLAA-GE----SVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             CCHHHHHHHHHHHHc-CC----CHHHHHHHHCCCHHHHHHhC
Confidence            566666666666653 22    46688999999999988874

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

>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators

Probab=80.46  E-value=4.3  Score=26.11  Aligned_cols=47  Identities=21%  Similarity=0.224  Sum_probs=35.4

Q ss_pred             CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      .||+.++.+|.-+..-..      ..++|..++++++.|..+..+=+.|..-.
T Consensus         3 ~LT~~E~~vl~~l~~G~~------~~eIA~~l~is~~tV~~~~~~i~~Kl~~~   49 (58)
T PF00196_consen    3 SLTERELEVLRLLAQGMS------NKEIAEELGISEKTVKSHRRRIMKKLGVK   49 (58)
T ss_dssp             SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT-S
T ss_pred             ccCHHHHHHHHHHHhcCC------cchhHHhcCcchhhHHHHHHHHHHHhCCC
Confidence            578889999887764433      78899999999999999887766665443

The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....

>PLN03162 golden-2 like transcription factor; Provisional

Probab=80.25  E-value=23  Score=32.22  Aligned_cols=67  Identities=13%  Similarity=0.068  Sum_probs=44.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHH-hhcC-CCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHHh
Q psy1901          33 RKQRRSRTTFTGDQLEELERA-FQRT-QYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQL   99 (205)
Q Consensus        33 ~k~rr~R~~~s~~q~~~Le~~-F~~~-~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~~   99 (205)
                      ..+||.|-++|.+.-..+-+. .+.. ..-+...+.+|-..-||+...|+.-.|--|...|+...++..
T Consensus       231 ~g~KKpRLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l~~rEaE  299 (526)
T PLN03162        231 PGKKKAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHLAAREAE  299 (526)
T ss_pred             CCCCCCcccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcccccchhhh
Confidence            445677888888854444333 3333 234556666666677999999999999888877765544443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	205
1fjl_A	81	Homeodomain From The Drosophila Paired Protein Boun		2e-31
3cmy_A	61	Structure Of A Homeodomain In Complex With Dna Leng		1e-23
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		5e-21
2m0c_A	75	Solution Nmr Structure Of Homeobox Domain Of Human		5e-19
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		1e-18
3a02_A	60	Crystal Structure Of Aristaless Homeodomain Length		1e-17
2cue_A	80	Solution Structure Of The Homeobox Domain Of The Hu		3e-15
2l7f_P	68	Solution Structure Of The Pitx2 Homeodomain Length		6e-15
2l7m_P	68	Solution Structure Of The Pitx2 Homeodomain R24h Mu		6e-15
2dms_A	80	Solution Structure Of The Homeobox Domain Of Homeob		3e-14
2dmu_A	70	Solution Structure Of The Homeobox Domain Of Homeob		7e-14
2k40_A	67	Nmr Structure Of Hesx-1 Homeodomain Double Mutant R		4e-10
2m34_A	71	Nmr Structure Of The Homeodomain Transcription Fact		6e-09
2djn_A	70	The Solution Structure Of The Homeobox Domain Of Hu		2e-08
1ig7_A	58	Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58		4e-07
2dmq_A	80	Solution Structure Of The Homeobox Domain Of LimHOM		5e-07
2dmt_A	80	Solution Structure Of The Homeobox Domain Of Homeob		9e-07
3a01_A	93	Crystal Structure Of Aristaless And Clawless Homeod		1e-06
1b8i_A	81	Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX		2e-06
2kt0_A	84	Solution Structure Of Human Stem Cell Transcription		4e-06
1zq3_P	68	Nmr Solution Structure Of The Bicoid Homeodomain Bo		5e-06
2hdd_A	61	Engrailed Homeodomain Q50k Variant Dna Complex Leng		5e-06
1hdd_C	61	Crystal Structure Of An Engrailed Homeodomain-Dna C		8e-06
2h1k_A	63	Crystal Structure Of The Pdx1 Homeodomain In Comple		9e-06
1jgg_A	60	Even-Skipped Homeodomain Complexed To At-Rich Dna L		9e-06
1nk2_P	77	VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES		1e-05
1du0_A	57	Engrailed Homeodomain Q50a Variant Dna Complex Leng		1e-05
1ztr_A	61	Solution Structure Of Engrailed Homeodomain L16a Mu		1e-05
3hdd_A	60	Engrailed Homeodomain Dna Complex Length = 60		1e-05
2hos_A	63	Phage-selected Homeodomain Bound To Unmodified Dna		1e-05
3a03_A	56	Crystal Structure Of Hox11l1 Homeodomain Length = 5		1e-05
1b72_A	97	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		2e-05
1p7j_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		2e-05
1p7i_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		2e-05
1qry_A	80	Homeobox Protein Vnd (Ventral Nervous System Defect		3e-05
1ftt_A	68	Thyroid Transcription Factor 1 Homeodomain (Rattus		3e-05
3rkq_A	58	Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Lengt		3e-05
2l9r_A	69	Solution Nmr Structure Of Homeobox Domain Of Homeob		3e-05
2r5y_A	88	Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO		5e-05
1enh_A	54	Structural Studies Of The Engrailed Homeodomain Len		7e-05
1hom_A	68	Determination Of The Three-Dimensional Structure Of		1e-04
2ld5_A	67	Solution Nmr-Derived Complex Structure Of Hoxa13 Dn		1e-04
2lp0_A	60	The Solution Structure Of Homeodomain-Protein Compl		1e-04
9ant_A	62	Antennapedia Homeodomain-Dna Complex Length = 62		1e-04
2e1o_A	70	Solution Structure Of Rsgi Ruh-028, A Homeobox Doma		1e-04
1ahd_P	68	Determination Of The Nmr Solution Structure Of An A		1e-04
1puf_A	77	Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo		1e-04
2l7z_A	73	Nmr Structure Of A13 Homedomain Length = 73		2e-04
2cra_A	70	Solution Structure Of The Homeobox Domain Of Human		6e-04
1bw5_A	66	The Nmr Solution Structure Of The Homeodomain Of Th		8e-04

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

Iteration: 1
 Score =  131 bits (330), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 62/75 (82%), Positives = 68/75 (90%)
Query: 19 DESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEAR 78
          D SD ESEPGI LKRKQRRSRTTF+  QL+ELERAF+RTQYPD+YTREELAQ+T LTEAR
Sbjct: 2  DISDCESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEAR 61
Query: 79 VQVWFSNRRARLRKQ 93
          +QVWF NRRARLRKQ
Sbjct: 62 IQVWFQNRRARLRKQ 76

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

Iteration: 1
 Score =  105 bits (263), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 51/59 (86%), Positives = 55/59 (93%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          QRRSRTTFT +QLEELERAF+RT YPD+YTREELAQ+ KLTEARVQVWFSNRRAR RKQ
Sbjct: 2  QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60

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

Iteration: 1
 Score = 97.4 bits (241), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 48/62 (77%), Positives = 52/62 (83%)
Query: 32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91
          KRKQRR RTTFT  QLEELE+AF RT YPDV+TREELA K  LTEAR+QVWF NRRA+ R
Sbjct: 3  KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 62
Query: 92 KQ 93
          KQ
Sbjct: 63 KQ 64

>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 = 90.9 bits (224), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 44/62 (70%), Positives = 52/62 (83%)
Query: 32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91
          K K+RR+RTTFT  QLEELE+ FQ+T YPDVY RE+LA +T LTEARVQVWF NRRA+ R
Sbjct: 6  KGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWR 65
Query: 92 KQ 93
          K+
Sbjct: 66 KR 67

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

Iteration: 1
 Score = 89.0 bits (219), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 43/57 (75%), Positives = 47/57 (82%)
Query: 37 RSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          R RTTFT  QLEELE+AF RT YPDV+TREELA K  LTEAR+QVWF NRRA+ RKQ
Sbjct: 1  RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

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

Iteration: 1
 Score = 86.3 bits (212), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 41/56 (73%), Positives = 45/56 (80%)
Query: 38 SRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          S  TFT  QLEELE+AF RT YPDV+TREELA K  LTEAR+QVWF NRRA+ RKQ
Sbjct: 2  SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

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

Iteration: 1
 Score = 78.2 bits (191), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 35/57 (61%), Positives = 46/57 (80%)
Query: 37 RSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          R+RT+FT +Q+E LE+ F+RT YPDV+ RE LA K  L EAR+QVWFSNRRA+ R++
Sbjct: 9  RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE 65

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

Iteration: 1
 Score = 77.4 bits (189), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 39/59 (66%), Positives = 46/59 (77%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          QRR RT FT  QL+ELE  FQR +YPD+ TREE+A  T LTEARV+VWF NRRA+ RK+
Sbjct: 3  QRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61

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

Iteration: 1
 Score = 77.0 bits (188), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 39/59 (66%), Positives = 45/59 (76%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          QRR RT FT  QL+ELE  FQR  YPD+ TREE+A  T LTEARV+VWF NRRA+ RK+
Sbjct: 3  QRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61

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

Iteration: 1
 Score = 75.1 bits (183), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 34/56 (60%), Positives = 42/56 (75%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91
          RR RTTFT  QL+ LE  F +T+YPD++ REE+A K  L E+RVQVWF NRRA+ R
Sbjct: 8  RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63

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

Iteration: 1
 Score = 73.6 bits (179), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 35/57 (61%), Positives = 43/57 (75%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          RR RT FT +QLE LE  FQ T+YPDV TRE+LA+K  L E +V+VWF NRRA+ R+
Sbjct: 8  RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRR 64

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

Iteration: 1
 Score = 61.2 bits (147), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 29/64 (45%), Positives = 39/64 (60%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95
          RR RT FT +Q+E LE  F+   YP +   E+LAQK  L   R+Q+WF NRRA+L++   
Sbjct: 2  RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61
Query: 96 SQQL 99
            Q 
Sbjct: 62 ESQF 65

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 26/56 (46%), Positives = 37/56 (66%)
Query: 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89
          K RR RT FT +QL ELE+ F   +Y  +  R ++A   KL+E +V++WF NRRA+
Sbjct: 6  KSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAK 61

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 39/57 (68%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          R+ RT ++  QL  L+R FQ+TQY  +  R ELA    LT+ +V++WF N+R++++K
Sbjct: 8  RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 36/57 (63%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          R+ RT FT  QL  LER F++ QY  +  R E +    LTE +V++WF NRRA+ ++
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 26/63 (41%), Positives = 37/63 (58%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95
          +R RT+F   QL  ++  F     PD    ++LAQKT LT+  +QVWF N RA+ R+ L 
Sbjct: 8  KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLL 67
Query: 96 SQQ 98
           Q+
Sbjct: 68 RQE 70

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

Iteration: 1
 Score = 50.1 bits (118), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 28/67 (41%), Positives = 41/67 (61%), Gaps = 1/67 (1%)
Query: 26 EPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSN 85
          EPG   K K RRSRT FT  QL  LE+ F++ +Y     R +LA+   L++ +V+ W+ N
Sbjct: 9  EPGTKAK-KGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQN 67
Query: 86 RRARLRK 92
          RR + +K
Sbjct: 68 RRMKWKK 74

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 40/60 (66%)
Query: 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          K+++ RT+FT  Q+ ELE+ F + +Y     R  LA+  K+T+A+V+ WF NRR + R+Q
Sbjct: 16 KRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQ 75

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/62 (38%), Positives = 37/62 (59%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94
          +RR R T+T  Q  ELE+ F    Y     R E+A    LTE ++++WF NRR +L+K++
Sbjct: 20 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEI 79
Query: 95 NS 96
           +
Sbjct: 80 QA 81

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 2/75 (2%)
Query: 15 PSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKL 74
          P+S + S  + E  +P+K+  +++RT F+  QL  L   FQR +Y  +   +EL+    L
Sbjct: 4  PTSAENSVAKKEDKVPVKK--QKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNL 61
Query: 75 TEARVQVWFSNRRAR 89
          +  +V+ WF N+R +
Sbjct: 62 SYKQVKTWFQNQRMK 76

>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 = 47.8 bits (112), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/54 (44%), Positives = 34/54 (62%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89
          RR+RTTFT  Q+ ELE+ F + +Y       +L+ K  L  A+V++WF NRR R
Sbjct: 3  RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRR 56

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 21/58 (36%), Positives = 39/58 (67%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          ++R RT F+ +QL  L+R F   +Y     R++L+ +  L EA++++WF N+RA+++K
Sbjct: 3  EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 21/58 (36%), Positives = 39/58 (67%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          ++R RT F+ +QL  L+R F   +Y     R++L+ +  L EA++++WF N+RA+++K
Sbjct: 3  EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 24/58 (41%), Positives = 35/58 (60%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          +R+RT +T  QL ELE+ F   +Y     R ELA    LTE  +++WF NRR + +K+
Sbjct: 4  KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 26/58 (44%), Positives = 35/58 (60%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          RR RT FT DQL  LE+ F +  Y     R ELA +  L E+ ++VWF NRR + ++Q
Sbjct: 2  RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/70 (37%), Positives = 41/70 (58%), Gaps = 2/70 (2%)
Query: 28 GIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRR 87
          G+P K+++RR    FT  Q  ELER F++ +Y     RE LA   +LT  +V++WF N R
Sbjct: 4  GLPNKKRKRR--VLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHR 61
Query: 88 ARLRKQLNSQ 97
           + ++  N +
Sbjct: 62 YKTKRAQNEK 71

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 21/56 (37%), Positives = 38/56 (67%)
Query: 37 RSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          R RT F+ +QL  L+R F   +Y     R++L+ +  L EA++++WF+N+RA+++K
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 38/58 (65%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          ++R RT F+ +QL   +R F   +Y     R++L+ +  L EA++++WF N+RA++R+
Sbjct: 3  EKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 21/58 (36%), Positives = 39/58 (67%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          ++R RT F+ +QL  L+R F   +Y     R++L+ +  L EA++++WF N+RA+++K
Sbjct: 1  EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 37/58 (63%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          ++R RT F+ +QL  L+R F   +Y     R++L+ +  L EA+V+ WF N RA+++K
Sbjct: 4  EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 35/54 (64%)
Query: 40 TTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          T+F+  Q+ ELER F R +Y     R  LA+  ++T+A+V+ WF NRR + R+Q
Sbjct: 2  TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 33/55 (60%)
Query: 39 RTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          RT FT  QL ELE+ F   +Y     R E+A   +L E +V++WF NRR + +K+
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKR 92

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 21/58 (36%), Positives = 38/58 (65%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          ++R RT F+ +QL  L+R F   +Y     R++L+ +  L EA++++WF N RA+++K
Sbjct: 1  EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 21/58 (36%), Positives = 38/58 (65%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          ++R RT F+ +QL  L+R F   +Y     R++L+ +  L EA++++WF N RA+++K
Sbjct: 1  EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 2/70 (2%)
Query: 28 GIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRR 87
          G+P K+++RR    FT  Q  ELER F++ +Y     RE L    +LT  +V++WF N R
Sbjct: 7  GLPNKKRKRR--VLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHR 64
Query: 88 ARLRKQLNSQ 97
           + ++  N +
Sbjct: 65 YKTKRAQNEK 74

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 35/58 (60%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          R+ R  F+  Q+ ELER F++ +Y     RE LA    LT  +V++WF N R ++++Q
Sbjct: 3  RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/53 (41%), Positives = 34/53 (64%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRR 87
          +R+ R  F+  Q+ ELER F++ +Y     R++LA   KLT  +V++WF NRR
Sbjct: 2  RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRR 54

>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 = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/53 (47%), Positives = 34/53 (64%), Gaps = 1/53 (1%)
Query: 46 QLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARL-RKQLNSQ 97
          Q+ ELER F   +Y     R  LA+  KLTE +V++WF NRR +  RKQL+S+
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSE 67

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 35/58 (60%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          +R RT++T  Q  ELE+ F   +Y     R E+A    LTE ++++WF NRR + +K+
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 86

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 20/54 (37%), Positives = 35/54 (64%)
Query: 37 RSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARL 90
          R RT F+ +QL  L+R F   +Y     R++L+ +  L EA++++WF N+RA++
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKI 54

>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 = 43.1 bits (100), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 22/59 (37%), Positives = 35/59 (59%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          ++R R T+T  Q  ELE+ F   +Y     R E+A    LTE ++++WF NRR + +K+
Sbjct: 2  RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 60

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 21/60 (35%), Positives = 35/60 (58%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95
          R+ R  +T  QL+ELER +   ++     R  ++  T L+E +V +WF NRR + +K +N
Sbjct: 2  RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVIN 61

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 22/57 (38%), Positives = 33/57 (57%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          R+ R  +T  Q  ELE+ F    Y     R E+A+   LTE +V++WF NRR +++K
Sbjct: 2  RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 22/60 (36%), Positives = 36/60 (60%)
Query: 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          +++R R T+T  Q  ELE+ F   +Y     R E+A    LTE ++++WF NRR + +K+
Sbjct: 2  ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 33/51 (64%)
Query: 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          F+ DQ  ELE+ F+  +Y     R+ LA+  +L+E +V+ WF NRRA+ R+
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 22/59 (37%), Positives = 35/59 (59%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          ++R R T+T  Q  ELE+ F   +Y     R E+A    LTE ++++WF NRR + +K+
Sbjct: 2  RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 60

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/60 (38%), Positives = 34/60 (56%)
Query: 33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          R  R+ R  +T  Q  ELE+ F    Y     R E+A+   LTE +V++WF NRR +++K
Sbjct: 11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 35/60 (58%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95
          R+ R  +T  QL+ELER +   ++     R  ++  T L+E +V +WF NRR + +K +N
Sbjct: 8  RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVIN 67

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 18/57 (31%), Positives = 33/57 (57%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          R+ R  ++  QL ELER +   ++     R +++  T L+E ++ +WF NRR + +K
Sbjct: 8  RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64

>pdb|1BW5|A Chain A, The Nmr Solution Structure Of The Homeodomain Of The Rat Insulin Gene Enhancer Protein Isl-1, 50 Structures Length = 66

Iteration: 1
 Score = 40.0 bits (92), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 19/60 (31%), Positives = 30/60 (50%)
Query: 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          K  R RT     QL  L   +     PD   +E+L + T L+   ++VWF N+R + +K+
Sbjct: 2  KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	205
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	9e-45
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	2e-39
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	2e-39
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	8e-39
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	3e-38
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	4e-38
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	3e-37
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	1e-35
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	3e-34
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	3e-34
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	1e-30
1uhs_A	72	HOP, homeodomain only protein; structural genomics	6e-30
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	1e-28
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	2e-28
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	4e-27
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	6e-26
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	7e-24
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	1e-23
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	2e-23
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	1e-21
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	7e-21
1lfb_A	99	Liver transcription factor (LFB1); transcription r	2e-20
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	2e-20
1e3o_C	160	Octamer-binding transcription factor 1; transcript	5e-20
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	2e-19
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	4e-19
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	7e-19
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	2e-18
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	2e-18
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	1e-17
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	1e-17
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	2e-17
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	3e-17
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	3e-17
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	5e-17
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	7e-17
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	2e-16
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	2e-16
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	3e-16
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	7e-16
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	1e-15
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	2e-15
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	1e-14
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	1e-14
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	2e-14
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	8e-14
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	4e-13
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	2e-12
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	4e-12
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	4e-12
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	6e-12
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	2e-11
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	3e-11
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	4e-11
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	8e-11
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	3e-10
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	3e-08
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	3e-06
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	1e-05
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	3e-05
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	3e-05
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	8e-05
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	9e-05
2e19_A	64	Transcription factor 8; homeobox domain, structura	2e-04
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	2e-04
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	5e-04

>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 =  142 bits (360), Expect = 9e-45
 Identities = 62/75 (82%), Positives = 68/75 (90%)

Query: 19 DESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEAR 78
          D SD ESEPGI LKRKQRRSRTTF+  QL+ELERAF+RTQYPD+YTREELAQ+T LTEAR
Sbjct: 2  DISDCESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEAR 61

Query: 79 VQVWFSNRRARLRKQ 93
          +QVWF NRRARLRKQ
Sbjct: 62 IQVWFQNRRARLRKQ 76

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

 Score =  129 bits (325), Expect = 2e-39
 Identities = 38/75 (50%), Positives = 48/75 (64%)

Query: 32  KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91
               RR RTTFT  QL+ LE  F +T+YPD++ REE+A K  L E+RVQVWF NRRA+ R
Sbjct: 4   GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63

Query: 92  KQLNSQQLNAFNSMS 106
           +Q   QQ    +  S
Sbjct: 64  QQQQQQQNGGQSGPS 78

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

 Score =  128 bits (324), Expect = 2e-39
 Identities = 36/77 (46%), Positives = 50/77 (64%)

Query: 30  PLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89
                 +R+RT+FT +Q+E LE+ F+RT YPDV+ RE LA K  L EAR+QVWFSNRRA+
Sbjct: 2   SSGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAK 61

Query: 90  LRKQLNSQQLNAFNSMS 106
            R++   +     +  S
Sbjct: 62  WRREEKLRNQRRQSGPS 78

>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 =  127 bits (320), Expect = 8e-39
 Identities = 35/62 (56%), Positives = 43/62 (69%)

Query: 32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91
              RR RT FT +QLE LE  FQ T+YPDV TRE+LA+K  L E +V+VWF NRRA+ R
Sbjct: 4  GSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 63

Query: 92 KQ 93
          + 
Sbjct: 64 RS 65

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

 Score =  125 bits (316), Expect = 3e-38
 Identities = 29/64 (45%), Positives = 39/64 (60%)

Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95
          RR RT FT +Q+E LE  F+   YP +   E+LAQK  L   R+Q+WF NRRA+L++   
Sbjct: 2  RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61

Query: 96 SQQL 99
            Q 
Sbjct: 62 ESQF 65

>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 =  125 bits (316), Expect = 4e-38
 Identities = 38/67 (56%), Positives = 47/67 (70%)

Query: 34  KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
            QRR RT FT  QL++LE  FQR +YPD+ TREE+A  T LTEARV+VWF NRRA+ RK+
Sbjct: 2   SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61

Query: 94  LNSQQLN 100
                 +
Sbjct: 62  EEFIVTD 68

>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 =  123 bits (311), Expect = 3e-37
 Identities = 27/75 (36%), Positives = 39/75 (52%)

Query: 32  KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91
               +R RT+F   QL  ++  F     PD    ++LAQKT LT+  +QVWF N RA+ R
Sbjct: 4   GSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFR 63

Query: 92  KQLNSQQLNAFNSMS 106
           + L  Q+    +  S
Sbjct: 64  RNLLRQENGGVSGPS 78

>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 =  118 bits (299), Expect = 1e-35
 Identities = 41/56 (73%), Positives = 45/56 (80%)

Query: 38 SRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          S  TFT  QLEELE+AF RT YPDV+TREELA K  LTEAR+QVWF NRRA+ RKQ
Sbjct: 2  SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

>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 =  115 bits (290), Expect = 3e-34
 Identities = 22/62 (35%), Positives = 27/62 (43%)

Query: 32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91
              R SRT FT  QL  L+  F    YP     E+L+    L    + VWF N R + R
Sbjct: 4  GSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKAR 63

Query: 92 KQ 93
          K 
Sbjct: 64 KS 65

>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 =  115 bits (290), Expect = 3e-34
 Identities = 19/65 (29%), Positives = 31/65 (47%)

Query: 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          K  R RT     QL  L   +     PD   +E+L + T L+   ++VWF N+R + +K+
Sbjct: 2  KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

Query: 94 LNSQQ 98
              +
Sbjct: 62 SIMMK 66

>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 =  106 bits (266), Expect = 1e-30
 Identities = 25/73 (34%), Positives = 36/73 (49%)

Query: 21 SDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQ 80
          S +    G    ++ +R RTT T +QLE L + +     P     + +A +  L +  VQ
Sbjct: 3  SGSSGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQ 62

Query: 81 VWFSNRRARLRKQ 93
          VWF N RAR RK 
Sbjct: 63 VWFQNTRARERKS 75

>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 =  104 bits (262), Expect = 6e-30
 Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 36 RRSRTTFTGDQLEELERAFQRT-QYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
               T T DQ+E LE  F +  ++PD  T   +A +  LTE + Q WF  R A  R+ 
Sbjct: 2  SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60

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

 Score =  100 bits (252), Expect = 1e-28
 Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 1/59 (1%)

Query: 36 RRSRTTFTGDQLEELERAFQRT-QYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
           ++ +  T DQ+E LE  F +  ++PD  T   +A +  LTE + Q WF  R A  R+ 
Sbjct: 3  AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 61

>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 =  100 bits (251), Expect = 2e-28
 Identities = 18/62 (29%), Positives = 28/62 (45%)

Query: 32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91
              +R RT  T DQL  L + F     P     +E+A K+ L +  ++ WF N   + R
Sbjct: 4  GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKER 63

Query: 92 KQ 93
          + 
Sbjct: 64 QS 65

>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 = 98.2 bits (244), Expect = 4e-27
 Identities = 24/90 (26%), Positives = 38/90 (42%), Gaps = 15/90 (16%)

Query: 32  KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELA---------------QKTKLTE 76
               R SR T+  + L  +E  F   QYPD   REE+A                  ++T 
Sbjct: 4   GSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTS 63

Query: 77  ARVQVWFSNRRARLRKQLNSQQLNAFNSMS 106
            +V  WF+NRR  ++++ N   +   +  S
Sbjct: 64  LKVYNWFANRRKEIKRRANIAAILESSGPS 93

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

 Score = 94.4 bits (235), Expect = 6e-26
 Identities = 19/67 (28%), Positives = 30/67 (44%)

Query: 32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91
                 +   + +QL  L+ +F R Q+P     E L + T L+   V+ WFS+RR   R
Sbjct: 5  SSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCR 64

Query: 92 KQLNSQQ 98
              S+ 
Sbjct: 65 NLKGSRS 71

>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 = 88.7 bits (220), Expect = 7e-24
 Identities = 15/60 (25%), Positives = 29/60 (48%)

Query: 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
                   T +Q+  L+ +F ++Q+PD      L + T L  + ++ WFS+ R R ++ 
Sbjct: 3  HHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRG 62

>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 = 90.9 bits (225), Expect = 1e-23
 Identities = 22/79 (27%), Positives = 35/79 (44%)

Query: 14  RPSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTK 73
              + +      E       K+R+ RT+FT   +E L   F++   P      E+A++  
Sbjct: 72  ELRNQEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELN 131

Query: 74  LTEARVQVWFSNRRARLRK 92
                V+VWFSNRR  L+ 
Sbjct: 132 YDREVVRVWFSNRRQTLKN 150

>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 = 90.4 bits (224), Expect = 2e-23
 Identities = 19/80 (23%), Positives = 34/80 (42%)

Query: 13  GRPSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKT 72
                 ++        +    ++R+ RTT +    + LER F     P       +A++ 
Sbjct: 65  KWLEEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEEL 124

Query: 73  KLTEARVQVWFSNRRARLRK 92
            L +  V+VWF NRR R ++
Sbjct: 125 NLEKEVVRVWFCNRRQREKR 144

>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 = 87.2 bits (215), Expect = 1e-21
 Identities = 21/95 (22%), Positives = 34/95 (35%), Gaps = 21/95 (22%)

Query: 16  SSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQK---- 71
           +       E        +K RR+R  +     + L +A++R + P    RE L ++    
Sbjct: 96  AGQGGLIEEPTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRA 155

Query: 72  -----------------TKLTEARVQVWFSNRRAR 89
                              +TE RV  WF+NRR  
Sbjct: 156 ECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE 190

>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 = 84.0 bits (207), Expect = 7e-21
 Identities = 20/78 (25%), Positives = 37/78 (47%)

Query: 15  PSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKL 74
            +  +E+  E      L + ++R RT+        LE  F ++  P +     +A +  L
Sbjct: 76  EADNNENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGL 135

Query: 75  TEARVQVWFSNRRARLRK 92
            +  V+VWFSNRR + ++
Sbjct: 136 EKDVVRVWFSNRRQKGKR 153

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

 Score = 81.0 bits (199), Expect = 2e-20
 Identities = 20/88 (22%), Positives = 33/88 (37%), Gaps = 21/88 (23%)

Query: 32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQK-------------------- 71
           +K RR+R  +     + L +A++R + P    RE L ++                    
Sbjct: 6  TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLG 65

Query: 72 -TKLTEARVQVWFSNRRARLRKQLNSQQ 98
             +TE RV  WF+NRR     +     
Sbjct: 66 SNLVTEVRVYNWFANRRKEEAFRHKLAM 93

>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-20
 Identities = 18/73 (24%), Positives = 33/73 (45%)

Query: 24  ESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWF 83
            +   I  + ++R+ RT+        LE  F +   P  +    LA   +L +  V+VWF
Sbjct: 88  TNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWF 147

Query: 84  SNRRARLRKQLNS 96
            NRR + ++   +
Sbjct: 148 CNRRQKEKRMTPA 160

>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 = 81.5 bits (201), Expect = 5e-20
 Identities = 19/74 (25%), Positives = 37/74 (50%)

Query: 19  DESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEAR 78
                 + PGI    ++R+ RT+   +    LE++F   Q P       +A++  + +  
Sbjct: 85  SSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEV 144

Query: 79  VQVWFSNRRARLRK 92
           ++VWFSNRR + ++
Sbjct: 145 IRVWFSNRRQKEKR 158

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

 Score = 81.6 bits (200), Expect = 2e-19
 Identities = 22/101 (21%), Positives = 36/101 (35%), Gaps = 21/101 (20%)

Query: 14  RPSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQK-- 71
              S     ++     P  +K RR+R  +     + L +A+ R + P    RE L ++  
Sbjct: 121 SQQSHGPGQSDDACSEPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECN 180

Query: 72  -------------------TKLTEARVQVWFSNRRARLRKQ 93
                                +TE RV  WF+NRR     +
Sbjct: 181 RAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEEAFR 221

>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 = 77.3 bits (190), Expect = 4e-19
 Identities = 20/89 (22%), Positives = 39/89 (43%), Gaps = 6/89 (6%)

Query: 18  GDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEA 77
           G    + + P    ++ + +     T  Q++ LE +F ++ +P     + L  +TKL+  
Sbjct: 1   GSSGSSGAYPDFAPQKFKEK-----TQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRR 55

Query: 78  RVQVWFSNRRARLRKQLNSQQLNAFNSMS 106
            +  WFS RR   R  +    L++  S  
Sbjct: 56  EIDSWFSERRKL-RDSMEQAVLDSMGSGK 83

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

 Score = 76.4 bits (188), Expect = 7e-19
 Identities = 24/80 (30%), Positives = 45/80 (56%), Gaps = 2/80 (2%)

Query: 14 RPSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTK 73
          +P+S + S  + E  +P   K++++RT F+  QL  L   FQR +Y  +   +EL+    
Sbjct: 3  QPTSAENSVAKKEDKVP--VKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILN 60

Query: 74 LTEARVQVWFSNRRARLRKQ 93
          L+  +V+ WF N+R + ++ 
Sbjct: 61 LSYKQVKTWFQNQRMKSKRW 80

>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 = 74.9 bits (185), Expect = 2e-18
 Identities = 19/58 (32%), Positives = 33/58 (56%)

Query: 32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89
          K K  + +++ +      LE  F+R Q  +   +EE+A+K  +T  +V+VWF N+R R
Sbjct: 2  KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 59

>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 = 75.2 bits (185), Expect = 2e-18
 Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 1/61 (1%)

Query: 34 KQRRSRTTFTGDQLEELERAFQRTQ-YPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
             RSRT  + + L  L+        YPD      L+ +  L +  +  +F N+R  ++ 
Sbjct: 6  SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH 65

Query: 93 Q 93
           
Sbjct: 66 S 66

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

 Score = 73.2 bits (180), Expect = 1e-17
 Identities = 22/66 (33%), Positives = 35/66 (53%)

Query: 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
                +  +  Q+ ELER F   +Y     R  LA+  KLTE +V++WF NRR + +++
Sbjct: 3  HHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRK 62

Query: 94 LNSQQL 99
            S +L
Sbjct: 63 QLSSEL 68

>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 = 72.9 bits (179), Expect = 1e-17
 Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 25 SEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFS 84
          +  G+P   K+R+ R  FT  Q  ELER F++ +Y     RE LA   +LT  +V++WF 
Sbjct: 1  ASDGLP--NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQ 58

Query: 85 NRRARLRKQLNSQQL 99
          N R + ++  N +  
Sbjct: 59 NHRYKTKRAQNEKGY 73

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

 Score = 72.0 bits (177), Expect = 2e-17
 Identities = 22/65 (33%), Positives = 37/65 (56%)

Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94
          +R+ R  F+  Q+ ELER F++ +Y     RE LA    LT  +V++WF N R ++++Q 
Sbjct: 2  RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61

Query: 95 NSQQL 99
            +  
Sbjct: 62 KDKAA 66

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

 Score = 72.1 bits (177), Expect = 3e-17
 Identities = 28/76 (36%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 18 GDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEA 77
          G    +  EPG    +K RRSRT FT  QL  LE+ F++ +Y     R +LA+   L++ 
Sbjct: 1  GSSGSSGGEPG-TKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQL 59

Query: 78 RVQVWFSNRRARLRKQ 93
          +V+ W+ NRR + +K 
Sbjct: 60 QVKTWYQNRRMKWKKS 75

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

 Score = 71.7 bits (176), Expect = 3e-17
 Identities = 25/65 (38%), Positives = 40/65 (61%)

Query: 33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
             R+ RT ++  QL  L+R FQ+TQY  +  R ELA    LT+ +V++WF N+R++++K
Sbjct: 5  SSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64

Query: 93 QLNSQ 97
             S 
Sbjct: 65 SGPSS 69

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

 Score = 71.2 bits (175), Expect = 5e-17
 Identities = 17/60 (28%), Positives = 34/60 (56%)

Query: 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
           +++ RT F+  QL  L+  FQ+ +Y  +   +EL+    L+  +V+ WF N+R + ++ 
Sbjct: 2  TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW 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 = 70.4 bits (173), Expect = 7e-17
 Identities = 25/57 (43%), Positives = 36/57 (63%)

Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          R+ RT FT  QL  LER F++ QY  +  R E +    LTE +V++WF NRRA+ ++
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

 Score = 70.4 bits (172), Expect = 2e-16
 Identities = 16/86 (18%), Positives = 35/86 (40%), Gaps = 5/86 (5%)

Query: 21  SDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQ 80
           S   S P    ++ + ++      +QL  L+ +F  +          L  +TKLT   + 
Sbjct: 2   SSGSSGPDFTPQKFKEKTA-----EQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREID 56

Query: 81  VWFSNRRARLRKQLNSQQLNAFNSMS 106
            WF+ ++     +    +++  N+ S
Sbjct: 57  AWFTEKKKSKALKEEKMEIDESNAGS 82

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

 Score = 69.2 bits (170), Expect = 2e-16
 Identities = 22/57 (38%), Positives = 36/57 (63%)

Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91
          +R+ R  F+  Q+ ELER F++ +Y     R++LA   KLT  +V++WF NRR + +
Sbjct: 2  RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

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

 Score = 69.9 bits (171), Expect = 3e-16
 Identities = 25/66 (37%), Positives = 42/66 (63%)

Query: 33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
           K+++ RT+FT  Q+ ELE+ F + +Y     R  LA+  K+T+A+V+ WF NRR + R+
Sbjct: 15 PKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRR 74

Query: 93 QLNSQQ 98
          Q   ++
Sbjct: 75 QTAEER 80

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

 Score = 71.1 bits (173), Expect = 7e-16
 Identities = 17/82 (20%), Positives = 29/82 (35%)

Query: 19  DESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEAR 78
                E E G       ++ R  FT  Q   L   F+  + P    +  ++Q+  L  + 
Sbjct: 81  ACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELST 140

Query: 79  VQVWFSNRRARLRKQLNSQQLN 100
           V  +F N R R   +      +
Sbjct: 141 VSNFFMNARRRSLDKWLEHHHH 162

>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 = 68.0 bits (166), Expect = 1e-15
 Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 5/74 (6%)

Query: 25 SEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFS 84
          S       + + R+      +QL  LE +F +   P     + L  +TK+T   +  WFS
Sbjct: 2  SSGSSGPTKYKERAP-----EQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFS 56

Query: 85 NRRARLRKQLNSQQ 98
           RR ++  +   + 
Sbjct: 57 ERRKKVNAEETKKS 70

>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 = 67.1 bits (164), Expect = 2e-15
 Identities = 21/61 (34%), Positives = 35/61 (57%)

Query: 33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
             +  +  F+ DQ  ELE+ F+  +Y     R+ LA+  +L+E +V+ WF NRRA+ R+
Sbjct: 5  SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64

Query: 93 Q 93
           
Sbjct: 65 S 65

>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 = 65.0 bits (159), Expect = 1e-14
 Identities = 21/58 (36%), Positives = 39/58 (67%)

Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          ++R RT F+ +QL  L+R F   +Y     R++L+ +  L EA++++WF N+RA+++K
Sbjct: 3  EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

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

 Score = 64.6 bits (158), Expect = 1e-14
 Identities = 23/54 (42%), Positives = 35/54 (64%)

Query: 40 TTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          T+F+  Q+ ELER F R +Y     R  LA+  ++T+A+V+ WF NRR + R+Q
Sbjct: 2  TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

>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 = 64.4 bits (157), Expect = 2e-14
 Identities = 25/64 (39%), Positives = 38/64 (59%)

Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94
           RR+RTTFT  Q+ ELE+ F + +Y       +L+ K  L  A+V++WF NRR R + Q 
Sbjct: 2  PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQS 61

Query: 95 NSQQ 98
          +  +
Sbjct: 62 DQHK 65

>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 = 62.8 bits (153), Expect = 8e-14
 Identities = 26/58 (44%), Positives = 35/58 (60%)

Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          RR RT FT DQL  LE+ F +  Y     R ELA +  L E+ ++VWF NRR + ++Q
Sbjct: 2  RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59

>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 = 62.1 bits (150), Expect = 4e-13
 Identities = 18/74 (24%), Positives = 29/74 (39%)

Query: 19 DESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEAR 78
                   G   K          T +QL  L+ AF RTQ+P     ++LA+++ L    
Sbjct: 9  SSGLEVLFQGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTD 68

Query: 79 VQVWFSNRRARLRK 92
          +  WF + R   + 
Sbjct: 69 IVSWFGDTRYAWKN 82

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

 Score = 58.9 bits (143), Expect = 2e-12
 Identities = 24/62 (38%), Positives = 36/62 (58%)

Query: 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
            +R+RT +T  QL ELE+ F   +Y     R ELA    LTE  +++WF NRR + +K+
Sbjct: 2  SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61

Query: 94 LN 95
           +
Sbjct: 62 ED 63

>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 = 59.1 bits (143), Expect = 4e-12
 Identities = 24/73 (32%), Positives = 36/73 (49%)

Query: 21 SDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQ 80
              ++   P        RT FT  QL ELE+ F   +Y     R E+A   +L E +V+
Sbjct: 20 PPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVK 79

Query: 81 VWFSNRRARLRKQ 93
          +WF NRR + +K+
Sbjct: 80 IWFQNRRMKQKKR 92

>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 = 58.2 bits (141), Expect = 4e-12
 Identities = 22/64 (34%), Positives = 37/64 (57%)

Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94
          ++R R T+T  Q  ELE+ F   +Y     R E+A    LTE ++++WF NRR + +K+ 
Sbjct: 2  RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61

Query: 95 NSQQ 98
           ++ 
Sbjct: 62 KTKG 65

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

 Score = 57.9 bits (140), Expect = 6e-12
 Identities = 21/69 (30%), Positives = 38/69 (55%)

Query: 33  RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
            + R+ R  +T  QL+ELER +   ++     R  ++  T L+E +V +WF NRR + +K
Sbjct: 5   LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64

Query: 93  QLNSQQLNA 101
            +N  +  +
Sbjct: 65  VINKLKTTS 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 = 56.4 bits (136), Expect = 2e-11
 Identities = 18/61 (29%), Positives = 33/61 (54%)

Query: 33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
             R+ R  ++  QL ELER +   ++     R +++  T L+E ++ +WF NRR + +K
Sbjct: 5  SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64

Query: 93 Q 93
           
Sbjct: 65 S 65

>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 76

 Score = 56.2 bits (135), Expect = 3e-11
 Identities = 15/56 (26%), Positives = 24/56 (42%)

Query: 37 RSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
           S    T +QL  L+  F + Q+      ++L Q T L    +  WF + R  L+ 
Sbjct: 5  SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH 60

>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 = 56.4 bits (136), Expect = 4e-11
 Identities = 24/61 (39%), Positives = 35/61 (57%)

Query: 33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
            +RR R T+T  Q  ELE+ F    Y     R E+A    LTE ++++WF NRR +L+K
Sbjct: 18 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKK 77

Query: 93 Q 93
          +
Sbjct: 78 E 78

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

 Score = 55.2 bits (133), Expect = 8e-11
 Identities = 22/60 (36%), Positives = 36/60 (60%)

Query: 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          + +R RT++T  Q  ELE+ F   +Y     R E+A    LTE ++++WF NRR + +K+
Sbjct: 27 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 86

>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 = 53.7 bits (129), Expect = 3e-10
 Identities = 23/66 (34%), Positives = 35/66 (53%)

Query: 33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          R  R+ R  +T  Q  ELE+ F    Y     R E+A+   LTE +V++WF NRR +++K
Sbjct: 11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70

Query: 93 QLNSQQ 98
              + 
Sbjct: 71 INKDRA 76

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

 Score = 48.3 bits (115), Expect = 3e-08
 Identities = 14/63 (22%), Positives = 28/63 (44%), Gaps = 6/63 (9%)

Query: 31 LKRKQRRSRTTFTGDQLEELERAFQR-TQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89
          +K               + LE+ F   T+YPD    + L+++   +  ++Q WF +RR +
Sbjct: 9  IKDSPVNKVE-----PNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQ 63

Query: 90 LRK 92
           + 
Sbjct: 64 DKP 66

>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 = 43.0 bits (100), Expect = 3e-06
 Identities = 14/70 (20%), Positives = 24/70 (34%), Gaps = 4/70 (5%)

Query: 28 GIPLKRKQRRSRTTFTGDQLEELERAFQR----TQYPDVYTREELAQKTKLTEARVQVWF 83
          G        + RT F+   L  L++ +               E +A +  +    V+ W 
Sbjct: 1  GSSGSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWI 60

Query: 84 SNRRARLRKQ 93
           NRR + R  
Sbjct: 61 GNRRRKYRLM 70

>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} Length = 102

 Score = 41.8 bits (97), Expect = 1e-05
 Identities = 18/76 (23%), Positives = 28/76 (36%), Gaps = 21/76 (27%)

Query: 33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQK--------------------- 71
              R+R  +     + L +A+ R + P    RE L ++                     
Sbjct: 4  GSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGS 63

Query: 72 TKLTEARVQVWFSNRR 87
            +TE RV  WF+NRR
Sbjct: 64 NLVTEVRVYNWFANRR 79

>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 = 39.8 bits (93), Expect = 3e-05
 Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 1/48 (2%)

Query: 46 QLEELERAFQR-TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
              LE+ F   T++PD    E L+++       +Q WF  RR + + 
Sbjct: 11 PNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 58

>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* Length = 83

 Score = 40.2 bits (94), Expect = 3e-05
 Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 5/77 (6%)

Query: 33  RKQRRSRTTFTGDQLEELERAFQRTQ---YPDVYTREELAQKTKLTEARVQVWFSNRRAR 89
           +  R  R  FT + +  LE  F +     Y D    E L + T L+  +++ W + RRA+
Sbjct: 2   KPYRGHR--FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAK 59

Query: 90  LRKQLNSQQLNAFNSMS 106
            +    + +L    S  
Sbjct: 60  EKTITIAPELADLLSGE 76

>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 Length = 60

 Score = 38.4 bits (90), Expect = 8e-05
 Identities = 11/34 (32%), Positives = 18/34 (52%)

Query: 59 YPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          Y D    E L + T L+  +++ W SNRR + + 
Sbjct: 25 YLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.1 Length = 87

 Score = 39.1 bits (91), Expect = 9e-05
 Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 4/79 (5%)

Query: 16 SSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQ---YPDVYTREELAQKT 72
          + G   +  ++  I    K  R    FT + +  LE  F +     Y D    E L + T
Sbjct: 9  ADGLVFNVVTQDMINKSTKPYR-GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNT 67

Query: 73 KLTEARVQVWFSNRRARLR 91
           L+  +++ W SNRR + +
Sbjct: 68 SLSRIQIKNWVSNRRRKEK 86

>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 64

 Score = 37.3 bits (86), Expect = 2e-04
 Identities = 10/52 (19%), Positives = 18/52 (34%)

Query: 45 DQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS 96
          + L  L+  +     P      ++A    L    V+ WF   +A      +S
Sbjct: 13 NLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISVQSS 64

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

 Score = 39.4 bits (91), Expect = 2e-04
 Identities = 19/91 (20%), Positives = 33/91 (36%), Gaps = 24/91 (26%)

Query: 16  SSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTK-- 73
           +  D    E E      RK R  +      +L+EL+ A +          +E  +K K  
Sbjct: 75  AQADRLTQEPES----IRKWREEQRK----RLQELDAASKVM-------EQEWREKAKKD 119

Query: 74  LTEARVQVWFSNRRARLRKQLNSQQLN--AF 102
           L E     W   +  ++ K   + ++   AF
Sbjct: 120 LEE-----WNQRQSEQVEKNKINNRIADKAF 145

>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* Length = 73

 Score = 36.2 bits (84), Expect = 5e-04
 Identities = 16/40 (40%), Positives = 24/40 (60%)

Query: 59 YPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQ 98
          YP    +EELA+K  +T ++V  WF N+R R +K +   Q
Sbjct: 28 YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQ 67

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	205
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.85
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.85
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.84
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.84
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.84
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.83
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.83
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.83
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.83
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.82
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.82
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.82
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.82
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.82
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.82
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.82
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.82
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.82
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.82
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.82
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.82
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.82
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.82
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.81
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.81
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.81
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.81
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.81
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.81
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.81
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.81
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.81
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.8
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.8
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.8
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.8
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.79
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.79
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.79
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.79
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.79
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.79
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.79
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.79
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.78
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.78
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.78
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.78
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.78
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.78
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.78
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.77
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.77
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.77
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.76
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.76
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.76
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.75
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.75
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.75
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.74
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.74
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.74
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.74
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.73
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.73
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.71
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.71
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.7
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.7
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.68
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.67
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.6
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.57
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.56
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.54
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.37
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.75
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	96.35
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	89.75
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	88.73
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	88.28
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	87.63
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	83.45
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	81.98
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	81.49

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

Probab=99.85  E-value=8.6e-22  Score=139.83  Aligned_cols=66  Identities=29%  Similarity=0.514  Sum_probs=61.7

Q ss_pred             CccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901          30 PLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN   95 (205)
Q Consensus        30 ~~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   95 (205)
                      ...+++||.|+.|+.+|+.+||.+|..++||+..+|.+||..|||++++|+|||||||+|+||..+
T Consensus        17 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k   82 (84)
T 2kt0_A           17 KVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK   82 (84)
T ss_dssp             CCCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhh
Confidence            346788899999999999999999999999999999999999999999999999999999998753

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

Probab=99.85  E-value=1.5e-21  Score=137.72  Aligned_cols=68  Identities=81%  Similarity=1.212  Sum_probs=60.0

Q ss_pred             CCCccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901          28 GIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN   95 (205)
Q Consensus        28 ~~~~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   95 (205)
                      +...++++||+|+.|+.+|+.+||.+|..++||+..+|.+||..|||++++|++||||||+|+|++..
T Consensus        11 ~~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~   78 (81)
T 1fjl_A           11 GIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   78 (81)
T ss_dssp             ------CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcccCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhcc
Confidence            44456788999999999999999999999999999999999999999999999999999999999854

>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=99.84  E-value=2.4e-21  Score=136.44  Aligned_cols=63  Identities=38%  Similarity=0.614  Sum_probs=60.1

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      .++.||.|+.|+.+|+.+||.+|..++||+..+|.+||..|||++++|+|||||||+|+||..
T Consensus        14 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   76 (80)
T 2dmt_A           14 AKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSG   76 (80)
T ss_dssp             CCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhccc
Confidence            567788999999999999999999999999999999999999999999999999999999863

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

Probab=99.84  E-value=2e-21  Score=136.54  Aligned_cols=63  Identities=37%  Similarity=0.500  Sum_probs=60.1

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      .+++||.|+.|+.+|+.+||.+|..++||+..++.+||.+|||++.+|++||||||+|+||..
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   76 (80)
T 2da3_A           14 PQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSG   76 (80)
T ss_dssp             CCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhc
Confidence            567788999999999999999999999999999999999999999999999999999999863

>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=99.84  E-value=7.8e-21  Score=132.90  Aligned_cols=66  Identities=38%  Similarity=0.628  Sum_probs=61.7

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901          31 LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS   96 (205)
Q Consensus        31 ~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   96 (205)
                      ..+++||.|+.|+.+|+.+||..|..++||+..+|.+||..|||++++|+|||||||+|+|+....
T Consensus         5 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~   70 (77)
T 1nk2_P            5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNE   70 (77)
T ss_dssp             CSCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhcc
Confidence            356778889999999999999999999999999999999999999999999999999999997654

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

Probab=99.83  E-value=1.4e-20  Score=132.58  Aligned_cols=67  Identities=52%  Similarity=0.896  Sum_probs=62.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHHh
Q psy1901          33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQL   99 (205)
Q Consensus        33 ~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~~   99 (205)
                      .++||+|+.|+.+|+.+||.+|..++||+..+|.+||..|||++++|+|||||||+|+|+..+....
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~~~   71 (80)
T 2cue_A            5 SSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQ   71 (80)
T ss_dssp             CSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhhhc
Confidence            5678899999999999999999999999999999999999999999999999999999998766543

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

Probab=99.83  E-value=8.7e-21  Score=127.70  Aligned_cols=61  Identities=39%  Similarity=0.624  Sum_probs=56.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        34 k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      +.||.|+.|+.+|+.+||..|..++||+..++.+||..|||++++|++||||||+|+|+.+
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            4678899999999999999999999999999999999999999999999999999999863

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

Probab=99.83  E-value=1.3e-20  Score=129.38  Aligned_cols=62  Identities=56%  Similarity=0.873  Sum_probs=59.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        33 ~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      .+.||+|+.|+.+|+.+||.+|..++||+..++.+||..|||++++|++||||||+|+|+..
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~   66 (70)
T 2dmu_A            5 SSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSG   66 (70)
T ss_dssp             TSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccC
Confidence            56688999999999999999999999999999999999999999999999999999999974

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

Probab=99.83  E-value=1.1e-20  Score=132.82  Aligned_cols=64  Identities=39%  Similarity=0.605  Sum_probs=60.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901          33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS   96 (205)
Q Consensus        33 ~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   96 (205)
                      .++||+|+.|+.+|+.+||.+|..++||+..++.+||.+|||++++|++||||||+|+||+...
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (80)
T 2dmq_A            5 SSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLR   68 (80)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHH
Confidence            5678899999999999999999999999999999999999999999999999999999998654

>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=99.82  E-value=2.8e-20  Score=130.08  Aligned_cols=65  Identities=35%  Similarity=0.550  Sum_probs=61.3

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS   96 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   96 (205)
                      .++.+|+|+.|+.+|+.+||..|..++||+..++.+||..|||++++|+|||||||+|+|+..+.
T Consensus        10 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k~   74 (77)
T 1puf_A           10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhhh
Confidence            46678899999999999999999999999999999999999999999999999999999998654

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

Probab=99.82  E-value=1.1e-20  Score=133.00  Aligned_cols=65  Identities=54%  Similarity=0.856  Sum_probs=61.2

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS   96 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   96 (205)
                      .++.||+|+.|+.+|+.+||.+|..++||+..+|.+||..|||++++|+|||||||+|+|+....
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~   68 (80)
T 2dms_A            4 GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQ   68 (80)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHc
Confidence            46778899999999999999999999999999999999999999999999999999999998544

>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=99.82  E-value=6.1e-21  Score=131.08  Aligned_cols=63  Identities=29%  Similarity=0.568  Sum_probs=59.6

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      ..+.||+|+.|+.+|+.+||..|..++||+..++.+||..|||++++|++||||||+|+|+..
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~   66 (70)
T 2cra_A            4 GSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSG   66 (70)
T ss_dssp             SCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccC
Confidence            356788999999999999999999999999999999999999999999999999999999864

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

Probab=99.82  E-value=7.3e-21  Score=134.19  Aligned_cols=61  Identities=25%  Similarity=0.337  Sum_probs=57.8

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhc----CCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQR----TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK   92 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~----~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   92 (205)
                      .+++||+|+.|+.+|+.+||.+|..    ++||+..+|++||..|||++++|+|||||||+|.|+
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           14 GGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            4677889999999999999999999    999999999999999999999999999999999764

>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=99.82  E-value=1.2e-20  Score=126.15  Aligned_cols=58  Identities=36%  Similarity=0.780  Sum_probs=53.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901          35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK   92 (205)
Q Consensus        35 ~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   92 (205)
                      .||.|+.|+.+|+.+||..|..++||+..++.+||..|||++.+|++||||||+|+||
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            5788999999999999999999999999999999999999999999999999999987

>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=99.82  E-value=7.2e-21  Score=130.58  Aligned_cols=64  Identities=28%  Similarity=0.404  Sum_probs=60.2

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN   95 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   95 (205)
                      .++.||+|+.|+.+|+.+||.+|..++||+..++.+||..|||++.+|++||||||+|+|+..+
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2da1_A            4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGP   67 (70)
T ss_dssp             SCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhcc
Confidence            4667889999999999999999999999999999999999999999999999999999998743

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

Probab=99.82  E-value=2.6e-20  Score=134.86  Aligned_cols=66  Identities=38%  Similarity=0.669  Sum_probs=61.9

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ   97 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~   97 (205)
                      ..++||+|+.|+.+|+.+||..|..++||+..+|.+||..|||++++|+|||||||+|+|+....+
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~   79 (93)
T 3a01_A           14 PPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEE   79 (93)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHH
Confidence            467788999999999999999999999999999999999999999999999999999999986554

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

Probab=99.82  E-value=1.1e-20  Score=133.00  Aligned_cols=62  Identities=21%  Similarity=0.300  Sum_probs=59.5

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcC----CCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRT----QYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~----~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      .+++||.|+.|+.+|+.+||.+|..+    +||+..+|++||.+|||++++|+|||||||+|+|+.
T Consensus         5 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~   70 (80)
T 2da4_A            5 SSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLM   70 (80)
T ss_dssp             CCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhc
Confidence            46778899999999999999999999    999999999999999999999999999999999986

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

Probab=99.82  E-value=2.3e-20  Score=123.41  Aligned_cols=57  Identities=44%  Similarity=0.779  Sum_probs=55.5

Q ss_pred             CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901          36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK   92 (205)
Q Consensus        36 rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   92 (205)
                      ||+|+.|+.+|+.+||..|..++||+..++.+||..|||++++|++||||||+|+||
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            578999999999999999999999999999999999999999999999999999987

>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=99.82  E-value=1.4e-20  Score=129.19  Aligned_cols=63  Identities=35%  Similarity=0.479  Sum_probs=59.7

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      .++.||+|+.|+.+|+.+||.+|..++||+..++.+||..|||++.+|++||||||+|+|+..
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2da2_A            4 GSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSG   66 (70)
T ss_dssp             SCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhcc
Confidence            456788999999999999999999999999999999999999999999999999999999864

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

Probab=99.82  E-value=2.7e-20  Score=127.18  Aligned_cols=62  Identities=40%  Similarity=0.644  Sum_probs=59.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901          35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS   96 (205)
Q Consensus        35 ~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   96 (205)
                      +||.|+.|+.+|+.+||..|..++||+..++.+||..|||++++|++||||||+|+|+....
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~   63 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ   63 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhcc
Confidence            57899999999999999999999999999999999999999999999999999999998654

>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=99.82  E-value=3.5e-20  Score=127.28  Aligned_cols=62  Identities=34%  Similarity=0.588  Sum_probs=58.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        33 ~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      .+.+++|+.|+.+|+.+||.+|..++||+..++.+||..|||++++|++||||||+|+|+..
T Consensus         5 ~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~   66 (70)
T 2e1o_A            5 SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSG   66 (70)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCC
Confidence            45677889999999999999999999999999999999999999999999999999999974

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

Probab=99.82  E-value=8.6e-21  Score=127.28  Aligned_cols=60  Identities=28%  Similarity=0.537  Sum_probs=53.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        34 k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      +++|.|+.|+.+|+.+||..|..++||+..++.+||..|||++.+|++||||||+|+|+.
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            567889999999999999999999999999999999999999999999999999999885

>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=99.82  E-value=1.1e-20  Score=129.12  Aligned_cols=63  Identities=60%  Similarity=0.904  Sum_probs=59.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901          34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS   96 (205)
Q Consensus        34 k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   96 (205)
                      ++||.|+.|+.+|+.+||..|..++||+..++.+||..|||++.+|++||||||+|+|+..+.
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~~   64 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEF   64 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhhc
Confidence            568899999999999999999999999999999999999999999999999999999998654

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

Probab=99.81  E-value=1.2e-20  Score=133.06  Aligned_cols=60  Identities=25%  Similarity=0.384  Sum_probs=56.5

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhc-----CCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQR-----TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK   92 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~-----~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   92 (205)
                      ..++||+|+.|+.+|+.+|| .|..     ++||+..+|++||.+|||++++|+|||||||+|+|+
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            46778899999999999999 7999     999999999999999999999999999999999764

>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=99.81  E-value=2e-20  Score=127.83  Aligned_cols=61  Identities=36%  Similarity=0.611  Sum_probs=58.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901          35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN   95 (205)
Q Consensus        35 ~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   95 (205)
                      +||.|+.|+.+|+.+||..|..++||+..++.+||..|||++++|++||||||+|+|+..+
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~   62 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK   62 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhcc
Confidence            5788999999999999999999999999999999999999999999999999999999854

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

Probab=99.81  E-value=1.7e-20  Score=128.11  Aligned_cols=62  Identities=35%  Similarity=0.660  Sum_probs=59.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901          35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS   96 (205)
Q Consensus        35 ~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   96 (205)
                      +||.|+.|+.+|+.+||..|..++||+..++.+||..|||++++|++||||||+|+|+..+.
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~~   63 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKD   63 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhhH
Confidence            57889999999999999999999999999999999999999999999999999999998644

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

Probab=99.81  E-value=1.4e-20  Score=130.57  Aligned_cols=66  Identities=67%  Similarity=0.980  Sum_probs=61.5

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901          31 LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS   96 (205)
Q Consensus        31 ~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   96 (205)
                      .+++++|.|+.|+.+|+.+||..|..++||+..++.+||..|||++.+|++||||||+|+|++.+.
T Consensus         5 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r~   70 (75)
T 2m0c_A            5 NKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRERF   70 (75)
T ss_dssp             CCSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHhh
Confidence            356778899999999999999999999999999999999999999999999999999999987543

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

Probab=99.81  E-value=3.7e-20  Score=123.38  Aligned_cols=58  Identities=45%  Similarity=0.717  Sum_probs=55.6

Q ss_pred             CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        36 rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      ||.|+.|+.+|+.+||..|..++||+..++.+||..|||++.+|++||||||+|+|++
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            5789999999999999999999999999999999999999999999999999999985

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

Probab=99.81  E-value=1.7e-20  Score=128.77  Aligned_cols=62  Identities=39%  Similarity=0.691  Sum_probs=59.1

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      ..+.||+|+.|+.+|+.+||.+|..++||+..++.+||..|||++++|++||||||+|+||.
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   65 (70)
T 2djn_A            4 GSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKS   65 (70)
T ss_dssp             CCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhccc
Confidence            45678899999999999999999999999999999999999999999999999999999886

>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=99.81  E-value=2.3e-20  Score=131.78  Aligned_cols=63  Identities=38%  Similarity=0.655  Sum_probs=54.7

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      .+++||+|+.|+.+|+.+||..|..++||+..+|.+||..|||++++|+|||||||+|+||..
T Consensus        17 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   79 (81)
T 1b8i_A           17 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEI   79 (81)
T ss_dssp             -------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhc
Confidence            356688999999999999999999999999999999999999999999999999999999874

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

Probab=99.81  E-value=4.3e-20  Score=127.88  Aligned_cols=64  Identities=33%  Similarity=0.604  Sum_probs=60.2

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN   95 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   95 (205)
                      ..+.||+|+.|+.+|+.+||..|..++||+..++.+||..|||++++|++||||||+|+|+...
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   67 (73)
T 2l7z_A            4 MLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVIN   67 (73)
T ss_dssp             SSCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHhc
Confidence            4567889999999999999999999999999999999999999999999999999999998743

>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=99.81  E-value=2.2e-20  Score=126.79  Aligned_cols=61  Identities=31%  Similarity=0.567  Sum_probs=58.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        34 k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      ++||.|+.|+.+|+.+||.+|..++||+..++.+||..|||++.+|++||||||+|+|+..
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   62 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHHh
Confidence            4688999999999999999999999999999999999999999999999999999998864

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

Probab=99.80  E-value=3.3e-20  Score=132.84  Aligned_cols=63  Identities=35%  Similarity=0.597  Sum_probs=55.5

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      .++.||+|+.|+.+|+.+||..|..++||+..+|.+||..|||++++|+|||||||+|+||..
T Consensus        25 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   87 (88)
T 2r5y_A           25 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH   87 (88)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhhc
Confidence            456788999999999999999999999999999999999999999999999999999999864

>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=99.80  E-value=2.9e-20  Score=124.21  Aligned_cols=60  Identities=32%  Similarity=0.529  Sum_probs=48.5

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR   91 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~k   91 (205)
                      +++++|.|+.|+.+|+.+||.+|..++||+..++.+||..|||++.+|++||||||+|+|
T Consensus         2 k~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            2 KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             ----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            456788999999999999999999999999999999999999999999999999999875

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

Probab=99.80  E-value=6.7e-20  Score=120.90  Aligned_cols=57  Identities=39%  Similarity=0.701  Sum_probs=54.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901          35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR   91 (205)
Q Consensus        35 ~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~k   91 (205)
                      +||.|+.|+.+|+.+||..|..++||+..++.+||..|||++.+|++||||||+|+|
T Consensus         2 ~rr~Rt~~t~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~k   58 (58)
T 3rkq_A            2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK   58 (58)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHC
T ss_pred             cCCCCCCcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhhccCC
Confidence            567899999999999999999999999999999999999999999999999999975

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

Probab=99.80  E-value=3.5e-20  Score=126.15  Aligned_cols=62  Identities=45%  Similarity=0.755  Sum_probs=58.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901          35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS   96 (205)
Q Consensus        35 ~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   96 (205)
                      +||+|+.|+.+|+.+||..|..++||+..++.+||..|||++++|++||||||+|+|+....
T Consensus         1 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~~   62 (67)
T 2k40_A            1 GRRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRE   62 (67)
T ss_dssp             CCCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCCT
T ss_pred             CcCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhchh
Confidence            37889999999999999999999999999999999999999999999999999999987543

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

Probab=99.79  E-value=1e-19  Score=126.73  Aligned_cols=58  Identities=26%  Similarity=0.341  Sum_probs=54.5

Q ss_pred             CCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          37 RSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        37 r~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      .+|..|+.+|+.+||+.|..|+||+..+|++||..+||++.||+|||||||+|+|+..
T Consensus         5 ~~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~   62 (76)
T 2ecc_A            5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ   62 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHH
Confidence            3456699999999999999999999999999999999999999999999999999874

>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=99.79  E-value=9.5e-20  Score=132.77  Aligned_cols=65  Identities=35%  Similarity=0.555  Sum_probs=56.9

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS   96 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   96 (205)
                      ..+.+++|+.|+.+|+.+||..|..++||+..+|.+||..|||++++|+|||||||+|+|+..+.
T Consensus        31 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~   95 (97)
T 1b72_A           31 LGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE   95 (97)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhcc
Confidence            35678889999999999999999999999999999999999999999999999999999998653

>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=99.79  E-value=1.6e-19  Score=124.54  Aligned_cols=59  Identities=36%  Similarity=0.481  Sum_probs=56.5

Q ss_pred             CCCCCCCCHHHHHHHHHHhhc-CCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          36 RRSRTTFTGDQLEELERAFQR-TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        36 rr~R~~~s~~q~~~Le~~F~~-~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      .++|+.|+.+|+.+||..|.. ++||+..+|.+||..|||++++|++||||||+|+|+..
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~   61 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhc
Confidence            578899999999999999996 99999999999999999999999999999999999975

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

Probab=99.79  E-value=5.9e-20  Score=133.67  Aligned_cols=64  Identities=27%  Similarity=0.380  Sum_probs=56.8

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN   95 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   95 (205)
                      ..+.+|+|+.|+.+|+.+||..|..++||+..+|++||.+|||++++|++||||||+|+||...
T Consensus        22 ~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~l   85 (96)
T 3nar_A           22 KSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNL   85 (96)
T ss_dssp             -----CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTCC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhcc
Confidence            4566788999999999999999999999999999999999999999999999999999998743

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

Probab=99.79  E-value=1.7e-19  Score=124.87  Aligned_cols=61  Identities=33%  Similarity=0.427  Sum_probs=57.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhc-CCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901          35 QRRSRTTFTGDQLEELERAFQR-TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN   95 (205)
Q Consensus        35 ~rr~R~~~s~~q~~~Le~~F~~-~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   95 (205)
                      .+++|+.|+.+|+.+||..|.. ++||+..+|.+||..|||++++|++||||||+|+|+...
T Consensus         2 ~~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~~   63 (73)
T 2hi3_A            2 SAQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   63 (73)
T ss_dssp             CCSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhcc
Confidence            3578899999999999999995 999999999999999999999999999999999999753

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

Probab=99.79  E-value=9.4e-20  Score=121.40  Aligned_cols=58  Identities=71%  Similarity=1.012  Sum_probs=50.7

Q ss_pred             CCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901          38 SRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN   95 (205)
Q Consensus        38 ~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   95 (205)
                      .|+.|+.+|+.+||..|..++||+..++.+||..|||++++|++||||||+|+|+..+
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            4789999999999999999999999999999999999999999999999999998753

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

Probab=99.79  E-value=1.6e-19  Score=131.16  Aligned_cols=65  Identities=35%  Similarity=0.585  Sum_probs=61.6

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhC---------------CchhhhhhhhhchHHHHHHHHhH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTK---------------LTEARVQVWFSNRRARLRKQLNS   96 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~---------------l~~~qV~~WFqNrR~k~kr~~~~   96 (205)
                      .+++||.|+.|+.+|+.+||.+|..++||+..+|++||..||               |++.+|++||||||+|+|++.+.
T Consensus         4 ~~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~~   83 (95)
T 2cuf_A            4 GSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANI   83 (95)
T ss_dssp             SSCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhhc
Confidence            467789999999999999999999999999999999999999               99999999999999999998654

>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=99.79  E-value=1.9e-19  Score=124.52  Aligned_cols=64  Identities=20%  Similarity=0.332  Sum_probs=59.5

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhc---CCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQR---TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN   95 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~---~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   95 (205)
                      .++.|++|+.|+.+|+.+||.+|..   ++||+..++++||.++||++.||++||||+|+|+|+...
T Consensus         4 ~~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~   70 (73)
T 1x2n_A            4 GSSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSGP   70 (73)
T ss_dssp             CSSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhcccccc
Confidence            4567888999999999999999976   999999999999999999999999999999999998743

>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=99.78  E-value=3e-19  Score=127.42  Aligned_cols=63  Identities=37%  Similarity=0.610  Sum_probs=58.5

Q ss_pred             CCCCCCCCHHHHHHHHHHh---hcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHH
Q psy1901          36 RRSRTTFTGDQLEELERAF---QRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQ   98 (205)
Q Consensus        36 rr~R~~~s~~q~~~Le~~F---~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~   98 (205)
                      ||+|+.|+.+|+.+||.+|   ..++||+..++.+||..|||++.||++||||||+|+|+......
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   89999999999999999999999999999999999999865543

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

Probab=99.78  E-value=2.4e-19  Score=124.00  Aligned_cols=63  Identities=35%  Similarity=0.595  Sum_probs=58.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHh---hcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901          35 QRRSRTTFTGDQLEELERAF---QRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ   97 (205)
Q Consensus        35 ~rr~R~~~s~~q~~~Le~~F---~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~   97 (205)
                      .||+|+.|+.+|+.+||.+|   ..++||+..++.+||..+||++.+|++||||||+|+|+.....
T Consensus         1 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~~   66 (73)
T 1puf_B            1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKF   66 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTTT
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcccccccc
Confidence            36889999999999999999   8999999999999999999999999999999999999976543

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

Probab=99.78  E-value=2.4e-19  Score=117.93  Aligned_cols=54  Identities=43%  Similarity=0.742  Sum_probs=51.1

Q ss_pred             CCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          40 TTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        40 ~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      +.|+.+|+.+||..|..++||+..+|.+||..|||++++|++||||||+|+||+
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            579999999999999999999999999999999999999999999999999986

>2da6_A Hepatocyte nuclear factor 1-beta; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=6.2e-19  Score=129.11  Aligned_cols=67  Identities=27%  Similarity=0.377  Sum_probs=62.2

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhh---------------------CCchhhhhhhhhchHHHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKT---------------------KLTEARVQVWFSNRRARL   90 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l---------------------~l~~~qV~~WFqNrR~k~   90 (205)
                      .+++||.|+.|++.|+.+||+.|..++||+..+|++||..|                     +|++.+|+|||||||+++
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            46778899999999999999999999999999999999999                     799999999999999999


Q ss_pred             HHHHhHHH
Q psy1901          91 RKQLNSQQ   98 (205)
Q Consensus        91 kr~~~~~~   98 (205)
                      |++.+...
T Consensus        83 kr~~~~~~   90 (102)
T 2da6_A           83 AFRQKLAM   90 (102)
T ss_dssp             HHHHHHHH
T ss_pred             HHhhHhhh
Confidence            99866643

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

Probab=99.78  E-value=1.2e-19  Score=126.55  Aligned_cols=61  Identities=30%  Similarity=0.451  Sum_probs=56.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901          35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN   95 (205)
Q Consensus        35 ~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   95 (205)
                      ..+.|+.|+.+|+.+||.+|..++||+..+|.+||.+|||++++|++||||||+|+|+...
T Consensus         8 ~~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~   68 (76)
T 2dn0_A            8 ASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKG   68 (76)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCS
T ss_pred             CCCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhcc
Confidence            3456899999999999999999999999999999999999999999999999999998744

>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=99.78  E-value=7.8e-20  Score=144.66  Aligned_cols=62  Identities=26%  Similarity=0.481  Sum_probs=55.0

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      ..++||+|+.|+.+|+.+||..|..++||+..+|.+||..|||++++|+|||||||+|+||.
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            46788899999999999999999999999999999999999999999999999999999985

>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=99.78  E-value=3e-19  Score=124.31  Aligned_cols=59  Identities=25%  Similarity=0.429  Sum_probs=55.4

Q ss_pred             CCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901          37 RSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN   95 (205)
Q Consensus        37 r~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   95 (205)
                      ++|+.|+.+|+.+||..|..|+||+..+|.+||..|||++++|++||||||+|+|++.+
T Consensus         9 ~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (75)
T 2da5_A            9 TKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEET   67 (75)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSC
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhh
Confidence            45667999999999999999999999999999999999999999999999999999854

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

Probab=99.77  E-value=4.8e-19  Score=127.11  Aligned_cols=57  Identities=21%  Similarity=0.321  Sum_probs=53.9

Q ss_pred             CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901          41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ   97 (205)
Q Consensus        41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~   97 (205)
                      .|+.+|+.+||+.|..|+||+..+|.+||..|||+++||+|||||||+|+|+++...
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~~~   73 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKM   73 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCC
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHHHh
Confidence            789999999999999999999999999999999999999999999999999875543

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

Probab=99.77  E-value=3.8e-19  Score=123.20  Aligned_cols=61  Identities=28%  Similarity=0.407  Sum_probs=57.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        34 k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      ..++.|+.|+.+|+.+||..|..++||+..++.+||.+|||++++|++||||||+|+||..
T Consensus         5 ~~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   65 (74)
T 2ly9_A            5 DSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSK   65 (74)
T ss_dssp             CCCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTT
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhC
Confidence            4467899999999999999999999999999999999999999999999999999999874

>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=99.77  E-value=3.8e-19  Score=127.09  Aligned_cols=60  Identities=28%  Similarity=0.464  Sum_probs=56.8

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhc---CCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQR---TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR   91 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~---~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~k   91 (205)
                      ..+++++|+.|+.+|+.+||.+|..   ++||+..+|.+||..+||+++||++||||||+|+|
T Consensus        24 ~~~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k   86 (87)
T 1mnm_C           24 KSTKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK   86 (87)
T ss_dssp             EESSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHT
T ss_pred             cCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcc
Confidence            4566778999999999999999999   99999999999999999999999999999999987

>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=99.76  E-value=6.5e-19  Score=124.91  Aligned_cols=65  Identities=18%  Similarity=0.397  Sum_probs=59.2

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhc---CCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQR---TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS   96 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~---~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   96 (205)
                      ..++||+|+.|+.+|+.+|+.+|..   ++||+..+|++||.++||+++||++||||+|+|.|+....
T Consensus         4 ~~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~~   71 (83)
T 2dmn_A            4 GSSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQ   71 (83)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHTC
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHHH
Confidence            3566788999999999999999987   5999999999999999999999999999999999887443

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

Probab=99.76  E-value=1.6e-19  Score=121.68  Aligned_cols=59  Identities=31%  Similarity=0.494  Sum_probs=55.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHh---hcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901          34 KQRRSRTTFTGDQLEELERAF---QRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK   92 (205)
Q Consensus        34 k~rr~R~~~s~~q~~~Le~~F---~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   92 (205)
                      .++++|+.|+.+|+.+||.+|   ..++||+..++.+||..|||++.||++||||+|+|+||
T Consensus         2 ~~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A            2 SGHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             CCCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            357889999999999999999   89999999999999999999999999999999999876

>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=99.76  E-value=8.6e-19  Score=118.48  Aligned_cols=60  Identities=23%  Similarity=0.346  Sum_probs=56.4

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhc-CCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQR-TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR   91 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~-~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~k   91 (205)
                      .+++||.||.|+.+|+.+|+..|.. +.||+.+.|+.||.+|||++++|+|||||||.-.|
T Consensus         4 ~~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~~~   64 (71)
T 1wi3_A            4 GSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVK   64 (71)
T ss_dssp             CCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceeeec
Confidence            4677899999999999999999999 99999999999999999999999999999997644

>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=99.75  E-value=1.1e-18  Score=116.16  Aligned_cols=56  Identities=29%  Similarity=0.475  Sum_probs=53.4

Q ss_pred             CCCCCCHHHHHHHHHHhhc---CCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          38 SRTTFTGDQLEELERAFQR---TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        38 ~R~~~s~~q~~~Le~~F~~---~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      +|+.|+.+|+.+||.+|..   ++||+..++.+||.++||++.+|++||||||+|+|+.
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            4688999999999999999   9999999999999999999999999999999999863

>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=99.75  E-value=4.5e-19  Score=138.33  Aligned_cols=63  Identities=30%  Similarity=0.505  Sum_probs=55.7

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          31 LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        31 ~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      ..+++||+|+.|+.+|+.+||..|..++||+..+|.+||..|||++++|+|||||||+|+||+
T Consensus        83 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           83 ANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             ------CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            356778899999999999999999999999999999999999999999999999999999875

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

Probab=99.75  E-value=5.5e-19  Score=140.34  Aligned_cols=65  Identities=26%  Similarity=0.426  Sum_probs=52.5

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901          31 LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN   95 (205)
Q Consensus        31 ~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   95 (205)
                      ..+++||+|+.|+..|+.+||..|..++||+..+|.+||..|||++++|+|||||||+|+||..+
T Consensus        95 ~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~  159 (164)
T 2xsd_C           95 AQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTP  159 (164)
T ss_dssp             -----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC
T ss_pred             ccccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhccC
Confidence            35778889999999999999999999999999999999999999999999999999999999754

>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=99.74  E-value=1.7e-18  Score=122.65  Aligned_cols=61  Identities=25%  Similarity=0.393  Sum_probs=55.3

Q ss_pred             CCCCCCCCHHHHHHHHHHhhc---CCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901          36 RRSRTTFTGDQLEELERAFQR---TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS   96 (205)
Q Consensus        36 rr~R~~~s~~q~~~Le~~F~~---~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   96 (205)
                      +++|++|+.+|+.+||.+|..   ++||+..++.+||..+||++.||++||||||+|+|+....
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            445667999999999999999   9999999999999999999999999999999999987544

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

Probab=99.74  E-value=6.4e-19  Score=128.92  Aligned_cols=66  Identities=30%  Similarity=0.431  Sum_probs=54.2

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHh------------------hC---CchhhhhhhhhchHHH
Q psy1901          31 LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQK------------------TK---LTEARVQVWFSNRRAR   89 (205)
Q Consensus        31 ~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~------------------l~---l~~~qV~~WFqNrR~k   89 (205)
                      .++++||.|+.|+.+|+.+||..|..++||+..+|++||..                  ||   |++.+|++||||||++
T Consensus         5 ~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k   84 (99)
T 1lfb_A            5 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE   84 (99)
T ss_dssp             --------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHH
Confidence            46788899999999999999999999999999999999999                  88   9999999999999999


Q ss_pred             HHHHHhH
Q psy1901          90 LRKQLNS   96 (205)
Q Consensus        90 ~kr~~~~   96 (205)
                      +|++.+.
T Consensus        85 ~k~k~~~   91 (99)
T 1lfb_A           85 EAFRHKL   91 (99)
T ss_dssp             TSCCC--
T ss_pred             HHHhchh
Confidence            8887544

>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=99.74  E-value=4e-18  Score=122.38  Aligned_cols=56  Identities=27%  Similarity=0.438  Sum_probs=52.9

Q ss_pred             CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901          41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS   96 (205)
Q Consensus        41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   96 (205)
                      .++.+|+.+||..|..++||+..+|++||.+|||++++|+|||||||+|+|+.+..
T Consensus        19 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~~   74 (89)
T 2dmp_A           19 EKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQA   74 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCSC
T ss_pred             cCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhHh
Confidence            48999999999999999999999999999999999999999999999999887544

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

Probab=99.74  E-value=1.1e-18  Score=120.61  Aligned_cols=59  Identities=22%  Similarity=0.421  Sum_probs=54.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHh-hcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          35 QRRSRTTFTGDQLEELERAF-QRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        35 ~rr~R~~~s~~q~~~Le~~F-~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      ..++|.+++.+|+.+||+.| ..++||+..+|.+||.+|||++++|+|||||||+|+|+.
T Consensus         8 g~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~   67 (72)
T 2cqx_A            8 GIKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPS   67 (72)
T ss_dssp             CCCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCC
Confidence            34556678888999999999 999999999999999999999999999999999999875

>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=99.73  E-value=2.8e-18  Score=134.46  Aligned_cols=61  Identities=34%  Similarity=0.602  Sum_probs=58.2

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK   92 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   92 (205)
                      .+++||+|+.|+.+|+.+||.+|..++||+..+|.+||.+|||++++|+|||||||+|+||
T Consensus        90 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           90 PSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            3577889999999999999999999999999999999999999999999999999999986

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

Probab=99.73  E-value=3.7e-18  Score=115.31  Aligned_cols=52  Identities=29%  Similarity=0.517  Sum_probs=50.2

Q ss_pred             CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      .+.+|+.+||+.|..++||+..+|.+||..+||++++|++||||||+|+|+.
T Consensus        11 ~~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg   62 (66)
T 3nau_A           11 KTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRG   62 (66)
T ss_dssp             CCHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhcc
Confidence            3789999999999999999999999999999999999999999999999986

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

Probab=99.71  E-value=2.6e-18  Score=117.79  Aligned_cols=56  Identities=36%  Similarity=0.622  Sum_probs=52.6

Q ss_pred             CCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901          40 TTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN   95 (205)
Q Consensus        40 ~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   95 (205)
                      ..++..|+..||+.|..++||+..+|.+||.+|||++++|+|||||||+|+||+..
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~~   64 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQL   64 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSSS
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhhh
Confidence            35799999999999999999999999999999999999999999999999998743

>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=99.71  E-value=3.9e-18  Score=115.02  Aligned_cols=50  Identities=26%  Similarity=0.403  Sum_probs=46.5

Q ss_pred             HHHHHHHHHHh-hcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          44 GDQLEELERAF-QRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        44 ~~q~~~Le~~F-~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      .+|+.+||+.| ..++||+..+|.+||.+|||+++||+|||||||+|+|+.
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            45899999999 679999999999999999999999999999999999864

>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=99.70  E-value=8.5e-18  Score=132.29  Aligned_cols=61  Identities=28%  Similarity=0.485  Sum_probs=57.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        33 ~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      +++||+|+.|+..|+.+||.+|..++||+..+|.+||.+|||++++|+|||||||+|+||.
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             cCCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            5677889999999999999999999999999999999999999999999999999999974

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

Probab=99.70  E-value=7.3e-18  Score=113.89  Aligned_cols=53  Identities=17%  Similarity=0.209  Sum_probs=49.5

Q ss_pred             CCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901          40 TTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK   92 (205)
Q Consensus        40 ~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   92 (205)
                      ..+..+|+.+||..|..++||+..+|.+||.+|||++++|+|||||||+|.++
T Consensus         8 ~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~   60 (64)
T 2e19_A            8 QPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS   60 (64)
T ss_dssp             CCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSC
T ss_pred             CCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCC
Confidence            34568999999999999999999999999999999999999999999998765

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

Probab=99.68  E-value=1.4e-17  Score=131.92  Aligned_cols=63  Identities=22%  Similarity=0.299  Sum_probs=55.0

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      ..++||+|+.|+.+|+.+||.+|..++||+..+|.+||.+|||++++|+|||||||+|.|+..
T Consensus        94 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~  156 (164)
T 2d5v_A           94 GNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKW  156 (164)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC-
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccC
Confidence            467788999999999999999999999999999999999999999999999999999998864

>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=99.67  E-value=4.7e-17  Score=110.82  Aligned_cols=57  Identities=28%  Similarity=0.396  Sum_probs=50.6

Q ss_pred             CCCHHHHHHHHHHhh---cCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901          41 TFTGDQLEELERAFQ---RTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ   97 (205)
Q Consensus        41 ~~s~~q~~~Le~~F~---~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~   97 (205)
                      .|+.+|+.+|+.+|.   .++||+..++.+||.++||+++||++||||+|+|.|+....+
T Consensus         4 ~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~   63 (67)
T 3k2a_A            4 IFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQ   63 (67)
T ss_dssp             --CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC---
T ss_pred             cCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHHHH
Confidence            689999999999999   999999999999999999999999999999999999875443

>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=99.60  E-value=1.8e-16  Score=128.79  Aligned_cols=62  Identities=32%  Similarity=0.482  Sum_probs=53.9

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhC---------------------CchhhhhhhhhchHHH
Q psy1901          31 LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTK---------------------LTEARVQVWFSNRRAR   89 (205)
Q Consensus        31 ~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~---------------------l~~~qV~~WFqNrR~k   89 (205)
                      ..+++||.|+.|++.|+.+||+.|..++||+..+|++||..|+                     |++.+|++||||||++
T Consensus       111 ~~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~  190 (194)
T 1ic8_A          111 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE  190 (194)
T ss_dssp             ------CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHH
T ss_pred             ccccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhh
Confidence            4578889999999999999999999999999999999999999                     9999999999999999


Q ss_pred             HHH
Q psy1901          90 LRK   92 (205)
Q Consensus        90 ~kr   92 (205)
                      .|.
T Consensus       191 ~k~  193 (194)
T 1ic8_A          191 EAF  193 (194)
T ss_dssp             CC-
T ss_pred             hhc
Confidence            764

>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=2e-15  Score=102.63  Aligned_cols=46  Identities=17%  Similarity=0.322  Sum_probs=44.0

Q ss_pred             HHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHH
Q psy1901          44 GDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR   89 (205)
Q Consensus        44 ~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k   89 (205)
                      ++|+.+|+.+|..|++|+.+++..||..+||++++|++||||||++
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~   59 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVY   59 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhcccc
Confidence            5689999999999999999999999999999999999999999973

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

Probab=99.56  E-value=7.9e-15  Score=104.79  Aligned_cols=58  Identities=24%  Similarity=0.397  Sum_probs=53.4

Q ss_pred             CCCCHHHHHHHHHHhhc---CCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901          40 TTFTGDQLEELERAFQR---TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ   97 (205)
Q Consensus        40 ~~~s~~q~~~Le~~F~~---~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~   97 (205)
                      ..|+++++.+|+.+|..   ++||+..+|.+||.++||+++||++||+|+|.|.|+.....
T Consensus        10 ~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~~~   70 (89)
T 2lk2_A           10 HMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRK   70 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHHHh
Confidence            45899999999999987   89999999999999999999999999999999999875544

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

Probab=99.54  E-value=4.1e-15  Score=122.45  Aligned_cols=62  Identities=34%  Similarity=0.541  Sum_probs=53.7

Q ss_pred             CCccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhC---------------------CchhhhhhhhhchH
Q psy1901          29 IPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTK---------------------LTEARVQVWFSNRR   87 (205)
Q Consensus        29 ~~~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~---------------------l~~~qV~~WFqNrR   87 (205)
                      .+.+++.||.|+.|++.|+.+||.+|..++||+..+|++||..||                     |++.+|++||||||
T Consensus       136 ~~~~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR  215 (221)
T 2h8r_A          136 EPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRR  215 (221)
T ss_dssp             ------CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHH
T ss_pred             ccccCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhh
Confidence            345688899999999999999999999999999999999999998                     89999999999999


Q ss_pred             HHH
Q psy1901          88 ARL   90 (205)
Q Consensus        88 ~k~   90 (205)
                      ++.
T Consensus       216 ~~~  218 (221)
T 2h8r_A          216 KEE  218 (221)
T ss_dssp             TTC
T ss_pred             hhh
Confidence            763

>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=99.37  E-value=1.5e-13  Score=121.18  Aligned_cols=57  Identities=32%  Similarity=0.497  Sum_probs=53.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901          35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR   91 (205)
Q Consensus        35 ~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~k   91 (205)
                      .++.|+.++.+|+..||+.|..++||+..+|++||.+|||+++||++||||||+|+|
T Consensus       365 ~~~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          365 QTAAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            355678899999999999999999999999999999999999999999999999865

>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=98.75  E-value=1.3e-09  Score=65.04  Aligned_cols=24  Identities=25%  Similarity=0.725  Sum_probs=20.4

Q ss_pred             hhhhhhhhchHHHHHHHHhHHHhh
Q psy1901          77 ARVQVWFSNRRARLRKQLNSQQLN  100 (205)
Q Consensus        77 ~qV~~WFqNrR~k~kr~~~~~~~~  100 (205)
                      +||+|||||||+|+||+.......
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~~~~   24 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFNDARD   24 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHHTTT
T ss_pred             CCceeccHHHHHHHHHHhHHHHHH
Confidence            589999999999999998775444

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

Probab=96.35  E-value=0.0032  Score=42.31  Aligned_cols=38  Identities=26%  Similarity=0.430  Sum_probs=36.4

Q ss_pred             HHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhh
Q psy1901          47 LEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFS   84 (205)
Q Consensus        47 ~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFq   84 (205)
                      ..+|+.+|...+.+..+....|+.+.+|+..||+-||-
T Consensus        18 ~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa   55 (70)
T 2ys9_A           18 IQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFD   55 (70)
T ss_dssp             CHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHH
T ss_pred             chHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHH
Confidence            57899999999999999999999999999999999995

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

Probab=89.75  E-value=0.48  Score=29.81  Aligned_cols=45  Identities=16%  Similarity=0.262  Sum_probs=32.7

Q ss_pred             CCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhh
Q psy1901          39 RTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFS   84 (205)
Q Consensus        39 R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFq   84 (205)
                      |..++.+++..+...+.. .........++|.++||....|..|..
T Consensus         3 r~~ys~efK~~~~~~~~~-g~s~~~~~~~vA~~~gIs~~tl~~W~~   47 (59)
T 2glo_A            3 RRIFTPHFKLQVLESYRN-DNDCKGNQRATARKYNIHRRQIQKWLQ   47 (59)
T ss_dssp             CCCCCHHHHHHHHHHHHH-CTTTTTCHHHHHHHTTSCHHHHHHHHT
T ss_pred             CCcCCHHHHHHHHHHHHc-CCCcchHHHHHHHHHCcCHHHHHHHHH
Confidence            456899988777555443 333233367999999999999999975

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

Probab=88.73  E-value=0.91  Score=30.87  Aligned_cols=47  Identities=13%  Similarity=0.229  Sum_probs=34.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhh
Q psy1901          33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFS   84 (205)
Q Consensus        33 ~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFq   84 (205)
                      +++|+.+..++.+++...-+.+.. ..    -..+||+++|++...|..|..
T Consensus        14 ~~~~~~~~~ys~e~k~~~v~~~~~-g~----s~~~iA~~~gIs~sTl~rW~k   60 (87)
T 2elh_A           14 TKGKRPLRSLTPRDKIHAIQRIHD-GE----SKASVARDIGVPESTLRGWCK   60 (87)
T ss_dssp             SCCSSCCSSCCHHHHHHHHHHHHH-TC----CHHHHHHHHTCCHHHHHHHHH
T ss_pred             ccCCCCCCCCCHHHHHHHHHHHHC-CC----CHHHHHHHHCcCHHHHHHHHH
Confidence            334456678899887666566643 22    366889999999999999984

>1hlv_A CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} SCOP: a.4.1.7 a.4.1.7 PDB: 1bw6_A

Probab=88.28  E-value=1.1  Score=32.28  Aligned_cols=49  Identities=14%  Similarity=0.225  Sum_probs=38.7

Q ss_pred             CCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHH
Q psy1901          38 SRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR   89 (205)
Q Consensus        38 ~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k   89 (205)
                      +|..++.+++..+-..+..+....   ..+||+.+|++...|..|..++...
T Consensus         4 ~r~~~t~e~K~~iv~~~~~~g~~~---~~~~A~~~gvs~stl~~~~~~~~~~   52 (131)
T 1hlv_A            4 KRRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNKRAI   52 (131)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTHHHH
T ss_pred             cceeCCHHHHHHHHHHHHHCCCCc---HHHHHHHhCCCHHHHHHHHhchhhh
Confidence            577899999988877776665544   3368999999999999999776654

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

Probab=87.63  E-value=1.5  Score=29.88  Aligned_cols=49  Identities=16%  Similarity=0.284  Sum_probs=37.0

Q ss_pred             CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      .++..++.+|.-.|....     ...+||+.||++...|+.+...-|.+.|+..
T Consensus        37 ~L~~~~r~vl~l~~~~g~-----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l   85 (92)
T 3hug_A           37 QLSAEHRAVIQRSYYRGW-----STAQIATDLGIAEGTVKSRLHYAVRALRLTL   85 (92)
T ss_dssp             TSCHHHHHHHHHHHTSCC-----CHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            377788888877654332     4678999999999999999887666666653

>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=83.45  E-value=2.4  Score=24.27  Aligned_cols=40  Identities=10%  Similarity=0.220  Sum_probs=29.0

Q ss_pred             CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhc
Q psy1901          41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSN   85 (205)
Q Consensus        41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqN   85 (205)
                      .++.++...+...+... +    ...+||+.+|++...|..|+..
T Consensus         5 ~l~~~~~~~i~~~~~~g-~----s~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C            5 ALSDTERAQLDVMKLLN-V----SLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             CCCHHHHHHHHHHHHTT-C----CHHHHHHHHTCCHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHcC-C----CHHHHHHHHCcCHHHHHHHHhh
Confidence            46777775555555433 2    3668999999999999999853

>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=81.98  E-value=1.7  Score=29.08  Aligned_cols=48  Identities=15%  Similarity=0.222  Sum_probs=36.2

Q ss_pred             CCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          40 TTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        40 ~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      ..++..++.+|.-++  ..    ....+||+.+|++...|+.+..+-+.|.+..
T Consensus        20 ~~Lt~~e~~vl~l~~--~g----~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~   67 (82)
T 1je8_A           20 NQLTPRERDILKLIA--QG----LPNKMIARRLDITESTVKVHVKHMLKKMKLK   67 (82)
T ss_dssp             GGSCHHHHHHHHHHT--TT----CCHHHHHHHHTSCHHHHHHHHHHHHHHTTCS
T ss_pred             ccCCHHHHHHHHHHH--cC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHcCC
Confidence            358999999998853  22    2467899999999999999887655555444

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=81.49  E-value=1.7  Score=27.48  Aligned_cols=48  Identities=17%  Similarity=0.075  Sum_probs=35.8

Q ss_pred             CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      .+++.+..+|.-.|...     ....+||..+|++...|+.+...-+.+.++.
T Consensus        15 ~L~~~~r~il~l~~~~g-----~s~~eIA~~lgis~~tv~~~~~ra~~~l~~~   62 (70)
T 2o8x_A           15 DLTTDQREALLLTQLLG-----LSYADAAAVCGCPVGTIRSRVARARDALLAD   62 (70)
T ss_dssp             SSCHHHHHHHHHHHTSC-----CCHHHHHHHHTSCHHHHHHHHHHHHHHHHC-
T ss_pred             hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            47888999998876443     2357899999999999999887555555443

---

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	205
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	3e-25
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	1e-24
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	6e-24
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	3e-23
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	5e-23
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	1e-22
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	1e-22
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	4e-22
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	2e-21
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	5e-21
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	1e-20
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	2e-20
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	3e-20
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	5e-20
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	9e-20
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	1e-19
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	2e-19
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	8e-19
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	8e-19
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	1e-18
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	1e-18
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	3e-18
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	9e-17
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	2e-16
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	3e-16
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	4e-16
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	6e-16
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	1e-15
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	1e-14
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	8e-13
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	6e-10
d1rp3a2	71	a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA)	6e-04

>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 = 91.4 bits (227), Expect = 3e-25
 Identities = 35/63 (55%), Positives = 48/63 (76%)

Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95
          +R+RT+FT +Q+E LE+ F+RT YPDV+ RE LA K  L EAR+QVWFSNRRA+ R++  
Sbjct: 2  QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 61

Query: 96 SQQ 98
           + 
Sbjct: 62 LRN 64

>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 = 90.3 bits (224), Expect = 1e-24
 Identities = 23/66 (34%), Positives = 35/66 (53%)

Query: 33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          R  R+ R  +T  Q  ELE+ F    Y     R E+A+   LTE +V++WF NRR +++K
Sbjct: 11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70

Query: 93 QLNSQQ 98
              + 
Sbjct: 71 INKDRA 76

>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 = 88.0 bits (218), Expect = 6e-24
 Identities = 19/60 (31%), Positives = 30/60 (50%)

Query: 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          K  R RT     QL  L   +     PD   +E+L + T L+   ++VWF N+R + +K+
Sbjct: 2  KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

>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 = 86.0 bits (213), Expect = 3e-23
 Identities = 21/57 (36%), Positives = 35/57 (61%)

Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          +  +  F+ DQ  ELE+ F+  +Y     R+ LA+  +L+E +V+ WF NRRA+ R+
Sbjct: 1  KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 57

>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 = 85.2 bits (211), Expect = 5e-23
 Identities = 21/55 (38%), Positives = 32/55 (58%)

Query: 39 RTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          R T+T  Q  ELE+ F   +Y     R E+A    LTE ++++WF NRR + +K+
Sbjct: 1  RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 55

>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 = 84.6 bits (209), Expect = 1e-22
 Identities = 50/60 (83%), Positives = 56/60 (93%)

Query: 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          KQRRSRTTF+  QL+ELERAF+RTQYPD+YTREELAQ+T LTEAR+QVWF NRRARLRKQ
Sbjct: 1  KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 60

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58

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

 Score = 84.2 bits (208), Expect = 1e-22
 Identities = 18/57 (31%), Positives = 33/57 (57%)

Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          R+ R  ++  QL ELER +   ++     R +++  T L+E ++ +WF NRR + +K
Sbjct: 2  RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 58

>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 = 83.1 bits (205), Expect = 4e-22
 Identities = 38/59 (64%), Positives = 46/59 (77%)

Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          QRR RT FT  QL++LE  FQR +YPD+ TREE+A  T LTEARV+VWF NRRA+ RK+
Sbjct: 1  QRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 59

>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 = 81.1 bits (200), Expect = 2e-21
 Identities = 25/57 (43%), Positives = 34/57 (59%)

Query: 37 RSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          R RT FT DQL  LE+ F +  Y     R ELA +  L E+ ++VWF NRR + ++Q
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 = 82.0 bits (202), Expect = 2e-21
 Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 15/79 (18%)

Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQK---------------TKLTEARVQ 80
          R SR T+  + L  +E  F   QYPD   REE+A                  ++T  +V 
Sbjct: 1  RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVY 60

Query: 81 VWFSNRRARLRKQLNSQQL 99
           WF+NRR  ++++ N   +
Sbjct: 61 NWFANRRKEIKRRANIAAI 79

>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 = 80.0 bits (197), Expect = 5e-21
 Identities = 25/57 (43%), Positives = 36/57 (63%)

Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          R+ RT FT  QL  LER F++ QY  +  R E +    LTE +V++WF NRRA+ ++
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>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 = 79.1 bits (195), Expect = 1e-20
 Identities = 20/53 (37%), Positives = 33/53 (62%)

Query: 37 RSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89
          R RT F+ +QL  L+R F   +Y     R++L+ +  L EA++++WF N RA+
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

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

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

 Score = 78.8 bits (194), Expect = 2e-20
 Identities = 25/63 (39%), Positives = 38/63 (60%)

Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95
          RR+RTTFT  Q+ ELE+ F + +Y       +L+ K  L  A+V++WF NRR R + Q +
Sbjct: 2  RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 61

Query: 96 SQQ 98
            +
Sbjct: 62 QHK 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 = 78.4 bits (193), Expect = 3e-20
 Identities = 22/63 (34%), Positives = 37/63 (58%)

Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94
          +R+ R  F+  Q+ ELER F++ +Y     RE LA    LT  +V++WF N R ++++Q 
Sbjct: 2  RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61

Query: 95 NSQ 97
            +
Sbjct: 62 KDK 64

>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 = 77.6 bits (191), Expect = 5e-20
 Identities = 18/57 (31%), Positives = 28/57 (49%)

Query: 37 RSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          + RTT +    + LER F     P       +A++  L +  V+VWF NRR R ++ 
Sbjct: 1  KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV 57

>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 = 77.4 bits (190), Expect = 9e-20
 Identities = 17/63 (26%), Positives = 30/63 (47%)

Query: 31 LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARL 90
          L + ++R RT+        LE  F +   P +     +A +  L +  V+VWF NRR + 
Sbjct: 4  LVQARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKG 63

Query: 91 RKQ 93
          ++ 
Sbjct: 64 KRS 66

>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 = 77.3 bits (190), Expect = 1e-19
 Identities = 24/69 (34%), Positives = 36/69 (52%)

Query: 25 SEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFS 84
          ++   P        RT FT  QL ELE+ F   +Y     R E+A   +L E +V++WF 
Sbjct: 17 AKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQ 76

Query: 85 NRRARLRKQ 93
          NRR + +K+
Sbjct: 77 NRRMKQKKR 85

>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 = 76.2 bits (187), Expect = 2e-19
 Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 36 RRSRTTFTGDQLEELERAFQRT-QYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
               T T DQ+E LE  F +  ++PD  T   +A +  LTE + Q WF  R A  R+ 
Sbjct: 2  SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60

>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 = 75.1 bits (184), Expect = 8e-19
 Identities = 25/70 (35%), Positives = 38/70 (54%)

Query: 31  LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARL 90
           L  K+R+ R  FT  Q  ELER F++ +Y     RE LA   +LT  +V++WF N R + 
Sbjct: 5   LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKT 64

Query: 91  RKQLNSQQLN 100
           ++  N +   
Sbjct: 65  KRAQNEKGYE 74

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

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

 Score = 74.1 bits (182), Expect = 8e-19
 Identities = 13/49 (26%), Positives = 21/49 (42%)

Query: 39 RTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRR 87
          R  FT  Q   L   F+  + P    +  ++Q+  L  + V  +F N R
Sbjct: 2  RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>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 = 74.6 bits (183), Expect = 1e-18
 Identities = 23/66 (34%), Positives = 31/66 (46%), Gaps = 3/66 (4%)

Query: 36 RRSRTTFTGDQLEELERAF---QRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          RR R  F     E L   F       YP    +EELA+K  +T ++V  WF N+R R +K
Sbjct: 2  RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61

Query: 93 QLNSQQ 98
           +   Q
Sbjct: 62 NIGKFQ 67

>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 = 73.8 bits (181), Expect = 1e-18
 Identities = 17/53 (32%), Positives = 32/53 (60%)

Query: 39 RTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91
          +++ +      LE+ F+R Q  +   +EE+A+K  +T  +V+VWF N+R R +
Sbjct: 1  KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53

>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 = 73.2 bits (180), Expect = 3e-18
 Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 3/60 (5%)

Query: 36 RRSRTTFTGDQLEELERAFQRTQ---YPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          +  R          +     +     YP    ++++A +T LT  +V  WF N R R+ +
Sbjct: 3  KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQ 62

>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 = 69.0 bits (169), Expect = 9e-17
 Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 5/60 (8%)

Query: 36 RRSRTTFTGDQLEELERAFQRTQ---YPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          R  R  FT + +  LE  F +     Y D    E L + T L+  +++ W SNRR + + 
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 = 67.8 bits (166), Expect = 2e-16
 Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 43 TGDQLEELERAFQR-TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
          T      LE+ F   T++PD    E L+++       +Q WF  RR + + 
Sbjct: 1  TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 51

>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 = 68.2 bits (166), Expect = 3e-16
 Identities = 15/64 (23%), Positives = 26/64 (40%), Gaps = 1/64 (1%)

Query: 34 KQRRSRTTFTGDQLEELERAFQRT-QYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
             RSRT  + + L  L+        YPD      L+ +  L +  +  +F N+R  ++ 
Sbjct: 6  SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH 65

Query: 93 QLNS 96
             S
Sbjct: 66 SGPS 69

>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 = 67.3 bits (164), Expect = 4e-16
 Identities = 15/55 (27%), Positives = 29/55 (52%)

Query: 39 RTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
          RT+   +    LE++F   Q P       +A++  + +  ++VWFSNRR + ++ 
Sbjct: 2  RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI 56

>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 = 66.7 bits (163), Expect = 6e-16
 Identities = 13/56 (23%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 37 RSRTTFTGDQLEELERAFQR-TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91
          +       +  + LE+ F   T+YPD    + L+++   +  ++Q WF +RR + +
Sbjct: 3  KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

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

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

 Score = 66.6 bits (162), Expect = 1e-15
 Identities = 19/82 (23%), Positives = 31/82 (37%), Gaps = 8/82 (9%)

Query: 16 SSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQR----TQYPDVYTREELAQK 71
          SSG      S  G       +R RT FT +Q E++    +R     Q  D    E+   +
Sbjct: 2  SSGSSGSNPSSSG----GTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAE 57

Query: 72 TKLTEARVQVWFSNRRARLRKQ 93
          T +    +++W  N +      
Sbjct: 58 TGVRRQVLKIWMHNNKNSGPSS 79

>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 = 64.4 bits (156), Expect = 1e-14
 Identities = 17/76 (22%), Positives = 28/76 (36%), Gaps = 21/76 (27%)

Query: 39 RTTFTGDQLEELERAFQRTQYPDVYTREELAQKT---------------------KLTEA 77
          R  +     + L +A++R + P    RE L ++                       +TE 
Sbjct: 1  RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 78 RVQVWFSNRRARLRKQ 93
          RV  WF+NRR     +
Sbjct: 61 RVYNWFANRRKEEAFR 76

>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 = 59.4 bits (143), Expect = 8e-13
 Identities = 14/71 (19%), Positives = 29/71 (40%)

Query: 36  RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95
            +     T +QL  L+ +F  +          L  +TKLT   +  WF+ ++     +  
Sbjct: 5   PQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEE 64

Query: 96  SQQLNAFNSMS 106
             +++  N+ S
Sbjct: 65  KMEIDESNAGS 75

>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 = 51.7 bits (123), Expect = 6e-10
 Identities = 15/63 (23%), Positives = 24/63 (38%)

Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95
            S    T +QL  L+  F + Q+      ++L Q T L    +  WF + R  L+    
Sbjct: 4  GSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQL 63

Query: 96 SQQ 98
             
Sbjct: 64 KWF 66

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 71

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

 Score = 34.8 bits (80), Expect = 6e-04
 Identities = 11/52 (21%), Positives = 26/52 (50%)

Query: 45 DQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS 96
           +L E E+   +  + +    +E+A+  + + +RV    +    RLR+ L++
Sbjct: 20 SKLPEREKLVIQLIFYEELPAKEVAKILETSVSRVSQLKAKALERLREMLSN 71

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	205
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.87
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.87
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.86
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.86
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.86
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.86
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.85
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.85
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.85
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.85
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.84
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.84
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.84
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.83
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.83
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.82
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.82
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.81
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.81
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.8
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.79
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.79
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.78
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.76
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.76
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.75
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.73
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.71
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.7
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.7
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.68
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.68
d1hlva1	66	DNA-binding domain of centromere binding protein B	93.14
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	84.63
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	84.3
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	83.9
d1iufa1	78	Ars-binding protein 1, ABP1 {Fission yeast (Schizo	81.19

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

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

Probab=99.87  E-value=2.2e-22  Score=139.18  Aligned_cols=66  Identities=35%  Similarity=0.550  Sum_probs=61.1

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ   97 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~   97 (205)
                      .+.+||+|++|+.+|+.+||.+|..|+||+..+|++||..|||++++|+|||||||+|+|+..+..
T Consensus        10 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~~   75 (77)
T d1pufa_          10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDR   75 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHHh
Confidence            345678899999999999999999999999999999999999999999999999999999976553

>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=99.87  E-value=4.6e-23  Score=135.23  Aligned_cols=58  Identities=31%  Similarity=0.647  Sum_probs=55.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901          35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK   92 (205)
Q Consensus        35 ~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   92 (205)
                      +||+|+.|+.+|+.+||.+|..|+||+..+|++||..|||++++|+|||||||+|+||
T Consensus         1 Grr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           1 GRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            3678999999999999999999999999999999999999999999999999999875

>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=99.86  E-value=2e-22  Score=132.24  Aligned_cols=57  Identities=44%  Similarity=0.779  Sum_probs=55.5

Q ss_pred             CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901          36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK   92 (205)
Q Consensus        36 rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   92 (205)
                      ||+|+.|+++|+.+||..|..|+||+..++.+||..|||++++|++||||||+|+||
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            578999999999999999999999999999999999999999999999999999997

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

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

Probab=99.86  E-value=2.2e-22  Score=135.71  Aligned_cols=61  Identities=41%  Similarity=0.656  Sum_probs=57.9

Q ss_pred             CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901          36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS   96 (205)
Q Consensus        36 rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   96 (205)
                      ||+|++|+.+|+.+||.+|..|+||+..++.+||..|||++++|+|||||||+|+|+....
T Consensus         2 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~~   62 (67)
T d1zq3p1           2 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ   62 (67)
T ss_dssp             SCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhhh
Confidence            5779999999999999999999999999999999999999999999999999999987544

>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=99.86  E-value=3.4e-22  Score=130.66  Aligned_cols=57  Identities=37%  Similarity=0.670  Sum_probs=55.2

Q ss_pred             CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901          36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK   92 (205)
Q Consensus        36 rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   92 (205)
                      |+.|++|+++|+.+||.+|..|+||+..++.+||..|||++++|+|||||||+|+||
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            578899999999999999999999999999999999999999999999999999986

>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=99.86  E-value=4.7e-22  Score=133.33  Aligned_cols=63  Identities=81%  Similarity=1.200  Sum_probs=59.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901          34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS   96 (205)
Q Consensus        34 k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   96 (205)
                      |+||.|+.|+.+|+.+||.+|..|+||+..++.+||..|||++++|++||||+|+|+|++...
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~~   63 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHTS   63 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhcccc
Confidence            467899999999999999999999999999999999999999999999999999999987543

>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=99.85  E-value=3.6e-22  Score=130.58  Aligned_cols=57  Identities=44%  Similarity=0.702  Sum_probs=55.2

Q ss_pred             CCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          37 RSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        37 r~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      |.|+.|+.+|+.+||..|..++||+..++.+||..|||++++|+|||||||+|.||+
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            679999999999999999999999999999999999999999999999999999974

>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=99.85  E-value=3.5e-22  Score=129.96  Aligned_cols=55  Identities=38%  Similarity=0.634  Sum_probs=53.8

Q ss_pred             CCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          39 RTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        39 R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      |+.|+.+|+.+||..|..|+||+..+|.+||..|||++++|+|||||||+|+||+
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=99.85  E-value=6.7e-22  Score=140.04  Aligned_cols=64  Identities=36%  Similarity=0.563  Sum_probs=56.3

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN   95 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   95 (205)
                      ..+++|.|+.|+.+|+.+||.+|..|+||+..+|++||..|||++++|+|||||||+|+||+.+
T Consensus        24 ~~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~~   87 (88)
T d1b72a_          24 LGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   87 (88)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhcc
Confidence            3455788999999999999999999999999999999999999999999999999999999754

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

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

Probab=99.85  E-value=1.6e-21  Score=131.80  Aligned_cols=63  Identities=56%  Similarity=0.958  Sum_probs=59.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901          35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ   97 (205)
Q Consensus        35 ~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~   97 (205)
                      +||+|+.|+.+|+.+||..|..|+||+..+|++||..|||++++|++||||+|+|.|+.....
T Consensus         1 grR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~~   63 (68)
T d2cuea1           1 GQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLR   63 (68)
T ss_dssp             SCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhhhh
Confidence            367899999999999999999999999999999999999999999999999999999876554

>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=99.84  E-value=2.6e-22  Score=138.86  Aligned_cols=63  Identities=37%  Similarity=0.615  Sum_probs=59.4

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      +.++||.|++|+.+|+.+||.+|..|+||+..+|++||..|||++++|+|||||||+|.|+..
T Consensus         6 p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   68 (77)
T d1vnda_           6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ   68 (77)
T ss_dssp             SSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHh
Confidence            467778899999999999999999999999999999999999999999999999999988764

>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=99.84  E-value=1e-21  Score=126.61  Aligned_cols=53  Identities=38%  Similarity=0.752  Sum_probs=51.5

Q ss_pred             CCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHH
Q psy1901          37 RSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR   89 (205)
Q Consensus        37 r~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k   89 (205)
                      |+|+.|+.+|+.+||..|..|+||+..+|.+||..|||++++|+|||||||+|
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            57999999999999999999999999999999999999999999999999986

>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=99.84  E-value=1.6e-21  Score=131.74  Aligned_cols=61  Identities=36%  Similarity=0.669  Sum_probs=58.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901          35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN   95 (205)
Q Consensus        35 ~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   95 (205)
                      +||.|+.|+..|+.+||..|..|+||+..+|.+||..|||++++|++||||+|+|+|+...
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~~   62 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK   62 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhccc
Confidence            4678999999999999999999999999999999999999999999999999999998743

>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=99.83  E-value=1.6e-21  Score=128.68  Aligned_cols=58  Identities=64%  Similarity=0.993  Sum_probs=56.3

Q ss_pred             CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        36 rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      ||.|++|+.+|+.+||.+|..|+||+..++.+||..|||++++|++||||+|+|.|+.
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            6789999999999999999999999999999999999999999999999999999986

>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=99.83  E-value=5.5e-21  Score=130.37  Aligned_cols=59  Identities=36%  Similarity=0.481  Sum_probs=55.9

Q ss_pred             CCCCCCCCHHHHHHHHHHhhc-CCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          36 RRSRTTFTGDQLEELERAFQR-TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        36 rr~R~~~s~~q~~~Le~~F~~-~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      ++.|++|+.+|+.+||..|.. ++||+..+|++||..|||++++|+|||||||+|+||..
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~   61 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhcc
Confidence            678999999999999999986 78999999999999999999999999999999999874

>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=99.82  E-value=4.3e-21  Score=128.92  Aligned_cols=61  Identities=31%  Similarity=0.567  Sum_probs=58.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        34 k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      |.+|.|+.|+.+|+.+||.+|..|+||+..++++||.+|||++++|++||||+|+|.|+..
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~~   62 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHHH
Confidence            5688999999999999999999999999999999999999999999999999999998864

>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=99.82  E-value=3.1e-21  Score=129.98  Aligned_cols=61  Identities=26%  Similarity=0.462  Sum_probs=57.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        33 ~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      ..+||+|++|+.+|+.+|+.+|..|+||+..++++||..|||++++|++||||+|+++||.
T Consensus         6 ~~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_           6 QARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             CCSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             hccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            4457889999999999999999999999999999999999999999999999999998864

>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=99.81  E-value=7.7e-21  Score=124.55  Aligned_cols=57  Identities=32%  Similarity=0.506  Sum_probs=55.0

Q ss_pred             CCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          37 RSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        37 r~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      |+|+.|+.+|+.+||.+|..|+||+..++.+||..|||++++|++||||+|+++|+.
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            679999999999999999999999999999999999999999999999999999874

>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=99.81  E-value=1.1e-20  Score=121.68  Aligned_cols=53  Identities=32%  Similarity=0.548  Sum_probs=51.4

Q ss_pred             CCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901          39 RTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR   91 (205)
Q Consensus        39 R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~k   91 (205)
                      |++|+++|+.+||..|..|+||+..++.+||..|||++++|++||||||+|.|
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            78999999999999999999999999999999999999999999999999865

>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=99.80  E-value=2.6e-20  Score=130.26  Aligned_cols=60  Identities=38%  Similarity=0.656  Sum_probs=56.8

Q ss_pred             CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhC---------------CchhhhhhhhhchHHHHHHHHh
Q psy1901          36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTK---------------LTEARVQVWFSNRRARLRKQLN   95 (205)
Q Consensus        36 rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~---------------l~~~qV~~WFqNrR~k~kr~~~   95 (205)
                      ||+|+.|+++|+.+||.+|..|+||+..+|++||..||               |++.+|++||||||+|+|++..
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~   75 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRAN   75 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhh
Confidence            67899999999999999999999999999999999875               9999999999999999999754

>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=99.79  E-value=3.3e-20  Score=121.07  Aligned_cols=56  Identities=27%  Similarity=0.477  Sum_probs=54.3

Q ss_pred             CCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          38 SRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        38 ~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      +||.|+.+|+.+||..|..|+||+..++.+||.+|||++++|++||||+|+|+||.
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            58999999999999999999999999999999999999999999999999999874

>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=99.79  E-value=2.6e-20  Score=126.80  Aligned_cols=61  Identities=23%  Similarity=0.342  Sum_probs=56.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhh-cCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          33 RKQRRSRTTFTGDQLEELERAFQ-RTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        33 ~k~rr~R~~~s~~q~~~Le~~F~-~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      ...+|+|++|+.+|+.+||++|. .++||+.+++++||.+|||++++|++||||+|+|.|+.
T Consensus         5 ~~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk~   66 (71)
T d1wi3a_           5 SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS   66 (71)
T ss_dssp             CCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCSS
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhccc
Confidence            34567899999999999999997 48999999999999999999999999999999998864

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

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

Probab=99.78  E-value=5.1e-20  Score=128.11  Aligned_cols=61  Identities=23%  Similarity=0.332  Sum_probs=55.4

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHhhc----CCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901          32 KRKQRRSRTTFTGDQLEELERAFQR----TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK   92 (205)
Q Consensus        32 ~~k~rr~R~~~s~~q~~~Le~~F~~----~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   92 (205)
                      ..++||.|++|+.+|+.+|+.+|+.    ++||+..++++||++|||++++|+|||||+|++.|+
T Consensus        14 ~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          14 GGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             ccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            3556789999999999999998886    899999999999999999999999999999987654

>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=99.76  E-value=1.9e-19  Score=124.06  Aligned_cols=55  Identities=22%  Similarity=0.339  Sum_probs=51.3

Q ss_pred             CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901          42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS   96 (205)
Q Consensus        42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   96 (205)
                      ++++|+.+||.+|..|+||+..++++||..|||++++|++||||||++.|+....
T Consensus        11 ~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~~   65 (76)
T d2ecba1          11 KTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEK   65 (76)
T ss_dssp             CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSC
T ss_pred             CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhHh
Confidence            5899999999999999999999999999999999999999999999988776443

>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=99.76  E-value=5.1e-19  Score=120.93  Aligned_cols=59  Identities=37%  Similarity=0.647  Sum_probs=55.4

Q ss_pred             CCCCCCCCHHHHHHHHHHhh---cCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901          36 RRSRTTFTGDQLEELERAFQ---RTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        36 rr~R~~~s~~q~~~Le~~F~---~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      ||+|+.|+++|+.+|+++|.   .++||+..++++||.++||+++||++||||+|+|.|+..
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~   63 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccc
Confidence            67889999999999999997   488999999999999999999999999999999999864

>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=99.75  E-value=2.5e-19  Score=113.82  Aligned_cols=50  Identities=26%  Similarity=0.339  Sum_probs=48.8

Q ss_pred             CCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchH
Q psy1901          38 SRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRR   87 (205)
Q Consensus        38 ~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR   87 (205)
                      .|+.|+.+|+.+||+.|..|+||+..++.+||.+|||++++|++||||||
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            48999999999999999999999999999999999999999999999997

>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=99.73  E-value=2.5e-18  Score=118.36  Aligned_cols=56  Identities=27%  Similarity=0.364  Sum_probs=52.7

Q ss_pred             CCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          38 SRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        38 ~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      .+.+++.+|+.+||.+|..|+||+..++.+||..|||++++|++||||+|+++|+.
T Consensus         6 ~~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~   61 (76)
T d2ecca1           6 SGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhc
Confidence            34457999999999999999999999999999999999999999999999999986

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

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

Probab=99.71  E-value=1.5e-18  Score=111.03  Aligned_cols=50  Identities=28%  Similarity=0.432  Sum_probs=46.5

Q ss_pred             CHHHHHHHHHHhhc-CCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901          43 TGDQLEELERAFQR-TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK   92 (205)
Q Consensus        43 s~~q~~~Le~~F~~-~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   92 (205)
                      |.+|..+||.+|.. ++||+..++.+||++|||++++|++||||||+|+|+
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            45789999999987 689999999999999999999999999999999874

>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=99.70  E-value=2.1e-18  Score=119.10  Aligned_cols=56  Identities=30%  Similarity=0.454  Sum_probs=52.9

Q ss_pred             CCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhC---------------------CchhhhhhhhhchHHHHHHHH
Q psy1901          39 RTTFTGDQLEELERAFQRTQYPDVYTREELAQKTK---------------------LTEARVQVWFSNRRARLRKQL   94 (205)
Q Consensus        39 R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~---------------------l~~~qV~~WFqNrR~k~kr~~   94 (205)
                      |++|+++|+.+||++|..|+||+..+|++||++|+                     |++.+|++||||||++.|++.
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            68899999999999999999999999999999995                     899999999999999998763

>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=99.70  E-value=1.8e-17  Score=109.63  Aligned_cols=56  Identities=23%  Similarity=0.414  Sum_probs=52.2

Q ss_pred             CCCCCCCCHHHHHHHHHHhhc---CCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901          36 RRSRTTFTGDQLEELERAFQR---TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR   91 (205)
Q Consensus        36 rr~R~~~s~~q~~~Le~~F~~---~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~k   91 (205)
                      |++|+.|+++++.+|+++|..   ++||+..++.+||.++||+.+||++||+|+|.|..
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   79999999999999999999999999999998865

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

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

Probab=99.68  E-value=6.7e-18  Score=110.64  Aligned_cols=55  Identities=24%  Similarity=0.476  Sum_probs=50.7

Q ss_pred             CCCCCCCHHHHHHHHHHhhc-CCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901          37 RSRTTFTGDQLEELERAFQR-TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR   91 (205)
Q Consensus        37 r~R~~~s~~q~~~Le~~F~~-~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~k   91 (205)
                      |.+.+++.++..+||++|.. ++||+..++.+||++|||++++|++||||||+++|
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            56677888899999999976 68999999999999999999999999999999976

>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=99.68  E-value=3.1e-17  Score=107.79  Aligned_cols=52  Identities=31%  Similarity=0.533  Sum_probs=48.6

Q ss_pred             CCCHHHHHHHHHHhhcC---CCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901          41 TFTGDQLEELERAFQRT---QYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK   92 (205)
Q Consensus        41 ~~s~~q~~~Le~~F~~~---~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   92 (205)
                      +|+.+|+.+|+.+|..+   +||+.+++++||.++||+++||++||||+|.|.|+
T Consensus         4 Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           4 RFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             SCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            49999999999999764   79999999999999999999999999999998875

>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=93.14  E-value=0.11  Score=32.92  Aligned_cols=48  Identities=15%  Similarity=0.246  Sum_probs=39.2

Q ss_pred             CCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHH
Q psy1901          38 SRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRA   88 (205)
Q Consensus        38 ~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~   88 (205)
                      +|..++-++...+-+.|+.++...   ..+||+.+|+....|..|..|+..
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            345689999888888888887554   567999999999999999988543

>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=84.63  E-value=1.1  Score=25.89  Aligned_cols=40  Identities=15%  Similarity=0.283  Sum_probs=33.8

Q ss_pred             CCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhh
Q psy1901          40 TTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFS   84 (205)
Q Consensus        40 ~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFq   84 (205)
                      ..++.+|+..+.+.+... .    -+.+||+.+|++...|-.||-
T Consensus         4 ~~lt~~q~~~a~~l~~~G-~----s~~~iA~~~gVSr~TiYry~p   43 (47)
T d1ijwc_           4 RAINKHEQEQISRLLEKG-H----PRQQLAIIFGIGVSTLYRYFP   43 (47)
T ss_dssp             CSSCHHHHHHHHHHHHTT-C----CHHHHHHHHTCCHHHHHHHSC
T ss_pred             CcCCHHHHHHHHHHHHCC-C----CHHHHHHHHCcCHHHHHhhCC
Confidence            458999999999999754 3    278899999999999999883

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=84.30  E-value=1.1  Score=27.27  Aligned_cols=48  Identities=17%  Similarity=0.170  Sum_probs=36.6

Q ss_pred             CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      .+++.+..+|.-.|....     ...+||+.+|++...|+.....-|.+.|+.
T Consensus        21 ~L~~~~r~v~~l~~~~~~-----s~~eIA~~lgis~~tv~~~~~ra~~~Lr~~   68 (71)
T d1rp3a2          21 KLPEREKLVIQLIFYEEL-----PAKEVAKILETSVSRVSQLKAKALERLREM   68 (71)
T ss_dssp             TSCHHHHHHHHHHHTSCC-----CHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhHhC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            367888888888775442     578899999999999998887666655543

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=83.90  E-value=1.2  Score=27.24  Aligned_cols=47  Identities=13%  Similarity=0.055  Sum_probs=35.7

Q ss_pred             CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901          42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ   93 (205)
Q Consensus        42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   93 (205)
                      +++.+..+|.-.|....     ...+||+.+|++...|+..++.-|.+.|+.
T Consensus        19 Lp~~~r~v~~l~~~~~~-----s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~   65 (68)
T d1or7a1          19 LPEDLRMAITLRELDGL-----SYEEIAAIMDCPVGTVRSRIFRAREAIDNK   65 (68)
T ss_dssp             SCHHHHHHHHHHHTTCC-----CHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            56677777777765543     367899999999999999998766666553