Psyllid ID: psy8148

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390
Protein Sequence
MKKLNPNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGYSSDDSSPVLYETNAHDFNKHYLEIQQKAQEYLNMKKLNPNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKNRTFDPYS
Secondary Structure (PSIPRED)
cccccccccccHHHHHHHHHHHHHcccccHHHHHHHcccccHHccccHHHHHHHHHHHHccccHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHcccHHHHHHHHHccccHHHcccccHHHHHHHHHHcccccHHHHHHHHHccccccccHHHHHHHHHHcHHHHHHHHccccccccHHHHHcccccccccccccccccccccHHcHHHHHHHHHccccccHHHHHHHHHHHccccHHHHHHHcccccccccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHcccccHHHHHccHHHHcccccHHHHccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccHHHHHHHHHHHHHcccHHHHHHHHHcccHHHHHcccHHHHHHHHHHHHHHccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHcHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHcccHHHHHHHHHcccHHHHHcccHHHHHHHHHHHHHcccHHHHHHHHHHccccHccHHHHHHHHHHHHHHHHHHHccccccccccEEEEEccccccEEEccccEEEEccHHHHHHHHHHHHccccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHccHHHHcccccccccHHcccccccccccHHHHHHHHccccHHEEccHHHccHccccccccccccccccccc
Coil and Loop (DISEMBL)
mkklnpnmsftpEQIDCLCEAMQQSGDFDKLAMFlwslppqeaiRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAkirgrdlgyssddsspvlyetnahdfNKHYLEIQQKAQEYLNMkklnpnmsftpEQIDCLCEAMQQSGDFDKLAMFlwslppqeaiRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAKirgrdlgavdkyrirkkfplpktiwdgeeTVYCFKERSRNAlkecydknrypnpdekrqlseitgltLTQVSNWfknrrqrdrtpqqrSIQRSRNALKecydknrypnpdekrqlseitgltLTQVSNWfknrrqrdrtpqqraknrtfdpys
Flexible Loop (DISEMBL)
MKKLNPNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGYSSDDSSPVLYETNAHDFNKHYLEIQQKAQEYLNMKKLNPNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAkirgrdlgavdkyrirkkfplpktiwdgeetvYCFKErsrnalkecydknrypnpdekrqlseitgltltqvsnwfknrrqrdrtpqqrsiqrsrnalkecydknrypnpdekrqlseitgltltqvsnwfknrrqrdrtpqqraknrtfdpys
Low Complexity Region (SEG)
MKKLNPNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGYSSDDSSPVLYETNAHDFNKHYLEIQQKAQEYLNMKKLNPNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKNRTFDPYS
Disordered region (IsUnstruct)
*************QIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGY*******VLYETNAHDFNKHYLEIQQKAQEYLNMKKLNPNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEETVYCFKERSRNALKECYD***************ITGLTLTQVSNWF*******************************************TGLTLTQVSNWF***********************
Disordered Region (DISOPRED)
*********FTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAK**************************************************FTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGH****************************************KERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT**********************************TGLTLTQVSNWFKN*********************
Disordered Region (DISEMBL)
MKKLNPNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGYSSDDSSPVLYETNAHDFNKHYLEIQQKAQEYLNMKKLNPNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKN***************SRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKN*********************
Disordered Region (DISPRO)
*****PNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGYSSDDSSPVLYETNAHDFNKHYLEIQQKAQEYLNMKKLNPNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR********************N*YPNPDEKRQLSEITGLTLTQVSNWFKNR********************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKKLNPNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGYSSDDSSPVLYETNAHDFNKHYLEIQQKAQEYLNMKKLNPNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKNRTFDPYS
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	390	2.2.26 [Sep-21-2011]
Q61321	775	Homeobox protein SIX4 OS=	yes	N/A	0.461	0.232	0.644	2e-71
Q9UIU6	781	Homeobox protein SIX4 OS=	yes	N/A	0.456	0.227	0.646	4e-71
P70178	719	Homeobox protein SIX5 OS=	no	N/A	0.451	0.244	0.647	1e-68
Q8N196	739	Homeobox protein SIX5 OS=	no	N/A	0.451	0.238	0.647	1e-68
Q62232	296	Homeobox protein SIX2 OS=	no	N/A	0.464	0.611	0.613	5e-64
Q9NPC8	291	Homeobox protein SIX2 OS=	no	N/A	0.464	0.621	0.613	6e-64
Q62231	284	Homeobox protein SIX1 OS=	no	N/A	0.464	0.637	0.607	8e-64
A2D5H2	284	Homeobox protein SIX1 OS=	N/A	N/A	0.464	0.637	0.607	8e-64
Q15475	284	Homeobox protein SIX1 OS=	no	N/A	0.464	0.637	0.607	8e-64
A1YER0	284	Homeobox protein SIX1 OS=	N/A	N/A	0.464	0.637	0.607	8e-64

>sp|Q61321|SIX4_MOUSE Homeobox protein SIX4 OS=Mus musculus GN=Six4 PE=2 SV=1

 Score =  270 bits (689), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 116/180 (64%), Positives = 148/180 (82%)

Query: 145 PNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFH 204
           P ++F+P+ + C+CEA+QQ G+ D+LA FLWSLP  + +RG ES+L+ARA+VA+ +  + 
Sbjct: 97  PPLAFSPDHVACVCEALQQGGNLDRLARFLWSLPQSDLLRGNESLLKARALVAFHQGIYP 156

Query: 205 ELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDG 264
           ELY+ILESH+F+S  H  LQQLW +  Y E  + RGR LGAVDKYR+R+KFPLP+TIWDG
Sbjct: 157 ELYSILESHSFESANHPLLQQLWYKARYTEAERARGRPLGAVDKYRLRRKFPLPRTIWDG 216

Query: 265 EETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ 324
           EETVYCFKE+SRNALKE Y +NRYP+P EKR L++ITGL+LTQVSNWFKNRRQRDR P +
Sbjct: 217 EETVYCFKEKSRNALKELYKQNRYPSPAEKRHLAKITGLSLTQVSNWFKNRRQRDRNPSE 276

Involved in skeletal muscle development. Also implicated in retina and kidney development.
Mus musculus (taxid: 10090)

>sp|Q9UIU6|SIX4_HUMAN Homeobox protein SIX4 OS=Homo sapiens GN=SIX4 PE=1 SV=2

 Score =  268 bits (686), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 115/178 (64%), Positives = 147/178 (82%)

Query: 147 MSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHEL 206
           ++F+P+ + C+CEA+QQ G+ D+LA FLWSLP  + +RG ES+L+ARA+VA+ +  + EL
Sbjct: 106 LAFSPDHVACVCEALQQGGNLDRLARFLWSLPQSDLLRGNESLLKARALVAFHQGIYPEL 165

Query: 207 YAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEE 266
           Y+ILESH+F+S  H  LQQLW +  Y E  + RGR LGAVDKYR+R+KFPLP+TIWDGEE
Sbjct: 166 YSILESHSFESANHPLLQQLWYKARYTEAERARGRPLGAVDKYRLRRKFPLPRTIWDGEE 225

Query: 267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ 324
           TVYCFKE+SRNALKE Y +NRYP+P EKR L++ITGL+LTQVSNWFKNRRQRDR P +
Sbjct: 226 TVYCFKEKSRNALKELYKQNRYPSPAEKRHLAKITGLSLTQVSNWFKNRRQRDRNPSE 283

Homo sapiens (taxid: 9606)

>sp|P70178|SIX5_MOUSE Homeobox protein SIX5 OS=Mus musculus GN=Six5 PE=1 SV=2

 Score =  260 bits (664), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 114/176 (64%), Positives = 140/176 (79%)

Query: 146 NMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHE 205
            + F+PEQ+ C+CEA+ Q+G   +L+ FL +LPP E +RG + VLRARA+VA++R  + E
Sbjct: 76  GLRFSPEQVACVCEALLQAGHAGRLSRFLGALPPAERLRGSDPVLRARALVAFQRGEYAE 135

Query: 206 LYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGE 265
           LY +LES  F + +HA LQ L++R  Y E  + RGR LGAVDKYR+RKKFPLPKTIWDGE
Sbjct: 136 LYQLLESRPFPAAHHAFLQDLYLRARYHEAERARGRALGAVDKYRLRKKFPLPKTIWDGE 195

Query: 266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT 321
           ETVYCFKERSR ALK CY  NRYP PDEKR+L+ +TGL+LTQVSNWFKNRRQRDRT
Sbjct: 196 ETVYCFKERSRAALKACYRGNRYPTPDEKRRLATLTGLSLTQVSNWFKNRRQRDRT 251

Transcription factor that is thought to be involved in regulation of organogenesis. May be involved in determination and maintenance of retina formation. Binds a 5'-GGTGTCAG-3' motif present in the ARE regulatory element of ATP1A1. Binds a 5'-TCA[AG][AG]TTNC-3' motif present in the MEF3 element in the myogenin promoter, and in the IGFBP5 promoter (By similarity). Thought to be regulated by association with Dach and Eya proteins, and seems to be coactivated by EYA1, EYA2 and EYA3.

Mus musculus (taxid: 10090)

>sp|Q8N196|SIX5_HUMAN Homeobox protein SIX5 OS=Homo sapiens GN=SIX5 PE=1 SV=3

 Score =  260 bits (664), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 114/176 (64%), Positives = 140/176 (79%)

Query: 146 NMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHE 205
            + F+PEQ+ C+CEA+ Q+G   +L+ FL +LPP E +RG + VLRARA+VA++R  + E
Sbjct: 83  GLRFSPEQVACVCEALLQAGHAGRLSRFLGALPPAERLRGSDPVLRARALVAFQRGEYAE 142

Query: 206 LYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGE 265
           LY +LES  F + +HA LQ L++R  Y E  + RGR LGAVDKYR+RKKFPLPKTIWDGE
Sbjct: 143 LYRLLESRPFPAAHHAFLQDLYLRARYHEAERARGRALGAVDKYRLRKKFPLPKTIWDGE 202

Query: 266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT 321
           ETVYCFKERSR ALK CY  NRYP PDEKR+L+ +TGL+LTQVSNWFKNRRQRDRT
Sbjct: 203 ETVYCFKERSRAALKACYRGNRYPTPDEKRRLATLTGLSLTQVSNWFKNRRQRDRT 258

Transcription factor that is thought to be involved in regulation of organogenesis. May be involved in determination and maintenance of retina formation. Binds a 5'-GGTGTCAG-3' motif present in the ARE regulatory element of ATP1A1. Binds a 5'-TCA[AG][AG]TTNC-3' motif present in the MEF3 element in the myogenin promoter, and in the IGFBP5 promoter (By similarity). Thought to be regulated by association with Dach and Eya proteins, and seems to be coactivated by EYA1, EYA2 and EYA3.

Homo sapiens (taxid: 9606)

>sp|Q62232|SIX2_MOUSE Homeobox protein SIX2 OS=Mus musculus GN=Six2 PE=1 SV=2

 Score =  245 bits (625), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 111/181 (61%), Positives = 137/181 (75%)

Query: 145 PNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFH 204
           P   FT EQ+ C+CE +QQ G+ ++L  FLWSLP  E +   ESVL+A+AVVA+ R  F 
Sbjct: 5   PTFGFTQEQVACVCEVLQQGGNIERLGRFLWSLPACEHLHKNESVLKAKAVVAFHRGNFR 64

Query: 205 ELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDG 264
           ELY ILESH F    HA+LQQLW++ HY E  K+RGR LGAV KYR+R+KFPLP++IWDG
Sbjct: 65  ELYKILESHQFSPHNHAKLQQLWLKAHYIEAEKLRGRPLGAVGKYRVRRKFPLPRSIWDG 124

Query: 265 EETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ 324
           EET YCFKE+SR+ L+E Y  N YP+P EKR+L+E TGLT TQVSNWFKNRRQRDR  + 
Sbjct: 125 EETSYCFKEKSRSVLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEA 184

Query: 325 R 325
           +
Sbjct: 185 K 185

May be involved in limb tendon and ligament development.

Mus musculus (taxid: 10090)

>sp|Q9NPC8|SIX2_HUMAN Homeobox protein SIX2 OS=Homo sapiens GN=SIX2 PE=2 SV=1

 Score =  244 bits (624), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 111/181 (61%), Positives = 137/181 (75%)

Query: 145 PNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFH 204
           P   FT EQ+ C+CE +QQ G+ ++L  FLWSLP  E +   ESVL+A+AVVA+ R  F 
Sbjct: 5   PTFGFTQEQVACVCEVLQQGGNIERLGRFLWSLPACEHLHKNESVLKAKAVVAFHRGNFR 64

Query: 205 ELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDG 264
           ELY ILESH F    HA+LQQLW++ HY E  K+RGR LGAV KYR+R+KFPLP++IWDG
Sbjct: 65  ELYKILESHQFSPHNHAKLQQLWLKAHYIEAEKLRGRPLGAVGKYRVRRKFPLPRSIWDG 124

Query: 265 EETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ 324
           EET YCFKE+SR+ L+E Y  N YP+P EKR+L+E TGLT TQVSNWFKNRRQRDR  + 
Sbjct: 125 EETSYCFKEKSRSVLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEA 184

Query: 325 R 325
           +
Sbjct: 185 K 185

May be involved in limb tendon and ligament development.

Homo sapiens (taxid: 9606)

>sp|Q62231|SIX1_MOUSE Homeobox protein SIX1 OS=Mus musculus GN=Six1 PE=1 SV=2

 Score =  244 bits (623), Expect = 8e-64,   Method: Compositional matrix adjust.
 Identities = 110/181 (60%), Positives = 136/181 (75%)

Query: 145 PNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFH 204
           P+  FT EQ+ C+CE +QQ G+ ++L  FLWSLP  + +   ESVL+A+AVVA+ R  F 
Sbjct: 5   PSFGFTQEQVACVCEVLQQGGNLERLGRFLWSLPACDHLHKNESVLKAKAVVAFHRGNFR 64

Query: 205 ELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDG 264
           ELY ILESH F    H +LQQLW++ HY E  K+RGR LGAV KYR+R+KFPLP+TIWDG
Sbjct: 65  ELYKILESHQFSPHNHPKLQQLWLKAHYVEAEKLRGRPLGAVGKYRVRRKFPLPRTIWDG 124

Query: 265 EETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ 324
           EET YCFKE+SR  L+E Y  N YP+P EKR+L+E TGLT TQVSNWFKNRRQRDR  + 
Sbjct: 125 EETSYCFKEKSRGVLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEA 184

Query: 325 R 325
           +
Sbjct: 185 K 185

Transcription factor that is involved in regulation of organogenesis. Seems to be required for development of kidney, muscle and inner ear. Seems to be involved in later steps of myogenic differentiation. May be involved in limb tendon and ligament development. Binds a 5'-TCA[AG][AG]TTNC-3' motif present in the MEF3 element in the myogenin promoter. Thought to be regulated by association with Dach and Eya proteins. Acts as activator of the IGFBP5 promoter, probably coactivated by EYA2. Repression of precursor cell proliferation in myoblasts is switched to activation through recruitment of EYA3 phosphatase to the SIX1-DACH1 complex. During myogenesis, seems to act together with EYA2 and DACH2.

Mus musculus (taxid: 10090)

>sp|A2D5H2|SIX1_LAGLA Homeobox protein SIX1 OS=Lagothrix lagotricha GN=SIX1 PE=3 SV=1

 Score =  244 bits (623), Expect = 8e-64,   Method: Compositional matrix adjust.
 Identities = 110/181 (60%), Positives = 136/181 (75%)

Query: 145 PNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFH 204
           P+  FT EQ+ C+CE +QQ G+ ++L  FLWSLP  + +   ESVL+A+AVVA+ R  F 
Sbjct: 5   PSFGFTQEQVACVCEVLQQGGNLERLGRFLWSLPACDHLHKNESVLKAKAVVAFHRGNFR 64

Query: 205 ELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDG 264
           ELY ILESH F    H +LQQLW++ HY E  K+RGR LGAV KYR+R+KFPLP+TIWDG
Sbjct: 65  ELYKILESHQFSPHNHPKLQQLWLKAHYVEAEKLRGRPLGAVGKYRVRRKFPLPRTIWDG 124

Query: 265 EETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ 324
           EET YCFKE+SR  L+E Y  N YP+P EKR+L+E TGLT TQVSNWFKNRRQRDR  + 
Sbjct: 125 EETSYCFKEKSRGVLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEA 184

Query: 325 R 325
           +
Sbjct: 185 K 185

May be involved in limb tendon and ligament development.

Lagothrix lagotricha (taxid: 9519)

>sp|Q15475|SIX1_HUMAN Homeobox protein SIX1 OS=Homo sapiens GN=SIX1 PE=1 SV=1

 Score =  244 bits (623), Expect = 8e-64,   Method: Compositional matrix adjust.
 Identities = 110/181 (60%), Positives = 136/181 (75%)

Query: 145 PNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFH 204
           P+  FT EQ+ C+CE +QQ G+ ++L  FLWSLP  + +   ESVL+A+AVVA+ R  F 
Sbjct: 5   PSFGFTQEQVACVCEVLQQGGNLERLGRFLWSLPACDHLHKNESVLKAKAVVAFHRGNFR 64

Query: 205 ELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDG 264
           ELY ILESH F    H +LQQLW++ HY E  K+RGR LGAV KYR+R+KFPLP+TIWDG
Sbjct: 65  ELYKILESHQFSPHNHPKLQQLWLKAHYVEAEKLRGRPLGAVGKYRVRRKFPLPRTIWDG 124

Query: 265 EETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ 324
           EET YCFKE+SR  L+E Y  N YP+P EKR+L+E TGLT TQVSNWFKNRRQRDR  + 
Sbjct: 125 EETSYCFKEKSRGVLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEA 184

Query: 325 R 325
           +
Sbjct: 185 K 185

May be involved in limb tendon and ligament development.

Homo sapiens (taxid: 9606)

>sp|A1YER0|SIX1_GORGO Homeobox protein SIX1 OS=Gorilla gorilla gorilla GN=SIX1 PE=3 SV=1

 Score =  244 bits (623), Expect = 8e-64,   Method: Compositional matrix adjust.
 Identities = 110/181 (60%), Positives = 136/181 (75%)

Query: 145 PNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFH 204
           P+  FT EQ+ C+CE +QQ G+ ++L  FLWSLP  + +   ESVL+A+AVVA+ R  F 
Sbjct: 5   PSFGFTQEQVACVCEVLQQGGNLERLGRFLWSLPACDHLHKNESVLKAKAVVAFHRGNFR 64

Query: 205 ELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDG 264
           ELY ILESH F    H +LQQLW++ HY E  K+RGR LGAV KYR+R+KFPLP+TIWDG
Sbjct: 65  ELYKILESHQFSPHNHPKLQQLWLKAHYVEAEKLRGRPLGAVGKYRVRRKFPLPRTIWDG 124

Query: 265 EETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ 324
           EET YCFKE+SR  L+E Y  N YP+P EKR+L+E TGLT TQVSNWFKNRRQRDR  + 
Sbjct: 125 EETSYCFKEKSRGVLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEA 184

Query: 325 R 325
           +
Sbjct: 185 K 185

May be involved in limb tendon and ligament development.

Gorilla gorilla gorilla (taxid: 9595)

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	390
193580188	359	PREDICTED: homeobox protein SIX5-like [A	0.487	0.529	0.720	7e-81
270004898	363	sine oculis-related homeobox 4 [Triboliu	0.458	0.493	0.726	7e-78
295798062	319	six4 protein [Tribolium castaneum]	0.458	0.561	0.726	2e-77
322789489	270	hypothetical protein SINV_09236 [Solenop	0.474	0.685	0.718	4e-77
307182948	429	Homeobox protein SIX4 [Camponotus florid	0.453	0.412	0.745	4e-77
357622768	381	hypothetical protein KGM_20665 [Danaus p	0.456	0.467	0.724	4e-76
307205328	267	Homeobox protein SIX4 [Harpegnathos salt	0.456	0.666	0.735	5e-76
312381801	433	hypothetical protein AND_05828 [Anophele	0.453	0.408	0.728	5e-76
158287585	224	AGAP011067-PA [Anopheles gambiae str. PE	0.453	0.790	0.734	6e-76
158287589	270	AGAP011065-PA [Anopheles gambiae str. PE	0.453	0.655	0.734	7e-76

>gi|193580188|ref|XP_001942738.1| PREDICTED: homeobox protein SIX5-like [Acyrthosiphon pisum]

 Score =  307 bits (786), Expect = 7e-81,   Method: Compositional matrix adjust.
 Identities = 139/193 (72%), Positives = 165/193 (85%), Gaps = 3/193 (1%)

Query: 134 AQEYLNMKKLNPNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRAR 193
             ++L  K+   ++SF+ EQ+ C+CEA+QQSGD D+LA FLW LPP E +RGQE+VLRAR
Sbjct: 44  VSDFLQTKR---SLSFSSEQVSCMCEALQQSGDVDRLARFLWYLPPSELLRGQETVLRAR 100

Query: 194 AVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRK 253
           A+VA+ R+AFHELYAILES +FDS++H +LQQLW + HY E  KIRGR LGAVDKYR+RK
Sbjct: 101 ALVAFHRNAFHELYAILESQSFDSRHHLQLQQLWFKAHYLEAEKIRGRSLGAVDKYRLRK 160

Query: 254 KFPLPKTIWDGEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFK 313
           K+PLPKTIWDGEETVYCFKE+SRNALK+CY KNRYP PDEKR+L+  TGLTLTQVSNWFK
Sbjct: 161 KYPLPKTIWDGEETVYCFKEKSRNALKDCYLKNRYPTPDEKRELARRTGLTLTQVSNWFK 220

Query: 314 NRRQRDRTPQQRS 326
           NRRQRDRTPQQ S
Sbjct: 221 NRRQRDRTPQQHS 233

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270004898|gb|EFA01346.1| sine oculis-related homeobox 4 [Tribolium castaneum]

 Score =  297 bits (760), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 130/179 (72%), Positives = 153/179 (85%)

Query: 147 MSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHEL 206
           + F+PEQ+ C+CEA+ Q GD ++LA FLWSLPP E +RG ES+LRARA VA+ R ++HEL
Sbjct: 134 IGFSPEQVQCMCEALHQRGDIERLATFLWSLPPSELLRGNESILRARAAVAFYRGSYHEL 193

Query: 207 YAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEE 266
           Y+ILESH F+ ++HAELQ LW + HY E  K+RGR LGAVDKYR+RKK+PLPKTIWDGEE
Sbjct: 194 YSILESHAFNQRWHAELQTLWFKAHYNEAEKVRGRPLGAVDKYRLRKKYPLPKTIWDGEE 253

Query: 267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR 325
           TVYCFKERSRNALKECY +NRYP PDEKR L++ TGLTLTQVSNWFKNRRQRDRTPQ R
Sbjct: 254 TVYCFKERSRNALKECYARNRYPTPDEKRALAKRTGLTLTQVSNWFKNRRQRDRTPQPR 312

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|295798062|emb|CBL87028.1| six4 protein [Tribolium castaneum]

 Score =  296 bits (757), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 130/179 (72%), Positives = 153/179 (85%)

Query: 147 MSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHEL 206
           + F+PEQ+ C+CEA+ Q GD ++LA FLWSLPP E +RG ES+LRARA VA+ R ++HEL
Sbjct: 90  IGFSPEQVQCMCEALHQRGDIERLATFLWSLPPSELLRGNESILRARAAVAFYRGSYHEL 149

Query: 207 YAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEE 266
           Y+ILESH F+ ++HAELQ LW + HY E  K+RGR LGAVDKYR+RKK+PLPKTIWDGEE
Sbjct: 150 YSILESHAFNQRWHAELQTLWFKAHYNEAEKVRGRPLGAVDKYRLRKKYPLPKTIWDGEE 209

Query: 267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR 325
           TVYCFKERSRNALKECY +NRYP PDEKR L++ TGLTLTQVSNWFKNRRQRDRTPQ R
Sbjct: 210 TVYCFKERSRNALKECYARNRYPTPDEKRALAKRTGLTLTQVSNWFKNRRQRDRTPQPR 268

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322789489|gb|EFZ14769.1| hypothetical protein SINV_09236 [Solenopsis invicta]

 Score =  294 bits (753), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 133/185 (71%), Positives = 154/185 (83%)

Query: 144 NPNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAF 203
           N   +FTPEQI C+CEA+ QS D ++LA FLWSLPP E +RG ESVL ARA VA+ R A+
Sbjct: 66  NATNNFTPEQISCMCEALSQSQDIERLARFLWSLPPGELLRGNESVLMARAAVAFHRGAY 125

Query: 204 HELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWD 263
           HELY+ILESH F  + H ELQQ+W + HY+E  KIRGR LGAVDKYR+RKK+PLPKTIWD
Sbjct: 126 HELYSILESHPFSPRRHPELQQMWFKSHYREAEKIRGRPLGAVDKYRLRKKYPLPKTIWD 185

Query: 264 GEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ 323
           GEETVYCFKERSRNALKECY +NRYP PDEK+ L++ TGLTLTQVSNWFKNRRQRDRTPQ
Sbjct: 186 GEETVYCFKERSRNALKECYMRNRYPTPDEKKNLAKKTGLTLTQVSNWFKNRRQRDRTPQ 245

Query: 324 QRSIQ 328
            R+ +
Sbjct: 246 ARTAE 250

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307182948|gb|EFN69948.1| Homeobox protein SIX4 [Camponotus floridanus]

 Score =  294 bits (753), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 132/177 (74%), Positives = 150/177 (84%)

Query: 149 FTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYA 208
           FTPEQI C+CEA+ QS D +KL+ FLWSLPP E +RG ESVL ARA VA+ R A+HELY+
Sbjct: 87  FTPEQISCMCEALSQSQDIEKLSRFLWSLPPGELLRGGESVLMARAAVAFHRGAYHELYS 146

Query: 209 ILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEETV 268
           ILESH F  + H ELQQ+W + HY+E  KIRGR LGAVDKYR+RKK+PLPKTIWDGEETV
Sbjct: 147 ILESHPFSPRRHPELQQMWFKSHYREAEKIRGRPLGAVDKYRLRKKYPLPKTIWDGEETV 206

Query: 269 YCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR 325
           YCFKERSRNALKECY +NRYP PDEK+ L++ TGLTLTQVSNWFKNRRQRDRTPQ R
Sbjct: 207 YCFKERSRNALKECYMRNRYPTPDEKKNLAKKTGLTLTQVSNWFKNRRQRDRTPQTR 263

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357622768|gb|EHJ74165.1| hypothetical protein KGM_20665 [Danaus plexippus]

 Score =  291 bits (745), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 129/178 (72%), Positives = 151/178 (84%)

Query: 147 MSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHEL 206
           ++F  EQ+ C+CEA+QQ GD +KLA FLWSLPP E +RG E+VLRARA+VAY R  F EL
Sbjct: 163 LNFNSEQVQCVCEALQQKGDIEKLAAFLWSLPPSELLRGNETVLRARALVAYHRGVFQEL 222

Query: 207 YAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEE 266
           YAILE+H F  ++H +LQ LW + HYKE  K+RGR LGAVDKYR+RKK+PLPKTIWDGEE
Sbjct: 223 YAILETHTFSPRHHTDLQNLWFKAHYKEAQKVRGRPLGAVDKYRLRKKYPLPKTIWDGEE 282

Query: 267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ 324
           TVYCFKE+SRNALK+CY +NRYP PDEKR L++ TGLTLTQVSNWFKNRRQRDRTPQQ
Sbjct: 283 TVYCFKEKSRNALKDCYYRNRYPTPDEKRALAQKTGLTLTQVSNWFKNRRQRDRTPQQ 340

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307205328|gb|EFN83676.1| Homeobox protein SIX4 [Harpegnathos saltator]

 Score =  291 bits (744), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 131/178 (73%), Positives = 150/178 (84%)

Query: 149 FTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYA 208
           FTPEQI C+CEA+ QS D +KL+ FLWSLPP E + G ESVL ARA VA+ R ++HELY+
Sbjct: 90  FTPEQISCMCEALSQSQDIEKLSRFLWSLPPGELLHGSESVLMARAAVAFHRGSYHELYS 149

Query: 209 ILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEETV 268
           ILESH F  + H ELQQ+W + HY+E  KIRGR LGAVDKYR+RKK+PLPKTIWDGEETV
Sbjct: 150 ILESHPFSPRRHPELQQMWFKSHYREAEKIRGRPLGAVDKYRLRKKYPLPKTIWDGEETV 209

Query: 269 YCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
           YCFKERSRNALKECY KNRYP PDEK+ L++ TGLTLTQVSNWFKNRRQRDRTPQ R+
Sbjct: 210 YCFKERSRNALKECYMKNRYPTPDEKKNLAKKTGLTLTQVSNWFKNRRQRDRTPQTRT 267

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312381801|gb|EFR27458.1| hypothetical protein AND_05828 [Anopheles darlingi]

 Score =  291 bits (744), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 129/177 (72%), Positives = 150/177 (84%)

Query: 147 MSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHEL 206
            SF+PEQI C+CEA+QQ GD +KLA FLWSL P + I G ES+LRARA+VAY R  +HEL
Sbjct: 209 FSFSPEQIQCMCEALQQEGDLEKLATFLWSLSPSDLISGNESLLRARALVAYHRGLYHEL 268

Query: 207 YAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEE 266
           YA+LESH F  KYH +LQ LW + HY+E  K+RGR LGAVDKYR+RKK+PLPKTIWDGEE
Sbjct: 269 YAVLESHFFSPKYHPDLQTLWFKAHYREAEKVRGRPLGAVDKYRLRKKYPLPKTIWDGEE 328

Query: 267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ 323
           TVYCFKE+SRNALK+CY +NRYP PDEK+ L++ TGLTLTQVSNWFKNRRQRDRTPQ
Sbjct: 329 TVYCFKEKSRNALKDCYTRNRYPTPDEKKTLAKKTGLTLTQVSNWFKNRRQRDRTPQ 385

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158287585|ref|XP_001237244.2| AGAP011067-PA [Anopheles gambiae str. PEST] gi|157019722|gb|EAU77547.2| AGAP011067-PA [Anopheles gambiae str. PEST]

 Score =  290 bits (743), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 130/177 (73%), Positives = 151/177 (85%)

Query: 147 MSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHEL 206
            SF+PEQI C+CEA+QQ GD +KLA FLWSL P + I G ES+LRARA+VAY R  +HEL
Sbjct: 44  FSFSPEQIQCMCEALQQEGDLEKLATFLWSLSPSDLISGNESLLRARALVAYHRGLYHEL 103

Query: 207 YAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEE 266
           YA+LESH F  KYHA+LQ LW + HY+E  K+RGR LGAVDKYR+RKK+PLPKTIWDGEE
Sbjct: 104 YAVLESHFFSPKYHADLQALWFKAHYREAEKVRGRPLGAVDKYRLRKKYPLPKTIWDGEE 163

Query: 267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ 323
           TVYCFKE+SRNALK+CY +NRYP PDEK+ L++ TGLTLTQVSNWFKNRRQRDRTPQ
Sbjct: 164 TVYCFKEKSRNALKDCYTRNRYPTPDEKKTLAKKTGLTLTQVSNWFKNRRQRDRTPQ 220

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158287589|ref|XP_309580.4| AGAP011065-PA [Anopheles gambiae str. PEST] gi|157019724|gb|EAA05081.4| AGAP011065-PA [Anopheles gambiae str. PEST]

 Score =  290 bits (743), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 130/177 (73%), Positives = 151/177 (85%)

Query: 147 MSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHEL 206
            SF+PEQI C+CEA+QQ GD +KLA FLWSL P + I G ES+LRARA+VAY R  +HEL
Sbjct: 48  FSFSPEQIQCMCEALQQEGDLEKLATFLWSLSPSDLISGNESLLRARALVAYHRGLYHEL 107

Query: 207 YAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEE 266
           YA+LESH F  KYHA+LQ LW + HY+E  K+RGR LGAVDKYR+RKK+PLPKTIWDGEE
Sbjct: 108 YAVLESHFFSPKYHADLQALWFKAHYREAEKVRGRPLGAVDKYRLRKKYPLPKTIWDGEE 167

Query: 267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ 323
           TVYCFKE+SRNALK+CY +NRYP PDEK+ L++ TGLTLTQVSNWFKNRRQRDRTPQ
Sbjct: 168 TVYCFKEKSRNALKDCYTRNRYPTPDEKKTLAKKTGLTLTQVSNWFKNRRQRDRTPQ 224

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	390
FB|FBgn0027364	392	Six4 "Six4" [Drosophila melano	0.458	0.456	0.703	6.3e-69
ZFIN|ZDB-GENE-010201-2	595	six4a "sine oculis homeobox ho	0.458	0.300	0.648	8.5e-65
MGI|MGI:106034	775	Six4 "sine oculis-related home	0.461	0.232	0.644	1.4e-64
RGD|1306726	775	Six4 "SIX homeobox 4" [Rattus	0.461	0.232	0.644	1.4e-64
UNIPROTKB|G3V2N2	521	SIX4 "Homeobox protein SIX4" [	0.561	0.420	0.552	3.7e-64
UNIPROTKB|Q9UIU6	781	SIX4 "Homeobox protein SIX4" [	0.561	0.280	0.552	3.7e-64
UNIPROTKB|E2QVI7	764	SIX4 "Uncharacterized protein"	0.456	0.232	0.646	4.7e-64
UNIPROTKB|F6XRS2	785	SIX4 "Uncharacterized protein"	0.456	0.226	0.646	4.7e-64
UNIPROTKB|J9NXQ2	775	SIX4 "Uncharacterized protein"	0.456	0.229	0.646	4.7e-64
UNIPROTKB|J9P424	644	SIX4 "Uncharacterized protein"	0.456	0.276	0.646	4.7e-64

FB|FBgn0027364 Six4 "Six4" [Drosophila melanogaster (taxid:7227)]

 Score = 699 (251.1 bits), Expect = 6.3e-69, P = 6.3e-69
 Identities = 126/179 (70%), Positives = 146/179 (81%)

Query:   147 MSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHEL 206
             + F+ +QI C+CEA+QQ GD +KL  FL SLPP E  +  ESVLRARA+VAY    FHEL
Sbjct:   179 LQFSTDQIQCMCEALQQKGDIEKLTTFLCSLPPSEFFKTNESVLRARAMVAYNLGQFHEL 238

Query:   207 YAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEE 266
             Y +LE+H F  KYH +LQ LW + HYKE  K+RGR LGAVDKYR+RKK+PLPKTIWDGEE
Sbjct:   239 YNLLETHCFSIKYHVDLQNLWFKAHYKEAEKVRGRPLGAVDKYRLRKKYPLPKTIWDGEE 298

Query:   267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR 325
             TVYCFKE+SRNALK+CY  NRYP PDEK+ L++ TGLTLTQVSNWFKNRRQRDRTPQQR
Sbjct:   299 TVYCFKEKSRNALKDCYLTNRYPTPDEKKTLAKKTGLTLTQVSNWFKNRRQRDRTPQQR 357

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

GO:0005634 "nucleus" evidence=ISS

GO:0008406 "gonad development" evidence=IMP;NAS

GO:0007520 "myoblast fusion" evidence=IMP

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

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

GO:0007498 "mesoderm development" evidence=IMP

GO:0007503 "fat body development" evidence=IMP

GO:0048812 "neuron projection morphogenesis" evidence=IMP

ZFIN|ZDB-GENE-010201-2 six4a "sine oculis homeobox homolog 4a" [Danio rerio (taxid:7955)]

 Score = 660 (237.4 bits), Expect = 8.5e-65, P = 8.5e-65
 Identities = 116/179 (64%), Positives = 147/179 (82%)

Query:   146 NMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHE 205
             +++F+PEQ+ C+CEA+QQ G+ D+LA FLWSLP  + +RG ES+LRA+A+VA+ +  + E
Sbjct:    79 SLAFSPEQVACVCEALQQGGNVDRLARFLWSLPQSDLLRGNESILRAQALVAFHQARYQE 138

Query:   206 LYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGE 265
             LY+ILESH+F    H+ LQ LW +  Y E  K RGR LGAVDKYR+R+KFPLP+TIWDGE
Sbjct:   139 LYSILESHSFSPSCHSALQDLWYKARYTEAEKARGRPLGAVDKYRLRRKFPLPRTIWDGE 198

Query:   266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ 324
             ETVYCFKERSRNALK+ Y +NRYP+P EKR L++ITGL+LTQVSNWFKNRRQRDR P +
Sbjct:   199 ETVYCFKERSRNALKDLYKQNRYPSPAEKRNLAKITGLSLTQVSNWFKNRRQRDRNPSE 257

GO:0003677 "DNA binding" evidence=IEA

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

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

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

GO:0005634 "nucleus" evidence=IEA

MGI|MGI:106034 Six4 "sine oculis-related homeobox 4" [Mus musculus (taxid:10090)]

 Score = 658 (236.7 bits), Expect = 1.4e-64, P = 1.4e-64
 Identities = 116/180 (64%), Positives = 148/180 (82%)

Query:   145 PNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFH 204
             P ++F+P+ + C+CEA+QQ G+ D+LA FLWSLP  + +RG ES+L+ARA+VA+ +  + 
Sbjct:    97 PPLAFSPDHVACVCEALQQGGNLDRLARFLWSLPQSDLLRGNESLLKARALVAFHQGIYP 156

Query:   205 ELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDG 264
             ELY+ILESH+F+S  H  LQQLW +  Y E  + RGR LGAVDKYR+R+KFPLP+TIWDG
Sbjct:   157 ELYSILESHSFESANHPLLQQLWYKARYTEAERARGRPLGAVDKYRLRRKFPLPRTIWDG 216

Query:   265 EETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ 324
             EETVYCFKE+SRNALKE Y +NRYP+P EKR L++ITGL+LTQVSNWFKNRRQRDR P +
Sbjct:   217 EETVYCFKEKSRNALKELYKQNRYPSPAEKRHLAKITGLSLTQVSNWFKNRRQRDRNPSE 276

GO:0003677 "DNA binding" evidence=IDA

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

GO:0005634 "nucleus" evidence=IC;IDA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0007275 "multicellular organismal development" evidence=IEA

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

GO:0008582 "regulation of synaptic growth at neuromuscular junction" evidence=IGI

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

GO:0032880 "regulation of protein localization" evidence=IGI

GO:0042472 "inner ear morphogenesis" evidence=IGI

GO:0043524 "negative regulation of neuron apoptotic process" evidence=IMP

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

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IMP;IDA

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

GO:0048538 "thymus development" evidence=IGI

GO:0048699 "generation of neurons" evidence=IMP

GO:0048701 "embryonic cranial skeleton morphogenesis" evidence=IGI

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

GO:0048856 "anatomical structure development" evidence=IGI

GO:0051451 "myoblast migration" evidence=IGI

GO:0072075 "metanephric mesenchyme development" evidence=IMP

GO:0072095 "regulation of branch elongation involved in ureteric bud branching" evidence=IMP

GO:0072107 "positive regulation of ureteric bud formation" evidence=IMP

GO:0090190 "positive regulation of branching involved in ureteric bud morphogenesis" evidence=IMP

RGD|1306726 Six4 "SIX homeobox 4" [Rattus norvegicus (taxid:10116)]

 Score = 658 (236.7 bits), Expect = 1.4e-64, P = 1.4e-64
 Identities = 116/180 (64%), Positives = 148/180 (82%)

Query:   145 PNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFH 204
             P ++F+P+ + C+CEA+QQ G+ D+LA FLWSLP  + +RG ES+L+ARA+VA+ +  + 
Sbjct:    97 PPLAFSPDHVACVCEALQQGGNLDRLARFLWSLPQSDLLRGNESLLKARALVAFHQGIYP 156

Query:   205 ELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDG 264
             ELY+ILESH+F+S  H  LQQLW +  Y E  + RGR LGAVDKYR+R+KFPLP+TIWDG
Sbjct:   157 ELYSILESHSFESANHPLLQQLWYKARYTEAERARGRPLGAVDKYRLRRKFPLPRTIWDG 216

Query:   265 EETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ 324
             EETVYCFKE+SRNALKE Y +NRYP+P EKR L++ITGL+LTQVSNWFKNRRQRDR P +
Sbjct:   217 EETVYCFKEKSRNALKELYKQNRYPSPAEKRHLAKITGLSLTQVSNWFKNRRQRDRNPSE 276

GO:0003677 "DNA binding" evidence=ISO

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

GO:0005634 "nucleus" evidence=IEA;ISO

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

GO:0008582 "regulation of synaptic growth at neuromuscular junction" evidence=ISO

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

GO:0032880 "regulation of protein localization" evidence=ISO

GO:0042472 "inner ear morphogenesis" evidence=ISO

GO:0043524 "negative regulation of neuron apoptotic process" evidence=ISO

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

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISO

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

GO:0048538 "thymus development" evidence=ISO

GO:0048699 "generation of neurons" evidence=ISO

GO:0048701 "embryonic cranial skeleton morphogenesis" evidence=ISO

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

GO:0048856 "anatomical structure development" evidence=ISO

GO:0051451 "myoblast migration" evidence=ISO

GO:0072075 "metanephric mesenchyme development" evidence=ISO

GO:0072095 "regulation of branch elongation involved in ureteric bud branching" evidence=ISO

GO:0072107 "positive regulation of ureteric bud formation" evidence=ISO

GO:0090190 "positive regulation of branching involved in ureteric bud morphogenesis" evidence=ISO

UNIPROTKB|G3V2N2 SIX4 "Homeobox protein SIX4" [Homo sapiens (taxid:9606)]

 Score = 654 (235.3 bits), Expect = 3.7e-64, P = 3.7e-64
 Identities = 122/221 (55%), Positives = 163/221 (73%)

Query:   147 MSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHEL 206
             ++F+P+ + C+CEA+QQ G+ D+LA FLWSLP  + +RG ES+L+ARA+VA+ +  + EL
Sbjct:    98 LAFSPDHVACVCEALQQGGNLDRLARFLWSLPQSDLLRGNESLLKARALVAFHQGIYPEL 157

Query:   207 YAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEE 266
             Y+ILESH+F+S  H  LQQLW +  Y E  + RGR LGAVDKYR+R+KFPLP+TIWDGEE
Sbjct:   158 YSILESHSFESANHPLLQQLWYKARYTEAERARGRPLGAVDKYRLRRKFPLPRTIWDGEE 217

Query:   267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
             TVYCFKE+SRNALKE Y +NRYP+P EKR L++ITGL+LTQVSNWFKNRRQRDR P +  
Sbjct:   218 TVYCFKEKSRNALKELYKQNRYPSPAEKRHLAKITGLSLTQVSNWFKNRRQRDRNPSETQ 277

Query:   327 IQRSRNALKECYDKNRYPNPD-EKRQLSEIT-GLTLTQVSN 365
              +   +      D++   + D     LS  + G+T   +S+
Sbjct:   278 SKSESDGNPSTEDESSKGHEDLSPHPLSSSSDGITNLSLSS 318

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

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

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|Q9UIU6 SIX4 "Homeobox protein SIX4" [Homo sapiens (taxid:9606)]

 Score = 654 (235.3 bits), Expect = 3.7e-64, P = 3.7e-64
 Identities = 122/221 (55%), Positives = 163/221 (73%)

Query:   147 MSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHEL 206
             ++F+P+ + C+CEA+QQ G+ D+LA FLWSLP  + +RG ES+L+ARA+VA+ +  + EL
Sbjct:   106 LAFSPDHVACVCEALQQGGNLDRLARFLWSLPQSDLLRGNESLLKARALVAFHQGIYPEL 165

Query:   207 YAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEE 266
             Y+ILESH+F+S  H  LQQLW +  Y E  + RGR LGAVDKYR+R+KFPLP+TIWDGEE
Sbjct:   166 YSILESHSFESANHPLLQQLWYKARYTEAERARGRPLGAVDKYRLRRKFPLPRTIWDGEE 225

Query:   267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
             TVYCFKE+SRNALKE Y +NRYP+P EKR L++ITGL+LTQVSNWFKNRRQRDR P +  
Sbjct:   226 TVYCFKEKSRNALKELYKQNRYPSPAEKRHLAKITGLSLTQVSNWFKNRRQRDRNPSETQ 285

Query:   327 IQRSRNALKECYDKNRYPNPD-EKRQLSEIT-GLTLTQVSN 365
              +   +      D++   + D     LS  + G+T   +S+
Sbjct:   286 SKSESDGNPSTEDESSKGHEDLSPHPLSSSSDGITNLSLSS 326

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

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

GO:0008582 "regulation of synaptic growth at neuromuscular junction" evidence=IEA

GO:0032880 "regulation of protein localization" evidence=IEA

GO:0042472 "inner ear morphogenesis" evidence=IEA

GO:0043524 "negative regulation of neuron apoptotic process" evidence=IEA

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

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

GO:0048538 "thymus development" evidence=IEA

GO:0048699 "generation of neurons" evidence=IEA

GO:0048701 "embryonic cranial skeleton morphogenesis" evidence=IEA

GO:0051451 "myoblast migration" evidence=IEA

GO:0072075 "metanephric mesenchyme development" evidence=IEA

GO:0072095 "regulation of branch elongation involved in ureteric bud branching" evidence=IEA

GO:0072107 "positive regulation of ureteric bud formation" evidence=IEA

GO:0090190 "positive regulation of branching involved in ureteric bud morphogenesis" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0009653 "anatomical structure morphogenesis" evidence=TAS

UNIPROTKB|E2QVI7 SIX4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 653 (234.9 bits), Expect = 4.7e-64, P = 4.7e-64
 Identities = 115/178 (64%), Positives = 147/178 (82%)

Query:   147 MSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHEL 206
             ++F+P+ + C+CEA+QQ G+ D+LA FLWSLP  + +RG ES+L+ARA+VA+ +  + EL
Sbjct:    89 LAFSPDHVACVCEALQQGGNLDRLARFLWSLPQSDLLRGNESLLKARALVAFHQGIYPEL 148

Query:   207 YAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEE 266
             Y+ILESH+F+S  H  LQQLW +  Y E  + RGR LGAVDKYR+R+KFPLP+TIWDGEE
Sbjct:   149 YSILESHSFESANHPLLQQLWYKARYTEAERARGRPLGAVDKYRLRRKFPLPRTIWDGEE 208

Query:   267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ 324
             TVYCFKE+SRNALKE Y +NRYP+P EKR L++ITGL+LTQVSNWFKNRRQRDR P +
Sbjct:   209 TVYCFKEKSRNALKELYKQNRYPSPAEKRHLAKITGLSLTQVSNWFKNRRQRDRNPSE 266

GO:0090190 "positive regulation of branching involved in ureteric bud morphogenesis" evidence=IEA

GO:0072107 "positive regulation of ureteric bud formation" evidence=IEA

GO:0072095 "regulation of branch elongation involved in ureteric bud branching" evidence=IEA

GO:0072075 "metanephric mesenchyme development" evidence=IEA

GO:0051451 "myoblast migration" evidence=IEA

GO:0048701 "embryonic cranial skeleton morphogenesis" evidence=IEA

GO:0048699 "generation of neurons" evidence=IEA

GO:0048538 "thymus development" evidence=IEA

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

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

GO:0043524 "negative regulation of neuron apoptotic process" evidence=IEA

GO:0042472 "inner ear morphogenesis" evidence=IEA

GO:0032880 "regulation of protein localization" evidence=IEA

GO:0008582 "regulation of synaptic growth at neuromuscular junction" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|F6XRS2 SIX4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 653 (234.9 bits), Expect = 4.7e-64, P = 4.7e-64
 Identities = 115/178 (64%), Positives = 147/178 (82%)

Query:   147 MSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHEL 206
             ++F+P+ + C+CEA+QQ G+ D+LA FLWSLP  + +RG ES+L+ARA+VA+ +  + EL
Sbjct:   110 LAFSPDHVACVCEALQQGGNLDRLARFLWSLPQSDLLRGNESLLKARALVAFHQGIYPEL 169

Query:   207 YAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEE 266
             Y+ILESH+F+S  H  LQQLW +  Y E  + RGR LGAVDKYR+R+KFPLP+TIWDGEE
Sbjct:   170 YSILESHSFESANHPLLQQLWYKARYTEAERARGRPLGAVDKYRLRRKFPLPRTIWDGEE 229

Query:   267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ 324
             TVYCFKE+SRNALKE Y +NRYP+P EKR L++ITGL+LTQVSNWFKNRRQRDR P +
Sbjct:   230 TVYCFKEKSRNALKELYKQNRYPSPAEKRHLAKITGLSLTQVSNWFKNRRQRDRNPSE 287

GO:0005634 "nucleus" evidence=IEA

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

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

UNIPROTKB|J9NXQ2 SIX4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 653 (234.9 bits), Expect = 4.7e-64, P = 4.7e-64
 Identities = 115/178 (64%), Positives = 147/178 (82%)

Query:   147 MSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHEL 206
             ++F+P+ + C+CEA+QQ G+ D+LA FLWSLP  + +RG ES+L+ARA+VA+ +  + EL
Sbjct:   100 LAFSPDHVACVCEALQQGGNLDRLARFLWSLPQSDLLRGNESLLKARALVAFHQGIYPEL 159

Query:   207 YAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEE 266
             Y+ILESH+F+S  H  LQQLW +  Y E  + RGR LGAVDKYR+R+KFPLP+TIWDGEE
Sbjct:   160 YSILESHSFESANHPLLQQLWYKARYTEAERARGRPLGAVDKYRLRRKFPLPRTIWDGEE 219

Query:   267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ 324
             TVYCFKE+SRNALKE Y +NRYP+P EKR L++ITGL+LTQVSNWFKNRRQRDR P +
Sbjct:   220 TVYCFKEKSRNALKELYKQNRYPSPAEKRHLAKITGLSLTQVSNWFKNRRQRDRNPSE 277

GO:0005634 "nucleus" evidence=IEA

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

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

UNIPROTKB|J9P424 SIX4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 653 (234.9 bits), Expect = 4.7e-64, P = 4.7e-64
 Identities = 115/178 (64%), Positives = 147/178 (82%)

Query:   147 MSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHEL 206
             ++F+P+ + C+CEA+QQ G+ D+LA FLWSLP  + +RG ES+L+ARA+VA+ +  + EL
Sbjct:   102 LAFSPDHVACVCEALQQGGNLDRLARFLWSLPQSDLLRGNESLLKARALVAFHQGIYPEL 161

Query:   207 YAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEE 266
             Y+ILESH+F+S  H  LQQLW +  Y E  + RGR LGAVDKYR+R+KFPLP+TIWDGEE
Sbjct:   162 YSILESHSFESANHPLLQQLWYKARYTEAERARGRPLGAVDKYRLRRKFPLPRTIWDGEE 221

Query:   267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ 324
             TVYCFKE+SRNALKE Y +NRYP+P EKR L++ITGL+LTQVSNWFKNRRQRDR P +
Sbjct:   222 TVYCFKEKSRNALKELYKQNRYPSPAEKRHLAKITGLSLTQVSNWFKNRRQRDRNPSE 279

GO:0005634 "nucleus" 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)
Q61321	SIX4_MOUSE	No assigned EC number	0.6444	0.4615	0.2322	yes	N/A
Q9UIU6	SIX4_HUMAN	No assigned EC number	0.6460	0.4564	0.2279	yes	N/A
Q94166	HM33_CAEEL	No assigned EC number	0.5433	0.4384	0.6551	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	390
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	2e-12
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	6e-12
smart00389	57	smart00389, HOX, Homeodomain	2e-11
smart00389	57	smart00389, HOX, Homeodomain	2e-11
pfam00046	57	pfam00046, Homeobox, Homeobox domain	2e-10
pfam00046	57	pfam00046, Homeobox, Homeobox domain	6e-10
pfam05920	40	pfam05920, Homeobox_KN, Homeobox KN domain	2e-08
pfam05920	40	pfam05920, Homeobox_KN, Homeobox KN domain	2e-08
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	3e-06
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	3e-04

>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 = 61.1 bits (149), Expect = 2e-12
 Identities = 18/55 (32%), Positives = 32/55 (58%)

Query: 269 YCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ 323
             F       L++ ++KN YP+ +E+ +L++  GLT  QV  WF+NRR + +  +
Sbjct: 5   TRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59

Length = 59

>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 = 59.9 bits (146), Expect = 6e-12
 Identities = 21/64 (32%), Positives = 38/64 (59%), Gaps = 6/64 (9%)

Query: 315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRD 374
           R++   TP+Q         L++ ++KN YP+ +E+ +L++  GLT  QV  WF+NRR + 
Sbjct: 2   RKRTRFTPEQLEE------LEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKL 55

Query: 375 RTPQ 378
           +  +
Sbjct: 56  KRSE 59

Length = 59

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 58.4 bits (142), Expect = 2e-11
 Identities = 17/50 (34%), Positives = 30/50 (60%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
           F       L++ + KN YP+ +E+ +L++  GL+  QV  WF+NRR + +
Sbjct: 8   FTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

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

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 58.4 bits (142), Expect = 2e-11
 Identities = 22/63 (34%), Positives = 37/63 (58%), Gaps = 7/63 (11%)

Query: 314 NRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQ 372
            RR+R   TP+Q         L++ + KN YP+ +E+ +L++  GL+  QV  WF+NRR 
Sbjct: 1   KRRKRTSFTPEQLEE------LEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRA 54

Query: 373 RDR 375
           + +
Sbjct: 55  KWK 57

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

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

 Score = 55.6 bits (135), Expect = 2e-10
 Identities = 24/62 (38%), Positives = 39/62 (62%), Gaps = 7/62 (11%)

Query: 315 RRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
           RR+R   TP+Q         L++ ++KNRYP+ +E+ +L++  GLT  QV  WF+NRR +
Sbjct: 1   RRKRTTFTPEQL------EELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAK 54

Query: 374 DR 375
            +
Sbjct: 55  WK 56

Length = 57

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

 Score = 54.4 bits (132), Expect = 6e-10
 Identities = 19/51 (37%), Positives = 32/51 (62%)

Query: 270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
            F       L++ ++KNRYP+ +E+ +L++  GLT  QV  WF+NRR + +
Sbjct: 6   TFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWK 56

Length = 57

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

 Score = 49.8 bits (120), Expect = 2e-08
 Identities = 16/34 (47%), Positives = 23/34 (67%)

Query: 285 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
            N YP+ +EK +L+  TGL+  Q+ NWF N R+R
Sbjct: 7   HNPYPSEEEKSELARQTGLSRKQIDNWFINARRR 40

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

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

 Score = 49.8 bits (120), Expect = 2e-08
 Identities = 16/34 (47%), Positives = 23/34 (67%)

Query: 340 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
            N YP+ +EK +L+  TGL+  Q+ NWF N R+R
Sbjct: 7   HNPYPSEEEKSELARQTGLSRKQIDNWFINARRR 40

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

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

 Score = 46.3 bits (110), Expect = 3e-06
 Identities = 18/95 (18%), Positives = 41/95 (43%), Gaps = 14/95 (14%)

Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNALKECY 338
           L+  ++ N YP+   + +LS +  +    V  WF+N+R +++  +   +++         
Sbjct: 66  LEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQR-------- 117

Query: 339 DKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
                   +E+  L++I  L+  Q+S        R
Sbjct: 118 ------PGEEEADLAKIGSLSTGQISIIETLEFSR 146

Length = 156

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

 Score = 40.5 bits (95), Expect = 3e-04
 Identities = 14/71 (19%), Positives = 33/71 (46%), Gaps = 6/71 (8%)

Query: 315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRD 374
            ++R  T +Q  +      L+  ++ N YP+   + +LS +  +    V  WF+N+R ++
Sbjct: 53  SKRRRTTDEQLMV------LEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKE 106

Query: 375 RTPQQRAKNRT 385
           +  +     + 
Sbjct: 107 KKKRSGKVEQR 117

Length = 156

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	390
KOG0775|consensus	304		100.0
KOG0775|consensus	304		100.0
KOG3802|consensus	398		99.32
KOG0488|consensus	309		99.17
KOG0487|consensus	308		99.12
KOG0842|consensus	307		99.11
KOG0843|consensus	197		99.11
KOG0489|consensus	261		99.1
KOG0850|consensus	245		99.08
KOG0490|consensus	235		99.07
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.02
KOG0494|consensus	332		99.0
KOG0484|consensus	125		98.99
KOG0848|consensus	317		98.98
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	98.98
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	98.98
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	98.97
KOG0485|consensus	268		98.96
KOG2251|consensus	228		98.95
KOG0492|consensus	246		98.9
KOG0850|consensus	245		98.88
KOG0491|consensus	194		98.85
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	98.83
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	98.82
KOG2251|consensus	228		98.81
KOG0843|consensus	197		98.79
KOG0488|consensus	309		98.77
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	98.74
KOG0844|consensus	408		98.71
KOG0842|consensus	307		98.71
KOG0492|consensus	246		98.71
KOG0483|consensus	198		98.71
KOG0489|consensus	261		98.7
KOG0487|consensus	308		98.65
KOG0483|consensus	198		98.63
KOG0485|consensus	268		98.62
KOG0493|consensus	342		98.61
KOG0848|consensus	317		98.6
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	98.6
KOG0486|consensus	351		98.59
KOG0493|consensus	342		98.59
KOG0484|consensus	125		98.56
COG5576	156	Homeodomain-containing transcription factor [Trans	98.54
KOG4577|consensus	383		98.53
COG5576	156	Homeodomain-containing transcription factor [Trans	98.53
KOG4577|consensus	383		98.46
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.41
KOG3802|consensus	398		98.41
KOG0491|consensus	194		98.4
KOG0847|consensus	288		98.36
KOG0486|consensus	351		98.34
KOG0494|consensus	332		98.32
KOG0844|consensus	408		98.14
KOG0774|consensus	334		98.1
KOG0490|consensus	235		98.08
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.08
KOG0849|consensus	354		97.92
KOG0847|consensus	288		97.89
KOG1168|consensus	385		97.74
KOG0774|consensus	334		97.74
KOG0849|consensus	354		97.27
KOG2252|consensus	558		96.9
KOG1168|consensus	385		96.84
KOG0773|consensus	342		96.04
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	95.46
KOG2252|consensus	558		95.23
KOG3623|consensus	1007		95.04
KOG0773|consensus	342		94.33
KOG1146|consensus	1406		93.25
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	92.8

>KOG0775|consensus

Probab=100.00  E-value=4.5e-68  Score=499.13  Aligned_cols=181  Identities=62%  Similarity=1.112  Sum_probs=177.4

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCChhHHHHHHHcCCCccccccchhhhhhHHHHHHhhhcHHHHHHHHhcCCCCccchHHH
Q psy8148         144 NPNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAEL  223 (390)
Q Consensus       144 ~~~~~~~~~q~~~~c~~l~~~~~~~~l~~fl~~lp~~~~~~~~e~v~rAra~v~~h~~~f~el~~~L~~~~F~~~~h~~l  223 (390)
                      .+++.||+|||+||||+|+|+||+|||++|||+||+++.+.+||+||||||+|+||.|+|+|||+|||+|.|++++|++|
T Consensus        56 ~pt~~fS~eQvacvCe~L~q~Gd~erL~rFlwsLp~~~~~~~nEsvLkArA~vafH~gnf~eLY~iLE~h~Fs~~~h~~L  135 (304)
T KOG0775|consen   56 LPTFGFSEEQVACVCESLQQGGDIERLGRFLWSLPVCEELLKNESVLKARAVVAFHSGNFRELYHILENHKFSPHNHPKL  135 (304)
T ss_pred             CCCcCCCHHHHHHHHHHHHhccCHHHHHHHHHcCchHHHHhhhHHHHHHHHHHHHhcccHHHHHHHHHhccCChhhhHHH
Confidence            38889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhhhHHHhhhCCCCCcccccccccCCCCCCcccCCCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCC
Q psy8148         224 QQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGL  303 (390)
Q Consensus       224 q~lw~~ahY~e~e~~rgrpL~~v~kyr~Rkk~p~P~ti~dge~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgL  303 (390)
                      |+||++|||.|+|+.||||||||+|||+|||+|+|+||||||+|+|||+++++.+|++||..++||++.+|++||+.|||
T Consensus       136 Q~lWl~AhY~EAek~RGR~LgaV~KYRvRrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgL  215 (304)
T KOG0775|consen  136 QALWLKAHYKEAEKLRGRPLGAVDKYRVRRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGL  215 (304)
T ss_pred             HHHHHHHHHHHHHHhcCCcCCccccceeeccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CchhcccccccccccCCCcch
Q psy8148         304 TLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       304 s~~QV~~WFqNRR~R~R~~~t  324 (390)
                      |.+||+|||||||+|+|....
T Consensus       216 t~tQVsNWFKNRRQRDRa~~a  236 (304)
T KOG0775|consen  216 TITQVSNWFKNRRQRDRAAAA  236 (304)
T ss_pred             chhhhhhhhhhhhhhhhhccc
Confidence            999999999999999996543

>KOG0775|consensus

Probab=100.00  E-value=8.2e-58  Score=429.81  Aligned_cols=154  Identities=39%  Similarity=0.701  Sum_probs=144.2

Q ss_pred             CCCCCCCChhhHHHHHHHHhhcCChhhHHHHHhcCCCcccccCCchHHHHHHHHHhhcCChHHHHHHHhcCCCCCCChHH
Q psy8148           4 LNPNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAE   83 (390)
Q Consensus         4 ~~~~~~~~~~q~~~~c~~l~~~~~~~~l~~f~~slp~~~~~~~~e~~l~a~a~v~~~~~~~~ely~~l~~~~f~~~~h~~   83 (390)
                      ..|++.||+|||+||||+|+|+||||||+|||||||+++.+.+||+||||||+||||.|||+|||+|||+|.|++++|++
T Consensus        55 ~~pt~~fS~eQvacvCe~L~q~Gd~erL~rFlwsLp~~~~~~~nEsvLkArA~vafH~gnf~eLY~iLE~h~Fs~~~h~~  134 (304)
T KOG0775|consen   55 ALPTFGFSEEQVACVCESLQQGGDIERLGRFLWSLPVCEELLKNESVLKARAVVAFHSGNFRELYHILENHKFSPHNHPK  134 (304)
T ss_pred             cCCCcCCCHHHHHHHHHHHHhccCHHHHHHHHHcCchHHHHhhhHHHHHHHHHHHHhcccHHHHHHHHHhccCChhhhHH
Confidence            46889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhhHHHHHhcCCCCCcc----ccCCCCe---ee--ecccccchhhhHHHH---HHHHHHhhh---hcCCCCCC
Q psy8148          84 LQQLWMRGHYKEHAKIRGRDLGYS----SDDSSPV---LY--ETNAHDFNKHYLEIQ---QKAQEYLNM---KKLNPNMS  148 (390)
Q Consensus        84 lq~~w~~ahy~eae~~rgr~lg~~----~~~~~~~---~~--~~~~~~~~~~~~~~~---~~~~~~~~~---~~~~~~~~  148 (390)
                      ||+||++|||.||||+||||||||    +|+|+|+   ||  |+.++|||+..+.++   +..++||++   ++++....
T Consensus       135 LQ~lWl~AhY~EAek~RGR~LgaV~KYRvRrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTg  214 (304)
T KOG0775|consen  135 LQALWLKAHYKEAEKLRGRPLGAVDKYRVRRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATG  214 (304)
T ss_pred             HHHHHHHHHHHHHHHhcCCcCCccccceeeccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhC
Confidence            999999999999999999999999    8999999   99  799999999876665   557999997   46778889


Q ss_pred             CCHHHHHHH
Q psy8148         149 FTPEQIDCL  157 (390)
Q Consensus       149 ~~~~q~~~~  157 (390)
                      +|+.||--.
T Consensus       215 Lt~tQVsNW  223 (304)
T KOG0775|consen  215 LTITQVSNW  223 (304)
T ss_pred             Cchhhhhhh
Confidence            999999433

>KOG3802|consensus

Probab=99.32  E-value=1.2e-12  Score=130.81  Aligned_cols=149  Identities=21%  Similarity=0.356  Sum_probs=119.7

Q ss_pred             hhcCChhHHHHHHHcCCCccccccchhhhhhHHHHHHhhhcHHHHHHHHhcCCCCccchHHHHHHHHhhhhhHHHhhhCC
Q psy8148         162 QQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGR  241 (390)
Q Consensus       162 ~~~~~~~~l~~fl~~lp~~~~~~~~e~v~rAra~v~~h~~~f~el~~~L~~~~F~~~~h~~lq~lw~~ahY~e~e~~rgr  241 (390)
                      .++.|+|.|..|-..+...            |..+.|-+++-..+...|.+..||..                       
T Consensus       200 ed~~~leELEqFAK~FKqR------------RIkLGfTQaDVGlALG~lyGn~FSQT-----------------------  244 (398)
T KOG3802|consen  200 EDTPDLEELEQFAKTFKQR------------RIKLGFTQADVGLALGALYGNVFSQT-----------------------  244 (398)
T ss_pred             ccccCHHHHHHHHHHHHhh------------eeccccchhHHHHHHHhhhCcccchh-----------------------
Confidence            3578899999999999886            88899999999999999999999777                       


Q ss_pred             CCCcccccccccCCCCCCcccCCCccccccCHHH--HHHHHHHHhhCC----CCCHHHHHHHHHHhCCCchhcccccccc
Q psy8148         242 DLGAVDKYRIRKKFPLPKTIWDGEETVYCFKERS--RNALKECYDKNR----YPNPDEKRQLSEITGLTLTQVSNWFKNR  315 (390)
Q Consensus       242 pL~~v~kyr~Rkk~p~P~ti~dge~t~~~Fs~~q--~~~Le~~F~~n~----YPs~~ek~~LA~~tgLs~~QV~~WFqNR  315 (390)
                                        |||+-|.-..+|++..  +-.|++|.+.--    -.+....+.++             =+.|
T Consensus       245 ------------------TIcRFEALqLSFKNMCKLKPLL~KWLeEAes~~~~~~~~~~e~i~-------------a~~R  293 (398)
T KOG3802|consen  245 ------------------TICRFEALQLSFKNMCKLKPLLEKWLEEAESRESTGSPNSIEKIG-------------AQSR  293 (398)
T ss_pred             ------------------hhhHhHhhccCHHHHhhhHHHHHHHHHHHhcccccCCCCCHHHhh-------------cccc
Confidence                              7888887778888866  567788865311    11111111111             1127


Q ss_pred             cccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhh
Q psy8148         316 RQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  379 (390)
Q Consensus       316 R~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~  379 (390)
                      |+|.|+++.....   ..||+.|..|+.|+.+|+..||+.++|..+.|+|||+|||.|+|+...
T Consensus       294 kRKKRTSie~~vr---~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  294 KRKKRTSIEVNVR---GALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             ccccccceeHHHH---HHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            7888888886666   999999999999999999999999999999999999999999999765

>KOG0488|consensus

Probab=99.17  E-value=7.7e-12  Score=123.70  Aligned_cols=66  Identities=26%  Similarity=0.467  Sum_probs=61.1

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhc
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAK  382 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~  382 (390)
                      .+++|.|+.|+..|+   ..||+.|++.+|.+..+|.+||..+||++.||++||||||+|||+......
T Consensus       170 kK~RksRTaFT~~Ql---~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~  235 (309)
T KOG0488|consen  170 KKRRKSRTAFSDHQL---FELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGG  235 (309)
T ss_pred             cccccchhhhhHHHH---HHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhh
Confidence            677888999998888   999999999999999999999999999999999999999999999876543

>KOG0487|consensus

Probab=99.12  E-value=1.5e-11  Score=120.49  Aligned_cols=73  Identities=25%  Similarity=0.413  Sum_probs=63.7

Q ss_pred             hcccccc-cccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhc
Q psy8148         307 QVSNWFK-NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAK  382 (390)
Q Consensus       307 QV~~WFq-NRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~  382 (390)
                      ...+|-. .+-+|.|.+-++.|+   .+||+.|--|.|.+.+.|-+|+..++|+++||+|||||||+|+||...+..
T Consensus       225 ~~~~~~~~~~~RKKRcPYTK~Qt---lELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r  298 (308)
T KOG0487|consen  225 HLPNASSARRGRKKRCPYTKHQT---LELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR  298 (308)
T ss_pred             CCcccccccccccccCCchHHHH---HHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence            4557877 444556778899888   999999999999999999999999999999999999999999999875443

>KOG0842|consensus

Probab=99.11  E-value=2.6e-11  Score=118.78  Aligned_cols=68  Identities=26%  Similarity=0.443  Sum_probs=61.9

Q ss_pred             ccccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhcc
Q psy8148         313 KNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKN  383 (390)
Q Consensus       313 qNRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~~  383 (390)
                      +.+|+|.|..|+..|.   .+||..|..++|.+..||+.||..++|+.+||||||||||.|.||..+....
T Consensus       150 ~~~kRKrRVLFSqAQV---~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~  217 (307)
T KOG0842|consen  150 KRKKRKRRVLFSQAQV---YELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKAL  217 (307)
T ss_pred             cccccccccccchhHH---HHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhh
Confidence            4678888999998887   9999999999999999999999999999999999999999999997755443

>KOG0843|consensus

Probab=99.11  E-value=2.8e-11  Score=109.27  Aligned_cols=65  Identities=34%  Similarity=0.495  Sum_probs=59.2

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhc
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAK  382 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~  382 (390)
                      |-+|.|+.|+..|+   ..||.+|+.++|....||+.||..++|++.||++||||||.|.|+.+.+.+
T Consensus       101 ~~kr~RT~ft~~Ql---~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~k  165 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQL---LKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQEDK  165 (197)
T ss_pred             CCCccccccCHHHH---HHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHhh
Confidence            56677888888777   999999999999999999999999999999999999999999999877643

>KOG0489|consensus

Probab=99.10  E-value=1.3e-11  Score=119.61  Aligned_cols=64  Identities=23%  Similarity=0.377  Sum_probs=58.6

Q ss_pred             cccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhc
Q psy8148         316 RQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAK  382 (390)
Q Consensus       316 R~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~  382 (390)
                      ++|.|+.+++.|+   .+||+.|.-|+|.+...|.+||..+.|+++||||||||||+|+||..+...
T Consensus       159 ~kR~RtayT~~Ql---lELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~  222 (261)
T KOG0489|consen  159 SKRRRTAFTRYQL---LELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS  222 (261)
T ss_pred             CCCCCcccchhhh---hhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence            5778888998887   999999999999999999999999999999999999999999998665544

>KOG0850|consensus

Probab=99.08  E-value=3.3e-11  Score=112.54  Aligned_cols=63  Identities=29%  Similarity=0.453  Sum_probs=55.2

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhh
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR  380 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r  380 (390)
                      +.+|-||..+..|+   ..|.+.|++.+|.-..||.+||..+||+..||++||||||.|.||..+.
T Consensus       121 K~RKPRTIYSS~QL---qaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~  183 (245)
T KOG0850|consen  121 KVRKPRTIYSSLQL---QALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQ  183 (245)
T ss_pred             cccCCcccccHHHH---HHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhc
Confidence            44455666665555   9999999999999999999999999999999999999999999998773

>KOG0490|consensus

Probab=99.07  E-value=7.2e-11  Score=110.74  Aligned_cols=112  Identities=25%  Similarity=0.422  Sum_probs=97.9

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch---------------------
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ---------------------  324 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t---------------------  324 (390)
                      +....|+..++..|+..|..++||+...++.||..+++++..|.+||+|+|++++....                     
T Consensus        62 r~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~~~~~~~~~~~~~~~~~~~~~~  141 (235)
T KOG0490|consen   62 CARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEERPLPEGENLPDLSGTAPPSASR  141 (235)
T ss_pred             ccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhccccccccCCCCCCCCCccccc
Confidence            34456888999999999999999999999999999999999999999999999875431                     


Q ss_pred             -----------------hhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccch
Q psy8148         325 -----------------RSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  377 (390)
Q Consensus       325 -----------------~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~  377 (390)
                                       .....+...+...|..+++|+...+..|+..+|++...|++||+|+|.+.++.
T Consensus       142 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~  211 (235)
T KOG0490|consen  142 DKLDKGPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKH  211 (235)
T ss_pred             cccccCCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhh
Confidence                             11123567888899999999999999999999999999999999999998864

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.02  E-value=9.8e-11  Score=87.08  Aligned_cols=54  Identities=35%  Similarity=0.708  Sum_probs=50.4

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCC
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR  320 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R  320 (390)
                      +...|+..++.+|+..|..++||+..++..||..+||+..+|.+||+|+|.+.|
T Consensus         3 ~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k   56 (57)
T PF00046_consen    3 KRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEK   56 (57)
T ss_dssp             SSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhC
Confidence            345789999999999999999999999999999999999999999999998865

; 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 ....

>KOG0494|consensus

Probab=99.00  E-value=1.2e-10  Score=110.22  Aligned_cols=67  Identities=25%  Similarity=0.439  Sum_probs=61.2

Q ss_pred             ccccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhc
Q psy8148         313 KNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAK  382 (390)
Q Consensus       313 qNRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~  382 (390)
                      +++|++.|+.|+..|+   ..||++|....||+...++-||.+++|.+..|+|||||||+||||..++..
T Consensus       138 k~kRRh~RTiFT~~Ql---e~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg  204 (332)
T KOG0494|consen  138 KKKRRHFRTIFTSYQL---EELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWG  204 (332)
T ss_pred             ccccccccchhhHHHH---HHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcC
Confidence            4567778999998888   999999999999999999999999999999999999999999999776653

>KOG0484|consensus

Probab=98.99  E-value=5.1e-11  Score=98.63  Aligned_cols=60  Identities=25%  Similarity=0.458  Sum_probs=54.0

Q ss_pred             cccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         316 RQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       316 R~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      .+|-|+.|+..|+   .+|+..|....||+...+++||.++.|++..|++||||||+|++|+.
T Consensus        17 QRRIRTTFTS~QL---kELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE   76 (125)
T KOG0484|consen   17 QRRIRTTFTSAQL---KELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE   76 (125)
T ss_pred             hhhhhhhhhHHHH---HHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence            4455677777666   99999999999999999999999999999999999999999999854

>KOG0848|consensus

Probab=98.98  E-value=8.5e-11  Score=111.81  Aligned_cols=53  Identities=30%  Similarity=0.569  Sum_probs=49.5

Q ss_pred             hhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhh
Q psy8148         329 RSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRA  381 (390)
Q Consensus       329 ~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~  381 (390)
                      .|+-+||+.|..++|+++..+.+||.-+||+++||++||||||+|+||..++.
T Consensus       209 hQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk  261 (317)
T KOG0848|consen  209 HQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK  261 (317)
T ss_pred             hhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence            35599999999999999999999999999999999999999999999987765

>smart00389 HOX Homeodomain

Probab=98.98  E-value=4.8e-10  Score=82.65  Aligned_cols=51  Identities=33%  Similarity=0.645  Sum_probs=48.6

Q ss_pred             ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCC
Q psy8148         270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR  320 (390)
Q Consensus       270 ~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R  320 (390)
                      .|+..++.+|+.+|..++||+..++..||..+||+..||.+||+|+|.+.+
T Consensus         6 ~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~   56 (56)
T smart00389        6 SFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK   56 (56)
T ss_pred             cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence            488999999999999999999999999999999999999999999998764

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

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

Probab=98.98  E-value=3.6e-10  Score=83.93  Aligned_cols=54  Identities=33%  Similarity=0.610  Sum_probs=50.5

Q ss_pred             cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         269 YCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       269 ~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      ..|+..++.+|+.+|..++||+..++..||..+||+..+|.+||+|+|.+.+..
T Consensus         5 ~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~   58 (59)
T cd00086           5 TRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS   58 (59)
T ss_pred             CcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence            468899999999999999999999999999999999999999999999987653

>PF00046 Homeobox: Homeobox domain not present here

Probab=98.97  E-value=8.1e-11  Score=87.53  Aligned_cols=56  Identities=38%  Similarity=0.729  Sum_probs=50.4

Q ss_pred             cCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccc
Q psy8148         318 RDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  376 (390)
Q Consensus       318 R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk  376 (390)
                      |.|+.++..+.   ..|+..|..++||+.++++.||..+||+..+|.+||+|+|.++|+
T Consensus         2 r~r~~~t~~q~---~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen    2 RKRTRFTKEQL---KVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             SSSSSSSHHHH---HHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCHHHH---HHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence            45666676666   999999999999999999999999999999999999999998874

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

>KOG0485|consensus

Probab=98.96  E-value=1.2e-10  Score=107.95  Aligned_cols=64  Identities=30%  Similarity=0.438  Sum_probs=60.1

Q ss_pred             cccccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         312 FKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       312 FqNRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      =.+|++|-|+.|++.|.   ..||..|+...|.+..++..||..+.|++.||++||||||.|||++-
T Consensus       100 g~~RKKktRTvFSraQV---~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~  163 (268)
T KOG0485|consen  100 GDDRKKKTRTVFSRAQV---FQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY  163 (268)
T ss_pred             cccccccchhhhhHHHH---HHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence            35889999999999988   88999999999999999999999999999999999999999999965

>KOG2251|consensus

Probab=98.95  E-value=3.5e-10  Score=105.27  Aligned_cols=65  Identities=31%  Similarity=0.519  Sum_probs=59.8

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhh
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRA  381 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~  381 (390)
                      .|.+|+|+.|+..|+   .+|+..|.+.+||+...+++||.+++|.+.+|+|||+|||+|+|+++..+
T Consensus        35 RkqRRERTtFtr~Ql---evLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   35 RKQRRERTTFTRKQL---EVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             hhcccccceecHHHH---HHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            467788999998888   99999999999999999999999999999999999999999999977653

>KOG0492|consensus

Probab=98.90  E-value=4.6e-10  Score=103.43  Aligned_cols=61  Identities=31%  Similarity=0.470  Sum_probs=55.6

Q ss_pred             ccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhh
Q psy8148         317 QRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR  380 (390)
Q Consensus       317 ~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r  380 (390)
                      ++-|++|+..|+   ..||+.|...+|.+..++.+++..+.|++.||++||||||+|.|+.++-
T Consensus       145 RkPRtPFTtqQL---laLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQea  205 (246)
T KOG0492|consen  145 RKPRTPFTTQQL---LALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEA  205 (246)
T ss_pred             CCCCCCCCHHHH---HHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHH
Confidence            346788888777   9999999999999999999999999999999999999999999997643

>KOG0850|consensus

Probab=98.88  E-value=7.8e-10  Score=103.47  Aligned_cols=54  Identities=30%  Similarity=0.517  Sum_probs=50.7

Q ss_pred             cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       271 Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      |+.-|+..|...|++++|....||.+||..+|||.+||++||||||.|.|+...
T Consensus       129 YSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k  182 (245)
T KOG0850|consen  129 YSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK  182 (245)
T ss_pred             ccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence            679999999999999999999999999999999999999999999999876544

>KOG0491|consensus

Probab=98.85  E-value=3.5e-10  Score=100.84  Aligned_cols=67  Identities=28%  Similarity=0.553  Sum_probs=62.0

Q ss_pred             ccccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhc
Q psy8148         313 KNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAK  382 (390)
Q Consensus       313 qNRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~  382 (390)
                      ..+|+|.|+.++..|+   ..|++.|+...|.+..++.+||..++|++.||+.||||||+|.||...+..
T Consensus        97 ~~~r~K~Rtvfs~~ql---~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~  163 (194)
T KOG0491|consen   97 HCRRRKARTVFSDPQL---SGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ  163 (194)
T ss_pred             HHHhhhhcccccCccc---cccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence            5688899999998887   999999999999999999999999999999999999999999999776654

>smart00389 HOX Homeodomain

Probab=98.83  E-value=1.5e-09  Score=79.98  Aligned_cols=53  Identities=34%  Similarity=0.594  Sum_probs=46.9

Q ss_pred             CCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCcccccccccccccccc
Q psy8148         320 RTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR  375 (390)
Q Consensus       320 R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~k  375 (390)
                      ++.++..+.   ..|+..|..++||+.+++..||..+|++..+|++||+|+|.+.+
T Consensus         4 r~~~~~~~~---~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~   56 (56)
T smart00389        4 RTSFTPEQL---EELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK   56 (56)
T ss_pred             CCcCCHHHH---HHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence            344555555   89999999999999999999999999999999999999998764

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

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

Probab=98.82  E-value=1.3e-09  Score=80.96  Aligned_cols=55  Identities=35%  Similarity=0.590  Sum_probs=48.4

Q ss_pred             CCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccch
Q psy8148         320 RTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  377 (390)
Q Consensus       320 R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~  377 (390)
                      +..++..+.   ..|+..|..++||+..++..||..+||+..+|++||+|+|.+.++.
T Consensus         4 r~~~~~~~~---~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~   58 (59)
T cd00086           4 RTRFTPEQL---EELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS   58 (59)
T ss_pred             CCcCCHHHH---HHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence            344554455   8999999999999999999999999999999999999999998763

>KOG2251|consensus

Probab=98.81  E-value=4e-09  Score=98.26  Aligned_cols=67  Identities=25%  Similarity=0.397  Sum_probs=58.7

Q ss_pred             CCcccCCCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         258 PKTIWDGEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       258 P~ti~dge~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      +.+.+...+-++.|+.+|+.+|+..|.++.||+...+++||.+++|.+.+|++||+|||.|+|....
T Consensus        31 ~~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~   97 (228)
T KOG2251|consen   31 SSGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQ   97 (228)
T ss_pred             CccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhh
Confidence            3445555555667999999999999999999999999999999999999999999999999987544

>KOG0843|consensus

Probab=98.79  E-value=2.7e-09  Score=96.57  Aligned_cols=61  Identities=30%  Similarity=0.488  Sum_probs=55.5

Q ss_pred             CccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcchh
Q psy8148         265 EETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR  325 (390)
Q Consensus       265 e~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t~  325 (390)
                      .++++.|+.+|+..|+..|..+.|-...+|+.||..++|+++||++||||||.|.|+....
T Consensus       103 kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e  163 (197)
T KOG0843|consen  103 KRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE  163 (197)
T ss_pred             CccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence            3456689999999999999999999999999999999999999999999999998876543

>KOG0488|consensus

Probab=98.77  E-value=2.9e-09  Score=105.43  Aligned_cols=58  Identities=26%  Similarity=0.489  Sum_probs=54.0

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      .+..|++.|+..||..|++.+|.+..+|.+||..+|||..||+.||||||+|+|+...
T Consensus       175 sRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a  232 (309)
T KOG0488|consen  175 SRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTA  232 (309)
T ss_pred             chhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHH
Confidence            3447999999999999999999999999999999999999999999999999998644

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=98.74  E-value=8.6e-09  Score=77.72  Aligned_cols=53  Identities=21%  Similarity=0.405  Sum_probs=49.1

Q ss_pred             cccCCCcchhhhhhhhhhhhhhhcCCCC----CCHHHHHHHHHhhCCCcccccccccccc
Q psy8148         316 RQRDRTPQQRSIQRSRNALKECYDKNRY----PNPDEKRQLSEITGLTLTQVSNWFKNRR  371 (390)
Q Consensus       316 R~R~R~~~t~~q~~q~~~Le~~F~~n~y----Ps~~er~eLA~~lgLs~~qVk~WFqNRR  371 (390)
                      ++|.|+.++..|.   ..|+..|+.++|    |+..++.+||..+||++.+|++||+|.+
T Consensus         1 ~kR~RT~Ft~~Q~---~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         1 KKRRRTKFTAEQK---EKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCCHHHH---HHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            3677888998777   999999999999    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.

>KOG0844|consensus

Probab=98.71  E-value=2.8e-09  Score=103.14  Aligned_cols=63  Identities=24%  Similarity=0.413  Sum_probs=57.6

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhh
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR  380 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r  380 (390)
                      .-+|.|+.|++.|+   ..||+.|-+-.|-+...|.+||..++|++..|++||||||+|+|++..-
T Consensus       180 qmRRYRTAFTReQI---aRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla  242 (408)
T KOG0844|consen  180 QMRRYRTAFTREQI---ARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA  242 (408)
T ss_pred             HHHHHHhhhhHHHH---HHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence            34567899999998   9999999999999999999999999999999999999999999996543

>KOG0842|consensus

Probab=98.71  E-value=8.6e-09  Score=101.26  Aligned_cols=61  Identities=28%  Similarity=0.454  Sum_probs=55.5

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcchhhh
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSI  327 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t~~q  327 (390)
                      .+--|+..|..+||..|...+|.+..||+.||..+.||++||++||||||-|.|+......
T Consensus       156 rRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~  216 (307)
T KOG0842|consen  156 RRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKA  216 (307)
T ss_pred             cccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhh
Confidence            3457999999999999999999999999999999999999999999999999988765443

>KOG0492|consensus

Probab=98.71  E-value=8.1e-09  Score=95.32  Aligned_cols=55  Identities=31%  Similarity=0.471  Sum_probs=52.1

Q ss_pred             ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       270 ~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      -|+..|+-.|+..|...+|.++.++.+++..+.||.+||++||||||.|.|+...
T Consensus       150 PFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe  204 (246)
T KOG0492|consen  150 PFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE  204 (246)
T ss_pred             CCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence            6999999999999999999999999999999999999999999999999887543

>KOG0483|consensus

Probab=98.71  E-value=6.5e-09  Score=96.64  Aligned_cols=65  Identities=25%  Similarity=0.450  Sum_probs=55.3

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhh
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRA  381 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~  381 (390)
                      +.....+..++..|.   ..|+..|+...+..+..+..||..+||+++||.+||||||+|||.++.-.
T Consensus        48 ~~~~~kk~Rlt~eQ~---~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~  112 (198)
T KOG0483|consen   48 SKGKGKKRRLTSEQV---KFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEK  112 (198)
T ss_pred             cccccccccccHHHH---HHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhh
Confidence            334455555666666   99999999999999999999999999999999999999999999966443

>KOG0489|consensus

Probab=98.70  E-value=3.8e-09  Score=102.47  Aligned_cols=63  Identities=19%  Similarity=0.344  Sum_probs=57.5

Q ss_pred             CCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcchhh
Q psy8148         264 GEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS  326 (390)
Q Consensus       264 ge~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t~~  326 (390)
                      ..+++..|+..|+..|+..|..|.|.+...|.++|..+.||++||+|||||||+|+|+.....
T Consensus       159 ~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~  221 (261)
T KOG0489|consen  159 SKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAK  221 (261)
T ss_pred             CCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccc
Confidence            446777899999999999999999999999999999999999999999999999999765543

>KOG0487|consensus

Probab=98.65  E-value=1.1e-08  Score=100.58  Aligned_cols=58  Identities=24%  Similarity=0.395  Sum_probs=53.0

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      ++--++.-|+..||..|.-|.|.+.+.|.+|+..++||.+||++||||||+|.|+...
T Consensus       238 KRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r  295 (308)
T KOG0487|consen  238 KRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR  295 (308)
T ss_pred             ccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence            3445678899999999999999999999999999999999999999999999998763

>KOG0483|consensus

Probab=98.63  E-value=2.5e-08  Score=92.79  Aligned_cols=70  Identities=26%  Similarity=0.402  Sum_probs=61.1

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcchhhhhhhhhhhhhhh
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNALKECY  338 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t~~q~~q~~~Le~~F  338 (390)
                      .....|+.+|...|+..|..+.+..+..|..||..+||.+.||.+||||||+|+|+.....+.   ..|+..|
T Consensus        52 ~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~---~~Lk~~~  121 (198)
T KOG0483|consen   52 GKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDY---ESLKRQL  121 (198)
T ss_pred             cccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhH---HHHHHHH
Confidence            344578999999999999999999999999999999999999999999999999998776655   4455544

>KOG0485|consensus

Probab=98.62  E-value=1.1e-08  Score=94.98  Aligned_cols=60  Identities=28%  Similarity=0.419  Sum_probs=56.4

Q ss_pred             CccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         265 EETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       265 e~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      ++|+++|+..|...|+..|+...|.+..+|..||..+.||++||++||||||.|+|+...
T Consensus       105 KktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a  164 (268)
T KOG0485|consen  105 KKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA  164 (268)
T ss_pred             ccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence            357889999999999999999999999999999999999999999999999999987655

>KOG0493|consensus

Probab=98.61  E-value=1.2e-08  Score=97.06  Aligned_cols=58  Identities=28%  Similarity=0.514  Sum_probs=51.1

Q ss_pred             cCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         318 RDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       318 R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      |.|+.|+..|+   ..|+..|..|.|.+...+.+||.+++|.+.||++||||+|+|.||..
T Consensus       248 RPRTAFtaeQL---~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT  305 (342)
T KOG0493|consen  248 RPRTAFTAEQL---QRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST  305 (342)
T ss_pred             CccccccHHHH---HHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence            34555665555   99999999999999999999999999999999999999999999843

>KOG0848|consensus

Probab=98.60  E-value=1.1e-08  Score=97.66  Aligned_cols=59  Identities=27%  Similarity=0.541  Sum_probs=54.9

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcchhh
Q psy8148         268 VYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS  326 (390)
Q Consensus       268 ~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t~~  326 (390)
                      +.++++-||-+|++.|..++|.++..|.+||.-+|||++||++||||||.|+|+...+.
T Consensus       203 RvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk  261 (317)
T KOG0848|consen  203 RVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK  261 (317)
T ss_pred             eEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence            34778999999999999999999999999999999999999999999999999876655

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=98.60  E-value=8e-08  Score=72.49  Aligned_cols=50  Identities=18%  Similarity=0.374  Sum_probs=47.1

Q ss_pred             cccccCHHHHHHHHHHHhhCCC----CCHHHHHHHHHHhCCCchhccccccccc
Q psy8148         267 TVYCFKERSRNALKECYDKNRY----PNPDEKRQLSEITGLTLTQVSNWFKNRR  316 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~Y----Ps~~ek~~LA~~tgLs~~QV~~WFqNRR  316 (390)
                      .++.|+.+|+..|+..|..++|    |+..++.+||..+||+..+|++||+|.+
T Consensus         4 ~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         4 RRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            3457999999999999999999    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.

>KOG0486|consensus

Probab=98.59  E-value=1.8e-08  Score=98.11  Aligned_cols=63  Identities=30%  Similarity=0.564  Sum_probs=54.8

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhh
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR  380 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r  380 (390)
                      |.+|.|+-|+..|+   ++||..|.++.||+...+++||.-+++++..|+|||+|||+||+|....
T Consensus       111 KqrrQrthFtSqql---qele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN  173 (351)
T KOG0486|consen  111 KQRRQRTHFTSQQL---QELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERN  173 (351)
T ss_pred             hhhhhhhhhHHHHH---HHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhh
Confidence            34455666776666   9999999999999999999999999999999999999999999985443

>KOG0493|consensus

Probab=98.59  E-value=3.3e-08  Score=94.01  Aligned_cols=63  Identities=22%  Similarity=0.470  Sum_probs=57.6

Q ss_pred             CCCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcchh
Q psy8148         263 DGEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR  325 (390)
Q Consensus       263 dge~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t~  325 (390)
                      +.++.++.|+.+|+..|+..|+.|.|.+...|.+||.++||.+.||++||||+|.|.|++-..
T Consensus       245 eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgs  307 (342)
T KOG0493|consen  245 EEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGS  307 (342)
T ss_pred             hhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCC
Confidence            455677899999999999999999999999999999999999999999999999998876443

>KOG0484|consensus

Probab=98.56  E-value=1.8e-08  Score=83.61  Aligned_cols=57  Identities=23%  Similarity=0.445  Sum_probs=52.9

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcc
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  323 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~  323 (390)
                      .+..|+..|+..|+..|..+.||++-.+++||....||+..|++||||||.|.|+..
T Consensus        20 IRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE   76 (125)
T KOG0484|consen   20 IRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE   76 (125)
T ss_pred             hhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence            445799999999999999999999999999999999999999999999999987653

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=98.54  E-value=3.8e-08  Score=88.47  Aligned_cols=53  Identities=21%  Similarity=0.454  Sum_probs=48.6

Q ss_pred             hhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhh
Q psy8148         328 QRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR  380 (390)
Q Consensus       328 ~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r  380 (390)
                      ..|+.+|+..|..+++|+..++..|+..++|+++.|++||||+|++.|+....
T Consensus        60 ~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~  112 (156)
T COG5576          60 DEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG  112 (156)
T ss_pred             HHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence            44559999999999999999999999999999999999999999999886654

>KOG4577|consensus

Probab=98.53  E-value=1.8e-08  Score=96.93  Aligned_cols=67  Identities=30%  Similarity=0.514  Sum_probs=54.6

Q ss_pred             cCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhccCCCC
Q psy8148         318 RDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKNRTFD  387 (390)
Q Consensus       318 R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~~~~~d  387 (390)
                      |.|+..+..|+   ..|+.+|..++.|..-.++.|+..+||..+.|++||||||+|+|+.++..-...|+
T Consensus       169 RPRTTItAKqL---ETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWg  235 (383)
T KOG4577|consen  169 RPRTTITAKQL---ETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWG  235 (383)
T ss_pred             CCcceeeHHHH---HHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHH
Confidence            34555554455   99999999999999999999999999999999999999999999866544332443

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=98.53  E-value=3.9e-08  Score=88.40  Aligned_cols=90  Identities=21%  Similarity=0.342  Sum_probs=73.0

Q ss_pred             cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHH
Q psy8148         271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKR  350 (390)
Q Consensus       271 Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~  350 (390)
                      -+..|+.+|+..|..++||+...+..|+..++|++..|++||||+|++.|....             +....++.. +..
T Consensus        58 ~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~-------------~~~~~~~~~-e~~  123 (156)
T COG5576          58 TTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRS-------------GKVEQRPGE-EEA  123 (156)
T ss_pred             chHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcc-------------cchhccccc-ccc
Confidence            458899999999999999999999999999999999999999999998876533             222333444 555


Q ss_pred             HHHHhhCCCccccccccccccccc
Q psy8148         351 QLSEITGLTLTQVSNWFKNRRQRD  374 (390)
Q Consensus       351 eLA~~lgLs~~qVk~WFqNRR~K~  374 (390)
                      .++....++..++.+|+.+...+.
T Consensus       124 ~~~~~~~~~~~~~~~~~~~~~s~~  147 (156)
T COG5576         124 DLAKIGSLSTGQISIIETLEFSRT  147 (156)
T ss_pred             cccccccccccchhhHHhhhcccc
Confidence            667777788888899988766653

>KOG4577|consensus

Probab=98.46  E-value=8.4e-08  Score=92.41  Aligned_cols=121  Identities=25%  Similarity=0.415  Sum_probs=87.3

Q ss_pred             chhhhhhHHHHHHhhhcHHHHH--HHHh-cCCCCccchHHHHHHHHhhhhhHHHhhhCCCCCcccccccccCCCCCCccc
Q psy8148         186 QESVLRARAVVAYKRHAFHELY--AILE-SHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIW  262 (390)
Q Consensus       186 ~e~v~rAra~v~~h~~~f~el~--~~L~-~~~F~~~~h~~lq~lw~~ahY~e~e~~rgrpL~~v~kyr~Rkk~p~P~ti~  262 (390)
                      ...|-||...| ||-+||..+.  +-|. +..|---   +-..|-.+..|..|...-.-.|..      -..+..|+|  
T Consensus       105 tqVVRkAqd~V-YHl~CF~C~iC~R~L~TGdEFYLm---eD~rLvCK~DYE~Ak~k~~~~l~g------d~~nKRPRT--  172 (383)
T KOG4577|consen  105 TQVVRKAQDFV-YHLHCFACFICKRQLATGDEFYLM---EDARLVCKDDYETAKQKHCNELEG------DASNKRPRT--  172 (383)
T ss_pred             HHHHHHhhcce-eehhhhhhHhhhcccccCCeeEEe---ccceeehhhhHHHHHhcccccccc------ccccCCCcc--
Confidence            45667799999 9999999763  2222 3344222   235677788888775533222222      111222333  


Q ss_pred             CCCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcchh
Q psy8148         263 DGEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR  325 (390)
Q Consensus       263 dge~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t~  325 (390)
                             ..+.+|++.|+..|+..+-|....|++|+..|||..+.|++||||||+|.|+....
T Consensus       173 -------TItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD  228 (383)
T KOG4577|consen  173 -------TITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD  228 (383)
T ss_pred             -------eeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence                   46789999999999999999999999999999999999999999999998876543

>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=98.41  E-value=5e-08  Score=68.22  Aligned_cols=34  Identities=50%  Similarity=0.908  Sum_probs=29.3

Q ss_pred             hCCCCCHHHHHHHHHHhCCCchhccccccccccc
Q psy8148         285 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR  318 (390)
Q Consensus       285 ~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R  318 (390)
                      .+|||+.++|..||..||++..||.+||.|.|+|
T Consensus         7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR   40 (40)
T PF05920_consen    7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR   40 (40)
T ss_dssp             TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence            5899999999999999999999999999998875

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

>KOG3802|consensus

Probab=98.41  E-value=3.1e-07  Score=92.34  Aligned_cols=55  Identities=29%  Similarity=0.445  Sum_probs=51.4

Q ss_pred             ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       270 ~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      ++....+..|+..|.+|+-|+..+...||+.++|..+.|++||+|||+|.|+...
T Consensus       300 Sie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  300 SIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             ceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            5667789999999999999999999999999999999999999999999998755

>KOG0491|consensus

Probab=98.40  E-value=3.3e-08  Score=88.35  Aligned_cols=62  Identities=26%  Similarity=0.549  Sum_probs=55.7

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcchhhh
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSI  327 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t~~q  327 (390)
                      +.+.+|+..|+..|++.|+...|.+..++.+||..++|+++||+.||+|||+|.|+.....+
T Consensus       102 K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~  163 (194)
T KOG0491|consen  102 KARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ  163 (194)
T ss_pred             hhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence            45567999999999999999999999999999999999999999999999999887655443

>KOG0847|consensus

Probab=98.36  E-value=9.8e-08  Score=88.83  Aligned_cols=62  Identities=24%  Similarity=0.441  Sum_probs=54.6

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      .+|...|..++-.++   ..|+..|+..+|+-..++.+||..+|++..+|++||||||.||||+.
T Consensus       165 G~rk~srPTf~g~qi---~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh  226 (288)
T KOG0847|consen  165 GQRKQSRPTFTGHQI---YQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH  226 (288)
T ss_pred             ccccccCCCccchhh---hhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence            345555566777777   99999999999999999999999999999999999999999999864

>KOG0486|consensus

Probab=98.34  E-value=2.3e-07  Score=90.46  Aligned_cols=62  Identities=27%  Similarity=0.514  Sum_probs=56.9

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcchhhh
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSI  327 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t~~q  327 (390)
                      +.+..|+..|+..|+.+|.+|.||+...++++|.-++||+..|++||+|||.|+|+.....+
T Consensus       114 rQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~  175 (351)
T KOG0486|consen  114 RQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ  175 (351)
T ss_pred             hhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence            45568999999999999999999999999999999999999999999999999998765444

>KOG0494|consensus

Probab=98.32  E-value=3.7e-07  Score=86.93  Aligned_cols=59  Identities=24%  Similarity=0.467  Sum_probs=54.9

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcchhh
Q psy8148         268 VYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS  326 (390)
Q Consensus       268 ~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t~~  326 (390)
                      ++.|+.-|+..|++.|+...||+...|+.||..|+|.+..|.+||+|||.|+|+.....
T Consensus       145 RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w  203 (332)
T KOG0494|consen  145 RTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW  203 (332)
T ss_pred             cchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence            45699999999999999999999999999999999999999999999999999876543

>KOG0844|consensus

Probab=98.14  E-value=1.1e-06  Score=85.42  Aligned_cols=56  Identities=21%  Similarity=0.417  Sum_probs=52.7

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      -++.|+.+|+..|++.|-+..|-+...|.+||..++|.++.|++||||||+|+|+.
T Consensus       184 YRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQ  239 (408)
T KOG0844|consen  184 YRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQ  239 (408)
T ss_pred             HHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhh
Confidence            44589999999999999999999999999999999999999999999999999874

>KOG0774|consensus

Probab=98.10  E-value=2.2e-06  Score=81.81  Aligned_cols=66  Identities=29%  Similarity=0.546  Sum_probs=57.4

Q ss_pred             CCCccccccCHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcchhhhh
Q psy8148         263 DGEETVYCFKERSRNALKECYD---KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQ  328 (390)
Q Consensus       263 dge~t~~~Fs~~q~~~Le~~F~---~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t~~q~  328 (390)
                      |..+++..|+.....+|.+||-   .||||+.+.|++||...|++..||++||.|+|-|.++...+.+.
T Consensus       187 darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~~e  255 (334)
T KOG0774|consen  187 DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKNQE  255 (334)
T ss_pred             HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhhhh
Confidence            4555666898989999999995   69999999999999999999999999999999999887665443

>KOG0490|consensus

Probab=98.08  E-value=1.7e-06  Score=81.19  Aligned_cols=62  Identities=23%  Similarity=0.314  Sum_probs=53.9

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      .++++.|+.++..+.   .+|+.+|+..+||+...++.|+..+++++..|++||||+|+++++..
T Consensus        58 ~~~rr~rt~~~~~ql---~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~  119 (235)
T KOG0490|consen   58 FSKRCARCKFTISQL---DELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE  119 (235)
T ss_pred             ccccccCCCCCcCHH---HHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence            344555666665555   99999999999999999999999999999999999999999999865

>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=98.08  E-value=5.7e-07  Score=62.91  Aligned_cols=34  Identities=50%  Similarity=0.908  Sum_probs=28.9

Q ss_pred             CCCCCCHHHHHHHHHhhCCCcccccccccccccc
Q psy8148         340 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR  373 (390)
Q Consensus       340 ~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K  373 (390)
                      .+|||+.+++.+|+..+|++..||.+||.|.|.|
T Consensus         7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR   40 (40)
T PF05920_consen    7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR   40 (40)
T ss_dssp             TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence            5799999999999999999999999999998864

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

>KOG0849|consensus

Probab=97.92  E-value=5.5e-06  Score=83.80  Aligned_cols=71  Identities=30%  Similarity=0.517  Sum_probs=63.5

Q ss_pred             hhcccccccccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhh
Q psy8148         306 TQVSNWFKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  379 (390)
Q Consensus       306 ~QV~~WFqNRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~  379 (390)
                      ..-.+|.+.+++|.|+.++..|.   ..|+++|+.++||+...++.|+..++++...|.+||+|||+++++...
T Consensus       166 ~~p~~~~~~~~rr~rtsft~~Q~---~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~  236 (354)
T KOG0849|consen  166 EPPGYALQRGGRRNRTSFSPSQL---EALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR  236 (354)
T ss_pred             ccccccccccccccccccccchH---HHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence            34457777777778888998888   999999999999999999999999999999999999999999999763

>KOG0847|consensus

Probab=97.89  E-value=3.7e-06  Score=78.48  Aligned_cols=56  Identities=25%  Similarity=0.441  Sum_probs=52.1

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      +.-.|+..|+..|+..|...+|+-..++.++|..+|++..||++||||||.|+|+.
T Consensus       170 srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKk  225 (288)
T KOG0847|consen  170 SRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKK  225 (288)
T ss_pred             cCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhh
Confidence            44568899999999999999999999999999999999999999999999999864

>KOG1168|consensus

Probab=97.74  E-value=2.4e-05  Score=75.85  Aligned_cols=108  Identities=17%  Similarity=0.246  Sum_probs=73.5

Q ss_pred             CCCcccCCCccccccCHH--HHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhccccccc-ccccCCCcchhhhhhhhhh
Q psy8148         257 LPKTIWDGEETVYCFKER--SRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKN-RRQRDRTPQQRSIQRSRNA  333 (390)
Q Consensus       257 ~P~ti~dge~t~~~Fs~~--q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqN-RR~R~R~~~t~~q~~q~~~  333 (390)
                      ...|||+-|--+.+.++.  -..+|..|.++         .+-+.+-..+.-.+..-|-+ -++|.|++......   ..
T Consensus       256 SQSTICRFESLTLSHNNMiALKPILqaWLEe---------AE~a~keK~~~pd~~~l~~~~ekKRKRTSIAAPEK---Rs  323 (385)
T KOG1168|consen  256 SQSTICRFESLTLSHNNMIALKPILQAWLEE---------AEAAMKEKDTKPDINELLPGGEKKRKRTSIAAPEK---RS  323 (385)
T ss_pred             cccceeeeeeeccccCcchhhhHHHHHHHHH---------HHHHHHhhccCCchhhccCccccccccccccCccc---cc
Confidence            356777766433333232  24566666432         22233333344434333333 35566666665555   78


Q ss_pred             hhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccc
Q psy8148         334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  376 (390)
Q Consensus       334 Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk  376 (390)
                      ||..|...+.|+.+....+|+++.|....|++||+|+|+|-|+
T Consensus       324 LEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR  366 (385)
T KOG1168|consen  324 LEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR  366 (385)
T ss_pred             HHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence            9999999999999999999999999999999999999999887

>KOG0774|consensus

Probab=97.74  E-value=1.8e-05  Score=75.68  Aligned_cols=58  Identities=31%  Similarity=0.564  Sum_probs=48.6

Q ss_pred             CCcchhhhhhhhhhhhhhh---cCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhh
Q psy8148         320 RTPQQRSIQRSRNALKECY---DKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR  380 (390)
Q Consensus       320 R~~~t~~q~~q~~~Le~~F---~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r  380 (390)
                      |+.|++...   .+|..+|   -.+|||+.+++++||.+.+++.+||.+||.|.|-+.+|...+
T Consensus       192 RRNFsK~aT---eiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k  252 (334)
T KOG0774|consen  192 RRNFSKQAT---EILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGK  252 (334)
T ss_pred             hcccchhHH---HHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhh
Confidence            344555555   7788888   578999999999999999999999999999999999886543

>KOG0849|consensus

Probab=97.27  E-value=0.0002  Score=72.57  Aligned_cols=56  Identities=32%  Similarity=0.611  Sum_probs=52.5

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcc
Q psy8148         268 VYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  323 (390)
Q Consensus       268 ~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~  323 (390)
                      ...|+..|...|+++|..++||+...++.||..+|++...|.+||+|+|.+.++..
T Consensus       180 rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~  235 (354)
T KOG0849|consen  180 RTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH  235 (354)
T ss_pred             ccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence            46799999999999999999999999999999999999999999999999887654

>KOG2252|consensus

Probab=96.90  E-value=0.0011  Score=69.43  Aligned_cols=56  Identities=23%  Similarity=0.459  Sum_probs=52.3

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      +.+.+|++.|+..|...|+.+++|+.+..+.|+..+||..+.|.|||-|-|+|...
T Consensus       422 KPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl~  477 (558)
T KOG2252|consen  422 KPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSLD  477 (558)
T ss_pred             CceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhccc
Confidence            45779999999999999999999999999999999999999999999999998644

>KOG1168|consensus

Probab=96.84  E-value=0.0011  Score=64.60  Aligned_cols=49  Identities=20%  Similarity=0.396  Sum_probs=45.0

Q ss_pred             HHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         274 RSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       274 ~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      .....|+.+|...|-|+.+....+|+++.|....|++||.|.|+|.|+.
T Consensus       319 PEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm  367 (385)
T KOG1168|consen  319 PEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM  367 (385)
T ss_pred             cccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence            3367899999999999999999999999999999999999999998764

>KOG0773|consensus

Probab=96.04  E-value=0.004  Score=62.49  Aligned_cols=54  Identities=37%  Similarity=0.518  Sum_probs=47.0

Q ss_pred             ccCHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcc
Q psy8148         270 CFKERSRNALKECYD---KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  323 (390)
Q Consensus       270 ~Fs~~q~~~Le~~F~---~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~  323 (390)
                      .+......+|+.|..   ..|||+..+|..|+..|||+..||.|||-|.|.|.-.+-
T Consensus       245 ~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~  301 (342)
T KOG0773|consen  245 GLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPM  301 (342)
T ss_pred             CCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCch
Confidence            566778889998854   469999999999999999999999999999998877653

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

Probab=95.46  E-value=0.0086  Score=44.86  Aligned_cols=43  Identities=23%  Similarity=0.491  Sum_probs=31.6

Q ss_pred             HHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhccccccccccc
Q psy8148         276 RNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR  318 (390)
Q Consensus       276 ~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R  318 (390)
                      ...|+++|...++....+-..|..+++|+..||+.||..+...
T Consensus        10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e   52 (56)
T PF11569_consen   10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE   52 (56)
T ss_dssp             -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred             hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence            4569999999999999999999999999999999999876543

>KOG2252|consensus

Probab=95.23  E-value=0.012  Score=61.97  Aligned_cols=54  Identities=24%  Similarity=0.421  Sum_probs=46.4

Q ss_pred             cCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccc
Q psy8148         318 RDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRD  374 (390)
Q Consensus       318 R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~  374 (390)
                      |-|..++..|.   ..|...|..+++|+.+..+.|+..++|....|.|||-|-|.|.
T Consensus       422 KPRlVfTd~Qk---rTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  422 KPRLVFTDIQK---RTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             CceeeecHHHH---HHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            33555665554   8999999999999999999999999999999999999977774

>KOG3623|consensus

Probab=95.04  E-value=0.03  Score=60.73  Aligned_cols=109  Identities=18%  Similarity=0.326  Sum_probs=78.2

Q ss_pred             HHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcchhhh---------------hhhhhhhhhhhcC
Q psy8148         276 RNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSI---------------QRSRNALKECYDK  340 (390)
Q Consensus       276 ~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t~~q---------------~~q~~~Le~~F~~  340 (390)
                      ..+|+.+|..|..|+..+-..+|...|++..-|+.||.+.+...+.......               ..+-..|..+++.
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps~psg~~p~kv~sp~k~~dq~ql~~a~el  647 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPSQPSGERPVKVRSPIKEEDQQQLKQAYEL  647 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCccCCCCCCCccccCCCCccchhhhHhhhhc
Confidence            6789999999999999999999999999999999999998876543221000               0111344555554


Q ss_pred             CCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhccC
Q psy8148         341 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKNR  384 (390)
Q Consensus       341 n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~~~  384 (390)
                      +-.++-.+-...+..+......|.+||.+|+...+...-...+.
T Consensus       648 q~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~pl~ltss  691 (1007)
T KOG3623|consen  648 QASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMPLFLTSS  691 (1007)
T ss_pred             ccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCccccccc
Confidence            44455555555556677778888999999999888765444433

>KOG0773|consensus

Probab=94.33  E-value=0.029  Score=56.28  Aligned_cols=41  Identities=46%  Similarity=0.658  Sum_probs=36.9

Q ss_pred             CCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhh
Q psy8148         340 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR  380 (390)
Q Consensus       340 ~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r  380 (390)
                      ..+||+..++..|+..+|++..||.+||.|.|.|..+....
T Consensus       263 ~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~  303 (342)
T KOG0773|consen  263 LHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIE  303 (342)
T ss_pred             cCCCCcchhccccchhcCCCcccCCchhhhcccccCCchHH
Confidence            36899999999999999999999999999999998776553

>KOG1146|consensus

Probab=93.25  E-value=0.048  Score=62.67  Aligned_cols=63  Identities=27%  Similarity=0.494  Sum_probs=54.8

Q ss_pred             cccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhh
Q psy8148         316 RQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRA  381 (390)
Q Consensus       316 R~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~  381 (390)
                      |+..|+.++..++   ..+...|....+|..++.+.|....+++.+.|.+||+|-|.|.++.....
T Consensus       903 r~a~~~~~~d~ql---k~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~  965 (1406)
T KOG1146|consen  903 RRAYRTQESDLQL---KIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG  965 (1406)
T ss_pred             hhhhccchhHHHH---HHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence            5556666666665   88899999999999999999999999999999999999999999977655

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

Probab=92.80  E-value=0.022  Score=42.69  Aligned_cols=42  Identities=24%  Similarity=0.521  Sum_probs=30.7

Q ss_pred             hhhhhhhcCCCCCCHHHHHHHHHhhCCCcccccccccccccc
Q psy8148         332 NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR  373 (390)
Q Consensus       332 ~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K  373 (390)
                      ..|++.|.....+...+...|..+++|+..||+.||-.++..
T Consensus        11 ~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e   52 (56)
T PF11569_consen   11 QPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE   52 (56)
T ss_dssp             HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred             HHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence            458999999999999999999999999999999999766543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	390
4egc_A	559	Crystal Structure Of Mbp-fused Human Six1 Bound To		9e-65
3k2a_A	67	Crystal Structure Of The Homeobox Domain Of Human H		2e-04
1x2n_A	73	Solution Structure Of The Homeobox Domain Of Human		6e-04
1x2n_A	73	Solution Structure Of The Homeobox Domain Of Human		6e-04

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

Iteration: 1
 Score =  243 bits (621), Expect = 9e-65,   Method: Compositional matrix adjust.
 Identities = 110/181 (60%), Positives = 136/181 (75%)
Query: 145 PNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFH 204
           P+  FT EQ+ C+CE +QQ G+ ++L  FLWSLP  + +   ESVL+A+AVVA+ R  F 
Sbjct: 375 PSFGFTQEQVACVCEVLQQGGNLERLGRFLWSLPACDHLHKNESVLKAKAVVAFHRGNFR 434
Query: 205 ELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDG 264
           ELY ILESH F    H +LQQLW++ HY E  K+RGR LGAV KYR+R+KFPLP+TIWDG
Sbjct: 435 ELYKILESHQFSPHNHPKLQQLWLKAHYVEAEKLRGRPLGAVGKYRVRRKFPLPRTIWDG 494
Query: 265 EETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ 324
           EET YCFKE+SR  L+E Y  N YP+P EKR+L+E TGLT TQVSNWFKNRRQRDR  + 
Sbjct: 495 EETSYCFKEKSRGVLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEA 554
Query: 325 R 325
           +
Sbjct: 555 K 555

>pdb|3K2A|A Chain A, Crystal Structure Of The Homeobox Domain Of Human Homeobox Protein Meis2 Length = 67

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/42 (47%), Positives = 29/42 (69%)
Query: 343 YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKNR 384
           YP+ ++K+QL++ TGLT+ QV+NWF N R+R   P     NR
Sbjct: 25  YPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPXIDQSNR 66

>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeobox Protein Pknox1 Length = 73

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 18/31 (58%), Positives = 23/31 (74%)
Query: 288 YPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
           YP  DEK+Q++  T LTL QV+NWF N R+R
Sbjct: 34  YPTEDEKKQIAAQTNLTLLQVNNWFINARRR 64

>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeobox Protein Pknox1 Length = 73

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 18/31 (58%), Positives = 23/31 (74%)
Query: 343 YPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
           YP  DEK+Q++  T LTL QV+NWF N R+R
Sbjct: 34  YPTEDEKKQIAAQTNLTLLQVNNWFINARRR 64

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	390
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	3e-13
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	2e-12
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	3e-13
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	2e-12
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	1e-12
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	4e-12
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	2e-12
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	3e-11
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	2e-12
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	6e-11
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	2e-12
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	6e-12
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	7e-12
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	7e-12
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	9e-12
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	3e-11
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	3e-11
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	1e-09
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	4e-11
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	5e-11
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	4e-11
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	4e-10
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	6e-11
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	2e-10
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	9e-11
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	2e-10
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	3e-10
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	3e-09
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	3e-10
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	2e-09
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	4e-10
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	5e-10
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	1e-08
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	9e-08
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	1e-08
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	3e-08
1e3o_C	160	Octamer-binding transcription factor 1; transcript	2e-08
1e3o_C	160	Octamer-binding transcription factor 1; transcript	2e-07
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	3e-08
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	4e-07
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	3e-08
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	5e-08
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	6e-08
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	9e-07
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	6e-08
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	2e-07
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	1e-07
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	3e-06
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	2e-07
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	2e-06
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	2e-07
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	5e-07
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	2e-07
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	7e-06
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	8e-07
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	9e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-05
2e19_A	64	Transcription factor 8; homeobox domain, structura	1e-06
2e19_A	64	Transcription factor 8; homeobox domain, structura	4e-05
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	2e-06
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	5e-06
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	2e-06
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	3e-05
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	4e-06
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	4e-06
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	4e-05
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	1e-04
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	4e-05
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	3e-04
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	3e-04
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	3e-04
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	7e-04
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	7e-04
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	8e-04
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	8e-04

>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 = 63.1 bits (154), Expect = 3e-13
 Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 271 FKERSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP 322
           F + +   L+  + KN    Y +      L + T L+  Q+ NW  NRR++++T 
Sbjct: 5   FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI 59

>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 = 61.2 bits (149), Expect = 2e-12
 Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 3/52 (5%)

Query: 329 RSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP 377
            +   L+  + KN    Y +      L + T L+  Q+ NW  NRR++++T 
Sbjct: 8   ENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI 59

>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 = 64.1 bits (156), Expect = 3e-13
 Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 3/54 (5%)

Query: 271 FKERSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT 321
           F + +   L+  + KN    Y +      L + T L+  Q+ NW  NRR++++T
Sbjct: 34  FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 87

>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 = 61.8 bits (150), Expect = 2e-12
 Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 3/51 (5%)

Query: 329 RSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT 376
            +   L+  + KN    Y +      L + T L+  Q+ NW  NRR++++T
Sbjct: 37  ENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 87

>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 = 62.1 bits (151), Expect = 1e-12
 Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 3/59 (5%)

Query: 271 FKERSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
           F + +   L+  + KN    Y +      L + T L+  Q+ NW   RR +++T     
Sbjct: 9   FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITIAP 67

>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 = 60.6 bits (147), Expect = 4e-12
 Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 6/66 (9%)

Query: 321 TPQQRSIQRSRNA---LKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRD 374
           T   R  + ++     L+  + KN    Y +      L + T L+  Q+ NW   RR ++
Sbjct: 1   TKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKE 60

Query: 375 RTPQQR 380
           +T    
Sbjct: 61  KTITIA 66

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

 Score = 60.9 bits (148), Expect = 2e-12
 Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 7/70 (10%)

Query: 313 KNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQ 372
              + + ++ +Q S       LK  + +N++P   E   L+++TGL+  +V  WF +RR 
Sbjct: 9   SIYKNK-KSHEQLSA------LKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRY 61

Query: 373 RDRTPQQRAK 382
             R  +    
Sbjct: 62  HCRNLKGSRS 71

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

 Score = 57.8 bits (140), Expect = 3e-11
 Identities = 16/48 (33%), Positives = 27/48 (56%)

Query: 278 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR 325
           ALK  + +N++P   E   L+++TGL+  +V  WF +RR   R  +  
Sbjct: 22  ALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGS 69

>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 = 61.1 bits (148), Expect = 2e-12
 Identities = 14/72 (19%), Positives = 31/72 (43%), Gaps = 6/72 (8%)

Query: 312 FKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
               + ++R P+Q         L+  + +N  P  +E  +L   T +T  ++ +WF  RR
Sbjct: 6   SGPTKYKERAPEQLRA------LESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERR 59

Query: 372 QRDRTPQQRAKN 383
           ++    + +   
Sbjct: 60  KKVNAEETKKSG 71

>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 = 57.2 bits (138), Expect = 6e-11
 Identities = 15/59 (25%), Positives = 30/59 (50%), Gaps = 3/59 (5%)

Query: 271 FKERSRN---ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
           +KER+     AL+  + +N  P  +E  +L   T +T  ++ +WF  RR++    + + 
Sbjct: 11  YKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETKK 69

>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 = 60.8 bits (148), Expect = 2e-12
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 8/74 (10%)

Query: 315 RRQRDRTPQQRSIQRSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
           RR+R    +Q     +   L E +  +    YP+ + K +L++  G+T++QVSNWF N+R
Sbjct: 2   RRKRRNFNKQ-----ATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKR 56

Query: 372 QRDRTPQQRAKNRT 385
            R +    + +   
Sbjct: 57  IRYKKNIGKFQEEA 70

>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 = 59.7 bits (145), Expect = 6e-12
 Identities = 18/63 (28%), Positives = 36/63 (57%), Gaps = 3/63 (4%)

Query: 271 FKERSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSI 327
           F +++   L E +  +    YP+ + K +L++  G+T++QVSNWF N+R R +    +  
Sbjct: 8   FNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQ 67

Query: 328 QRS 330
           + +
Sbjct: 68  EEA 70

>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 Length = 87

 Score = 60.2 bits (146), Expect = 7e-12
 Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 3/65 (4%)

Query: 271 FKERSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSI 327
           F +++   L E +  +    YP+ + K +L++  G+T++QVSNWF N+R R +    +  
Sbjct: 8   FNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQ 67

Query: 328 QRSRN 332
           + +  
Sbjct: 68  EEANI 72

>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 Length = 87

 Score = 60.2 bits (146), Expect = 7e-12
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 8/73 (10%)

Query: 315 RRQRDRTPQQRSIQRSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
           RR+R    +Q     +   L E +  +    YP+ + K +L++  G+T++QVSNWF N+R
Sbjct: 2   RRKRRNFNKQ-----ATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKR 56

Query: 372 QRDRTPQQRAKNR 384
            R +    + +  
Sbjct: 57  IRYKKNIGKFQEE 69

>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 Length = 73

 Score = 59.3 bits (144), Expect = 9e-12
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 8/72 (11%)

Query: 313 KNRRQRDRTPQQRSIQRSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKN 369
             + +R   P+      + N ++    ++    YP  DEK+Q++  T LTL QV+NWF N
Sbjct: 6   SGKNKRGVLPKH-----ATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFIN 60

Query: 370 RRQRDRTPQQRA 381
            R+R       +
Sbjct: 61  ARRRILQSGPSS 72

>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 Length = 73

 Score = 58.2 bits (141), Expect = 3e-11
 Identities = 19/42 (45%), Positives = 25/42 (59%)

Query: 285 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
            + YP  DEK+Q++  T LTL QV+NWF N R+R       S
Sbjct: 31  GHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSGPSS 72

>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 = 58.5 bits (141), Expect = 3e-11
 Identities = 17/79 (21%), Positives = 36/79 (45%), Gaps = 6/79 (7%)

Query: 312 FKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
           F  ++ +++T  Q  I      L++ + K+ +P   E  +L   T L+  ++ +WF  RR
Sbjct: 12  FAPQKFKEKTQGQVKI------LEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERR 65

Query: 372 QRDRTPQQRAKNRTFDPYS 390
           +   + +Q   +      S
Sbjct: 66  KLRDSMEQAVLDSMGSGKS 84

>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 = 53.8 bits (129), Expect = 1e-09
 Identities = 15/63 (23%), Positives = 32/63 (50%), Gaps = 3/63 (4%)

Query: 271 FKERSR---NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSI 327
           FKE+++     L++ + K+ +P   E  +L   T L+  ++ +WF  RR+   + +Q  +
Sbjct: 17  FKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAVL 76

Query: 328 QRS 330
              
Sbjct: 77  DSM 79

>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} Length = 83

 Score = 57.8 bits (140), Expect = 4e-11
 Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 8/75 (10%)

Query: 313 KNRRQRDRTPQQRSIQRSRNALKE---CYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKN 369
             ++++   P +     S   L++    +    YP+ +EK+ LSE T L+L Q+SNWF N
Sbjct: 6   SGKKRKGNLPAE-----SVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFIN 60

Query: 370 RRQRDRTPQQRAKNR 384
            R+R      + +  
Sbjct: 61  ARRRILPDMLQQRRN 75

>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} Length = 83

 Score = 57.5 bits (139), Expect = 5e-11
 Identities = 18/49 (36%), Positives = 27/49 (55%)

Query: 285 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNA 333
              YP+ +EK+ LSE T L+L Q+SNWF N R+R      +  +   + 
Sbjct: 31  FKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQRRNDPSG 79

>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 = 58.1 bits (140), Expect = 4e-11
 Identities = 11/73 (15%), Positives = 32/73 (43%), Gaps = 6/73 (8%)

Query: 312 FKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
           F  ++ +++T +Q  +      L+  +  +     +E  +L   T LT  ++  WF  ++
Sbjct: 10  FTPQKFKEKTAEQLRV------LQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKK 63

Query: 372 QRDRTPQQRAKNR 384
           +     +++ +  
Sbjct: 64  KSKALKEEKMEID 76

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

 Score = 55.0 bits (132), Expect = 4e-10
 Identities = 13/66 (19%), Positives = 28/66 (42%), Gaps = 3/66 (4%)

Query: 271 FKERSRN---ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSI 327
           FKE++      L+  +  +     +E  +L   T LT  ++  WF  +++     +++  
Sbjct: 15  FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKME 74

Query: 328 QRSRNA 333
               NA
Sbjct: 75  IDESNA 80

>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding, transcription, nucleus, phosphoprotein, DNA bindi protein; 1.95A {Homo sapiens} Length = 67

 Score = 57.0 bits (138), Expect = 6e-11
 Identities = 20/45 (44%), Positives = 30/45 (66%)

Query: 340 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKNR 384
            + YP+ ++K+QL++ TGLT+ QV+NWF N R+R   P     NR
Sbjct: 22  THPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQSNR 66

>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding, transcription, nucleus, phosphoprotein, DNA bindi protein; 1.95A {Homo sapiens} Length = 67

 Score = 55.0 bits (133), Expect = 2e-10
 Identities = 19/46 (41%), Positives = 30/46 (65%)

Query: 285 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRS 330
            + YP+ ++K+QL++ TGLT+ QV+NWF N R+R   P      R+
Sbjct: 22  THPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQSNRA 67

>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens} Length = 89

 Score = 57.1 bits (138), Expect = 9e-11
 Identities = 19/49 (38%), Positives = 24/49 (48%)

Query: 285 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNA 333
            N YP+  EK  LS+ T L+  QV NWF N R+R      R   +  N 
Sbjct: 29  YNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRKDGKDPNQ 77

>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens} Length = 89

 Score = 56.3 bits (136), Expect = 2e-10
 Identities = 21/77 (27%), Positives = 32/77 (41%), Gaps = 8/77 (10%)

Query: 312 FKNRRQRDRTPQQRSIQRSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFK 368
             +       P+      S   L++   ++R   YP+  EK  LS+ T L+  QV NWF 
Sbjct: 3   HHHHHHSHMLPK-----ESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFI 57

Query: 369 NRRQRDRTPQQRAKNRT 385
           N R+R      R   + 
Sbjct: 58  NARRRLLPDMLRKDGKD 74

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

 Score = 58.0 bits (139), Expect = 3e-10
 Identities = 19/115 (16%), Positives = 43/115 (37%), Gaps = 6/115 (5%)

Query: 211 ESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEETVYC 270
                  +    + +      ++  + +R       ++   + +   PK      +    
Sbjct: 50  SKLKSGRETFRRMWKWLQEPEFQRMSALRLAACKRKEQEHGKDRGNTPK------KPRLV 103

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR 325
           F +  R  L   + +N+ P+ + +  +S+  GL L+ VSN+F N R+R       
Sbjct: 104 FTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWLE 158

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

 Score = 54.9 bits (131), Expect = 3e-09
 Identities = 20/95 (21%), Positives = 38/95 (40%)

Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPN 345
                P+ +R  +        +     K+R    + P+       R  L   + +N+ P+
Sbjct: 64  KWLQEPEFQRMSALRLAACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPS 123

Query: 346 PDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR 380
            + +  +S+  GL L+ VSN+F N R+R       
Sbjct: 124 KELQITISQQLGLELSTVSNFFMNARRRSLDKWLE 158

>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 = 54.8 bits (132), Expect = 3e-10
 Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 6/61 (9%)

Query: 315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRD 374
              R +T +Q +       LK  + ++++P+  E  +L E+TGL  +++  WF + R R 
Sbjct: 6   HHHRKKTKEQIAH------LKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRC 59

Query: 375 R 375
           +
Sbjct: 60  Q 60

>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 = 52.5 bits (126), Expect = 2e-09
 Identities = 13/44 (29%), Positives = 26/44 (59%)

Query: 277 NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
             LK  + ++++P+  E  +L E+TGL  +++  WF + R R +
Sbjct: 17  AHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQ 60

>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1 Length = 64

 Score = 54.6 bits (132), Expect = 4e-10
 Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 8/64 (12%)

Query: 313 KNRRQRDRTPQQRSIQRSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKN 369
               +     +Q     +   L E +  +    YP+ + K +L++  G+T++QVSNWF N
Sbjct: 2   SGHIEGRHMNKQ-----ATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGN 56

Query: 370 RRQR 373
           +R R
Sbjct: 57  KRIR 60

>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1 Length = 64

 Score = 53.9 bits (130), Expect = 5e-10
 Identities = 17/51 (33%), Positives = 31/51 (60%), Gaps = 3/51 (5%)

Query: 271 FKERSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
             +++   L E +  +    YP+ + K +L++  G+T++QVSNWF N+R R
Sbjct: 10  MNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR 60

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

 Score = 53.1 bits (127), Expect = 1e-08
 Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 7/76 (9%)

Query: 307 QVSNWFKNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSN 365
           +++   + R++R       +       AL+  + K   P+  E   L++   L    V  
Sbjct: 92  KIAAQGRKRKKRTSIEVGVK------GALESHFLKCPKPSAHEITGLADSLQLEKEVVRV 145

Query: 366 WFKNRRQRDRTPQQRA 381
           WF NRRQ+++     A
Sbjct: 146 WFCNRRQKEKRMTPAA 161

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

 Score = 50.4 bits (120), Expect = 9e-08
 Identities = 14/57 (24%), Positives = 25/57 (43%)

Query: 270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
             +   + AL+  + K   P+  E   L++   L    V  WF NRRQ+++     +
Sbjct: 105 SIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTPAA 161

>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 = 50.4 bits (121), Expect = 1e-08
 Identities = 15/64 (23%), Positives = 34/64 (53%), Gaps = 7/64 (10%)

Query: 313 KNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
             +R R R T  Q  +      L++ +D N  P+ ++ +++++ +GL    + +WF+N  
Sbjct: 6   SGKRPRTRITDDQLRV------LRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTL 59

Query: 372 QRDR 375
            ++R
Sbjct: 60  FKER 63

>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 = 49.3 bits (118), Expect = 3e-08
 Identities = 11/56 (19%), Positives = 29/56 (51%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
             +     L++ +D N  P+ ++ +++++ +GL    + +WF+N   ++R     S
Sbjct: 14  ITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGPSS 69

>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 = 52.3 bits (125), Expect = 2e-08
 Identities = 17/64 (26%), Positives = 36/64 (56%), Gaps = 3/64 (4%)

Query: 312 FKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
             +RR++ RT  + +I   R AL++ + +N+ P  ++   ++E   +    +  WF NRR
Sbjct: 97  GLSRRRKKRTSIETNI---RVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRR 153

Query: 372 QRDR 375
           Q+++
Sbjct: 154 QKEK 157

>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 = 49.6 bits (118), Expect = 2e-07
 Identities = 12/51 (23%), Positives = 27/51 (52%)

Query: 270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
             +   R AL++ + +N+ P  ++   ++E   +    +  WF NRRQ+++
Sbjct: 107 SIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEK 157

>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 = 49.6 bits (118), Expect = 3e-08
 Identities = 14/66 (21%), Positives = 32/66 (48%), Gaps = 6/66 (9%)

Query: 315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRD 374
              + +T +Q +I      LK  + + ++   ++ ++L +ITGL   ++  WF + R   
Sbjct: 5   SSGKRKTKEQLAI------LKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYAL 58

Query: 375 RTPQQR 380
           +  Q +
Sbjct: 59  KHGQLK 64

>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 = 46.2 bits (109), Expect = 4e-07
 Identities = 11/55 (20%), Positives = 28/55 (50%)

Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNA 333
           LK  + + ++   ++ ++L +ITGL   ++  WF + R   +  Q +  + + + 
Sbjct: 18  LKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLKWFRDNASG 72

>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 = 51.1 bits (122), Expect = 3e-08
 Identities = 18/78 (23%), Positives = 37/78 (47%), Gaps = 5/78 (6%)

Query: 298 SEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITG 357
            ++  L   +V    + R++R           +++AL+  + ++  P+  E  +++E   
Sbjct: 71  EQVGALYNEKVGANERKRKRRTTISIA-----AKDALERHFGEHSKPSSQEIMRMAEELN 125

Query: 358 LTLTQVSNWFKNRRQRDR 375
           L    V  WF NRRQR++
Sbjct: 126 LEKEVVRVWFCNRRQREK 143

>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 = 50.8 bits (121), Expect = 5e-08
 Identities = 14/51 (27%), Positives = 27/51 (52%)

Query: 270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
                +++AL+  + ++  P+  E  +++E   L    V  WF NRRQR++
Sbjct: 93  TISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREK 143

>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 = 49.4 bits (117), Expect = 6e-08
 Identities = 15/70 (21%), Positives = 34/70 (48%), Gaps = 6/70 (8%)

Query: 311 WFKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNR 370
                +   +TP+Q  +      LK  + + ++P+P+E  +L++ +GL  T + +WF + 
Sbjct: 23  SGSTGKICKKTPEQLHM------LKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDT 76

Query: 371 RQRDRTPQQR 380
           R   +    +
Sbjct: 77  RYAWKNGNLK 86

>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 = 45.9 bits (108), Expect = 9e-07
 Identities = 14/78 (17%), Positives = 33/78 (42%)

Query: 256 PLPKTIWDGEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNR 315
             P         +        + LK  + + ++P+P+E  +L++ +GL  T + +WF + 
Sbjct: 17  QGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDT 76

Query: 316 RQRDRTPQQRSIQRSRNA 333
           R   +    +     ++A
Sbjct: 77  RYAWKNGNLKWYYYYQSA 94

>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 = 48.6 bits (116), Expect = 6e-08
 Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 7/64 (10%)

Query: 313 KNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
           +++R R   TP+Q         L + Y  +  P       ++   GL    V  WF+N R
Sbjct: 16  RDKRLRTTITPEQL------EILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTR 69

Query: 372 QRDR 375
            R+R
Sbjct: 70  ARER 73

>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 = 47.1 bits (112), Expect = 2e-07
 Identities = 13/56 (23%), Positives = 19/56 (33%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
                   L + Y  +  P       ++   GL    V  WF+N R R+R     S
Sbjct: 24  ITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSGPSS 79

>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 = 47.4 bits (113), Expect = 1e-07
 Identities = 23/68 (33%), Positives = 31/68 (45%), Gaps = 7/68 (10%)

Query: 309 SNWFKNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWF 367
           S+    R  R R T  Q         L++ +D N YP  DE  QLS +  L    +  WF
Sbjct: 2   SSGSSGRSSRTRFTDYQL------RVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWF 55

Query: 368 KNRRQRDR 375
           +N RQ+ R
Sbjct: 56  QNARQKAR 63

>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 = 43.9 bits (104), Expect = 3e-06
 Identities = 19/56 (33%), Positives = 27/56 (48%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
           F +     L++ +D N YP  DE  QLS +  L    +  WF+N RQ+ R     S
Sbjct: 14  FTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGPSS 69

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

 Score = 46.8 bits (112), Expect = 2e-07
 Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 7/62 (11%)

Query: 313 KNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
           K+ + +   +PQ R+       L+E + + +  N  EK ++++  G+T  QV  WF N+R
Sbjct: 4   KSPKGKSSISPQARAF------LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKR 57

Query: 372 QR 373
            R
Sbjct: 58  MR 59

>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 = 43.7 bits (104), Expect = 2e-06
 Identities = 14/42 (33%), Positives = 24/42 (57%)

Query: 277 NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
             L+E + + +  N  EK ++++  G+T  QV  WF N+R R
Sbjct: 18  AFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 59

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

 Score = 49.3 bits (117), Expect = 2e-07
 Identities = 17/85 (20%), Positives = 35/85 (41%), Gaps = 3/85 (3%)

Query: 292 DEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQ 351
           +E    ++     L +      +++++ RT       ++  AL   ++KN  P   E  +
Sbjct: 69  NEAELRNQEGQQNLMEFVGGEPSKKRKRRTSFT---PQAIEALNAYFEKNPLPTGQEITE 125

Query: 352 LSEITGLTLTQVSNWFKNRRQRDRT 376
           +++        V  WF NRRQ  + 
Sbjct: 126 MAKELNYDREVVRVWFSNRRQTLKN 150

>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 = 48.1 bits (114), Expect = 5e-07
 Identities = 14/52 (26%), Positives = 23/52 (44%)

Query: 270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT 321
            F  ++  AL   ++KN  P   E  ++++        V  WF NRRQ  + 
Sbjct: 99  SFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN 150

>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 = 47.1 bits (112), Expect = 2e-07
 Identities = 14/68 (20%), Positives = 26/68 (38%), Gaps = 6/68 (8%)

Query: 309 SNWFKNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWF 367
           S+     R R + + +   I +S        D   YP+ +    LS    L    +  +F
Sbjct: 2   SSGSSGPRSRTKISLEALGILQSFIH-----DVGLYPDQEAIHTLSAQLDLPKHTIIKFF 56

Query: 368 KNRRQRDR 375
           +N+R   +
Sbjct: 57  QNQRYHVK 64

>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 = 42.5 bits (100), Expect = 7e-06
 Identities = 9/37 (24%), Positives = 16/37 (43%)

Query: 284 DKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
           D   YP+ +    LS    L    +  +F+N+R   +
Sbjct: 28  DVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVK 64

>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 = 45.0 bits (107), Expect = 8e-07
 Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 7/71 (9%)

Query: 313 KNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
           K  R R     +Q       + L+ CY  N  P+   K QL E+TGL+   +  WF+N+R
Sbjct: 2   KTTRVRTVLNEKQL------HTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKR 55

Query: 372 QRDRTPQQRAK 382
            +D+      K
Sbjct: 56  CKDKKRSIMMK 66

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

 Score = 45.0 bits (107), Expect = 9e-07
 Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQ 328
             E+  + L+ CY  N  P+   K QL E+TGL+   +  WF+N+R +D+  +   ++
Sbjct: 10  LNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKK-RSIMMK 66

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 49.5 bits (117), Expect = 1e-06
 Identities = 42/241 (17%), Positives = 78/241 (32%), Gaps = 61/241 (25%)

Query: 136 EYLNMKKLNPNMSFTPEQIDCLCEA-MQQSGDFDKLAMF-------------LWSLPPQE 181
           +++N  KL   +  +   ++ L  A  ++   FD+L++F             +W    + 
Sbjct: 348 KHVNCDKLTTIIESS---LNVLEPAEYRKM--FDRLSVFPPSAHIPTILLSLIWFDVIKS 402

Query: 182 AIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAE-LQQLWMRGHYKEHAKIRG 240
            +    + L   ++V  ++       +I   +  + K   E    L        H  I  
Sbjct: 403 DVMVVVNKLHKYSLV--EKQPKESTISIPSIY-LELKVKLENEYAL--------HRSI-- 449

Query: 241 RDLGAVDKYRIRKKFP---LPKTIWDGEETVYCFKERSRNALKECYDKNRYPNPDEKRQL 297
                VD Y I K F    L     D     Y +     + LK            E+  L
Sbjct: 450 -----VDHYNIPKTFDSDDLIPPYLDQ----YFYSHIGHH-LKNI-------EHPERMTL 492

Query: 298 SEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNALK--ECYDKNRYPN-PDEKRQLSE 354
             +  L       + + + + D T    S     N L+  + Y      N P  +R ++ 
Sbjct: 493 FRMVFLDF----RFLEQKIRHDSTAWNAS-GSILNTLQQLKFYKPYICDNDPKYERLVNA 547

Query: 355 I 355
           I
Sbjct: 548 I 548

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 43.7 bits (102), Expect = 9e-05
 Identities = 42/270 (15%), Positives = 83/270 (30%), Gaps = 86/270 (31%)

Query: 15  IDCLCEA-MQQSGDFDKLAMF-------------LWSLPPQEAIRGQESVLRARAVVAYK 60
           ++ L  A  ++   FD+L++F             +W    +  +    + L   ++V  +
Sbjct: 363 LNVLEPAEYRKM--FDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLV--E 418

Query: 61  RHAFHELYAILESHNFDSKYHAE-LQQLWMRGHYKEHAKIRGRD---LGYSSDDSSPVLY 116
           +       +I   +  + K   E    L        H  I         + SDD  P   
Sbjct: 419 KQPKESTISIPSIY-LELKVKLENEYAL--------HRSIVDHYNIPKTFDSDDLIPPYL 469

Query: 117 ETNAHDFNKHYLEIQQKAQEYLNMKKLNPNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWS 176
           +   +    H+L+  +  +     + +     F                DF     FL  
Sbjct: 470 DQYFYSHIGHHLKNIEHPERMTLFRMV-----FL---------------DFR----FL-- 503

Query: 177 LPPQEAIRGQESVLRARAVVA--------YKRH------AFHEL-YAIL------ESHNF 215
              ++ IR   +   A   +         YK +       +  L  AIL      E +  
Sbjct: 504 ---EQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLI 560

Query: 216 DSKYHAELQQLWM----RGHYKEHAKIRGR 241
            SK + +L ++ +       ++E  K   R
Sbjct: 561 CSK-YTDLLRIALMAEDEAIFEEAHKQVQR 589

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

 Score = 44.3 bits (104), Expect = 1e-06
 Identities = 13/58 (22%), Positives = 26/58 (44%)

Query: 321 TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ 378
           +  Q  ++   + LK  Y  N  P+ +E  ++++   L L  V  WF+  +    + Q
Sbjct: 5   SSGQPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISVQ 62

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

 Score = 40.4 bits (94), Expect = 4e-05
 Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 5/58 (8%)

Query: 273 ERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRS 330
           +   + LK  Y  N  P+ +E  ++++   L L  V  WF+  +       Q S+Q S
Sbjct: 12  KNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAG-----QISVQSS 64

>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 = 46.6 bits (110), Expect = 2e-06
 Identities = 14/51 (27%), Positives = 25/51 (49%)

Query: 270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
             + R R +L+  + K+  P+  +   ++   GL    V  WF NRRQ+ +
Sbjct: 102 SIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGK 152

>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 = 45.1 bits (106), Expect = 5e-06
 Identities = 15/80 (18%), Positives = 31/80 (38%), Gaps = 8/80 (10%)

Query: 304 TLTQVSNWFKNRRQRDRTPQQRSIQRSR--------NALKECYDKNRYPNPDEKRQLSEI 355
            + +  N    +         ++ +R R         +L+  + K+  P+  +   ++  
Sbjct: 73  WVEEADNNENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQ 132

Query: 356 TGLTLTQVSNWFKNRRQRDR 375
            GL    V  WF NRRQ+ +
Sbjct: 133 LGLEKDVVRVWFSNRRQKGK 152

>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 = 45.0 bits (106), Expect = 2e-06
 Identities = 15/87 (17%), Positives = 35/87 (40%), Gaps = 22/87 (25%)

Query: 313 KNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQL---------------SEIT 356
             R  R     +  ++      ++  +++N+YP+  ++ ++               S++ 
Sbjct: 6   SGRGSRFTWRKECLAV------MESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLE 59

Query: 357 GLTLTQVSNWFKNRRQRDRTPQQRAKN 383
            +T  +V NWF NRR+  +     A  
Sbjct: 60  RVTSLKVYNWFANRRKEIKRRANIAAI 86

>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 = 41.5 bits (97), Expect = 3e-05
 Identities = 12/65 (18%), Positives = 32/65 (49%), Gaps = 15/65 (23%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQL---------------SEITGLTLTQVSNWFKNR 315
           +++     ++  +++N+YP+  ++ ++               S++  +T  +V NWF NR
Sbjct: 14  WRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANR 73

Query: 316 RQRDR 320
           R+  +
Sbjct: 74  RKEIK 78

>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 = 43.2 bits (102), Expect = 4e-06
 Identities = 10/43 (23%), Positives = 25/43 (58%), Gaps = 1/43 (2%)

Query: 279 LKECYDK-NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
           L++ +    +YP+    + LS+    ++ ++  WF++RR +D+
Sbjct: 23  LEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 65

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

 Score = 43.2 bits (102), Expect = 4e-06
 Identities = 10/43 (23%), Positives = 25/43 (58%), Gaps = 1/43 (2%)

Query: 334 LKECYDK-NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
           L++ +    +YP+    + LS+    ++ ++  WF++RR +D+
Sbjct: 23  LEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 65

>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 = 40.9 bits (96), Expect = 4e-05
 Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 9/76 (11%)

Query: 313 KNRRQRDRT---PQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKN 369
            +  +R RT     Q         +K  +  N  P+  + +QL++ TGLT   +  WF+N
Sbjct: 4   GSSGKRMRTSFKHHQL------RTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQN 57

Query: 370 RRQRDRTPQQRAKNRT 385
            R + R    R +N  
Sbjct: 58  ARAKFRRNLLRQENGG 73

>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 = 39.4 bits (92), Expect = 1e-04
 Identities = 17/63 (26%), Positives = 28/63 (44%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRS 330
           FK      +K  +  N  P+  + +QL++ TGLT   +  WF+N R + R    R     
Sbjct: 14  FKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQENGG 73

Query: 331 RNA 333
            + 
Sbjct: 74  VSG 76

>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} Length = 71

 Score = 40.5 bits (94), Expect = 4e-05
 Identities = 15/56 (26%), Positives = 22/56 (39%)

Query: 321 TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT 376
                  +   + LK  Y  N  PN DE  ++S   GL    V  WF+ R+    +
Sbjct: 7   GSPINPYKDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVYQYS 62

>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} Length = 71

 Score = 38.2 bits (88), Expect = 3e-04
 Identities = 15/43 (34%), Positives = 20/43 (46%)

Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT 321
           LK  Y  N  PN DE  ++S   GL    V  WF+ R+    +
Sbjct: 20  LKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVYQYS 62

>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 = 37.9 bits (88), Expect = 3e-04
 Identities = 7/36 (19%), Positives = 17/36 (47%)

Query: 285 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
             ++P+      LS+     +  +  WF+ RR +++
Sbjct: 22  ITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 57

>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 = 37.9 bits (88), Expect = 3e-04
 Identities = 7/36 (19%), Positives = 17/36 (47%)

Query: 340 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
             ++P+      LS+     +  +  WF+ RR +++
Sbjct: 22  ITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 57

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

 Score = 37.0 bits (86), Expect = 7e-04
 Identities = 12/44 (27%), Positives = 19/44 (43%)

Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQR 329
           N++P+P     ++   GLT  Q   WFK R    R  +    + 
Sbjct: 25  NKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLPSEC 68

>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 = 37.0 bits (86), Expect = 7e-04
 Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 7/79 (8%)

Query: 313 KNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
             RR+R   T  Q       + L+  + K RYP+   + +++    L  ++V  WFKNRR
Sbjct: 6   SGRRERTTFTRAQL------DVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRR 59

Query: 372 QRDRTPQQRAKNRTFDPYS 390
            + R  QQ+ +N      S
Sbjct: 60  AKCRQQQQQQQNGGQSGPS 78

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

 Score = 36.5 bits (85), Expect = 8e-04
 Identities = 12/38 (31%), Positives = 21/38 (55%)

Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
           L+  + + +Y    E+  L++   +T  QV  WF+NRR
Sbjct: 12  LERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRR 49

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

 Score = 36.5 bits (85), Expect = 8e-04
 Identities = 12/38 (31%), Positives = 21/38 (55%)

Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
           L+  + + +Y    E+  L++   +T  QV  WF+NRR
Sbjct: 12  LERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRR 49

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	390
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.47
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.33
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.31
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.3
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.3
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.3
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.28
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.28
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.27
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.26
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.26
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.25
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.24
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.24
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.24
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.24
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.24
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.24
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.24
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.24
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.23
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.23
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.23
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.23
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.23
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.23
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.23
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.23
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.23
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.23
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.23
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.23
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.23
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.22
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.22
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.22
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.22
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.21
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.21
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.21
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.21
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.21
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.21
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.21
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.21
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.21
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.21
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.21
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.2
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.2
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.2
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.2
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.2
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.19
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.19
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.19
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.19
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.19
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.19
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.18
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.18
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.18
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.18
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.18
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.18
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.18
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.18
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.18
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.18
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.17
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.17
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.17
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.16
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.16
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.15
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.15
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.15
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.15
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.14
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.14
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.14
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.14
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.14
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.14
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.14
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.14
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.13
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.13
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.13
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.13
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.13
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.12
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.12
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.12
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.12
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.12
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.12
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.11
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.11
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.11
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.11
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.11
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.11
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.1
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.1
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.1
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.1
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.09
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.09
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.09
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.09
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.08
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.08
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.08
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.08
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.08
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.08
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.08
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.07
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.07
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.07
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.06
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.06
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.06
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.05
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.05
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.04
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.03
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.03
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.02
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.01
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.01
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.0
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.0
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.0
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.0
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	98.96
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	98.96
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	98.96
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	98.95
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	98.94
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	98.92
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	98.91
1lfb_A	99	Liver transcription factor (LFB1); transcription r	98.89
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	98.84
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	98.84
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	98.72
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	98.71
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	98.66
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	98.52
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	98.52
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	98.48
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	98.46
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	98.43
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	97.82
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	96.14
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	89.85
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	84.18

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

Probab=99.47  E-value=2.9e-14  Score=127.76  Aligned_cols=141  Identities=18%  Similarity=0.239  Sum_probs=95.3

Q ss_pred             hhcCChhHHHHHHHcCCCccccccchhhhhhHHHHHHhhhcHHHHHHHHhcCCCCcc----------chHHHHHHH--Hh
Q psy8148         162 QQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSK----------YHAELQQLW--MR  229 (390)
Q Consensus       162 ~~~~~~~~l~~fl~~lp~~~~~~~~e~v~rAra~v~~h~~~f~el~~~L~~~~F~~~----------~h~~lq~lw--~~  229 (390)
                      ..+.+++.|..|...+...            |..+.|.+.+...++..|.+..|+..          ++..+..||  +.
T Consensus         7 ~~~~~~~~l~~fa~~fk~~------------ri~lg~tQ~~vg~alg~l~g~~~Sqtti~rFE~l~ls~kn~~klkPlL~   74 (164)
T 2xsd_C            7 EDAPSSDDLEQFAKQFKQR------------RIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPLLN   74 (164)
T ss_dssp             --CCCHHHHHHHHHHHHHH------------HHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHTTCSBHHHHHHHHHHHH
T ss_pred             ccccchhHHHHHHHHHHHH------------HhhcCCcccccccccccccCCCcCcchhhhhhccCCCHHHHHHcchhHH
Confidence            4678889999998876543            55667778777777788777777632          233445555  67


Q ss_pred             hhhhHHHhhhCCCCCcccccccccCCCCCCcccCCCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcc
Q psy8148         230 GHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVS  309 (390)
Q Consensus       230 ahY~e~e~~rgrpL~~v~kyr~Rkk~p~P~ti~dge~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~  309 (390)
                      .++.+++...|.+ +.++++...++..         +.+..|+..|+.+|+..|..++||+..++..||..+||++.||+
T Consensus        75 ~wl~eae~~~~~~-~~~~~~~~~~~~r---------r~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~  144 (164)
T 2xsd_C           75 KWLEETDSSSGSP-TNLDKIAAQGRKR---------KKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVR  144 (164)
T ss_dssp             HHHHHHCC---------------------------------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             HHHhhhccccCCC-cccccccccccCC---------CCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhh
Confidence            7788888766655 3344443322222         23347999999999999999999999999999999999999999


Q ss_pred             cccccccccCCCcch
Q psy8148         310 NWFKNRRQRDRTPQQ  324 (390)
Q Consensus       310 ~WFqNRR~R~R~~~t  324 (390)
                      +||+|||+|+|+...
T Consensus       145 vWFqNRR~k~kr~~~  159 (164)
T 2xsd_C          145 VWFCNRRQKEKRMTP  159 (164)
T ss_dssp             HHHHHHHHHHTBSCC
T ss_pred             hhhHHhhHHHhhccC
Confidence            999999999987643

>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=99.33  E-value=2e-13  Score=111.91  Aligned_cols=75  Identities=23%  Similarity=0.405  Sum_probs=57.9

Q ss_pred             hCCCchhccccccccccc----------------CCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccc
Q psy8148         301 TGLTLTQVSNWFKNRRQR----------------DRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVS  364 (390)
Q Consensus       301 tgLs~~QV~~WFqNRR~R----------------~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk  364 (390)
                      .+.+..+|-.||++.|..                .|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|+
T Consensus         3 ~~~~~~~~~~W~~~~r~~~~~~~~~~~~~~~~rr~Rt~ft~~Ql---~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~   79 (97)
T 1b72_A            3 PNTPTARTFDWMKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQL---TELEKEFHFNKYLSRARRVEIAATLELNETQVK   79 (97)
T ss_dssp             -----CCCCGGGGC--------------------CCCCCCHHHH---HHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CCCCCcccccccccccCCCCCCCCCCCCCCCCCCCCcCcCHHHH---HHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhH
Confidence            455667777888877643                3455565555   999999999999999999999999999999999


Q ss_pred             cccccccccccchh
Q psy8148         365 NWFKNRRQRDRTPQ  378 (390)
Q Consensus       365 ~WFqNRR~K~kk~~  378 (390)
                      +||||||+|+|+..
T Consensus        80 vWFqNRR~k~kk~~   93 (97)
T 1b72_A           80 IWFQNRRMKQKKRE   93 (97)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHhHHHhHHh
Confidence            99999999999854

>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=99.31  E-value=1.7e-12  Score=114.14  Aligned_cols=117  Identities=20%  Similarity=0.297  Sum_probs=76.7

Q ss_pred             HHHHHHhhhcHHHHHHHHhcCCCC-------------ccchHHHHHHHHhhhhhHHHhhhCCCCCcccccccccCCCCCC
Q psy8148         193 RAVVAYKRHAFHELYAILESHNFD-------------SKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPK  259 (390)
Q Consensus       193 ra~v~~h~~~f~el~~~L~~~~F~-------------~~~h~~lq~lw~~ahY~e~e~~rgrpL~~v~kyr~Rkk~p~P~  259 (390)
                      |....|.+.+...++..|.+..||             ..++..|.- ++...+.+++...+...+.++..+.+       
T Consensus        16 ri~lg~tQ~~vg~al~~l~g~~~Sqtti~rfe~l~ls~knm~kLkP-lL~~wl~e~e~~~~~~~~~~~~~~~~-------   87 (146)
T 1au7_A           16 RIKLGYTQTNVGEALAAVHGSEFSQTTICRFENLQLSFKNACKLKA-ILSKWLEEAEQVGALYNEKVGANERK-------   87 (146)
T ss_dssp             HHHHTCCHHHHHHHHHHTTSSCCCHHHHHHHHTTCSBHHHHHHHHH-HHHHHHHHCCC----------------------
T ss_pred             HHhccCcHHhhhhhcchhccCCCCcchHHHHhccCCChHHHHhcch-HHHHHHHHhhcccCccCcccCCCCCC-------
Confidence            344556666666666666666655             333444443 25566677776554444433332111       


Q ss_pred             cccCCCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         260 TIWDGEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       260 ti~dge~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                           .+.+..|+..|+.+|+..|..++||+..++..||..+||++.||++||+|||+|+|..
T Consensus        88 -----rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           88 -----RKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             ------CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             -----CCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence                 1233479999999999999999999999999999999999999999999999998864

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

Probab=99.30  E-value=3.2e-13  Score=101.58  Aligned_cols=60  Identities=30%  Similarity=0.484  Sum_probs=51.4

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccch
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  377 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~  377 (390)
                      ++++.|+.++..+.   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+.
T Consensus         2 ~~rr~Rt~ft~~q~---~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A            2 TKQKMRTVFSQAQL---CALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             ------CCCCHHHH---HHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             CCCCCCCCCCHHHH---HHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            45667788887777   9999999999999999999999999999999999999999999985

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

Probab=99.30  E-value=4.5e-13  Score=102.68  Aligned_cols=65  Identities=31%  Similarity=0.450  Sum_probs=58.5

Q ss_pred             cccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhcc
Q psy8148         316 RQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKN  383 (390)
Q Consensus       316 R~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~~  383 (390)
                      +++.|+.++..+.   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+.....+.
T Consensus         2 ~rr~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~~~~   66 (68)
T 1zq3_P            2 PRRTRTTFTSSQI---AELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQHKD   66 (68)
T ss_dssp             CSCCSCCCCHHHH---HHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             cCCCCCCcCHHHH---HHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhccccc
Confidence            4567788887777   9999999999999999999999999999999999999999999997766554

>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=99.30  E-value=4.4e-13  Score=105.76  Aligned_cols=69  Identities=28%  Similarity=0.422  Sum_probs=62.0

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhccCCC
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKNRTF  386 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~~~~~  386 (390)
                      +++|.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+...++.++.-
T Consensus         6 ~~rr~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~~~~~   74 (80)
T 2dmq_A            6 SGKRMRTSFKHHQL---RTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQENGGV   74 (80)
T ss_dssp             CCCCCCCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHSSCCCSS
T ss_pred             CCCCCCCCCCHHHH---HHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHHHhcCCC
Confidence            45667788887777   9999999999999999999999999999999999999999999998887777654

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

Probab=99.28  E-value=5.7e-13  Score=105.24  Aligned_cols=68  Identities=31%  Similarity=0.501  Sum_probs=60.4

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhccCC
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKNRT  385 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~~~~  385 (390)
                      +.+|.|+.++..|.   ..|+..|..++||+..++.+||..+||++.+|++||+|||+|+|+......++.
T Consensus         6 ~~rr~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~~~~~~   73 (80)
T 2dms_A            6 SGRRERTTFTRAQL---DVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQQNGG   73 (80)
T ss_dssp             CCCCCCSSCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCSCCCCC
T ss_pred             CCCCCCCCCCHHHH---HHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHccCCCC
Confidence            45667788887777   999999999999999999999999999999999999999999999877666554

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

Probab=99.28  E-value=2.5e-12  Score=97.20  Aligned_cols=57  Identities=32%  Similarity=0.575  Sum_probs=52.6

Q ss_pred             CccccccCHHHHHHHHHHH---hhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         265 EETVYCFKERSRNALKECY---DKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       265 e~t~~~Fs~~q~~~Le~~F---~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      ......|+..++.+|+.+|   ..++||+..++..||..+||+..||.+||+|+|+|.|.
T Consensus         4 rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A            4 HIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             CCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            3445578999999999999   89999999999999999999999999999999999875

>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=99.27  E-value=7.9e-13  Score=101.84  Aligned_cols=61  Identities=26%  Similarity=0.564  Sum_probs=55.6

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      +.++.|+.++..|.   ..|+..|..++||+..++.+||..+||++.+|++||+|||+|+|+..
T Consensus         6 ~~rr~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~   66 (70)
T 2cra_A            6 SGRKKRIPYSKGQL---RELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSG   66 (70)
T ss_dssp             CCCCSCCCSCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCcCCHHHH---HHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccC
Confidence            45567788887777   99999999999999999999999999999999999999999999854

>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=99.26  E-value=7.5e-13  Score=100.73  Aligned_cols=61  Identities=33%  Similarity=0.578  Sum_probs=55.6

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      ++++.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+..
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 KTTRVRTVLNEKQL---HTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             CCSCCCCCCSHHHH---HHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             CCCCCCCCCCHHHH---HHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHHh
Confidence            35667888887777   99999999999999999999999999999999999999999999854

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

Probab=99.26  E-value=8.1e-13  Score=102.71  Aligned_cols=65  Identities=28%  Similarity=0.547  Sum_probs=57.5

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhc
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAK  382 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~  382 (390)
                      +.++.|+.++..|.   ..|+..|..++||+..++.+||..+||++.+|++||||||+|+|+.....+
T Consensus         6 ~~rr~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~~   70 (73)
T 2l7z_A            6 EGRKKRVPYTKVQL---KELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINKLK   70 (73)
T ss_dssp             CCCCCCCCSCHHHH---HHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSSSSSS
T ss_pred             CCCCCCCCCCHHHH---HHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHhcccC
Confidence            34566777887777   999999999999999999999999999999999999999999999765543

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

Probab=99.25  E-value=1.5e-12  Score=100.28  Aligned_cols=61  Identities=30%  Similarity=0.439  Sum_probs=55.5

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      ..++.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+..
T Consensus         6 ~~rr~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2djn_A            6 SGRKPRTIYSSFQL---AALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSG   66 (70)
T ss_dssp             CCCCSSCSSCHHHH---HHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSS
T ss_pred             CCCCCCCCCCHHHH---HHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccC
Confidence            45567788887777   99999999999999999999999999999999999999999999854

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

Probab=99.24  E-value=3.6e-12  Score=99.01  Aligned_cols=63  Identities=25%  Similarity=0.506  Sum_probs=57.1

Q ss_pred             cCCCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         262 WDGEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       262 ~dge~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      ..+.+....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|||+++|....
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   67 (73)
T 2l7z_A            5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVIN   67 (73)
T ss_dssp             SCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHhc
Confidence            345556678999999999999999999999999999999999999999999999999987644

>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=99.24  E-value=1.9e-12  Score=96.94  Aligned_cols=55  Identities=31%  Similarity=0.529  Sum_probs=51.2

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      ....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|||++.|.
T Consensus         6 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            6 PRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             -CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            4457999999999999999999999999999999999999999999999998775

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

Probab=99.24  E-value=7e-13  Score=100.07  Aligned_cols=59  Identities=25%  Similarity=0.403  Sum_probs=53.2

Q ss_pred             cccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccch
Q psy8148         316 RQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  377 (390)
Q Consensus       316 R~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~  377 (390)
                      .++.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+.
T Consensus         3 ~rr~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   61 (63)
T 2h1k_A            3 NKRTRTAYTRAQL---LELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE   61 (63)
T ss_dssp             --CCCCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCHHHH---HHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhh
Confidence            4566778887777   9999999999999999999999999999999999999999999885

>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=99.24  E-value=7.6e-13  Score=99.17  Aligned_cols=58  Identities=33%  Similarity=0.531  Sum_probs=50.9

Q ss_pred             cccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccc
Q psy8148         316 RQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  376 (390)
Q Consensus       316 R~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk  376 (390)
                      .+|.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+
T Consensus         3 ~rr~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            3 EKRPRTAFSSEQL---ARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             ----CCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHH---HHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            3556777887777   999999999999999999999999999999999999999999886

>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=99.24  E-value=9.1e-13  Score=101.33  Aligned_cols=62  Identities=31%  Similarity=0.497  Sum_probs=55.7

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhh
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  379 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~  379 (390)
                      ++++.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+...
T Consensus         6 ~~rr~Rt~ft~~q~---~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2da2_A            6 SGRSSRTRFTDYQL---RVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGP   67 (70)
T ss_dssp             CSCCCCCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCSS
T ss_pred             CCCCCCCCCCHHHH---HHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhccc
Confidence            45567778887777   999999999999999999999999999999999999999999998543

>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=99.24  E-value=1e-12  Score=103.85  Aligned_cols=62  Identities=26%  Similarity=0.472  Sum_probs=56.2

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      .+.++.|+.++..|+   ..|+..|..++||+..++.+||..+||+..+|++||||||+|+|+..
T Consensus        15 ~~~rr~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   76 (80)
T 2dmt_A           15 KKGRRSRTVFTELQL---MGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSG   76 (80)
T ss_dssp             CCCCCSCCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCC
T ss_pred             CCCCCCCCCCCHHHH---HHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhccc
Confidence            355667788887777   99999999999999999999999999999999999999999999854

>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=99.24  E-value=5.8e-12  Score=96.97  Aligned_cols=59  Identities=24%  Similarity=0.501  Sum_probs=54.3

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      +....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|||+++|....
T Consensus         9 r~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (70)
T 2cra_A            9 KKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGP   67 (70)
T ss_dssp             CSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSCT
T ss_pred             CCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccCC
Confidence            34557999999999999999999999999999999999999999999999999987643

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

Probab=99.24  E-value=1.9e-12  Score=100.62  Aligned_cols=66  Identities=18%  Similarity=0.415  Sum_probs=60.1

Q ss_pred             CCcccCCCccccccCHHHHHHHHHHH-hhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcc
Q psy8148         258 PKTIWDGEETVYCFKERSRNALKECY-DKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  323 (390)
Q Consensus       258 P~ti~dge~t~~~Fs~~q~~~Le~~F-~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~  323 (390)
                      |-.++.|......++..|+.+|+..| ..++||+..++.+||..+||++.||++||+|||+++|...
T Consensus         2 P~~~~~g~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~~   68 (72)
T 2cqx_A            2 SSGSSGGIKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSG   68 (72)
T ss_dssp             CCCCCCCCCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSCC
T ss_pred             CccccCCCCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCCC
Confidence            55667777777788899999999999 9999999999999999999999999999999999998754

>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=99.23  E-value=5.9e-13  Score=101.99  Aligned_cols=64  Identities=30%  Similarity=0.518  Sum_probs=57.2

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhh
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRA  381 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~  381 (390)
                      ++++.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+.....
T Consensus         2 ~~rr~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~~~   65 (68)
T 1yz8_P            2 SQRRQRTHFTSQQL---QQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEFI   65 (68)
T ss_dssp             CSSCSCCCCCHHHH---HHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCCHHHH---HHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhhcc
Confidence            45667788887777   99999999999999999999999999999999999999999999865443

>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=99.23  E-value=6.7e-13  Score=101.81  Aligned_cols=61  Identities=26%  Similarity=0.435  Sum_probs=55.5

Q ss_pred             cccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhh
Q psy8148         316 RQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  379 (390)
Q Consensus       316 R~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~  379 (390)
                      +++.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||||||+|+|+...
T Consensus         2 ~rr~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~   62 (68)
T 1ahd_P            2 RKRGRQTYTRYQT---LELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK   62 (68)
T ss_dssp             CSCTTCCCCHHHH---HHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCcCHHHH---HHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhcc
Confidence            4567788887777   999999999999999999999999999999999999999999998653

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

Probab=99.23  E-value=9e-13  Score=97.63  Aligned_cols=56  Identities=32%  Similarity=0.508  Sum_probs=51.6

Q ss_pred             cCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccc
Q psy8148         318 RDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  376 (390)
Q Consensus       318 R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk  376 (390)
                      |.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+
T Consensus         2 r~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A            2 KPRTPFTTAQL---LALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCHHHH---HHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHH---HHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            45677777777   999999999999999999999999999999999999999999876

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

Probab=99.23  E-value=1.6e-12  Score=95.89  Aligned_cols=57  Identities=32%  Similarity=0.545  Sum_probs=52.1

Q ss_pred             cccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCcccccccccccccccc
Q psy8148         316 RQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR  375 (390)
Q Consensus       316 R~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~k  375 (390)
                      +++.|+.++..+.   ..|+..|..++||+..++.+||..+||+..+|++||||||+|+|
T Consensus         2 ~rr~Rt~~t~~q~---~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~k   58 (58)
T 3rkq_A            2 RRKPRVLFSQAQV---YELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK   58 (58)
T ss_dssp             CCCCCCCCCHHHH---HHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHC
T ss_pred             cCCCCCCcCHHHH---HHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhhccCC
Confidence            4566788887777   99999999999999999999999999999999999999999875

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

Probab=99.23  E-value=1.6e-12  Score=102.72  Aligned_cols=65  Identities=25%  Similarity=0.460  Sum_probs=58.1

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhc
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAK  382 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~  382 (390)
                      .+++.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||||||+|+|+......
T Consensus         6 ~~rr~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~~   70 (80)
T 2cue_A            6 SGQRNRTSFTQEQI---EALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRN   70 (80)
T ss_dssp             SSCCCCCCSCHHHH---HHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCccCHHHH---HHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhhh
Confidence            45667788887777   999999999999999999999999999999999999999999999765443

>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=99.23  E-value=4.4e-12  Score=96.46  Aligned_cols=56  Identities=32%  Similarity=0.613  Sum_probs=52.6

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      ....|+..|+.+|+.+|..++||+..++..||..+||++.||.+||+|+|+++|..
T Consensus         6 ~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   61 (66)
T 1bw5_A            6 VRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR   61 (66)
T ss_dssp             CCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSC
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHH
Confidence            44579999999999999999999999999999999999999999999999998864

>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=99.23  E-value=9.8e-13  Score=98.40  Aligned_cols=59  Identities=24%  Similarity=0.481  Sum_probs=46.8

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCcccccccccccccccc
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR  375 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~k  375 (390)
                      .+..+.|+.++..+.   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|
T Consensus         3 ~k~rr~Rt~ft~~q~---~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            3 EKSPKGKSSISPQAR---AFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             ---------CCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCCHHHH---HHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            345566777887777   99999999999999999999999999999999999999999875

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

Probab=99.23  E-value=1e-12  Score=100.68  Aligned_cols=62  Identities=24%  Similarity=0.448  Sum_probs=56.1

Q ss_pred             cccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhh
Q psy8148         316 RQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR  380 (390)
Q Consensus       316 R~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r  380 (390)
                      +++.|+.++..+.   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+....
T Consensus         2 ~rr~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~~   63 (68)
T 1ftt_A            2 RRKRRVLFSQAQV---YELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKD   63 (68)
T ss_dssp             CSSSCSSCCHHHH---HHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCccCHHHH---HHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhhH
Confidence            4567788887777   9999999999999999999999999999999999999999999986543

>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=99.23  E-value=1.5e-12  Score=102.17  Aligned_cols=65  Identities=26%  Similarity=0.503  Sum_probs=57.8

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhh
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRA  381 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~  381 (390)
                      .++++.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||||||+|+|+.....
T Consensus         7 ~~~rr~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~~   71 (77)
T 1nk2_P            7 NKKRKRRVLFTKAQT---YELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEK   71 (77)
T ss_dssp             CCCCCCCCCCCHHHH---HHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCccCCHHHH---HHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhccc
Confidence            456667888887777   99999999999999999999999999999999999999999999865443

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

Probab=99.23  E-value=1.6e-12  Score=103.52  Aligned_cols=62  Identities=26%  Similarity=0.491  Sum_probs=56.8

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      .++++.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||||||+|+|+..
T Consensus        20 ~~~rr~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   81 (84)
T 2kt0_A           20 VKKQKTRTVFSSTQL---CVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQ   81 (84)
T ss_dssp             SCSCCCSSCCCHHHH---HHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCC
T ss_pred             CCCCCCCCCCCHHHH---HHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHh
Confidence            456677888888777   99999999999999999999999999999999999999999999854

>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=99.23  E-value=3.4e-12  Score=95.47  Aligned_cols=54  Identities=28%  Similarity=0.491  Sum_probs=48.0

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCC
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR  320 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R  320 (390)
                      ....|+..|+.+|+.+|..++||+..++..||..+||++.||.+||+|+|++.|
T Consensus         8 ~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            8 GKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             ----CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            345799999999999999999999999999999999999999999999998865

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

Probab=99.23  E-value=3e-12  Score=95.57  Aligned_cols=55  Identities=25%  Similarity=0.512  Sum_probs=49.9

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         268 VYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       268 ~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      ...|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|||+|.|..
T Consensus         3 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~   57 (60)
T 3a02_A            3 HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ   57 (60)
T ss_dssp             --CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC--
T ss_pred             CcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhh
Confidence            3469999999999999999999999999999999999999999999999998764

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

Probab=99.23  E-value=2.4e-12  Score=94.91  Aligned_cols=53  Identities=26%  Similarity=0.453  Sum_probs=49.2

Q ss_pred             cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         269 YCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       269 ~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      ..|+..|+..|+..|..++||+..++..||..+||++.||.+||+|||.|.|.
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr   54 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRR   54 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhhcc
Confidence            46899999999999999999999999999999999999999999999998764

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

Probab=99.22  E-value=1.2e-12  Score=100.76  Aligned_cols=62  Identities=29%  Similarity=0.475  Sum_probs=55.5

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhh
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  379 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~  379 (390)
                      ..+|.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+...
T Consensus         6 ~~rr~Rt~ft~~q~---~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2dmu_A            6 SGRRHRTIFTDEQL---EALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP   67 (70)
T ss_dssp             SSCCCCCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTST
T ss_pred             CCCCCCCCCCHHHH---HHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccCC
Confidence            34566788887777   999999999999999999999999999999999999999999988543

>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=99.22  E-value=2.4e-12  Score=102.07  Aligned_cols=60  Identities=13%  Similarity=0.271  Sum_probs=55.0

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcC----CCCCCHHHHHHHHHhhCCCccccccccccccccccc
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDK----NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  376 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~----n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk  376 (390)
                      .+++|.|+.++..|.   ..|+..|+.    ++||+..++++||..+||++.+|++||||||+|.++
T Consensus        15 ~~~rR~Rt~ft~~Ql---~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           15 GIRKRHRTKFTAEQK---ERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCSCCCSCCCCHHHH---HHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCccCCHHHH---HHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            356677888888777   999999999    999999999999999999999999999999999986

>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=99.22  E-value=1.5e-12  Score=102.32  Aligned_cols=59  Identities=19%  Similarity=0.382  Sum_probs=51.9

Q ss_pred             CCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhh
Q psy8148         319 DRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR  380 (390)
Q Consensus       319 ~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r  380 (390)
                      .+..++..|+   .+|++.|..++||+..++++||..+||++.+|++||+|+|+|+|+..-+
T Consensus         6 ~r~kfT~~Ql---~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~l~   64 (76)
T 2ecc_A            6 SGKRKTKEQL---AILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLK   64 (76)
T ss_dssp             CCCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCCS
T ss_pred             CCCCCCHHHH---HHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHHHH
Confidence            3445666666   9999999999999999999999999999999999999999999886533

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

Probab=99.22  E-value=6.7e-12  Score=97.46  Aligned_cols=64  Identities=28%  Similarity=0.413  Sum_probs=57.8

Q ss_pred             ccCCCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         261 IWDGEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       261 i~dge~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      +++.......|+..|+.+|+..|..++||+..++..||..+||+..||.+||+|||.+.|....
T Consensus         3 ~~~~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   66 (74)
T 2ly9_A            3 MPDSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKS   66 (74)
T ss_dssp             CCCCCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTTC
T ss_pred             CCCCCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhCc
Confidence            4455566678999999999999999999999999999999999999999999999999987644

>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=99.21  E-value=1.1e-12  Score=100.98  Aligned_cols=61  Identities=21%  Similarity=0.485  Sum_probs=55.6

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      +.++.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+..
T Consensus         6 ~~rr~Rt~ft~~q~---~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2da1_A            6 SGKRPRTRITDDQL---RVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSG   66 (70)
T ss_dssp             CCCSCSCCCCHHHH---HHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCC
T ss_pred             CCCCCCCCCCHHHH---HHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhc
Confidence            45667788887777   99999999999999999999999999999999999999999999854

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

Probab=99.21  E-value=1.9e-12  Score=98.83  Aligned_cols=61  Identities=26%  Similarity=0.489  Sum_probs=54.7

Q ss_pred             ccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhh
Q psy8148         317 QRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR  380 (390)
Q Consensus       317 ~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r  380 (390)
                      ++.|+.++..+.   ..|+..|..++||+..++..||..+||+..+|++||+|||+|+|+....
T Consensus         2 rr~Rt~ft~~q~---~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~~   62 (67)
T 2k40_A            2 RRPRTAFTQNQI---EVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRE   62 (67)
T ss_dssp             CCCSCCCCHHHH---HHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCCT
T ss_pred             cCCCCCCCHHHH---HHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhchh
Confidence            356777887777   9999999999999999999999999999999999999999999986543

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

Probab=99.21  E-value=5.2e-12  Score=94.87  Aligned_cols=55  Identities=29%  Similarity=0.526  Sum_probs=51.0

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      ....|+..|+.+|+..|..++||+..++..||..+||++.+|.+||+|||+++|.
T Consensus         6 ~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   60 (62)
T 2vi6_A            6 MRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR   60 (62)
T ss_dssp             --CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGG
T ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhh
Confidence            3457999999999999999999999999999999999999999999999999876

>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=99.21  E-value=1.5e-12  Score=102.44  Aligned_cols=62  Identities=26%  Similarity=0.370  Sum_probs=56.4

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      .+++|.|+.++..|+   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+..
T Consensus        15 ~~~rr~Rt~ft~~Ql---~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   76 (80)
T 2da3_A           15 QRDKRLRTTITPEQL---EILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSG   76 (80)
T ss_dssp             CCCTTCCSSCCTTTH---HHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCCCHHHH---HHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhc
Confidence            456677888887777   99999999999999999999999999999999999999999999854

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

Probab=99.21  E-value=1.3e-12  Score=97.57  Aligned_cols=57  Identities=26%  Similarity=0.451  Sum_probs=52.3

Q ss_pred             cCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccch
Q psy8148         318 RDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  377 (390)
Q Consensus       318 R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~  377 (390)
                      |.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+.
T Consensus         3 r~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (60)
T 1jgg_A            3 RYRTAFTRDQL---GRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   59 (60)
T ss_dssp             CCCCCCCHHHH---HHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCHHHH---HHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHhHhhcc
Confidence            55677777776   9999999999999999999999999999999999999999998874

>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=99.21  E-value=3.3e-12  Score=100.29  Aligned_cols=54  Identities=19%  Similarity=0.347  Sum_probs=50.9

Q ss_pred             cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         269 YCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       269 ~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      ..|+.+|+.+|+.+|..++||+..++.+||..|||+..||.+||+|+|+|.|..
T Consensus         8 ~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~   61 (76)
T 2ecc_A            8 KRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             CCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHH
Confidence            358999999999999999999999999999999999999999999999988754

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

Probab=99.21  E-value=4.1e-12  Score=95.96  Aligned_cols=58  Identities=31%  Similarity=0.581  Sum_probs=52.2

Q ss_pred             cccCCCcchhhhhhhhhhhhhhh---cCCCCCCHHHHHHHHHhhCCCccccccccccccccccc
Q psy8148         316 RQRDRTPQQRSIQRSRNALKECY---DKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  376 (390)
Q Consensus       316 R~R~R~~~t~~q~~q~~~Le~~F---~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk  376 (390)
                      ..+.|+.++..+.   ..|+..|   ..++||+..++.+||..+||+..+|++||+|+|+|+|+
T Consensus         3 ~rr~R~~ft~~q~---~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A            3 GHIEGRHMNKQAT---EILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             CCCCCCSSTTTHH---HHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCcCCHHHH---HHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            3456677776666   9999999   99999999999999999999999999999999999987

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

Probab=99.21  E-value=7.5e-12  Score=96.33  Aligned_cols=58  Identities=28%  Similarity=0.448  Sum_probs=53.9

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcc
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  323 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~  323 (390)
                      +....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|||+++|...
T Consensus         9 r~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2djn_A            9 KPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSG   66 (70)
T ss_dssp             CSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSS
T ss_pred             CCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccC
Confidence            3455799999999999999999999999999999999999999999999999998754

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

Probab=99.21  E-value=1.1e-12  Score=100.10  Aligned_cols=50  Identities=26%  Similarity=0.527  Sum_probs=46.5

Q ss_pred             hhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         329 RSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       329 ~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      .|+..|+..|..++||+..++.+||..+||+.++|++||||||+|+|+..
T Consensus        14 ~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg~   63 (66)
T 3nau_A           14 EQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGI   63 (66)
T ss_dssp             HHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhccC
Confidence            34599999999999999999999999999999999999999999998743

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

Probab=99.21  E-value=1.5e-12  Score=105.93  Aligned_cols=68  Identities=26%  Similarity=0.439  Sum_probs=59.5

Q ss_pred             ccccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhcc
Q psy8148         313 KNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKN  383 (390)
Q Consensus       313 qNRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~~  383 (390)
                      ..++++.|+.++..+.   ..|+..|..++||+..++.+||..+||+..+|++||||||+|+|+....++.
T Consensus        14 ~~~~rr~Rt~ft~~Ql---~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~~   81 (93)
T 3a01_A           14 PPKRKKPRTSFTRIQV---AELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEERE   81 (93)
T ss_dssp             CCCCCCCCCCCCHHHH---HHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC--
T ss_pred             CCCCCCCCcCCCHHHH---HHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHHHH
Confidence            3456677888888777   9999999999999999999999999999999999999999999997765543

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

Probab=99.21  E-value=3.9e-12  Score=94.19  Aligned_cols=54  Identities=30%  Similarity=0.439  Sum_probs=50.5

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         268 VYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       268 ~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      ...|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|+|++.|.
T Consensus         4 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A            4 RTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            346999999999999999999999999999999999999999999999988753

>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=99.20  E-value=4.3e-12  Score=94.67  Aligned_cols=54  Identities=28%  Similarity=0.482  Sum_probs=50.7

Q ss_pred             cccCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         269 YCFKERSRNALKECYDK---NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       269 ~~Fs~~q~~~Le~~F~~---n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      ..|+..|+.+|+.+|..   ++||+..++..||..+||+..||.+||+|+|+|.|..
T Consensus         3 ~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A            3 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             CcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            36899999999999999   9999999999999999999999999999999988753

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

Probab=99.20  E-value=4.6e-12  Score=96.62  Aligned_cols=58  Identities=24%  Similarity=0.481  Sum_probs=53.6

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      ....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|+|++.|....
T Consensus         4 ~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~   61 (67)
T 2k40_A            4 PRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR   61 (67)
T ss_dssp             CSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCC
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhch
Confidence            3457999999999999999999999999999999999999999999999999887654

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

Probab=99.20  E-value=1.6e-12  Score=97.09  Aligned_cols=56  Identities=23%  Similarity=0.463  Sum_probs=48.1

Q ss_pred             CCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         320 RTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       320 R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      |+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+..
T Consensus         3 Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~   58 (60)
T 3a02_A            3 HMTFTSFQL---EELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE   58 (60)
T ss_dssp             --CCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC---
T ss_pred             CcccCHHHH---HHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhc
Confidence            456666666   99999999999999999999999999999999999999999999854

>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=99.20  E-value=2.1e-12  Score=101.35  Aligned_cols=69  Identities=26%  Similarity=0.499  Sum_probs=59.0

Q ss_pred             ccccccc-cccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhh
Q psy8148         309 SNWFKNR-RQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR  380 (390)
Q Consensus       309 ~~WFqNR-R~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r  380 (390)
                      .+|...+ +++.|+.++..|.   ..|+..|..++||+..++.+||..+||++.+|++||||||+|+|+..+.
T Consensus         5 ~~~~~~~~~rr~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k~   74 (77)
T 1puf_A            5 ANWLHARSTRKKRCPYTKHQT---LELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             TTSCCCCTTSCCCCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccCCCCCCCCCCCCHHHH---HHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhhh
Confidence            4555554 3456777887777   9999999999999999999999999999999999999999999986643

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

Probab=99.20  E-value=6.5e-12  Score=92.62  Aligned_cols=54  Identities=31%  Similarity=0.541  Sum_probs=50.3

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCC
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR  320 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R  320 (390)
                      ....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|+|+|.|
T Consensus         5 ~Rt~~t~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~k   58 (58)
T 3rkq_A            5 PRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK   58 (58)
T ss_dssp             CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHC
T ss_pred             CCCCcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhhccCC
Confidence            345689999999999999999999999999999999999999999999998864

>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=99.19  E-value=2.3e-12  Score=101.99  Aligned_cols=65  Identities=29%  Similarity=0.583  Sum_probs=57.1

Q ss_pred             cccccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhh
Q psy8148         312 FKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  379 (390)
Q Consensus       312 FqNRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~  379 (390)
                      ...++++.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+...
T Consensus        14 ~~~~~rr~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~   78 (81)
T 1fjl_A           14 LKRKQRRSRTTFSASQL---DELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   78 (81)
T ss_dssp             ---CCCCCCCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCCCCCCCCCHHHH---HHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhcc
Confidence            34567778888888777   999999999999999999999999999999999999999999998653

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

Probab=99.19  E-value=1.5e-12  Score=96.03  Aligned_cols=48  Identities=27%  Similarity=0.460  Sum_probs=45.5

Q ss_pred             hhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccch
Q psy8148         330 SRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  377 (390)
Q Consensus       330 q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~  377 (390)
                      |+..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+.
T Consensus         8 Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~   55 (56)
T 3a03_A            8 QVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ   55 (56)
T ss_dssp             HHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhhccc
Confidence            349999999999999999999999999999999999999999999874

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

Probab=99.19  E-value=5.2e-12  Score=95.24  Aligned_cols=55  Identities=22%  Similarity=0.360  Sum_probs=51.5

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      ....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|||++.|.
T Consensus         6 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk   60 (63)
T 2h1k_A            6 TRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK   60 (63)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhh
Confidence            4457999999999999999999999999999999999999999999999998764

>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=99.19  E-value=9.2e-12  Score=95.69  Aligned_cols=57  Identities=32%  Similarity=0.558  Sum_probs=53.1

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcc
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  323 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~  323 (390)
                      ....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|||++.|...
T Consensus        10 ~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2da2_A           10 SRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSG   66 (70)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCS
T ss_pred             CCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhcc
Confidence            445799999999999999999999999999999999999999999999999988753

>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=99.19  E-value=3.3e-12  Score=99.08  Aligned_cols=62  Identities=32%  Similarity=0.582  Sum_probs=55.1

Q ss_pred             ccCCCcchhhhhhhhhhhhhhh---cCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhh
Q psy8148         317 QRDRTPQQRSIQRSRNALKECY---DKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRA  381 (390)
Q Consensus       317 ~R~R~~~t~~q~~q~~~Le~~F---~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~  381 (390)
                      +|.|+.++..+.   ..|+..|   ..++||+..++..||..+||+..+|++||+|+|+|+|+.....
T Consensus         2 rr~R~~ft~~q~---~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~~   66 (73)
T 1puf_B            2 RRKRRNFNKQAT---EILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKF   66 (73)
T ss_dssp             CCCCCCCCHHHH---HHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTTT
T ss_pred             CCCCCcCCHHHH---HHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcccccccc
Confidence            456777777666   9999999   9999999999999999999999999999999999998866554

>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=99.19  E-value=2.3e-12  Score=99.21  Aligned_cols=61  Identities=23%  Similarity=0.467  Sum_probs=54.6

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      ...+.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+..
T Consensus         6 ~~~r~R~~ft~~q~---~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~   66 (70)
T 2e1o_A            6 SGKGGQVRFSNDQT---IELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSG   66 (70)
T ss_dssp             CCCCCCCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCHHHH---HHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCC
Confidence            34556777887777   99999999999999999999999999999999999999999998854

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

Probab=99.18  E-value=2.2e-12  Score=99.58  Aligned_cols=54  Identities=28%  Similarity=0.453  Sum_probs=49.4

Q ss_pred             hhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhc
Q psy8148         329 RSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAK  382 (390)
Q Consensus       329 ~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~  382 (390)
                      .|+..|+..|..++||+..++.+||..+||++.+|++||||||+|+|+.....+
T Consensus        14 ~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~~~~~   67 (69)
T 2l9r_A           14 TQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSE   67 (69)
T ss_dssp             HHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSSSSCC
T ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhhhhhh
Confidence            455999999999999999999999999999999999999999999999765554

>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=99.18  E-value=2.1e-12  Score=102.41  Aligned_cols=61  Identities=25%  Similarity=0.403  Sum_probs=52.7

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      .++|.|+.++..+.   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+..
T Consensus        19 ~~rr~Rt~ft~~Ql---~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   79 (81)
T 1b8i_A           19 LRRRGRQTYTRYQT---LELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEI   79 (81)
T ss_dssp             -----CCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCcccCHHHH---HHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhc
Confidence            45667888888777   99999999999999999999999999999999999999999999854

>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=99.18  E-value=6.1e-12  Score=97.37  Aligned_cols=58  Identities=28%  Similarity=0.424  Sum_probs=53.3

Q ss_pred             CccccccCHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         265 EETVYCFKERSRNALKECYDK-NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       265 e~t~~~Fs~~q~~~Le~~F~~-n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      .++...|+..|+.+|+..|.. ++||+..++..||..+||++.||.+||+|||+++|..
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~   60 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS   60 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhh
Confidence            345567999999999999996 9999999999999999999999999999999998764

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

Probab=99.18  E-value=5.9e-12  Score=93.96  Aligned_cols=54  Identities=22%  Similarity=0.436  Sum_probs=50.7

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         268 VYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       268 ~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      ...|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|+|++.|.
T Consensus         5 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   58 (60)
T 1jgg_A            5 RTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR   58 (60)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHhHhhc
Confidence            346999999999999999999999999999999999999999999999988764

>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=99.18  E-value=5.3e-12  Score=100.09  Aligned_cols=59  Identities=14%  Similarity=0.217  Sum_probs=53.6

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcC-----CCCCCHHHHHHHHHhhCCCccccccccccccccccc
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDK-----NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  376 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~-----n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk  376 (390)
                      .+++|.|+.++..|.   ..|+ .|..     ++||+..++++||..+||++.+|++||||||+|+++
T Consensus        15 ~~~rR~Rt~ft~~Ql---~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           15 GTTKRFRTKFTAEQK---EKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCSSCCCCCCCHHHH---HHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCCccCCHHHH---HHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            356677888888777   8999 7998     999999999999999999999999999999999986

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

Probab=99.18  E-value=2.9e-12  Score=102.99  Aligned_cols=61  Identities=26%  Similarity=0.425  Sum_probs=53.2

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      ..+|.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||||||+|+|+..
T Consensus        27 ~~rr~Rt~ft~~Ql---~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   87 (88)
T 2r5y_A           27 ETKRQRTSYTRYQT---LELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH   87 (88)
T ss_dssp             ----CCCCCCHHHH---HHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCcCHHHH---HHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhhc
Confidence            45667788887777   99999999999999999999999999999999999999999998854

>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=99.18  E-value=3.1e-12  Score=99.05  Aligned_cols=59  Identities=24%  Similarity=0.385  Sum_probs=53.4

Q ss_pred             cCCCcchhhhhhhhhhhhhhhcC-CCCCCHHHHHHHHHhhCCCccccccccccccccccchhh
Q psy8148         318 RDRTPQQRSIQRSRNALKECYDK-NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  379 (390)
Q Consensus       318 R~R~~~t~~q~~q~~~Le~~F~~-n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~  379 (390)
                      +.|+.++..|.   ..|+..|.. ++||+..++.+||..+||++.+|++||+|||+|+|+...
T Consensus         3 k~Rt~ft~~Q~---~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~~   62 (72)
T 1uhs_A            3 EGAATMTEDQV---EILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   62 (72)
T ss_dssp             CCCCCCCHHHH---HHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCccCCHHHH---HHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhcc
Confidence            45677777776   999999996 999999999999999999999999999999999998663

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

Probab=99.18  E-value=2.9e-12  Score=99.55  Aligned_cols=63  Identities=30%  Similarity=0.533  Sum_probs=56.4

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhh
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  379 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~  379 (390)
                      .++++.|+.++..+.   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+...
T Consensus         7 ~~~rr~Rt~ft~~q~---~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r   69 (75)
T 2m0c_A            7 GKKRRNRTTFTSYQL---EELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRER   69 (75)
T ss_dssp             SCCCSCSCSSCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCC
T ss_pred             CCCCCCCCCCCHHHH---HHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHh
Confidence            345666788887777   999999999999999999999999999999999999999999998544

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

Probab=99.18  E-value=8.7e-12  Score=95.87  Aligned_cols=58  Identities=28%  Similarity=0.505  Sum_probs=53.2

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcc
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  323 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~  323 (390)
                      +....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|||+|+|...
T Consensus         9 r~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~   66 (70)
T 2dmu_A            9 RHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSG   66 (70)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTS
T ss_pred             CCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccC
Confidence            3455799999999999999999999999999999999999999999999999987643

>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=99.18  E-value=3.4e-12  Score=99.75  Aligned_cols=60  Identities=20%  Similarity=0.407  Sum_probs=52.5

Q ss_pred             CcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhcc
Q psy8148         321 TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKN  383 (390)
Q Consensus       321 ~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~~  383 (390)
                      +.++..|+   ..|+..|..++||+..++.+||..+||+..+|++||||||+|+|+......+
T Consensus        12 ~~~t~~Ql---~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~~~~~   71 (75)
T 2da5_A           12 KERAPEQL---RALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETKKSG   71 (75)
T ss_dssp             CCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSCSSCC
T ss_pred             ccCCHHHH---HHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhhcccC
Confidence            34555555   9999999999999999999999999999999999999999999987655443

>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=99.17  E-value=8e-12  Score=96.03  Aligned_cols=58  Identities=17%  Similarity=0.456  Sum_probs=53.4

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcc
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  323 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~  323 (390)
                      +....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|+|++.|...
T Consensus         9 r~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2da1_A            9 RPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSG   66 (70)
T ss_dssp             SCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCC
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhc
Confidence            3455799999999999999999999999999999999999999999999999987653

>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=99.17  E-value=1.6e-11  Score=96.90  Aligned_cols=58  Identities=26%  Similarity=0.491  Sum_probs=53.6

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcc
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  323 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~  323 (390)
                      +....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|||+|.|...
T Consensus        19 r~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   76 (80)
T 2dmt_A           19 RSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSG   76 (80)
T ss_dssp             CSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCC
T ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhccc
Confidence            3445799999999999999999999999999999999999999999999999988754

>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=99.17  E-value=1e-11  Score=95.57  Aligned_cols=57  Identities=26%  Similarity=0.531  Sum_probs=52.6

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      +....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|||+|+|..
T Consensus         9 r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~   65 (70)
T 2e1o_A            9 GGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRS   65 (70)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCC
Confidence            344579999999999999999999999999999999999999999999999998754

>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=99.16  E-value=5.9e-12  Score=100.35  Aligned_cols=65  Identities=31%  Similarity=0.468  Sum_probs=55.5

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcC---CCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhc
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDK---NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAK  382 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~---n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~  382 (390)
                      ++++.|+.++..+.   ..|+.+|..   ++||+..++.+||..+||+..||++||+|+|+|.++....+.
T Consensus         6 ~~rk~R~~~s~~q~---~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~~~~   73 (83)
T 2dmn_A            6 SGKKRKGNLPAESV---KILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQR   73 (83)
T ss_dssp             CCCCCCSSCCHHHH---HHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHTCCC
T ss_pred             CCCCCCCcCCHHHH---HHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHHHhc
Confidence            45566777777776   889998865   699999999999999999999999999999999988765543

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

Probab=99.16  E-value=2.1e-12  Score=101.93  Aligned_cols=62  Identities=19%  Similarity=0.245  Sum_probs=56.2

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcCC----CCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDKN----RYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~n----~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      .++++.|+.++..|.   ..|+..|..+    +||+..++.+||..+||+..+|++||||||+|+|+..
T Consensus         6 ~~~rr~Rt~ft~~Q~---~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~~   71 (80)
T 2da4_A            6 SGALQDRTQFSDRDL---ATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMG   71 (80)
T ss_dssp             CCCCCSSCCCCHHHH---HHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCHHHH---HHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhcc
Confidence            456677888888777   9999999999    9999999999999999999999999999999998843

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

Probab=99.15  E-value=4.3e-12  Score=98.55  Aligned_cols=59  Identities=22%  Similarity=0.356  Sum_probs=53.4

Q ss_pred             cCCCcchhhhhhhhhhhhhhhc-CCCCCCHHHHHHHHHhhCCCccccccccccccccccchhh
Q psy8148         318 RDRTPQQRSIQRSRNALKECYD-KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  379 (390)
Q Consensus       318 R~R~~~t~~q~~q~~~Le~~F~-~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~  379 (390)
                      +.|+.++..|.   ..|+..|. .++||+..++.+||..+||++.+|++||+|||+|+|+...
T Consensus         4 k~Rt~ft~~Q~---~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~~   63 (73)
T 2hi3_A            4 QTVSGPTEDQV---EILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   63 (73)
T ss_dssp             SCCSSCCHHHH---HHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHH---HHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhcc
Confidence            55677777777   99999999 4999999999999999999999999999999999998664

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

Probab=99.15  E-value=1.8e-11  Score=95.79  Aligned_cols=57  Identities=28%  Similarity=0.509  Sum_probs=53.4

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         268 VYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       268 ~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      ...|+..|+.+|+..|..++||+..++..||..+||+..||.+||+|||++.|....
T Consensus        12 R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~   68 (76)
T 2dn0_A           12 KNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKG   68 (76)
T ss_dssp             CCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCS
T ss_pred             CccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhcc
Confidence            456999999999999999999999999999999999999999999999999987644

>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=99.15  E-value=2.6e-11  Score=96.06  Aligned_cols=57  Identities=9%  Similarity=0.237  Sum_probs=52.9

Q ss_pred             ccccccCHHHHHHHHHHHhh----CCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         266 ETVYCFKERSRNALKECYDK----NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~----n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      +....|+..|+..|+..|..    ++||+..++.+||..+||++.||++||+|||+|.|.+
T Consensus        19 R~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~~   79 (80)
T 1wh5_A           19 RHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPSS   79 (80)
T ss_dssp             CCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSCC
T ss_pred             CCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCCC
Confidence            34457999999999999999    9999999999999999999999999999999998864

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

Probab=99.15  E-value=4.8e-12  Score=99.02  Aligned_cols=60  Identities=27%  Similarity=0.530  Sum_probs=53.9

Q ss_pred             CCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhh
Q psy8148         319 DRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRA  381 (390)
Q Consensus       319 ~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~  381 (390)
                      .|+.++..|+   ..|+..|..++||+..++.+||..+||+..+|++||+|||+|+|+.....
T Consensus        11 ~R~~ft~~Ql---~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~~~   70 (76)
T 2dn0_A           11 YKNKKSHEQL---SALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGSR   70 (76)
T ss_dssp             CCCCCCHHHH---HHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCSSS
T ss_pred             CCccCCHHHH---HHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhcccC
Confidence            4677777776   99999999999999999999999999999999999999999999965443

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

Probab=99.14  E-value=5.9e-12  Score=101.83  Aligned_cols=58  Identities=14%  Similarity=0.312  Sum_probs=50.8

Q ss_pred             cchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhc
Q psy8148         322 PQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAK  382 (390)
Q Consensus       322 ~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~  382 (390)
                      .++..|+   .+|+..|..++||+..++.+||..+||++.+|++||||||+|+++.....+
T Consensus        17 ~~t~~Ql---~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~~~~   74 (89)
T 2ecb_A           17 EKTAEQL---RVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKME   74 (89)
T ss_dssp             CCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCCC
T ss_pred             cCCHHHH---HHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHHHhh
Confidence            4455555   999999999999999999999999999999999999999999988555443

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

Probab=99.14  E-value=3e-11  Score=96.00  Aligned_cols=58  Identities=26%  Similarity=0.499  Sum_probs=54.0

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcc
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  323 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~  323 (390)
                      +....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|||+|+|...
T Consensus        24 r~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   81 (84)
T 2kt0_A           24 KTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQ   81 (84)
T ss_dssp             CCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCC
T ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHh
Confidence            3455799999999999999999999999999999999999999999999999998754

>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=99.14  E-value=5.4e-12  Score=97.83  Aligned_cols=62  Identities=32%  Similarity=0.497  Sum_probs=54.4

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcC---CCCCCHHHHHHHHHhhCCCccccccccccccccccchhh
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDK---NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  379 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~---n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~  379 (390)
                      ++++.|+.++..+.   ..|+..|..   ++||+..++.+||..+||+..+|++||+|+|+|+++...
T Consensus         6 ~~rr~R~~~~~~q~---~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~   70 (73)
T 1x2n_A            6 SGKNKRGVLPKHAT---NVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSGP   70 (73)
T ss_dssp             SSCCSSCCCCHHHH---HHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCcCCHHHH---HHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhcccccc
Confidence            45566777777776   999999965   999999999999999999999999999999999988654

>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=99.14  E-value=3.1e-11  Score=107.47  Aligned_cols=139  Identities=16%  Similarity=0.298  Sum_probs=86.3

Q ss_pred             hcCChhHHHHHHHcCCCccccccchhhhhhHHHHHHhhhcHHHHHHHHhcCCCCccc-----------------hHHHHH
Q psy8148         163 QSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKY-----------------HAELQQ  225 (390)
Q Consensus       163 ~~~~~~~l~~fl~~lp~~~~~~~~e~v~rAra~v~~h~~~f~el~~~L~~~~F~~~~-----------------h~~lq~  225 (390)
                      +.+|++.|..|-+.+..            .|....+.+.+...++..|.+..|+...                 .+.|+ 
T Consensus         2 ~~~~~~~~~~~~~~~k~------------~r~~lg~tQ~~vg~~lg~l~g~~~sq~ti~rfE~l~lS~knm~klkPlL~-   68 (160)
T 1e3o_C            2 EPSDLEELEQFAKTFKQ------------RRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMSKLKPLLE-   68 (160)
T ss_dssp             CSCCHHHHHHHHHHHHH------------HHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHHTCSCHHHHHHHHHHHH-
T ss_pred             CCCcHHHHHHHHHHHHH------------HHHHcCCCHHHHHHhhccccCCCcCccccccccccCCChHHHHhcchhHH-
Confidence            45788888888776633            2445566777777777888777776421                 12222 


Q ss_pred             HHHh-hhhhHH-HhhhCCCCCcccccccccCCCCCCcccCCCccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCC
Q psy8148         226 LWMR-GHYKEH-AKIRGRDLGAVDKYRIRKKFPLPKTIWDGEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGL  303 (390)
Q Consensus       226 lw~~-ahY~e~-e~~rgrpL~~v~kyr~Rkk~p~P~ti~dge~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgL  303 (390)
                      .|++ +.-... ....+.+ +.+..       |.........+.+..|+..|+.+|+..|..++||+..++..||..+||
T Consensus        69 ~WL~e~e~~~~~~~~~~s~-~~~~~-------~~~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L  140 (160)
T 1e3o_C           69 KWLNDAEANLSSDSSLSSP-SALNS-------PGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNM  140 (160)
T ss_dssp             HHHHHHC------------------------------------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTC
T ss_pred             HHHHhhhcccccCCCCCCC-CCcCC-------CCCCCCCCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCC
Confidence            4443 211100 0000000 00000       000000112345567999999999999999999999999999999999


Q ss_pred             CchhcccccccccccCCCc
Q psy8148         304 TLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       304 s~~QV~~WFqNRR~R~R~~  322 (390)
                      ++.||++||+|||+|.|+.
T Consensus       141 ~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C          141 EKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             CHHHHHHHHHHHHHHHTSC
T ss_pred             ChHHhhHhhHHhhhhhhcc
Confidence            9999999999999998863

>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=99.14  E-value=7.3e-12  Score=100.24  Aligned_cols=62  Identities=32%  Similarity=0.582  Sum_probs=54.4

Q ss_pred             ccCCCcchhhhhhhhhhhhhhh---cCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhh
Q psy8148         317 QRDRTPQQRSIQRSRNALKECY---DKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRA  381 (390)
Q Consensus       317 ~R~R~~~t~~q~~q~~~Le~~F---~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~  381 (390)
                      +|.|+.++..+.   ..|+..|   ..++||+..++.+||..+||+..+|++||+|||+|+|+.....
T Consensus         2 rr~R~~ft~~q~---~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~   66 (87)
T 1b72_B            2 RRKRRNFNKQAT---EILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKF   66 (87)
T ss_dssp             -CCCCCCCHHHH---HHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGGG
T ss_pred             CCCCCCCCHHHH---HHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhccccc
Confidence            456777777666   9999999   8999999999999999999999999999999999998865443

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

Probab=99.14  E-value=6.7e-12  Score=97.50  Aligned_cols=61  Identities=30%  Similarity=0.498  Sum_probs=54.6

Q ss_pred             ccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhh
Q psy8148         317 QRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR  380 (390)
Q Consensus       317 ~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r  380 (390)
                      .+.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||||||+|+|+....
T Consensus         7 ~~~Rt~ft~~Ql---~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~   67 (74)
T 2ly9_A            7 FGIRAKKTKEQL---AELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKSN   67 (74)
T ss_dssp             CCTTCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTTCS
T ss_pred             CCCCcCCCHHHH---HHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhCcC
Confidence            456777777777   9999999999999999999999999999999999999999999986543

>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=99.14  E-value=1.1e-11  Score=94.89  Aligned_cols=56  Identities=21%  Similarity=0.363  Sum_probs=52.1

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      ....|+..|+..|+..|..++||+..++..||..+||++.||.+||+|||++.|..
T Consensus         5 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~   60 (68)
T 1ahd_P            5 GRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   60 (68)
T ss_dssp             TTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHh
Confidence            34569999999999999999999999999999999999999999999999988754

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

Probab=99.14  E-value=1.4e-11  Score=94.32  Aligned_cols=56  Identities=30%  Similarity=0.449  Sum_probs=52.2

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      ....|+..|+.+|+..|..++||+..++..||..+||++.+|.+||+|||++.|..
T Consensus         5 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~   60 (68)
T 1zq3_P            5 TRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQ   60 (68)
T ss_dssp             CSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHH
Confidence            34579999999999999999999999999999999999999999999999998764

>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=99.13  E-value=1.3e-11  Score=95.58  Aligned_cols=58  Identities=33%  Similarity=0.608  Sum_probs=53.0

Q ss_pred             ccccCHHHHHHHHHHH---hhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcchh
Q psy8148         268 VYCFKERSRNALKECY---DKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR  325 (390)
Q Consensus       268 ~~~Fs~~q~~~Le~~F---~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t~  325 (390)
                      ...|+..++.+|+.+|   ..++||+..++..||..+||+..||.+||+|+|+|.|.....
T Consensus         5 R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~   65 (73)
T 1puf_B            5 RRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGK   65 (73)
T ss_dssp             CCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTT
T ss_pred             CCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccccccc
Confidence            3468999999999999   899999999999999999999999999999999998765443

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

Probab=99.13  E-value=1.4e-11  Score=94.25  Aligned_cols=56  Identities=25%  Similarity=0.453  Sum_probs=52.2

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcc
Q psy8148         268 VYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  323 (390)
Q Consensus       268 ~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~  323 (390)
                      ...|+..|+.+|+..|..++||+..++..||..+||++.+|.+||+|||.+.|...
T Consensus         6 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~   61 (68)
T 1ftt_A            6 RVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA   61 (68)
T ss_dssp             CSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhh
Confidence            34699999999999999999999999999999999999999999999999987654

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

Probab=99.13  E-value=1.8e-11  Score=96.59  Aligned_cols=58  Identities=22%  Similarity=0.477  Sum_probs=53.6

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcc
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  323 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~  323 (390)
                      +....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|||+|+|...
T Consensus         9 r~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   66 (80)
T 2cue_A            9 RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREE   66 (80)
T ss_dssp             CCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHh
Confidence            4455799999999999999999999999999999999999999999999999988754

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

Probab=99.13  E-value=1.1e-11  Score=94.59  Aligned_cols=50  Identities=26%  Similarity=0.559  Sum_probs=47.3

Q ss_pred             CHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         272 KERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       272 s~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      +..|+.+|+..|..++||+..++.+||..+|||.+||++||+|||.+.|.
T Consensus        12 ~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kk   61 (66)
T 3nau_A           12 TKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR   61 (66)
T ss_dssp             CHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhc
Confidence            46899999999999999999999999999999999999999999988764

>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=99.13  E-value=2e-11  Score=96.03  Aligned_cols=58  Identities=21%  Similarity=0.310  Sum_probs=53.3

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcc
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  323 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~  323 (390)
                      +....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|||+|.|...
T Consensus        19 r~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   76 (80)
T 2da3_A           19 RLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSG   76 (80)
T ss_dssp             TCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhc
Confidence            3445799999999999999999999999999999999999999999999999987753

>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=99.12  E-value=2.3e-11  Score=97.48  Aligned_cols=54  Identities=28%  Similarity=0.477  Sum_probs=50.9

Q ss_pred             ccccCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         268 VYCFKERSRNALKECYDK---NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       268 ~~~Fs~~q~~~Le~~F~~---n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      ...|+..|+.+|+.+|..   ++||+..++..||..+||+..||.+||+|+|+|.|.
T Consensus        31 r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k~   87 (87)
T 1mnm_C           31 GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   87 (87)
T ss_dssp             TCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTC
T ss_pred             CCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccC
Confidence            347999999999999999   999999999999999999999999999999998874

>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=99.12  E-value=8.5e-12  Score=94.85  Aligned_cols=48  Identities=17%  Similarity=0.475  Sum_probs=44.7

Q ss_pred             hhhhhhhhh-cCCCCCCHHHHHHHHHhhCCCccccccccccccccccch
Q psy8148         330 SRNALKECY-DKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  377 (390)
Q Consensus       330 q~~~Le~~F-~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~  377 (390)
                      +..+||+.| ..++||+..++.+||..+||+++||++||||||+|+|+.
T Consensus        11 ~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~~   59 (64)
T 1x2m_A           11 PNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPS   59 (64)
T ss_dssp             HHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCCS
T ss_pred             HHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCCC
Confidence            348999999 679999999999999999999999999999999999874

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

Probab=99.12  E-value=2.5e-11  Score=95.79  Aligned_cols=59  Identities=29%  Similarity=0.473  Sum_probs=53.8

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      +....|+..|+.+|+..|..++||+..++..||..+||++.+|.+||+|||+|.|....
T Consensus         9 r~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~   67 (80)
T 2dms_A            9 RERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQ   67 (80)
T ss_dssp             CCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTC
T ss_pred             CCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHH
Confidence            34457999999999999999999999999999999999999999999999999876543

>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=99.12  E-value=1.7e-11  Score=94.97  Aligned_cols=56  Identities=34%  Similarity=0.530  Sum_probs=51.4

Q ss_pred             cccccCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         267 TVYCFKERSRNALKECYDK---NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~---n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      ....|+..++.+|+.+|..   ++||+..++..||..+||+..||.+||+|+|+|.+..
T Consensus        10 ~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~   68 (73)
T 1x2n_A           10 KRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQS   68 (73)
T ss_dssp             SSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhcccc
Confidence            3447899999999999976   9999999999999999999999999999999988754

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

Probab=99.12  E-value=1.8e-11  Score=94.93  Aligned_cols=56  Identities=30%  Similarity=0.418  Sum_probs=52.0

Q ss_pred             cccccCHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         267 TVYCFKERSRNALKECYDK-NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~-n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      +...|+..|+.+|+..|.. ++||+..++..||..+||++.||.+||+|||+++|..
T Consensus         5 ~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~   61 (73)
T 2hi3_A            5 TVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS   61 (73)
T ss_dssp             CCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence            4457999999999999995 9999999999999999999999999999999998764

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

Probab=99.12  E-value=8.9e-12  Score=96.82  Aligned_cols=48  Identities=21%  Similarity=0.608  Sum_probs=45.4

Q ss_pred             hhhhhhhh-cCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         331 RNALKECY-DKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       331 ~~~Le~~F-~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      ...|+..| ..++||+..++.+||..+||++.+|++||||||+|+|+..
T Consensus        20 l~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~~   68 (72)
T 2cqx_A           20 NDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSG   68 (72)
T ss_dssp             TTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSCC
T ss_pred             HHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCCC
Confidence            38999999 9999999999999999999999999999999999999743

>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=99.11  E-value=2.7e-11  Score=94.90  Aligned_cols=56  Identities=27%  Similarity=0.493  Sum_probs=52.3

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      ....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|||+|.|..
T Consensus        12 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~   67 (77)
T 1nk2_P           12 RRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRA   67 (77)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhh
Confidence            44579999999999999999999999999999999999999999999999998764

>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=99.11  E-value=7.6e-12  Score=93.28  Aligned_cols=54  Identities=26%  Similarity=0.430  Sum_probs=48.5

Q ss_pred             CcchhhhhhhhhhhhhhhcC---CCCCCHHHHHHHHHhhCCCccccccccccccccccch
Q psy8148         321 TPQQRSIQRSRNALKECYDK---NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  377 (390)
Q Consensus       321 ~~~t~~q~~q~~~Le~~F~~---n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~  377 (390)
                      +.++..+.   ..|+..|..   ++||+..++.+||..+||+..+|++||+|||+|+|+.
T Consensus         3 ~~ft~~q~---~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A            3 HRFTKENV---RILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CSCCHHHH---HHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             CcCCHHHH---HHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            45555555   999999999   9999999999999999999999999999999999873

>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=99.11  E-value=1.9e-11  Score=93.54  Aligned_cols=55  Identities=36%  Similarity=0.610  Sum_probs=49.7

Q ss_pred             ccCHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         270 CFKERSRNALKECYD---KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       270 ~Fs~~q~~~Le~~F~---~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      .|+..++.+|+.+|.   .++||+..++..||..+||+..||.+||+|+|+|.+....
T Consensus         4 ~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~   61 (67)
T 3k2a_A            4 IFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMI   61 (67)
T ss_dssp             --CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC-
T ss_pred             cCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHH
Confidence            588999999999999   9999999999999999999999999999999999877543

>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=99.11  E-value=1e-11  Score=94.96  Aligned_cols=56  Identities=30%  Similarity=0.555  Sum_probs=52.1

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      ....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|+|++.|..
T Consensus         6 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~   61 (68)
T 1yz8_P            6 QRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   61 (68)
T ss_dssp             SCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHH
Confidence            34579999999999999999999999999999999999999999999999998754

>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=99.11  E-value=2.6e-11  Score=95.05  Aligned_cols=56  Identities=23%  Similarity=0.367  Sum_probs=52.3

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      ....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|||++.|..
T Consensus        16 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   71 (77)
T 1puf_A           16 KRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKI   71 (77)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence            44579999999999999999999999999999999999999999999999998754

>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=99.11  E-value=2.7e-11  Score=95.43  Aligned_cols=57  Identities=28%  Similarity=0.484  Sum_probs=53.0

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      +....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|||+|.|..
T Consensus         9 r~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   65 (80)
T 2dmq_A            9 RMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRN   65 (80)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHH
Confidence            445579999999999999999999999999999999999999999999999998764

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

Probab=99.10  E-value=1.3e-11  Score=93.70  Aligned_cols=49  Identities=22%  Similarity=0.407  Sum_probs=45.8

Q ss_pred             hhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccch
Q psy8148         329 RSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  377 (390)
Q Consensus       329 ~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~  377 (390)
                      .|+..|+..|..++||+..++.+||..+||++.+|++||||||+|.++.
T Consensus        13 ~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~~   61 (64)
T 2e19_A           13 NLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISV   61 (64)
T ss_dssp             HHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSCS
T ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCCC
Confidence            3459999999999999999999999999999999999999999998873

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

Probab=99.10  E-value=4.3e-11  Score=90.89  Aligned_cols=53  Identities=21%  Similarity=0.328  Sum_probs=49.7

Q ss_pred             ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       270 ~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      .+...|+..|+..|..++||+..++..||..+||+..+|++||+|||+|.+..
T Consensus         9 ~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~~   61 (64)
T 2e19_A            9 PPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISV   61 (64)
T ss_dssp             CCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSCS
T ss_pred             CccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCCC
Confidence            45688999999999999999999999999999999999999999999998764

>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=99.10  E-value=2.7e-11  Score=95.81  Aligned_cols=56  Identities=27%  Similarity=0.566  Sum_probs=52.1

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      ....|+..|+.+|+.+|..++||+..++..||..+||++.||.+||+|||+|.|..
T Consensus        21 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~   76 (81)
T 1fjl_A           21 SRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ   76 (81)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhh
Confidence            34569999999999999999999999999999999999999999999999998754

>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=99.10  E-value=6.9e-11  Score=93.68  Aligned_cols=56  Identities=11%  Similarity=0.213  Sum_probs=51.7

Q ss_pred             ccccccCHHHHHHHHHHHhh-----CCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         266 ETVYCFKERSRNALKECYDK-----NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~-----n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      +....|+..|+..|+ .|..     ++||+..++.+||..+||++.||++||+|||+|.+.+
T Consensus        19 R~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~s   79 (80)
T 1wh7_A           19 RFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPSS   79 (80)
T ss_dssp             CCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCCC
T ss_pred             CCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCCC
Confidence            345579999999999 7998     9999999999999999999999999999999998864

>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=99.09  E-value=4.6e-11  Score=95.13  Aligned_cols=56  Identities=38%  Similarity=0.513  Sum_probs=51.0

Q ss_pred             cccccCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         267 TVYCFKERSRNALKECYDK---NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~---n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      ....|+..++.+|+.+|..   ++||+..++..||..+||+..||.+||+|+|+|.+..
T Consensus        10 ~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~   68 (83)
T 2dmn_A           10 RKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPD   68 (83)
T ss_dssp             CCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHH
T ss_pred             CCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHH
Confidence            4456899999999999987   6999999999999999999999999999999998653

>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=99.09  E-value=2.8e-11  Score=95.86  Aligned_cols=57  Identities=19%  Similarity=0.362  Sum_probs=52.1

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      +....|+..|+.+|+..|..++||+..++..||..+||++.+|.+||+|||+|.|..
T Consensus        22 r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   78 (81)
T 1b8i_A           22 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE   78 (81)
T ss_dssp             --CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTT
T ss_pred             CCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhh
Confidence            345579999999999999999999999999999999999999999999999998764

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

Probab=99.09  E-value=3.9e-11  Score=93.12  Aligned_cols=58  Identities=29%  Similarity=0.500  Sum_probs=53.5

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      ....|+..++.+|+..|..++||+..++..||..+||++.+|.+||+|+|++.|....
T Consensus        12 ~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r   69 (75)
T 2m0c_A           12 NRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRER   69 (75)
T ss_dssp             CSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCC
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHh
Confidence            3457999999999999999999999999999999999999999999999999887544

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

Probab=99.09  E-value=1.5e-11  Score=100.20  Aligned_cols=63  Identities=19%  Similarity=0.450  Sum_probs=56.8

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhC---------------CCccccccccccccccccchhh
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITG---------------LTLTQVSNWFKNRRQRDRTPQQ  379 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lg---------------Ls~~qVk~WFqNRR~K~kk~~~  379 (390)
                      +++|.|+.++..++   ..|+..|..++||+..++++||..++               |+..+|++||||||+|+|+...
T Consensus         6 ~~rr~R~~ft~~ql---~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~   82 (95)
T 2cuf_A            6 SGRGSRFTWRKECL---AVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRAN   82 (95)
T ss_dssp             CCCCCSCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCCHHHH---HHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhh
Confidence            45667778887776   99999999999999999999999999               9999999999999999998765


Q ss_pred             h
Q psy8148         380 R  380 (390)
Q Consensus       380 r  380 (390)
                      .
T Consensus        83 ~   83 (95)
T 2cuf_A           83 I   83 (95)
T ss_dssp             C
T ss_pred             c
Confidence            4

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

Probab=99.08  E-value=1.4e-11  Score=100.74  Aligned_cols=60  Identities=20%  Similarity=0.424  Sum_probs=53.7

Q ss_pred             cccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         316 RQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       316 R~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      ..+.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||||||+|+|+..
T Consensus        25 ~~r~Rt~ft~~Ql---~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   84 (96)
T 3nar_A           25 STGKICKKTPEQL---HMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGN   84 (96)
T ss_dssp             --CCSSSSCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTC
T ss_pred             CCCCCccCCHHHH---HHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhc
Confidence            4456777887777   99999999999999999999999999999999999999999999865

>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=99.08  E-value=4.7e-11  Score=105.81  Aligned_cols=56  Identities=25%  Similarity=0.429  Sum_probs=51.6

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      .++.|+..|+..|+..|..++||+..++..||..+||++.||++||+|||+|.|+.
T Consensus        99 ~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A           99 KRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             CCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             CCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            34578999999999999999999999999999999999999999999999998763

>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=99.08  E-value=3.1e-11  Score=96.53  Aligned_cols=58  Identities=33%  Similarity=0.608  Sum_probs=53.3

Q ss_pred             ccccCHHHHHHHHHHH---hhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcchh
Q psy8148         268 VYCFKERSRNALKECY---DKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR  325 (390)
Q Consensus       268 ~~~Fs~~q~~~Le~~F---~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t~  325 (390)
                      ...|+..++.+|+.+|   ..++||+..++..||..+||+..||.+||+|+|+|.|.....
T Consensus         5 R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~   65 (87)
T 1b72_B            5 RRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGK   65 (87)
T ss_dssp             CCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGG
T ss_pred             CCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhcccc
Confidence            3468999999999999   899999999999999999999999999999999999876543

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

Probab=99.08  E-value=3e-11  Score=97.67  Aligned_cols=55  Identities=15%  Similarity=0.280  Sum_probs=51.6

Q ss_pred             ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       270 ~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      .|+..|+.+|+..|..++||+..++.+||..+||+..||++||+|||+|++....
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~   71 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEE   71 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCS
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHH
Confidence            6889999999999999999999999999999999999999999999998876544

>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=99.08  E-value=1.8e-11  Score=98.11  Aligned_cols=60  Identities=23%  Similarity=0.402  Sum_probs=53.6

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcC---CCCCCHHHHHHHHHhhCCCccccccccccccccccc
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDK---NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  376 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~---n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk  376 (390)
                      ..+.+.|+.++..+.   ..|+..|..   ++||+..++.+||..+||+..+|++||+|||+|+|.
T Consensus        25 ~~~~k~r~~ft~~q~---~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k~   87 (87)
T 1mnm_C           25 STKPYRGHRFTKENV---RILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   87 (87)
T ss_dssp             ESSCCTTCCCCHHHH---HHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCcCCHHHH---HHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccC
Confidence            445556777887777   999999999   999999999999999999999999999999999873

>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=99.08  E-value=4.3e-11  Score=95.19  Aligned_cols=55  Identities=25%  Similarity=0.437  Sum_probs=52.0

Q ss_pred             ccCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         270 CFKERSRNALKECYDK---NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       270 ~Fs~~q~~~Le~~F~~---n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      .|+..|+.+|+.+|..   ++||+..++..||..+||+..||.+||+|+|+|.|....
T Consensus         8 rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~~   65 (83)
T 1le8_B            8 RFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITI   65 (83)
T ss_dssp             CCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHcccccccc
Confidence            4899999999999999   999999999999999999999999999999999987644

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

Probab=99.08  E-value=4.6e-11  Score=92.14  Aligned_cols=55  Identities=27%  Similarity=0.437  Sum_probs=51.3

Q ss_pred             ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       270 ~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      ..+..++..|+..|..++||+..++..||..+||++.||++||+|||+|+|....
T Consensus        10 ~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~~   64 (69)
T 2l9r_A           10 HMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQL   64 (69)
T ss_dssp             CCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSSS
T ss_pred             cCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhhh
Confidence            4578899999999999999999999999999999999999999999999987644

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

Probab=99.07  E-value=5.4e-11  Score=96.70  Aligned_cols=58  Identities=26%  Similarity=0.418  Sum_probs=53.5

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcc
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  323 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~  323 (390)
                      +....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|||.|+|...
T Consensus        19 r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~   76 (93)
T 3a01_A           19 KPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQT   76 (93)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhh
Confidence            3455799999999999999999999999999999999999999999999999987653

>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=99.07  E-value=4.7e-11  Score=93.19  Aligned_cols=55  Identities=22%  Similarity=0.381  Sum_probs=51.4

Q ss_pred             cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcc
Q psy8148         269 YCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  323 (390)
Q Consensus       269 ~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~  323 (390)
                      ..|+..|+.+|+..|..++||+..++..||..+||+..||.+||+|||++.|...
T Consensus        12 ~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~   66 (75)
T 2da5_A           12 KERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEE   66 (75)
T ss_dssp             CCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSS
T ss_pred             ccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhh
Confidence            3588999999999999999999999999999999999999999999999987654

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

Probab=99.07  E-value=3.6e-11  Score=96.62  Aligned_cols=57  Identities=21%  Similarity=0.367  Sum_probs=52.6

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      +....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|||+|.|..
T Consensus        30 r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~   86 (88)
T 2r5y_A           30 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   86 (88)
T ss_dssp             -CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhh
Confidence            455679999999999999999999999999999999999999999999999998764

>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=99.06  E-value=1.8e-11  Score=97.46  Aligned_cols=57  Identities=23%  Similarity=0.354  Sum_probs=50.9

Q ss_pred             CCcchhhhhhhhhhhhhhhcC---CCCCCHHHHHHHHHhhCCCccccccccccccccccchhh
Q psy8148         320 RTPQQRSIQRSRNALKECYDK---NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  379 (390)
Q Consensus       320 R~~~t~~q~~q~~~Le~~F~~---n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~  379 (390)
                      ++.++..+.   ..|+..|..   ++||+..++.+||..+||+..+|++||+|||+|+|+...
T Consensus         6 r~rft~~q~---~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~~   65 (83)
T 1le8_B            6 GHRFTKENV---RILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITI   65 (83)
T ss_dssp             CCCCCHHHH---HHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCHHHH---HHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHcccccccc
Confidence            344676666   999999999   999999999999999999999999999999999998653

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

Probab=99.06  E-value=1.5e-11  Score=110.10  Aligned_cols=65  Identities=28%  Similarity=0.438  Sum_probs=51.3

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhh
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRA  381 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~  381 (390)
                      .+++|.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||||||+|+|+.....
T Consensus        97 ~~~rr~Rt~ft~~Ql---~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~  161 (164)
T 2xsd_C           97 GRKRKKRTSIEVGVK---GALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTPAA  161 (164)
T ss_dssp             ---------CCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC--
T ss_pred             ccCCCCceeccHHHH---HHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhccCCC
Confidence            456667888888777   99999999999999999999999999999999999999999999966543

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

Probab=99.06  E-value=5.5e-11  Score=97.14  Aligned_cols=59  Identities=20%  Similarity=0.426  Sum_probs=54.3

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      +....|+..|+.+|+..|..++||+..++..||..+||+..||++||+|||.|.|....
T Consensus        27 r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~l   85 (96)
T 3nar_A           27 GKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNL   85 (96)
T ss_dssp             CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTCC
T ss_pred             CCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhcc
Confidence            34457999999999999999999999999999999999999999999999999988644

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

Probab=99.05  E-value=2.3e-11  Score=96.02  Aligned_cols=56  Identities=20%  Similarity=0.325  Sum_probs=52.1

Q ss_pred             ccccccCHHHHHHHHHHHhhC----CCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         266 ETVYCFKERSRNALKECYDKN----RYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n----~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      +....|+..|+.+|+.+|..+    +||+..++..||..+||++.||.+||+|||+|.|.
T Consensus        10 r~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk   69 (80)
T 2da4_A           10 QDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRL   69 (80)
T ss_dssp             CSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhh
Confidence            344579999999999999999    99999999999999999999999999999998875

>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=99.05  E-value=3.7e-11  Score=105.91  Aligned_cols=55  Identities=25%  Similarity=0.423  Sum_probs=51.7

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      .+..|+..|+.+|+.+|..++||+..++..||..+||++.||++||+|||+|.|+
T Consensus        96 ~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           96 RRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            3457999999999999999999999999999999999999999999999999875

>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=99.04  E-value=6.1e-11  Score=90.11  Aligned_cols=51  Identities=16%  Similarity=0.451  Sum_probs=46.8

Q ss_pred             HHHHHHHHHHH-hhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcc
Q psy8148         273 ERSRNALKECY-DKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  323 (390)
Q Consensus       273 ~~q~~~Le~~F-~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~  323 (390)
                      ..++.+|+..| ..++||+..++.+||..+||++.||++||+|||+++|...
T Consensus         9 ~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~~~   60 (64)
T 1x2m_A            9 AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPSG   60 (64)
T ss_dssp             SCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCCSS
T ss_pred             chHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCCCC
Confidence            45689999999 5799999999999999999999999999999999998653

>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=99.03  E-value=3.2e-11  Score=105.88  Aligned_cols=103  Identities=23%  Similarity=0.337  Sum_probs=70.6

Q ss_pred             CcccCCCccccccCHHH--HHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcchhhhhhhhhhhhh
Q psy8148         259 KTIWDGEETVYCFKERS--RNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNALKE  336 (390)
Q Consensus       259 ~ti~dge~t~~~Fs~~q--~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t~~q~~q~~~Le~  336 (390)
                      .||+.-+....+|++..  ...|+.|+....-.....           ...+.  -..+++|.|+.++..|.   ..|+.
T Consensus        41 tti~rfe~l~ls~knm~kLkPlL~~wl~e~e~~~~~~-----------~~~~~--~~~~~rr~Rt~ft~~Q~---~~Le~  104 (146)
T 1au7_A           41 TTICRFENLQLSFKNACKLKAILSKWLEEAEQVGALY-----------NEKVG--ANERKRKRRTTISIAAK---DALER  104 (146)
T ss_dssp             HHHHHHHTTCSBHHHHHHHHHHHHHHHHHCCC-----------------------------CCCCCCCHHHH---HHHHH
T ss_pred             chHHHHhccCCChHHHHhcchHHHHHHHHhhcccCcc-----------CcccC--CCCCCCCCCcCccHHHH---HHHHH
Confidence            35555555455555443  356778877554222110           00111  12456667888888777   99999


Q ss_pred             hhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccch
Q psy8148         337 CYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  377 (390)
Q Consensus       337 ~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~  377 (390)
                      .|..++||+..++.+||..+||+..+|++||||||+|+|+.
T Consensus       105 ~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A          105 HFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             HHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             HHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            99999999999999999999999999999999999999984

>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=99.03  E-value=3.9e-11  Score=96.83  Aligned_cols=56  Identities=21%  Similarity=0.427  Sum_probs=50.1

Q ss_pred             chhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhh
Q psy8148         323 QQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRA  381 (390)
Q Consensus       323 ~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~  381 (390)
                      ++..|+   ..|+..|..++||+..++.+||..+||+..+|++||||||+|+++.....
T Consensus        20 ~t~~Ql---~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~~~   75 (89)
T 2dmp_A           20 KTQGQV---KILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAV   75 (89)
T ss_dssp             CCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCSCC
T ss_pred             CCHHHH---HHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhHhh
Confidence            454555   99999999999999999999999999999999999999999998866554

>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=99.02  E-value=2.8e-11  Score=92.63  Aligned_cols=54  Identities=37%  Similarity=0.615  Sum_probs=46.3

Q ss_pred             hhhhhhhhhc---CCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhcc
Q psy8148         330 SRNALKECYD---KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKN  383 (390)
Q Consensus       330 q~~~Le~~F~---~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~~  383 (390)
                      +...|+..|.   .++||+..++.+||..+||+..||++||+|+|+|.++....+++
T Consensus         9 ~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~~~   65 (67)
T 3k2a_A            9 ATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQSN   65 (67)
T ss_dssp             HHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC-----
T ss_pred             HHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHHHHhc
Confidence            4488999998   99999999999999999999999999999999999997766554

>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=99.01  E-value=3.8e-11  Score=106.93  Aligned_cols=61  Identities=26%  Similarity=0.540  Sum_probs=53.2

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccch
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  377 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~  377 (390)
                      .+++|.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||||||+|+|+.
T Consensus        99 ~~~rr~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C           99 SRRRKKRTSIETNIR---VALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             -----CCCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCcCccccCHHHH---HHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            366777888888777   9999999999999999999999999999999999999999999984

>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=99.01  E-value=8.1e-11  Score=96.25  Aligned_cols=57  Identities=25%  Similarity=0.420  Sum_probs=52.5

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      +....|+..|+.+|+..|..++||+..++..||..+||++.||.+||+|||+|.|..
T Consensus        36 r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   92 (97)
T 1b72_A           36 GLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKR   92 (97)
T ss_dssp             -CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHH
Confidence            345679999999999999999999999999999999999999999999999988753

>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=99.00  E-value=9e-11  Score=94.68  Aligned_cols=55  Identities=22%  Similarity=0.394  Sum_probs=51.2

Q ss_pred             ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       270 ~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      .|+..|+.+|+..|..++||+..++..||..+||+..||.+||+|||+|.|....
T Consensus        19 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~   73 (89)
T 2dmp_A           19 EKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQ   73 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCS
T ss_pred             cCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhH
Confidence            3789999999999999999999999999999999999999999999999876543

>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=99.00  E-value=7e-11  Score=97.63  Aligned_cols=64  Identities=31%  Similarity=0.468  Sum_probs=56.3

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhh---------------------CCCcccccccccccccc
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEIT---------------------GLTLTQVSNWFKNRRQR  373 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~l---------------------gLs~~qVk~WFqNRR~K  373 (390)
                      +.+|.|+.++..+.   .+|++.|..++||+..++++||..+                     ++++.+|++||||||++
T Consensus         5 ~~Rr~Rt~ft~~ql---~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k   81 (102)
T 2da6_A            5 SSGRNRFKWGPASQ---QILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKE   81 (102)
T ss_dssp             CSCCCCCCCCHHHH---HHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCccCCHHHH---HHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHH
Confidence            45667788887666   9999999999999999999999999                     79999999999999999


Q ss_pred             ccchhhhh
Q psy8148         374 DRTPQQRA  381 (390)
Q Consensus       374 ~kk~~~r~  381 (390)
                      +++.....
T Consensus        82 ~kr~~~~~   89 (102)
T 2da6_A           82 EAFRQKLA   89 (102)
T ss_dssp             HHHHHHHH
T ss_pred             HHHhhHhh
Confidence            98866443

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

Probab=99.00  E-value=6.5e-11  Score=97.51  Aligned_cols=62  Identities=29%  Similarity=0.537  Sum_probs=51.8

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHh------------------hC---CCcccccccccccccc
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEI------------------TG---LTLTQVSNWFKNRRQR  373 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~------------------lg---Ls~~qVk~WFqNRR~K  373 (390)
                      +++|.|+.++..++   ..|+..|..++||+..++++||..                  +|   |+..+|++||||||++
T Consensus         8 k~rr~Rt~ft~~Ql---~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k   84 (99)
T 1lfb_A            8 KGRRNRFKWGPASQ---QILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE   84 (99)
T ss_dssp             -----CCCCCHHHH---HHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCcCcCHHHH---HHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHH
Confidence            45566778887776   999999999999999999999999                  88   9999999999999999


Q ss_pred             ccchhh
Q psy8148         374 DRTPQQ  379 (390)
Q Consensus       374 ~kk~~~  379 (390)
                      +++...
T Consensus        85 ~k~k~~   90 (99)
T 1lfb_A           85 EAFRHK   90 (99)
T ss_dssp             TSCCC-
T ss_pred             HHHhch
Confidence            987553

>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=99.00  E-value=5.7e-11  Score=104.70  Aligned_cols=60  Identities=25%  Similarity=0.438  Sum_probs=55.0

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccc
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  376 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk  376 (390)
                      .+++|.|+.++..+.   ..|+..|..++||+..++.+||..+||+..+|++||||||+|+|+
T Consensus        91 ~~~rr~Rt~ft~~q~---~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           91 SKKRKRRTSFTPQAI---EALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             CCCCCCCCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCcccCHHHH---HHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            356667888887777   999999999999999999999999999999999999999999987

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

Probab=98.96  E-value=1.8e-10  Score=93.86  Aligned_cols=58  Identities=19%  Similarity=0.543  Sum_probs=53.2

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhC---------------CCchhcccccccccccCCCcc
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITG---------------LTLTQVSNWFKNRRQRDRTPQ  323 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tg---------------Ls~~QV~~WFqNRR~R~R~~~  323 (390)
                      +....|+..|+.+|+.+|..++||+..++..||..+|               |+..+|.+||+|||++.|...
T Consensus         9 r~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~   81 (95)
T 2cuf_A            9 GSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRA   81 (95)
T ss_dssp             CCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHh
Confidence            3455789999999999999999999999999999999               999999999999999987643

>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=98.96  E-value=1.1e-10  Score=103.50  Aligned_cols=61  Identities=26%  Similarity=0.480  Sum_probs=55.6

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccch
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  377 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~  377 (390)
                      .+++|.|+.++..+.   ..|+..|..++||+..++.+||..+||+..+|++||||||+|+|+.
T Consensus        94 ~~~rr~Rt~ft~~Q~---~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A           94 QARKRKRTSIENRVR---WSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             CCSCCCCCCCCHHHH---HHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             cCCCCCCcccCHHHH---HHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            466677888888777   9999999999999999999999999999999999999999999874

>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens}

Probab=98.96  E-value=1.2e-10  Score=93.95  Aligned_cols=56  Identities=34%  Similarity=0.456  Sum_probs=51.2

Q ss_pred             cccccCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         267 TVYCFKERSRNALKECYDK---NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~---n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      ....|+.+++.+|+.||..   +|||+..+|..||..|||+..||++||+|+|+|.+..
T Consensus         8 ~~~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~   66 (89)
T 2lk2_A            8 HSHMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPD   66 (89)
T ss_dssp             CCCCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHH
T ss_pred             ccccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhH
Confidence            3456889999999999986   9999999999999999999999999999999988654

>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=98.95  E-value=1.3e-10  Score=88.91  Aligned_cols=59  Identities=20%  Similarity=0.302  Sum_probs=52.8

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcC-CCCCCHHHHHHHHHhhCCCccccccccccccccccc
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDK-NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  376 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~-n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk  376 (390)
                      ..+|.|+.++..|+   ..|+..|+. ++||+.+++..||..+||++.+|++||||+|.-.+-
T Consensus         6 ~~kR~RT~~s~eQL---~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~~~~   65 (71)
T 1wi3_A            6 SGPRSRTKISLEAL---GILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             CCCCCCCCCCSHHH---HHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             CCCCCCccCCHHHH---HHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceeeecC
Confidence            45667788887777   999999999 999999999999999999999999999999986554

>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=98.94  E-value=4.5e-10  Score=85.83  Aligned_cols=54  Identities=17%  Similarity=0.244  Sum_probs=49.4

Q ss_pred             ccccccCHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhCCCchhcccccccccccC
Q psy8148         266 ETVYCFKERSRNALKECYDK-NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRD  319 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~-n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~  319 (390)
                      +.+..|+.+|+.+|+..|.. ++||+...+..||..|||++.+|.+||||+|---
T Consensus         9 R~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~~   63 (71)
T 1wi3_A            9 RSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHV   63 (71)
T ss_dssp             CCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHC
T ss_pred             CCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceeee
Confidence            34457999999999999999 9999999999999999999999999999998543

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

Probab=98.92  E-value=1.8e-10  Score=102.67  Aligned_cols=64  Identities=25%  Similarity=0.378  Sum_probs=53.0

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhh
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR  380 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r  380 (390)
                      .+.+|.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||||||+|.|+....
T Consensus        95 ~~~rr~Rt~ft~~q~---~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~~  158 (164)
T 2d5v_A           95 NTPKKPRLVFTDVQR---RTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWLE  158 (164)
T ss_dssp             -----CCCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC---
T ss_pred             CCCCCCCCcCCHHHH---HHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccCCC
Confidence            345667788887777   9999999999999999999999999999999999999999999985543

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

Probab=98.91  E-value=5.7e-10  Score=99.41  Aligned_cols=59  Identities=27%  Similarity=0.455  Sum_probs=53.3

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      +.+..|+..|+.+|+.+|..++||+..++..||..+||++.||++||+|||+|.|....
T Consensus        99 r~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~  157 (164)
T 2d5v_A           99 KPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWL  157 (164)
T ss_dssp             -CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC--
T ss_pred             CCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccCC
Confidence            45567999999999999999999999999999999999999999999999999987644

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

Probab=98.89  E-value=6.5e-10  Score=91.53  Aligned_cols=58  Identities=28%  Similarity=0.554  Sum_probs=52.1

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHH------------------hC---CCchhcccccccccccCCCcch
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEI------------------TG---LTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~------------------tg---Ls~~QV~~WFqNRR~R~R~~~t  324 (390)
                      ..+.|+..|+.+|+..|..++||+..++.+||..                  +|   |++.+|.+||+|||++.+....
T Consensus        12 ~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k~k~k~~   90 (99)
T 1lfb_A           12 NRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFRHK   90 (99)
T ss_dssp             -CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCCC-
T ss_pred             CCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHHHHHhch
Confidence            4457899999999999999999999999999999                  88   9999999999999998876543

>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=98.84  E-value=1e-09  Score=90.71  Aligned_cols=57  Identities=28%  Similarity=0.508  Sum_probs=51.8

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHh---------------------CCCchhcccccccccccCCCc
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEIT---------------------GLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~t---------------------gLs~~QV~~WFqNRR~R~R~~  322 (390)
                      +.++.|+..|+.+|+..|..++||+..++++||..+                     ++++.+|.+||+|||++.+..
T Consensus         8 r~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k~kr~   85 (102)
T 2da6_A            8 RNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEEAFR   85 (102)
T ss_dssp             CCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHHHHHh
Confidence            344568899999999999999999999999999999                     799999999999999988654

>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens}

Probab=98.84  E-value=3.8e-10  Score=91.04  Aligned_cols=54  Identities=37%  Similarity=0.497  Sum_probs=47.8

Q ss_pred             hhhhhhhhhcC---CCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhcc
Q psy8148         330 SRNALKECYDK---NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKN  383 (390)
Q Consensus       330 q~~~Le~~F~~---n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~~  383 (390)
                      +...|+.+|..   ++||+.+++.+||..+||+..||++||+|+|.|.++...+...
T Consensus        16 ~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~~~~~   72 (89)
T 2lk2_A           16 SVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRKDG   72 (89)
T ss_dssp             HHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHHHhcC
Confidence            34788888865   9999999999999999999999999999999999987766653

>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=98.72  E-value=2.6e-09  Score=82.09  Aligned_cols=44  Identities=34%  Similarity=0.528  Sum_probs=42.0

Q ss_pred             hhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccc
Q psy8148         329 RSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQ  372 (390)
Q Consensus       329 ~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~  372 (390)
                      .|+..|+.+|..+++|+.+++..||..+||+.+.|++||+|||+
T Consensus        15 ~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa   58 (71)
T 2da7_A           15 DHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKV   58 (71)
T ss_dssp             HHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhccc
Confidence            45699999999999999999999999999999999999999997

>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=98.71  E-value=1.1e-09  Score=100.36  Aligned_cols=61  Identities=28%  Similarity=0.512  Sum_probs=51.7

Q ss_pred             ccccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhC---------------------CCcccccccccccc
Q psy8148         313 KNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITG---------------------LTLTQVSNWFKNRR  371 (390)
Q Consensus       313 qNRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lg---------------------Ls~~qVk~WFqNRR  371 (390)
                      ..+++|.|+.++..+.   ..|++.|..++||+..++++||..++                     ++..+|++||+|||
T Consensus       112 ~~k~rr~R~~ft~~ql---~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR  188 (194)
T 1ic8_A          112 TKKGRRNRFKWGPASQ---QILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRR  188 (194)
T ss_dssp             -----CCCCCCCHHHH---HHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHH
T ss_pred             cccCCCCCcccCHHHH---HHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhh
Confidence            3456677888887777   99999999999999999999999999                     99999999999999


Q ss_pred             ccccc
Q psy8148         372 QRDRT  376 (390)
Q Consensus       372 ~K~kk  376 (390)
                      ++++.
T Consensus       189 ~~~k~  193 (194)
T 1ic8_A          189 KEEAF  193 (194)
T ss_dssp             HHCC-
T ss_pred             hhhhc
Confidence            99875

>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=98.66  E-value=8.1e-09  Score=79.32  Aligned_cols=47  Identities=32%  Similarity=0.497  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccC
Q psy8148         273 ERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRD  319 (390)
Q Consensus       273 ~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~  319 (390)
                      .+++.+|+.+|..|++|+.+++..||..+||+.+.|++||+|+|.+.
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~~   60 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVYQ   60 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhccccc
Confidence            45799999999999999999999999999999999999999999754

>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=98.52  E-value=1.6e-08  Score=92.74  Aligned_cols=56  Identities=27%  Similarity=0.533  Sum_probs=51.3

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhC---------------------CCchhcccccccccccCCC
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITG---------------------LTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tg---------------------Ls~~QV~~WFqNRR~R~R~  321 (390)
                      +.++.|+..|+.+|+..|..++||+..+|.+||..++                     ||..+|.+||+|||++.+.
T Consensus       117 r~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~~k~  193 (194)
T 1ic8_A          117 RNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAF  193 (194)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHHCC-
T ss_pred             CCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhhhhc
Confidence            4456789999999999999999999999999999999                     9999999999999998763

>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=98.52  E-value=4.1e-08  Score=97.38  Aligned_cols=51  Identities=27%  Similarity=0.541  Sum_probs=48.8

Q ss_pred             ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCC
Q psy8148         270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR  320 (390)
Q Consensus       270 ~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R  320 (390)
                      .|+..++..|+..|..++||+..+|.+||..+||+.+||++||+|||+|.|
T Consensus       371 ~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          371 AISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             SSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            477899999999999999999999999999999999999999999999976

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

Probab=98.48  E-value=5.9e-08  Score=90.33  Aligned_cols=55  Identities=29%  Similarity=0.575  Sum_probs=50.0

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhC---------------------CCchhcccccccccccCC
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITG---------------------LTLTQVSNWFKNRRQRDR  320 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tg---------------------Ls~~QV~~WFqNRR~R~R  320 (390)
                      +.++.|+..|+.+|+.+|..++||+..+|++||..+|                     ||..+|.+||+|||+...
T Consensus       144 R~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~~~~  219 (221)
T 2h8r_A          144 RNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEEA  219 (221)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHTTCC
T ss_pred             CCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhhhhh
Confidence            4455789999999999999999999999999999987                     899999999999998753

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

Probab=98.46  E-value=2.8e-08  Score=92.50  Aligned_cols=59  Identities=31%  Similarity=0.554  Sum_probs=51.1

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhC---------------------CCccccccccccccc
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITG---------------------LTLTQVSNWFKNRRQ  372 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lg---------------------Ls~~qVk~WFqNRR~  372 (390)
                      .+++|.|+.++..+.   ..|+..|..++||+..++++||..++                     |+..+|++||+|||+
T Consensus       140 ~k~RR~R~~ft~~ql---~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~  216 (221)
T 2h8r_A          140 KKMRRNRFKWGPASQ---QILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRK  216 (221)
T ss_dssp             --CCCCCCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHT
T ss_pred             CCCCCCCcCCCHHHH---HHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhh
Confidence            345667788887777   99999999999999999999999887                     889999999999999


Q ss_pred             ccc
Q psy8148         373 RDR  375 (390)
Q Consensus       373 K~k  375 (390)
                      +..
T Consensus       217 ~~~  219 (221)
T 2h8r_A          217 EEA  219 (221)
T ss_dssp             TCC
T ss_pred             hhh
Confidence            764

>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=98.43  E-value=2.5e-08  Score=98.89  Aligned_cols=47  Identities=30%  Similarity=0.579  Sum_probs=44.4

Q ss_pred             hhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCcccccccccccccccc
Q psy8148         329 RSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR  375 (390)
Q Consensus       329 ~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~k  375 (390)
                      .++..|++.|..++||+..++.+||..+||+.+||++||||||+|+|
T Consensus       375 ~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          375 QARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            34589999999999999999999999999999999999999999986

>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=97.82  E-value=3.5e-06  Score=56.90  Aligned_cols=21  Identities=29%  Similarity=0.526  Sum_probs=18.3

Q ss_pred             cccccccccccccccchhhhh
Q psy8148         361 TQVSNWFKNRRQRDRTPQQRA  381 (390)
Q Consensus       361 ~qVk~WFqNRR~K~kk~~~r~  381 (390)
                      +||++||||||+|+|+.....
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~   21 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFND   21 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHH
T ss_pred             CCceeccHHHHHHHHHHhHHH
Confidence            589999999999999977654

>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=96.14  E-value=0.00068  Score=45.66  Aligned_cols=20  Identities=30%  Similarity=0.557  Sum_probs=17.4

Q ss_pred             hhcccccccccccCCCcchh
Q psy8148         306 TQVSNWFKNRRQRDRTPQQR  325 (390)
Q Consensus       306 ~QV~~WFqNRR~R~R~~~t~  325 (390)
                      .||.+||+|||.|.|+....
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~   20 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFN   20 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHH
T ss_pred             CCceeccHHHHHHHHHHhHH
Confidence            48999999999999987664

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

Probab=89.85  E-value=0.17  Score=38.54  Aligned_cols=40  Identities=25%  Similarity=0.445  Sum_probs=37.6

Q ss_pred             HHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccc
Q psy8148         276 RNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNR  315 (390)
Q Consensus       276 ~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNR  315 (390)
                      +++|+.+|..........-..|+.+++|+..||+.||..|
T Consensus        18 ~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~k   57 (70)
T 2ys9_A           18 IQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSR   57 (70)
T ss_dssp             CHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             chHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHhc
Confidence            6899999999999999999999999999999999999654

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

Probab=84.18  E-value=0.28  Score=37.38  Aligned_cols=37  Identities=24%  Similarity=0.452  Sum_probs=35.2

Q ss_pred             hhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccc
Q psy8148         332 NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFK  368 (390)
Q Consensus       332 ~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFq  368 (390)
                      ..|++.|...+....++...|+.+++|+..||+-||-
T Consensus        19 e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa   55 (70)
T 2ys9_A           19 QPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFD   55 (70)
T ss_dssp             HHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHH
T ss_pred             hHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHH
Confidence            6789999999999999999999999999999999995

---

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	390
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	5e-10
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	8e-10
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	8e-10
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	4e-09
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	2e-09
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	4e-08
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	4e-09
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	1e-08
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	4e-09
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	7e-09
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	7e-09
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	4e-08
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	8e-09
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	8e-09
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	1e-08
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	1e-08
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	1e-08
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	5e-08
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	1e-08
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	6e-08
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	3e-08
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	1e-07
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	3e-08
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	1e-07
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	6e-08
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	3e-07
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	1e-07
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	1e-07
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	1e-07
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	4e-06
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	1e-07
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	2e-07
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	2e-07
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	5e-07
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	4e-07
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	2e-06
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	1e-06
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	1e-06
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	1e-06
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	1e-06
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	1e-06
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	2e-06
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	2e-06
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	3e-06
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	2e-06
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	4e-06
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	4e-06
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	5e-06
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	5e-06
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	1e-05
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	7e-06
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	2e-05
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	1e-05
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	1e-05
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	1e-05
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	2e-05
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	1e-05
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	3e-05
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	5e-05
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	7e-05
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	1e-04
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	3e-04
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	2e-04
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	2e-04

>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 = 52.8 bits (127), Expect = 5e-10
 Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 3/51 (5%)

Query: 271 FKERSRNALKECYD---KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
             + + N ++        + YP  DEK+Q++  T LTL QV+NWF N R+R
Sbjct: 9   LPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRR 59

>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 = 52.0 bits (125), Expect = 8e-10
 Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 8/63 (12%)

Query: 314 NRRQRDRTPQQRSIQRSRNALKECYD---KNRYPNPDEKRQLSEITGLTLTQVSNWFKNR 370
            + +R   P+      + N ++        + YP  DEK+Q++  T LTL QV+NWF N 
Sbjct: 2   GKNKRGVLPKH-----ATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINA 56

Query: 371 RQR 373
           R+R
Sbjct: 57  RRR 59

>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 = 52.1 bits (125), Expect = 8e-10
 Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 3/54 (5%)

Query: 271 FKERSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT 321
           F + +   L+  + KN    Y +      L + T L+  Q+ NW  NRR++++T
Sbjct: 5   FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

>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 = 50.2 bits (120), Expect = 4e-09
 Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 3/52 (5%)

Query: 328 QRSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT 376
           + +   L+  + KN    Y +      L + T L+  Q+ NW  NRR++++T
Sbjct: 7   KENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

>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 = 51.3 bits (123), Expect = 2e-09
 Identities = 11/52 (21%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 270 CFKERSRNALKECYDK-NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
             K    + L++ +    +YP+    + LS+    ++ ++  WF++RR +D+
Sbjct: 7   VNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

>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 = 47.5 bits (113), Expect = 4e-08
 Identities = 10/62 (16%), Positives = 27/62 (43%), Gaps = 7/62 (11%)

Query: 315 RRQRDRTPQQRSIQRSRNALKECYDK-NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
           +       +          L++ +    +YP+    + LS+    ++ ++  WF++RR +
Sbjct: 3   KDSPVNKVEPNDT------LEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQ 56

Query: 374 DR 375
           D+
Sbjct: 57  DK 58

>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 = 50.7 bits (121), Expect = 4e-09
 Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 4/71 (5%)

Query: 315 RRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
           RR+R     Q   I          +  N YP+ + K +L++  G+T++QVSNWF N+R R
Sbjct: 2   RRKRRNFNKQATEILN---EYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR 58

Query: 374 DRTPQQRAKNR 384
            +    + +  
Sbjct: 59  YKKNIGKFQEE 69

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Length = 73

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.6 bits (118), Expect = 1e-08
 Identities = 19/63 (30%), Positives = 36/63 (57%), Gaps = 3/63 (4%)

Query: 271 FKERSRNALKECYD---KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSI 327
           F +++   L E +     N YP+ + K +L++  G+T++QVSNWF N+R R +    +  
Sbjct: 8   FNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQ 67

Query: 328 QRS 330
           + +
Sbjct: 68  EEA 70

>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 = 49.9 bits (119), Expect = 4e-09
 Identities = 14/50 (28%), Positives = 28/50 (56%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
              ++R  L++ + + +  N  EK ++++  G+T  QV  WF N+R R +
Sbjct: 4   ISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53

>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 = 49.5 bits (118), Expect = 7e-09
 Identities = 16/55 (29%), Positives = 30/55 (54%), Gaps = 6/55 (10%)

Query: 321 TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
           +PQ R+       L++ + + +  N  EK ++++  G+T  QV  WF N+R R +
Sbjct: 5   SPQARAF------LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53

>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 = 50.0 bits (119), Expect = 7e-09
 Identities = 8/63 (12%), Positives = 19/63 (30%), Gaps = 2/63 (3%)

Query: 313 KNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQ 372
             R +   T +Q   ++     +    + +  +     Q    TG+    +  W  N + 
Sbjct: 17  TKRFRTKFTAEQ--KEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKN 74

Query: 373 RDR 375
              
Sbjct: 75  SGP 77

>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 = 48.1 bits (114), Expect = 4e-08
 Identities = 7/49 (14%), Positives = 15/49 (30%)

Query: 272 KERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
           KE+     +    + +  +     Q    TG+    +  W  N +    
Sbjct: 29  KEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGP 77

>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 = 49.4 bits (118), Expect = 8e-09
 Identities = 15/59 (25%), Positives = 30/59 (50%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQR 329
           F +    AL++ +++  YP+   + +L+    L   ++  WF NRR + R  ++   QR
Sbjct: 8   FTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQR 66

>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 = 49.4 bits (118), Expect = 8e-09
 Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 7/71 (9%)

Query: 315 RRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
           +R R   T +Q         L++ +++  YP+   + +L+    L   ++  WF NRR +
Sbjct: 2   QRNRTSFTQEQIEA------LEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAK 55

Query: 374 DRTPQQRAKNR 384
            R  ++    R
Sbjct: 56  WRREEKLRNQR 66

>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 = 49.5 bits (118), Expect = 1e-08
 Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQ 328
             E+  + L+ CY  N  P+   K QL E+TGL+   +  WF+N+R +D+  +   ++
Sbjct: 10  LNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKK-RSIMMK 66

>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 = 49.1 bits (117), Expect = 1e-08
 Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 7/64 (10%)

Query: 313 KNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
           K  R R     +Q         L+ CY  N  P+   K QL E+TGL+   +  WF+N+R
Sbjct: 2   KTTRVRTVLNEKQLHT------LRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKR 55

Query: 372 QRDR 375
            +D+
Sbjct: 56  CKDK 59

>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 = 48.9 bits (117), Expect = 1e-08
 Identities = 11/56 (19%), Positives = 25/56 (44%), Gaps = 7/56 (12%)

Query: 321 TPQQRSIQRSRNALKECYDK-NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
           T Q  +I      L++ +    ++P+      LS+     +  +  WF+ RR +++
Sbjct: 1   TAQPNAI------LEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 50

>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 = 47.0 bits (112), Expect = 5e-08
 Identities = 7/35 (20%), Positives = 17/35 (48%)

Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
            ++P+      LS+     +  +  WF+ RR +++
Sbjct: 16  TKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 50

>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 = 48.7 bits (116), Expect = 1e-08
 Identities = 15/46 (32%), Positives = 26/46 (56%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
           F +  R  L   + +N+ P+ + +  +S+  GL L+ VSN+F N R
Sbjct: 5   FTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>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 = 46.4 bits (110), Expect = 6e-08
 Identities = 14/41 (34%), Positives = 24/41 (58%)

Query: 331 RNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
           R  L   + +N+ P+ + +  +S+  GL L+ VSN+F N R
Sbjct: 10  RRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>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 = 48.3 bits (115), Expect = 3e-08
 Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 11/80 (13%)

Query: 309 SNWFKNRRQRDR----TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVS 364
           +NW   R  R +    T  Q         L++ +  N Y   D + +++ +  LT  QV 
Sbjct: 5   ANWLHARSTRKKRCPYTKHQT------LELEKEFLFNMYLTRDRRYEVARLLNLTERQVK 58

Query: 365 NWFKNRRQRDRTPQQRAKNR 384
            WF+NRR + +    + + +
Sbjct: 59  IWFQNRRMKMKK-INKDRAK 77

>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 = 46.4 bits (110), Expect = 1e-07
 Identities = 13/54 (24%), Positives = 27/54 (50%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ 324
           + +     L++ +  N Y   D + +++ +  LT  QV  WF+NRR + +   +
Sbjct: 20  YTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINK 73

>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 = 48.0 bits (114), Expect = 3e-08
 Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 7/68 (10%)

Query: 313 KNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
           K RR R   +  Q         L+  +++ +YP+   + +L++ T LT  ++  WF+NRR
Sbjct: 1   KQRRSRTTFSASQLDE------LERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRR 54

Query: 372 QRDRTPQQ 379
            R R    
Sbjct: 55  ARLRKQHT 62

>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 = 46.4 bits (110), Expect = 1e-07
 Identities = 15/54 (27%), Positives = 29/54 (53%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ 324
           F     + L+  +++ +YP+   + +L++ T LT  ++  WF+NRR R R    
Sbjct: 9   FSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT 62

>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 = 47.7 bits (113), Expect = 6e-08
 Identities = 15/72 (20%), Positives = 30/72 (41%), Gaps = 7/72 (9%)

Query: 309 SNWFKNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWF 367
                    R   T +Q         L++ +  N+Y +   + +++    L  TQV  WF
Sbjct: 22  PGLGSPSGLRTNFTTRQL------TELEKEFHFNKYLSRARRVEIAATLELNETQVKIWF 75

Query: 368 KNRRQRDRTPQQ 379
           +NRR + +  ++
Sbjct: 76  QNRRMKQKKRER 87

>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 = 45.8 bits (108), Expect = 3e-07
 Identities = 14/54 (25%), Positives = 28/54 (51%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ 324
           F  R    L++ +  N+Y +   + +++    L  TQV  WF+NRR + +  ++
Sbjct: 34  FTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER 87

>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 = 46.0 bits (109), Expect = 1e-07
 Identities = 15/50 (30%), Positives = 30/50 (60%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
           F       L++ ++  +Y +P E+++L+++  L+  QV  WF+NRR + R
Sbjct: 7   FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 56

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein prh
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.0 bits (109), Expect = 1e-07
 Identities = 16/62 (25%), Positives = 34/62 (54%), Gaps = 7/62 (11%)

Query: 315 RRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
           +  + R +  Q         L++ ++  +Y +P E+++L+++  L+  QV  WF+NRR +
Sbjct: 1   KGGQVRFSNDQTIE------LEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAK 54

Query: 374 DR 375
            R
Sbjct: 55  WR 56

>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 = 46.6 bits (110), Expect = 1e-07
 Identities = 11/72 (15%), Positives = 32/72 (44%), Gaps = 6/72 (8%)

Query: 312 FKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
           F  ++ +++T +Q  +      L+  +  +     +E  +L   T LT  ++  WF  ++
Sbjct: 3   FTPQKFKEKTAEQLRV------LQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKK 56

Query: 372 QRDRTPQQRAKN 383
           +     +++ + 
Sbjct: 57  KSKALKEEKMEI 68

>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 = 42.0 bits (98), Expect = 4e-06
 Identities = 13/66 (19%), Positives = 28/66 (42%), Gaps = 3/66 (4%)

Query: 271 FKERSRN---ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSI 327
           FKE++      L+  +  +     +E  +L   T LT  ++  WF  +++     +++  
Sbjct: 8   FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKME 67

Query: 328 QRSRNA 333
               NA
Sbjct: 68  IDESNA 73

>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 = 45.5 bits (108), Expect = 1e-07
 Identities = 12/50 (24%), Positives = 24/50 (48%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
           +       L++ +  NRY     + +++    LT  Q+  WF+NRR + +
Sbjct: 4   YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 53

>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 = 45.2 bits (107), Expect = 2e-07
 Identities = 12/44 (27%), Positives = 23/44 (52%)

Query: 332 NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
             L++ +  NRY     + +++    LT  Q+  WF+NRR + +
Sbjct: 10  LELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 53

>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 = 45.2 bits (107), Expect = 2e-07
 Identities = 16/48 (33%), Positives = 24/48 (50%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
           F       LK  +++NRY     ++QLS   GL   Q+  WF+N R +
Sbjct: 6   FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>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 = 44.1 bits (104), Expect = 5e-07
 Identities = 15/43 (34%), Positives = 23/43 (53%)

Query: 331 RNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
              LK  +++NRY     ++QLS   GL   Q+  WF+N R +
Sbjct: 11  LARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>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 = 44.9 bits (106), Expect = 4e-07
 Identities = 14/59 (23%), Positives = 28/59 (47%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQR 329
           F +     L+  + + +Y +  E+  L+ +  LT TQV  WF+N R + +   +    +
Sbjct: 9   FSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDKAAQ 67

>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 = 43.0 bits (101), Expect = 2e-06
 Identities = 13/50 (26%), Positives = 25/50 (50%)

Query: 331 RNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR 380
              L+  + + +Y +  E+  L+ +  LT TQV  WF+N R + +   + 
Sbjct: 14  VYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKD 63

>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 = 43.3 bits (102), Expect = 1e-06
 Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 7/62 (11%)

Query: 315 RRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
           R++R   +  Q         L+  Y  N++   D++R++S  T L+  Q++ WF+NRR +
Sbjct: 2   RKKRIPYSKGQLRE------LEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVK 55

Query: 374 DR 375
           ++
Sbjct: 56  EK 57

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.3 bits (102), Expect = 1e-06
 Identities = 14/50 (28%), Positives = 30/50 (60%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
           + +     L+  Y  N++   D++R++S  T L+  Q++ WF+NRR +++
Sbjct: 8   YSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK 57

>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 = 43.4 bits (102), Expect = 1e-06
 Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 7/65 (10%)

Query: 315 RRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
           RRQR   T QQ         L+  + +NRYP+   + +++  T LT  +V  WFKNRR +
Sbjct: 2   RRQRTHFTSQQLQQ------LEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAK 55

Query: 374 DRTPQ 378
            R  +
Sbjct: 56  WRKRE 60

>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 = 43.4 bits (102), Expect = 1e-06
 Identities = 17/53 (32%), Positives = 29/53 (54%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ 323
           F  +    L+  + +NRYP+   + +++  T LT  +V  WFKNRR + R  +
Sbjct: 8   FTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 60

>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 = 43.4 bits (102), Expect = 1e-06
 Identities = 21/72 (29%), Positives = 31/72 (43%), Gaps = 7/72 (9%)

Query: 315 RRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
           RR R   T  Q         L++ + + RY        LS    L   QV  WFKNRR+R
Sbjct: 2   RRTRTTFTSSQI------AELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRR 55

Query: 374 DRTPQQRAKNRT 385
            +    + K+++
Sbjct: 56  HKIQSDQHKDQS 67

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 67

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 42.6 bits (100), Expect = 2e-06
 Identities = 17/60 (28%), Positives = 25/60 (41%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRS 330
           F       L++ + + RY        LS    L   QV  WFKNRR+R +    +   +S
Sbjct: 8   FTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQHKDQS 67

>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 = 43.0 bits (101), Expect = 2e-06
 Identities = 12/50 (24%), Positives = 24/50 (48%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
           F       L++ + K  Y +   + +L+    L  + +  WF+NRR +D+
Sbjct: 6   FTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDK 55

>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 = 41.8 bits (98), Expect = 3e-06
 Identities = 11/45 (24%), Positives = 23/45 (51%)

Query: 331 RNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
              L++ + K  Y +   + +L+    L  + +  WF+NRR +D+
Sbjct: 11  LGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDK 55

>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 = 42.6 bits (100), Expect = 2e-06
 Identities = 14/50 (28%), Positives = 27/50 (54%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
               +++AL+  + ++  P+  E  +++E   L    V  WF NRRQR++
Sbjct: 6   ISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREK 55

>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 = 41.8 bits (98), Expect = 4e-06
 Identities = 14/45 (31%), Positives = 26/45 (57%)

Query: 331 RNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
           ++AL+  + ++  P+  E  +++E   L    V  WF NRRQR++
Sbjct: 11  KDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREK 55

>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 = 41.4 bits (97), Expect = 4e-06
 Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 7/62 (11%)

Query: 315 RRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
           R+ R   T  Q         L+  + + +Y +  E+ + S    LT TQV  WF+NRR +
Sbjct: 1   RKPRTPFTTAQLLA------LERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAK 54

Query: 374 DR 375
            +
Sbjct: 55  AK 56

>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 = 41.4 bits (97), Expect = 5e-06
 Identities = 16/50 (32%), Positives = 26/50 (52%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
           F      AL+  + + +Y +  E+ + S    LT TQV  WF+NRR + +
Sbjct: 7   FTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56

>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 = 41.5 bits (97), Expect = 5e-06
 Identities = 12/50 (24%), Positives = 27/50 (54%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
            +   R AL++ + +N+ P  ++   ++E   +    +  WF NRRQ+++
Sbjct: 5   IETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEK 54

>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 = 40.3 bits (94), Expect = 1e-05
 Identities = 12/45 (26%), Positives = 26/45 (57%)

Query: 331 RNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
           R AL++ + +N+ P  ++   ++E   +    +  WF NRRQ+++
Sbjct: 10  RVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEK 54

>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 = 41.6 bits (97), Expect = 7e-06
 Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 7/69 (10%)

Query: 313 KNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
           K R++R   T  Q         L+  + + RY +  E+  L+ +  LT TQV  WF+N R
Sbjct: 8   KKRKRRVLFTKAQT------YELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHR 61

Query: 372 QRDRTPQQR 380
            + +  Q  
Sbjct: 62  YKTKRAQNE 70

>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 = 40.8 bits (95), Expect = 2e-05
 Identities = 16/56 (28%), Positives = 27/56 (48%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
           F +     L+  + + RY +  E+  L+ +  LT TQV  WF+N R + +  Q   
Sbjct: 16  FTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEK 71

>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 = 41.2 bits (96), Expect = 1e-05
 Identities = 15/84 (17%), Positives = 35/84 (41%), Gaps = 22/84 (26%)

Query: 315 RRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQL---------------SEITGL 358
           R  R     +  ++      ++  +++N+YP+  ++ ++               S++  +
Sbjct: 1   RGSRFTWRKECLAV------MESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERV 54

Query: 359 TLTQVSNWFKNRRQRDRTPQQRAK 382
           T  +V NWF NRR+  +     A 
Sbjct: 55  TSLKVYNWFANRRKEIKRRANIAA 78

>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 = 41.2 bits (96), Expect = 1e-05
 Identities = 12/67 (17%), Positives = 33/67 (49%), Gaps = 15/67 (22%)

Query: 269 YCFKERSRNALKECYDKNRYPNPDEKRQL---------------SEITGLTLTQVSNWFK 313
           + +++     ++  +++N+YP+  ++ ++               S++  +T  +V NWF 
Sbjct: 5   FTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFA 64

Query: 314 NRRQRDR 320
           NRR+  +
Sbjct: 65  NRRKEIK 71

>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 = 40.8 bits (95), Expect = 1e-05
 Identities = 11/55 (20%), Positives = 19/55 (34%)

Query: 272 KERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
            E         +D   YP+ +    LS    L    +  +F+N+R   +     S
Sbjct: 16  LEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHSGPSS 70

>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 = 40.5 bits (94), Expect = 2e-05
 Identities = 12/63 (19%), Positives = 23/63 (36%), Gaps = 4/63 (6%)

Query: 313 KNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQ 372
              R R +     S++         +D   YP+ +    LS    L    +  +F+N+R 
Sbjct: 6   SGPRSRTKI----SLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRY 61

Query: 373 RDR 375
             +
Sbjct: 62  HVK 64

>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 = 40.9 bits (95), Expect = 1e-05
 Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 21/75 (28%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEIT---------------------GLTLTQVS 309
           +   S+  L + Y++ + P+ +E+  L E                        +T  +V 
Sbjct: 4   WGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVY 63

Query: 310 NWFKNRRQRDRTPQQ 324
           NWF NRR+ +    +
Sbjct: 64  NWFANRRKEEAFRHK 78

>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 = 40.1 bits (93), Expect = 3e-05
 Identities = 16/80 (20%), Positives = 29/80 (36%), Gaps = 27/80 (33%)

Query: 321 TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEIT---------------------GLT 359
            P  + I      L + Y++ + P+ +E+  L E                        +T
Sbjct: 5   GPASQQI------LFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVT 58

Query: 360 LTQVSNWFKNRRQRDRTPQQ 379
             +V NWF NRR+ +    +
Sbjct: 59  EVRVYNWFANRRKEEAFRHK 78

>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 = 38.8 bits (90), Expect = 5e-05
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
            + R R +L+  + K   P+  +   ++   GL    V  WF NRRQ+ +
Sbjct: 15  IENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGK 64

>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 = 38.4 bits (89), Expect = 7e-05
 Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 3/64 (4%)

Query: 312 FKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
               R+R RT  +  +   R +L+  + K   P+  +   ++   GL    V  WF NRR
Sbjct: 4   LVQARKRKRTSIENRV---RWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRR 60

Query: 372 QRDR 375
           Q+ +
Sbjct: 61  QKGK 64

>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 = 38.2 bits (88), Expect = 1e-04
 Identities = 14/71 (19%), Positives = 32/71 (45%), Gaps = 6/71 (8%)

Query: 315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRD 374
              + +T +Q +I      LK  + + ++   ++ ++L +ITGL   ++  WF + R   
Sbjct: 5   SSGKRKTKEQLAI------LKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYAL 58

Query: 375 RTPQQRAKNRT 385
           +  Q +     
Sbjct: 59  KHGQLKWFRDN 69

>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 = 37.0 bits (85), Expect = 3e-04
 Identities = 11/62 (17%), Positives = 29/62 (46%)

Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRS 330
             +     LK  + + ++   ++ ++L +ITGL   ++  WF + R   +  Q +  + +
Sbjct: 10  KTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLKWFRDN 69

Query: 331 RN 332
            +
Sbjct: 70  AS 71

>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 = 37.3 bits (86), Expect = 2e-04
 Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 1/68 (1%)

Query: 264 GEETVYCFKERSRNALKECYDK-NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP 322
           G E      E     L+  ++K N++P+P     ++   GLT  Q   WFK R    R  
Sbjct: 1   GSEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60

Query: 323 QQRSIQRS 330
           +    +  
Sbjct: 61  EGLPSECR 68

>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 = 37.3 bits (86), Expect = 2e-04
 Identities = 12/50 (24%), Positives = 18/50 (36%)

Query: 335 KECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKNR 384
                 N++P+P     ++   GLT  Q   WFK R    R  +      
Sbjct: 18  YNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLPSEC 67

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	390
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.43
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.4
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.39
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.38
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.37
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.36
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.35
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.35
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.34
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.34
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.33
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.33
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.33
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.32
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.32
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.31
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.31
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.3
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.3
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.28
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.27
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.27
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.27
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.26
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.26
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.26
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.26
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.26
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.26
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.25
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.25
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.25
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.24
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.23
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.23
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.22
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.22
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.21
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.21
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.19
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.19
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.18
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.16
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.15
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.15
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.14
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.13
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.13
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.13
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.12
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.12
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.1
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.1
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.07
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.06
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.06
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.06
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.04
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.02
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.02
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.02
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	98.98
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	98.91
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	98.83
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	82.96

>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=99.43  E-value=3.5e-14  Score=104.29  Aligned_cols=56  Identities=25%  Similarity=0.532  Sum_probs=52.3

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      +....|+..|+.+|+..|..++||+..++..||..+||++.||++||+|||+|+|+
T Consensus         3 r~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           3 KKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            44557999999999999999999999999999999999999999999999999874

>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=99.40  E-value=2e-14  Score=105.64  Aligned_cols=56  Identities=29%  Similarity=0.616  Sum_probs=51.7

Q ss_pred             cCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccc
Q psy8148         318 RDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  376 (390)
Q Consensus       318 R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk  376 (390)
                      |.|+.++..|.   .+|+..|..++||+.+++++||..+||++.+|++||||||+|+||
T Consensus         3 r~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           3 KKRIPYSKGQL---RELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CSCCCSCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCHHHH---HHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            45677887777   999999999999999999999999999999999999999999986

>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=99.39  E-value=2.6e-14  Score=107.96  Aligned_cols=63  Identities=32%  Similarity=0.461  Sum_probs=57.1

Q ss_pred             cCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhcc
Q psy8148         318 RDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKN  383 (390)
Q Consensus       318 R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~~  383 (390)
                      |.|+.++..|.   .+|+..|..++||+..++.+||..+||++.+|++||||||+|+|+.....+.
T Consensus         3 r~Rt~ft~~Ql---~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~~~~~   65 (67)
T d1zq3p1           3 RTRTTFTSSQI---AELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQHKD   65 (67)
T ss_dssp             CCSCCCCHHHH---HHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             CCCCcCCHHHH---HHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhhhccc
Confidence            45778887777   9999999999999999999999999999999999999999999987766554

>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=99.38  E-value=2.3e-14  Score=104.49  Aligned_cols=55  Identities=25%  Similarity=0.402  Sum_probs=50.8

Q ss_pred             CCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccch
Q psy8148         320 RTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  377 (390)
Q Consensus       320 R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~  377 (390)
                      |+.++..|.   ..|+..|..++||+..++.+||..+||++.+|++||||||+|+|++
T Consensus         1 Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk~   55 (56)
T d9anta_           1 RQTYTRYQT---LELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   55 (56)
T ss_dssp             CCCCCHHHH---HHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCcCCHHHH---HHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhhc
Confidence            466777676   9999999999999999999999999999999999999999999874

>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=99.37  E-value=1.2e-13  Score=99.62  Aligned_cols=51  Identities=31%  Similarity=0.543  Sum_probs=48.4

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhccccccccccc
Q psy8148         268 VYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR  318 (390)
Q Consensus       268 ~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R  318 (390)
                      +..|+..|+.+|+..|..++||+..++.+||..+||++.||++||+|||+|
T Consensus         3 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~lgL~~~qV~vWFqNrRaK   53 (53)
T d1p7ia_           3 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK   53 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             CccCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChHHhhhcccccCCC
Confidence            346999999999999999999999999999999999999999999999975

>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=99.36  E-value=2.9e-14  Score=104.32  Aligned_cols=56  Identities=27%  Similarity=0.461  Sum_probs=52.2

Q ss_pred             cCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccc
Q psy8148         318 RDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  376 (390)
Q Consensus       318 R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk  376 (390)
                      |.|+.++..|.   ..|+..|..++||+..++.+||..+||++.+|++||||+|+|+|+
T Consensus         1 R~Rt~fT~~Ql---~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk   56 (57)
T d1jgga_           1 RYRTAFTRDQL---GRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR   56 (57)
T ss_dssp             CCCCCCCHHHH---HHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHH---HHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhc
Confidence            45778887777   999999999999999999999999999999999999999999886

>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=99.35  E-value=3.7e-14  Score=104.11  Aligned_cols=56  Identities=32%  Similarity=0.508  Sum_probs=52.0

Q ss_pred             cCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccc
Q psy8148         318 RDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  376 (390)
Q Consensus       318 R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk  376 (390)
                      |.|+.++..|.   ..|+..|+.++||+.+++++||..+||++.+|++||||+|+|+|+
T Consensus         2 r~Rt~ft~~Ql---~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           2 KPRTPFTTAQL---LALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCHHHH---HHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHH---HHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            45778887777   999999999999999999999999999999999999999999886

>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=99.35  E-value=5.7e-14  Score=101.27  Aligned_cols=53  Identities=34%  Similarity=0.543  Sum_probs=49.1

Q ss_pred             cCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCcccccccccccccc
Q psy8148         318 RDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR  373 (390)
Q Consensus       318 R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K  373 (390)
                      |.|+.++..|.   ..|+..|..++||+.+++.+||..+||++.+|++||||||+|
T Consensus         1 R~Rt~ft~~Q~---~~Le~~F~~~~yp~~~~r~~LA~~lgL~~~qV~vWFqNrRaK   53 (53)
T d1p7ia_           1 RPRTAFSSEQL---ARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK   53 (53)
T ss_dssp             CCCCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             CCCccCCHHHH---HHHHHHHHHCCCCCHHHHHHHHHHhCCChHHhhhcccccCCC
Confidence            45777887777   999999999999999999999999999999999999999986

>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=99.34  E-value=1.5e-13  Score=106.51  Aligned_cols=62  Identities=27%  Similarity=0.524  Sum_probs=56.7

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      .+++|.|+.++..|.   .+|+..|..++||+..++++||..+||++.+|++||||+|+|.|+..
T Consensus         7 ~k~rr~Rt~ft~~Q~---~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   68 (77)
T d1vnda_           7 NKKRKRRVLFTKAQT---YELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ   68 (77)
T ss_dssp             SSSCSSCCCCCTTHH---HHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSC
T ss_pred             CCCCCCCCCCCHHHH---HHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHh
Confidence            456677888888777   99999999999999999999999999999999999999999999754

>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=99.34  E-value=2.3e-13  Score=98.02  Aligned_cols=52  Identities=27%  Similarity=0.516  Sum_probs=49.7

Q ss_pred             cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCC
Q psy8148         269 YCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR  320 (390)
Q Consensus       269 ~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R  320 (390)
                      ..|+++|+.+|+..|..++||+..++..||..+||++.||.+||+|+|+|.|
T Consensus         2 t~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~K   53 (53)
T d1le8a_           2 SSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   53 (53)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTTC
T ss_pred             CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhccC
Confidence            3689999999999999999999999999999999999999999999999875

>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=99.33  E-value=6.7e-14  Score=105.03  Aligned_cols=62  Identities=29%  Similarity=0.581  Sum_probs=55.8

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhh
Q psy8148         315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  379 (390)
Q Consensus       315 RR~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~  379 (390)
                      +++|.|+.++..|.   ..|+..|..++||+..++.+||..+||+..+|++||||+|+|+|+...
T Consensus         1 k~rr~Rt~ft~~Q~---~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~   62 (65)
T d1fjla_           1 KQRRSRTTFSASQL---DELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   62 (65)
T ss_dssp             CCCCCCCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHH---HHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhccc
Confidence            35667888887777   999999999999999999999999999999999999999999988543

>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=99.33  E-value=1.5e-13  Score=100.46  Aligned_cols=54  Identities=22%  Similarity=0.436  Sum_probs=50.8

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         268 VYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       268 ~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      ...|+..|+.+|+..|..++||+..++.+||..+||++.+|.+||+|+|.|.|.
T Consensus         3 Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk   56 (57)
T d1jgga_           3 RTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR   56 (57)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhc
Confidence            456999999999999999999999999999999999999999999999998763

>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=99.33  E-value=6.4e-14  Score=102.48  Aligned_cols=56  Identities=25%  Similarity=0.510  Sum_probs=51.5

Q ss_pred             cCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccc
Q psy8148         318 RDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  376 (390)
Q Consensus       318 R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk  376 (390)
                      +.|+.++..|.   ..|+..|..++||+.+++.+||..+||++.+|++||||||+|+|+
T Consensus         2 ~~R~~ft~~Q~---~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k~kk   57 (57)
T d2e1oa1           2 GGQVRFSNDQT---IELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR   57 (57)
T ss_dssp             CCCCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCccCCHHHH---HHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhhccC
Confidence            45677887777   999999999999999999999999999999999999999999875

>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=99.32  E-value=1.8e-13  Score=99.73  Aligned_cols=53  Identities=23%  Similarity=0.406  Sum_probs=50.2

Q ss_pred             cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         269 YCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       269 ~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      ..|+..|+.+|+..|..++||+..++.+||..+||++.+|++||+|||+|.|+
T Consensus         2 t~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk   54 (56)
T d9anta_           2 QTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK   54 (56)
T ss_dssp             CCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhh
Confidence            36899999999999999999999999999999999999999999999998764

>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=99.32  E-value=2.1e-13  Score=100.01  Aligned_cols=54  Identities=30%  Similarity=0.439  Sum_probs=50.6

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         268 VYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       268 ~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      ...|+..|+.+|+..|..++||+..++.+||..+||++.+|.+||+|+|.|.|.
T Consensus         4 Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           4 RTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            347999999999999999999999999999999999999999999999988763

>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=99.31  E-value=9.5e-14  Score=105.11  Aligned_cols=62  Identities=24%  Similarity=0.448  Sum_probs=56.1

Q ss_pred             cccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhh
Q psy8148         316 RQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR  380 (390)
Q Consensus       316 R~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r  380 (390)
                      ++|.|+.++..|.   .+|+..|..++||+..++.+||..+||+..+|++||+|+|+|+|+....
T Consensus         2 krr~Rt~ft~~Ql---~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~~~   63 (68)
T d1ftta_           2 RRKRRVLFSQAQV---YELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKD   63 (68)
T ss_dssp             CSSSCSSCCHHHH---HHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCCHHHH---HHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhcccc
Confidence            4567888888777   9999999999999999999999999999999999999999999886543

>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=99.31  E-value=2.6e-13  Score=99.15  Aligned_cols=53  Identities=28%  Similarity=0.582  Sum_probs=50.1

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCC
Q psy8148         268 VYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR  320 (390)
Q Consensus       268 ~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R  320 (390)
                      ...|+..|+.+|+..|..|+||+..++..||..+||++.||.+||+|+|.+.|
T Consensus         4 R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k~k   56 (57)
T d2e1oa1           4 QVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR   56 (57)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHH
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhhcc
Confidence            44699999999999999999999999999999999999999999999998865

>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=99.30  E-value=1.5e-13  Score=106.50  Aligned_cols=63  Identities=24%  Similarity=0.406  Sum_probs=56.2

Q ss_pred             cccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhh
Q psy8148         316 RQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRA  381 (390)
Q Consensus       316 R~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~  381 (390)
                      .+|.|+.++..|+   .+|+..|..++||+..++++||..+||++.+|++||||||+|+|+..+.+
T Consensus        13 ~rr~Rt~ft~~Ql---~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~~   75 (77)
T d1pufa_          13 TRKKRCPYTKHQT---LELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDR   75 (77)
T ss_dssp             TSCCCCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHH---HHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHHh
Confidence            3455778887777   99999999999999999999999999999999999999999999866543

>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=99.30  E-value=5e-13  Score=97.95  Aligned_cols=55  Identities=25%  Similarity=0.425  Sum_probs=51.8

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         268 VYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       268 ~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      ..+|+..|+.+|+..|..++||+..++..||..+||++.+|.+||+|+|++.|..
T Consensus         3 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr~   57 (58)
T d1au7a1           3 RTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV   57 (58)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHhc
Confidence            4569999999999999999999999999999999999999999999999998763

>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=99.28  E-value=4.1e-13  Score=101.23  Aligned_cols=59  Identities=27%  Similarity=0.464  Sum_probs=54.4

Q ss_pred             cccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccch
Q psy8148         316 RQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  377 (390)
Q Consensus       316 R~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~  377 (390)
                      ++|.|+.++..+.   ..|+..|..++||+..++++||..+||+..+|++||+|+|+++|+.
T Consensus         8 ~rr~Rt~~t~~q~---~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_           8 RKRKRTSIENRVR---WSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             SSSCCSSCCHHHH---HHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             cCCCCCCCCHHHH---HHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            4567888887777   9999999999999999999999999999999999999999999874

>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=99.27  E-value=4.9e-13  Score=101.12  Aligned_cols=58  Identities=22%  Similarity=0.477  Sum_probs=53.4

Q ss_pred             CccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         265 EETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       265 e~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      .+....|+..|+.+|+..|..|+||+..++..||..+||++.+|.+||+|+|.+.|..
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~   59 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE   59 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhh
Confidence            3445679999999999999999999999999999999999999999999999998754

>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=99.27  E-value=9.9e-13  Score=98.82  Aligned_cols=58  Identities=31%  Similarity=0.595  Sum_probs=53.4

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcc
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  323 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~  323 (390)
                      +....|+.+|+.+|+..|..|+||+..++..||..+||++.+|.+||+|+|.+.|...
T Consensus         5 R~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~~   62 (66)
T d1bw5a_           5 RVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             CCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             CCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHHH
Confidence            3445799999999999999999999999999999999999999999999999988753

>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=99.27  E-value=1.5e-12  Score=100.77  Aligned_cols=57  Identities=28%  Similarity=0.500  Sum_probs=53.2

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcc
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  323 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~  323 (390)
                      +...|+..|+.+|+..|..++||+..++..||..+||++.||++||+|+|.|.|...
T Consensus        12 ~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   68 (77)
T d1vnda_          12 RRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ   68 (77)
T ss_dssp             SCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHh
Confidence            445799999999999999999999999999999999999999999999999988654

>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=99.26  E-value=3.2e-13  Score=101.56  Aligned_cols=60  Identities=33%  Similarity=0.573  Sum_probs=54.8

Q ss_pred             cccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         316 RQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       316 R~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      ..|.|+.++..|.   ..|+..|..++||+.+++++||..+||+..+|++||+|+|+|.|+..
T Consensus         3 ~kR~Rt~~t~~Q~---~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~~   62 (66)
T d1bw5a_           3 TTRVRTVLNEKQL---HTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             CSCCCCCCSHHHH---HHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             CCCCCcCcCHHHH---HHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHHH
Confidence            4567788887777   99999999999999999999999999999999999999999998854

>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=99.26  E-value=6.7e-13  Score=100.07  Aligned_cols=55  Identities=29%  Similarity=0.442  Sum_probs=51.7

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         268 VYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       268 ~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      ...|+..|+.+|+..|..++||+..++..||..+||++.+|.+||+|||.+.|..
T Consensus         5 Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~   59 (67)
T d1zq3p1           5 RTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQ   59 (67)
T ss_dssp             SCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhh
Confidence            3469999999999999999999999999999999999999999999999998753

>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=99.26  E-value=3.2e-13  Score=107.10  Aligned_cols=60  Identities=23%  Similarity=0.366  Sum_probs=53.4

Q ss_pred             cccCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         316 RQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       316 R~R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      .+|.|+.++..|+   .+|+..|..++||+.+++++||..+||+..+|++||||+|+|+|+..
T Consensus        27 ~kr~Rt~ft~~Ql---~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~   86 (88)
T d1b72a_          27 PSGLRTNFTTRQL---TELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRE   86 (88)
T ss_dssp             ---CCCCCCHHHH---HHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCCHHHH---HHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhc
Confidence            4566888887777   99999999999999999999999999999999999999999999854

>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=99.26  E-value=3.5e-13  Score=97.05  Aligned_cols=53  Identities=25%  Similarity=0.486  Sum_probs=47.5

Q ss_pred             CCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCcccccccccccccccc
Q psy8148         320 RTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR  375 (390)
Q Consensus       320 R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~k  375 (390)
                      |+.++..+.   .+|+..|..++||+..++.+||..+||++.+|++||+|+|+|.|
T Consensus         1 Rt~~s~~q~---~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~K   53 (53)
T d1le8a_           1 KSSISPQAR---AFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   53 (53)
T ss_dssp             CCCCCHHHH---HHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTTC
T ss_pred             CCCCCHHHH---HHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhccC
Confidence            345555555   99999999999999999999999999999999999999999876

>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=99.26  E-value=3.6e-13  Score=98.75  Aligned_cols=57  Identities=28%  Similarity=0.470  Sum_probs=51.9

Q ss_pred             cCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccch
Q psy8148         318 RDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  377 (390)
Q Consensus       318 R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~  377 (390)
                      |.|+.++..+.   ..|+..|..++||+..++.+||..+||++.+|++||+|+|+++|+.
T Consensus         1 r~Rt~~s~~q~---~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr~   57 (58)
T d1au7a1           1 KRRTTISIAAK---DALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV   57 (58)
T ss_dssp             CCCCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCHHHH---HHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHhc
Confidence            35677776666   9999999999999999999999999999999999999999999874

>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=99.26  E-value=3.8e-13  Score=101.74  Aligned_cols=60  Identities=25%  Similarity=0.489  Sum_probs=54.7

Q ss_pred             cCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhh
Q psy8148         318 RDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR  380 (390)
Q Consensus       318 R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r  380 (390)
                      |.|+.++..|.   ..|+..|..++||+..++++||..+||++.+|++||+|+|+|+|+....
T Consensus         3 R~Rt~ft~~Ql---~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~   62 (68)
T d2cuea1           3 RNRTSFTQEQI---EALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL   62 (68)
T ss_dssp             CCCCCSCHHHH---HHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCcCCHHHH---HHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhhh
Confidence            45788887777   9999999999999999999999999999999999999999999986544

>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=99.25  E-value=3.3e-13  Score=103.13  Aligned_cols=60  Identities=23%  Similarity=0.380  Sum_probs=53.8

Q ss_pred             ccCCCcchhhhhhhhhhhhhhhcC-CCCCCHHHHHHHHHhhCCCccccccccccccccccchhh
Q psy8148         317 QRDRTPQQRSIQRSRNALKECYDK-NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  379 (390)
Q Consensus       317 ~R~R~~~t~~q~~q~~~Le~~F~~-n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~  379 (390)
                      .+.|+.++..|+   ..|+..|.. ++||+..++++||..+||++.+|++||||||+|+|+..+
T Consensus         2 ~~~r~~fT~~Ql---~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~~   62 (72)
T d1uhsa_           2 SEGAATMTEDQV---EILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   62 (72)
T ss_dssp             CCCCCCCCHHHH---HHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHH---HHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhccC
Confidence            356778887777   999999985 789999999999999999999999999999999988654

>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=99.25  E-value=1.6e-12  Score=97.90  Aligned_cols=56  Identities=25%  Similarity=0.395  Sum_probs=52.5

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      ....|+..|+.+|+..|..++||+..++..||..+||++.+|.+||+|+|++.|..
T Consensus        11 ~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_          11 KRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             CCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            44579999999999999999999999999999999999999999999999998864

>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=99.25  E-value=8.3e-13  Score=98.95  Aligned_cols=56  Identities=27%  Similarity=0.566  Sum_probs=51.9

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      +...|+..|+.+|+.+|..|+||+..++..||..+||++.+|.+||+|+|.|.|..
T Consensus         5 ~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~   60 (65)
T d1fjla_           5 SRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ   60 (65)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhc
Confidence            34469999999999999999999999999999999999999999999999988753

>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=99.24  E-value=2.2e-13  Score=100.54  Aligned_cols=57  Identities=33%  Similarity=0.569  Sum_probs=52.3

Q ss_pred             cCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccch
Q psy8148         318 RDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  377 (390)
Q Consensus       318 R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~  377 (390)
                      |.|+.++..|.   ..|+..|..++||+..++..||..+||+..+|++||+|+|+|.|+.
T Consensus         3 r~Rt~ft~~Q~---~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1           3 RQRTHFTSQQL---QQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             CSCCCCCHHHH---HHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHH---HHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            45677887776   9999999999999999999999999999999999999999998874

>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=99.23  E-value=1.4e-12  Score=95.22  Aligned_cols=53  Identities=23%  Similarity=0.480  Sum_probs=50.6

Q ss_pred             cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         269 YCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       269 ~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      ..|+..++.+|+..|..++||+..++..||..+||++.||.+||+|+|++.|.
T Consensus         3 T~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk   55 (57)
T d1e3oc1           3 TSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR   55 (57)
T ss_dssp             CCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTS
T ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHc
Confidence            46889999999999999999999999999999999999999999999999875

>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=99.23  E-value=1.1e-12  Score=100.14  Aligned_cols=58  Identities=28%  Similarity=0.424  Sum_probs=52.7

Q ss_pred             CccccccCHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         265 EETVYCFKERSRNALKECYDK-NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       265 e~t~~~Fs~~q~~~Le~~F~~-n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      .++...|+..|+.+|+..|.. ++||+...+..||..+||++.+|.+||+|||+|.|..
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~   60 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS   60 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhc
Confidence            345668999999999999986 7899999999999999999999999999999988653

>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=99.22  E-value=1.6e-12  Score=92.26  Aligned_cols=47  Identities=32%  Similarity=0.579  Sum_probs=46.0

Q ss_pred             ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhccccccccc
Q psy8148         270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR  316 (390)
Q Consensus       270 ~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR  316 (390)
                      .|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|+|
T Consensus         4 ~ft~~Q~~~Le~~F~~n~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1           4 VFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             CCCHHHHHHHHHHTTSSCSSTHHHHHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             CCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhhcCCcCc
Confidence            69999999999999999999999999999999999999999999997

>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=99.22  E-value=2.9e-12  Score=97.52  Aligned_cols=59  Identities=17%  Similarity=0.262  Sum_probs=53.3

Q ss_pred             CCccccccCHHHHHHHHHHHh-hCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         264 GEETVYCFKERSRNALKECYD-KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       264 ge~t~~~Fs~~q~~~Le~~F~-~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      +.+....|+++|+.+|+.+|. .++||+..++..||..+||++.||.+||+|+|++.|..
T Consensus         7 ~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk~   66 (71)
T d1wi3a_           7 GPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS   66 (71)
T ss_dssp             CCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCSS
T ss_pred             CCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhccc
Confidence            334556799999999999997 59999999999999999999999999999999998865

>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=99.21  E-value=1.5e-12  Score=98.32  Aligned_cols=55  Identities=25%  Similarity=0.463  Sum_probs=51.7

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         268 VYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       268 ~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      ...|++.|+.+|+..|..++||+..++..||..+||++.+|.+||+|+|.+.|..
T Consensus         6 Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~   60 (68)
T d1ftta_           6 RVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ   60 (68)
T ss_dssp             CSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhc
Confidence            3469999999999999999999999999999999999999999999999988754

>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=99.21  E-value=7.7e-13  Score=97.56  Aligned_cols=54  Identities=31%  Similarity=0.581  Sum_probs=50.7

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         268 VYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       268 ~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      ...|+..|+.+|+.+|..++||+..++..||..+||++.+|.+||+|+|.+.|.
T Consensus         5 Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   58 (60)
T d1yz8p1           5 RTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK   58 (60)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHh
Confidence            446999999999999999999999999999999999999999999999988764

>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=99.19  E-value=2e-12  Score=102.47  Aligned_cols=56  Identities=25%  Similarity=0.433  Sum_probs=51.9

Q ss_pred             ccccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         266 ETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      +....|+..|+.+|+..|..|+||+..++.+||..+||++.+|.+||+|+|+|.|.
T Consensus        29 r~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk   84 (88)
T d1b72a_          29 GLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK   84 (88)
T ss_dssp             -CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHH
Confidence            34557999999999999999999999999999999999999999999999998875

>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=99.19  E-value=2.4e-12  Score=99.51  Aligned_cols=55  Identities=24%  Similarity=0.390  Sum_probs=51.9

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      ....|+..|+.+|+..|..++||+..++..||..+||++.||++||+|+|.|.|.
T Consensus        16 ~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr   70 (77)
T d1pufa_          16 KRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK   70 (77)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHH
Confidence            4457999999999999999999999999999999999999999999999999875

>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=99.18  E-value=1.2e-12  Score=95.51  Aligned_cols=55  Identities=25%  Similarity=0.508  Sum_probs=49.8

Q ss_pred             CCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccch
Q psy8148         320 RTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  377 (390)
Q Consensus       320 R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~  377 (390)
                      |+.++..+.   ..|+..|..++||+.+++.+||..+||+..+|++||+|+|+|+|+.
T Consensus         2 RT~~~~~q~---~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk~   56 (57)
T d1e3oc1           2 RTSIETNIR---VALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI   56 (57)
T ss_dssp             CCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCHHHH---HHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHcc
Confidence            455665555   8999999999999999999999999999999999999999999874

>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=99.16  E-value=4.3e-12  Score=90.91  Aligned_cols=50  Identities=16%  Similarity=0.480  Sum_probs=46.2

Q ss_pred             HHHHHHHHHHHhh-CCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         273 ERSRNALKECYDK-NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       273 ~~q~~~Le~~F~~-n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      ..+..+|+.+|.. ++||+..++..||..+||+..+|.+||+|||.++|.+
T Consensus         2 ~~q~~iLE~~F~~~~~~P~~~~~~~LA~~~~ls~~qV~~WFqNrR~k~k~s   52 (52)
T d1x2ma1           2 AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPS   52 (52)
T ss_dssp             SCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCCS
T ss_pred             hhHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccCcC
Confidence            4578999999986 7999999999999999999999999999999999863

>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=99.15  E-value=5.2e-12  Score=93.03  Aligned_cols=52  Identities=29%  Similarity=0.531  Sum_probs=48.1

Q ss_pred             ccCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         270 CFKERSRNALKECYDK---NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       270 ~Fs~~q~~~Le~~F~~---n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      .|+.+++.+|+.+|..   +|||+..++..||..+||++.||.+||+|+|+|.|.
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            4889999999999975   589999999999999999999999999999998765

>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=99.15  E-value=5.2e-12  Score=96.57  Aligned_cols=56  Identities=34%  Similarity=0.627  Sum_probs=51.0

Q ss_pred             ccccCHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcc
Q psy8148         268 VYCFKERSRNALKECYD---KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  323 (390)
Q Consensus       268 ~~~Fs~~q~~~Le~~F~---~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~  323 (390)
                      ...|+..++.+|+.+|.   .+|||+..++..||..+||+..||.+||+|+|+|.+...
T Consensus         5 R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~   63 (73)
T d1pufb_           5 RRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (73)
T ss_dssp             CCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccc
Confidence            34689999999999997   589999999999999999999999999999999987544

>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=99.14  E-value=5e-12  Score=89.71  Aligned_cols=49  Identities=29%  Similarity=0.451  Sum_probs=45.4

Q ss_pred             CCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCcccccccccccc
Q psy8148         320 RTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR  371 (390)
Q Consensus       320 R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR  371 (390)
                      |+.++..|.   ..|+..|..++||+.+++.+||..+||+.++|++||||+|
T Consensus         2 Rt~ft~~Q~---~~Le~~F~~n~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1           2 RLVFTDVQR---RTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             CSCCCHHHH---HHHHHHTTSSCSSTHHHHHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             CCCCCHHHH---HHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhhcCCcCc
Confidence            566776666   9999999999999999999999999999999999999998

>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=99.13  E-value=3.5e-12  Score=97.03  Aligned_cols=58  Identities=21%  Similarity=0.304  Sum_probs=51.3

Q ss_pred             ccCCCcchhhhhhhhhhhhhhhc-CCCCCCHHHHHHHHHhhCCCccccccccccccccccch
Q psy8148         317 QRDRTPQQRSIQRSRNALKECYD-KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  377 (390)
Q Consensus       317 ~R~R~~~t~~q~~q~~~Le~~F~-~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~  377 (390)
                      .+.|+.++..|.   .+|+..|. .++||+.+++++||..+||+..+|++||+|+|+|.|+.
T Consensus         8 ~r~R~~~t~~Q~---~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk~   66 (71)
T d1wi3a_           8 PRSRTKISLEAL---GILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS   66 (71)
T ss_dssp             CCCCCCCCSHHH---HHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCSS
T ss_pred             CCCCccCCHHHH---HHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhccc
Confidence            345667776666   99999997 58999999999999999999999999999999999873

>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=99.13  E-value=3.6e-12  Score=98.23  Aligned_cols=55  Identities=15%  Similarity=0.315  Sum_probs=49.4

Q ss_pred             hhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhhhccC
Q psy8148         330 SRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKNR  384 (390)
Q Consensus       330 q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r~~~~  384 (390)
                      |+..|+..|..++||+..++++||..+||+..+|++||||||++.++.....+..
T Consensus        15 Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~~~~~~   69 (76)
T d2ecba1          15 QLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEID   69 (76)
T ss_dssp             HHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCCCCC
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhHhhhcc
Confidence            4499999999999999999999999999999999999999999988766655544

>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=99.13  E-value=4.1e-12  Score=93.34  Aligned_cols=55  Identities=20%  Similarity=0.501  Sum_probs=49.0

Q ss_pred             ccccccCHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhCCCchhcccccccccccCC
Q psy8148         266 ETVYCFKERSRNALKECYDK-NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR  320 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~-n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R  320 (390)
                      +....++.++..+|+.+|.. ++||+..++..||..+||++.||.+||+|||.++|
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            33446777788999999986 68999999999999999999999999999999876

>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=99.12  E-value=2.4e-12  Score=100.64  Aligned_cols=60  Identities=20%  Similarity=0.471  Sum_probs=53.0

Q ss_pred             cCCCcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhC---------------CCccccccccccccccccchhhh
Q psy8148         318 RDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITG---------------LTLTQVSNWFKNRRQRDRTPQQR  380 (390)
Q Consensus       318 R~R~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lg---------------Ls~~qVk~WFqNRR~K~kk~~~r  380 (390)
                      |.|+.++..|+   .+|+..|..++||+..++++||..+|               |+..+|++||||||+|+|+....
T Consensus         2 r~R~~ft~~Ql---~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~~   76 (82)
T d2cufa1           2 GSRFTWRKECL---AVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANI   76 (82)
T ss_dssp             CCSCCCCHHHH---HHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             cCCCCCCHHHH---HHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhhH
Confidence            55777887777   99999999999999999999999875               99999999999999999985543

>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=99.12  E-value=3.6e-12  Score=91.33  Aligned_cols=47  Identities=17%  Similarity=0.497  Sum_probs=43.9

Q ss_pred             hhhhhhhhhcC-CCCCCHHHHHHHHHhhCCCccccccccccccccccc
Q psy8148         330 SRNALKECYDK-NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  376 (390)
Q Consensus       330 q~~~Le~~F~~-n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk  376 (390)
                      |..+|+..|.. ++||+..++++||..+||+.++|++||+|||+|+|+
T Consensus         4 q~~iLE~~F~~~~~~P~~~~~~~LA~~~~ls~~qV~~WFqNrR~k~k~   51 (52)
T d1x2ma1           4 PNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   51 (52)
T ss_dssp             HHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccCc
Confidence            45899999976 789999999999999999999999999999999986

>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=99.10  E-value=7.9e-12  Score=97.68  Aligned_cols=56  Identities=20%  Similarity=0.568  Sum_probs=51.2

Q ss_pred             cccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhC---------------CCchhcccccccccccCCCc
Q psy8148         267 TVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITG---------------LTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       267 t~~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tg---------------Ls~~QV~~WFqNRR~R~R~~  322 (390)
                      ..+.|+..|+.+|+..|..|+||+..++++||..+|               +++.+|.+||+|||++.|..
T Consensus         3 ~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~   73 (82)
T d2cufa1           3 SRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRR   73 (82)
T ss_dssp             CSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHh
Confidence            345799999999999999999999999999999875               99999999999999998763

>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=99.10  E-value=2e-11  Score=90.49  Aligned_cols=51  Identities=37%  Similarity=0.617  Sum_probs=47.2

Q ss_pred             ccccCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCchhccccccccccc
Q psy8148         268 VYCFKERSRNALKECYDK---NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR  318 (390)
Q Consensus       268 ~~~Fs~~q~~~Le~~F~~---n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R  318 (390)
                      ...|+.+++.+|+.||..   +|||+..++..||..+||+..||.+||+|+|+|
T Consensus         6 R~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R   59 (62)
T d1x2na1           6 RGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRR   59 (62)
T ss_dssp             SCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHH
Confidence            346889999999999984   899999999999999999999999999999976

>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=99.07  E-value=1.4e-11  Score=94.84  Aligned_cols=52  Identities=19%  Similarity=0.384  Sum_probs=49.4

Q ss_pred             ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCC
Q psy8148         270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  321 (390)
Q Consensus       270 ~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~  321 (390)
                      .|+.+|+.+|+.+|..|+||+..++..||..+||+..||.+||+|+|.+.|.
T Consensus         9 r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~   60 (76)
T d2ecca1           9 RKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH   60 (76)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHh
Confidence            4789999999999999999999999999999999999999999999998775

>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=99.06  E-value=1.8e-11  Score=95.13  Aligned_cols=60  Identities=13%  Similarity=0.190  Sum_probs=53.2

Q ss_pred             cccccCCCcchhhhhhhhhhhhhhhc----CCCCCCHHHHHHHHHhhCCCccccccccccccccccc
Q psy8148         314 NRRQRDRTPQQRSIQRSRNALKECYD----KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  376 (390)
Q Consensus       314 NRR~R~R~~~t~~q~~q~~~Le~~F~----~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk  376 (390)
                      .+++|.|+.++..|.   ..|+..|+    .++||+.+++++||..+||+..+|++||||+|++.|.
T Consensus        15 ~~~kR~Rt~ft~~Q~---~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          15 GTTKRFRTKFTAEQK---EKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCSSCCCCCCCHHHH---HHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             cCCCCccccCCHHHH---HHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            456678899998887   88877776    4899999999999999999999999999999998876

>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=99.06  E-value=1.9e-11  Score=94.04  Aligned_cols=54  Identities=15%  Similarity=0.303  Sum_probs=49.6

Q ss_pred             cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchhcccccccccccCCCcch
Q psy8148         271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ  324 (390)
Q Consensus       271 Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~~t  324 (390)
                      ++..|+.+|+..|..++||+..++..||..+||+..+|.+||+|+|++.+....
T Consensus        11 ~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~   64 (76)
T d2ecba1          11 KTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEE   64 (76)
T ss_dssp             CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCS
T ss_pred             CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhH
Confidence            468999999999999999999999999999999999999999999988765433

>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=99.06  E-value=1.1e-11  Score=94.67  Aligned_cols=60  Identities=33%  Similarity=0.612  Sum_probs=51.7

Q ss_pred             cCCCcchhhhhhhhhhhhhhhc---CCCCCCHHHHHHHHHhhCCCccccccccccccccccchhhh
Q psy8148         318 RDRTPQQRSIQRSRNALKECYD---KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR  380 (390)
Q Consensus       318 R~R~~~t~~q~~q~~~Le~~F~---~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~~r  380 (390)
                      |.|+.++..+.   ..|+..|.   .+|||+.+++.+||..+||+..+|++||+|+|+|.++...+
T Consensus         3 k~R~~~t~~q~---~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~~~   65 (73)
T d1pufb_           3 RKRRNFNKQAT---EILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGK   65 (73)
T ss_dssp             CCCCCCCHHHH---HHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTT
T ss_pred             CCCCCCCHHHH---HHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccchh
Confidence            44666776666   99999995   58999999999999999999999999999999998875443

>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=99.04  E-value=4.5e-11  Score=92.47  Aligned_cols=54  Identities=28%  Similarity=0.525  Sum_probs=50.2

Q ss_pred             cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHh---------------------CCCchhcccccccccccCCCc
Q psy8148         269 YCFKERSRNALKECYDKNRYPNPDEKRQLSEIT---------------------GLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       269 ~~Fs~~q~~~Le~~F~~n~YPs~~ek~~LA~~t---------------------gLs~~QV~~WFqNRR~R~R~~  322 (390)
                      +.|+..|+.+|+..|..|+||+..+++.||..+                     ++|+.+|.+||+|||++++..
T Consensus         2 ~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr~   76 (78)
T d1lfba_           2 FKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFR   76 (78)
T ss_dssp             CCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCC
T ss_pred             ccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHHh
Confidence            468999999999999999999999999999998                     489999999999999998864

>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=99.02  E-value=1.4e-10  Score=89.99  Aligned_cols=57  Identities=11%  Similarity=0.185  Sum_probs=51.7

Q ss_pred             ccccccCHHHHHHHHHHHhh----CCCCCHHHHHHHHHHhCCCchhcccccccccccCCCc
Q psy8148         266 ETVYCFKERSRNALKECYDK----NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP  322 (390)
Q Consensus       266 ~t~~~Fs~~q~~~Le~~F~~----n~YPs~~ek~~LA~~tgLs~~QV~~WFqNRR~R~R~~  322 (390)
                      +.+..|+..|+..|+..|..    ++||+..++.+||..+||++.+|++||+|+|++.+..
T Consensus        19 R~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~~   79 (80)
T d1wh7a_          19 RFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPSS   79 (80)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCCC
T ss_pred             CccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCCC
Confidence            45567999999999988885    8999999999999999999999999999999988753

>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=99.02  E-value=2e-11  Score=93.99  Aligned_cols=50  Identities=22%  Similarity=0.434  Sum_probs=46.4

Q ss_pred             hhhhhhhhhhcCCCCCCHHHHHHHHHhhCCCccccccccccccccccchh
Q psy8148         329 RSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       329 ~q~~~Le~~F~~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk~~  378 (390)
                      +|+.+|+..|..++||+.+++.+||..+||+..+|++||+|+|+++|+..
T Consensus        13 eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~~   62 (76)
T d2ecca1          13 EQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ   62 (76)
T ss_dssp             HHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhch
Confidence            34499999999999999999999999999999999999999999998754

>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=99.02  E-value=1.6e-11  Score=90.05  Aligned_cols=44  Identities=23%  Similarity=0.653  Sum_probs=41.6

Q ss_pred             hhhhhhhcC-CCCCCHHHHHHHHHhhCCCcccccccccccccccc
Q psy8148         332 NALKECYDK-NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR  375 (390)
Q Consensus       332 ~~Le~~F~~-n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~k  375 (390)
                      .+|+..|.. ++||+..++++||..+||+..+|++||+|||+++|
T Consensus        14 ~iLE~~F~~~~~yPs~~~~~~LA~~lgls~~qV~~WFqNrR~k~r   58 (59)
T d2cqxa1          14 DTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK   58 (59)
T ss_dssp             THHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccC
Confidence            889999975 68999999999999999999999999999999876

>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=98.98  E-value=3.9e-11  Score=92.82  Aligned_cols=55  Identities=27%  Similarity=0.474  Sum_probs=47.8

Q ss_pred             CcchhhhhhhhhhhhhhhcCCCCCCHHHHHHHHHhhC---------------------CCccccccccccccccccchh
Q psy8148         321 TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITG---------------------LTLTQVSNWFKNRRQRDRTPQ  378 (390)
Q Consensus       321 ~~~t~~q~~q~~~Le~~F~~n~yPs~~er~eLA~~lg---------------------Ls~~qVk~WFqNRR~K~kk~~  378 (390)
                      ..++..|.   .+|+..|+.++||+..+++.||..++                     |++.+|++||+|||++.|+..
T Consensus         2 ~~~tp~Ql---~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr~~   77 (78)
T d1lfba_           2 FKWGPASQ---QILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFRH   77 (78)
T ss_dssp             CCCCHHHH---HHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCCC
T ss_pred             ccCCHHHH---HHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHHhc
Confidence            34454555   99999999999999999999999984                     888999999999999998753

>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=98.91  E-value=1e-10  Score=85.91  Aligned_cols=51  Identities=25%  Similarity=0.467  Sum_probs=44.4

Q ss_pred             chhhhhhhhhhhhhhhc---CCCCCCHHHHHHHHHhhCCCccccccccccccccccc
Q psy8148         323 QQRSIQRSRNALKECYD---KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT  376 (390)
Q Consensus       323 ~t~~q~~q~~~Le~~F~---~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~kk  376 (390)
                      ++..+.   ..|+.+|.   .+|||+.+++++||..+||+..+|++||+|+|+|.|+
T Consensus         5 ft~~q~---~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           5 FTKENV---RILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             CCHHHH---HHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCHHHH---HHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            454455   88999995   4589999999999999999999999999999998765

>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=98.83  E-value=3.5e-10  Score=83.60  Aligned_cols=52  Identities=38%  Similarity=0.588  Sum_probs=44.7

Q ss_pred             CCcchhhhhhhhhhhhhhhc---CCCCCCHHHHHHHHHhhCCCccccccccccccccc
Q psy8148         320 RTPQQRSIQRSRNALKECYD---KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRD  374 (390)
Q Consensus       320 R~~~t~~q~~q~~~Le~~F~---~n~yPs~~er~eLA~~lgLs~~qVk~WFqNRR~K~  374 (390)
                      |+.++..+.   ..|+..|.   .+|||+.+++..||..+||+..+|++||+|+|+|.
T Consensus         6 R~~~~~~~~---~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R~   60 (62)
T d1x2na1           6 RGVLPKHAT---NVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRI   60 (62)
T ss_dssp             SCCCCHHHH---HHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHH---HHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHHh
Confidence            345555555   88999886   48999999999999999999999999999999864

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.96  E-value=0.018  Score=35.46  Aligned_cols=21  Identities=38%  Similarity=0.591  Sum_probs=17.9

Q ss_pred             ccccchhhhhhHHHHHHhhhcH
Q psy8148         182 AIRGQESVLRARAVVAYKRHAF  203 (390)
Q Consensus       182 ~~~~~e~v~rAra~v~~h~~~f  203 (390)
                      .+..+|.||||+..| ||-.+|
T Consensus        11 ~I~~~e~VmRA~~~V-yHl~CF   31 (31)
T d1rutx3          11 SIPASELVMRAQGNV-YHLKCF   31 (31)
T ss_dssp             EECTTSEEEEETTEE-ECGGGC
T ss_pred             cCChhHhheecccce-eeeccC
Confidence            356789999999999 998876