Psyllid ID: psy15514

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------
Protein Sequence
MCWGDRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKLSDGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG
Secondary Structure (PSIPRED)
cccccHHHHcccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccHHHHHHHHcccccccHHHcccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHccccccEEEccccccccc
Secondary Structure Prediction (SSPRO)
ccccHHHHHcccccccccccHHHHHHHcHHHHccHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHccccccccccccccccccccccccccccHHHccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHc
Coil and Loop (DISEMBL)
mcwgdrlikeglcdrgsapsvSAISRLLrghegddtssekklsdgegsdcdsepgiplkrkqrrsrttfSAQQLDELERAFErtqypdiytREELAQRTKLFPHFLIIIEqqssgegsdcdsepgiplkrkqrrsrttfSAQQLDELERAFErtqypdiytREELAQRTKLTEARIQTIFIVRKMRG
Flexible Loop (DISEMBL)
MCWGDRLIKeglcdrgsapsvSAISRllrghegddtssekklsdgegsdcdsepgiplkrkqrrsrttfsaqqldelerafertqypdiYTREELAQRTKLFPHFLIIIEqqssgegsdcdsepgiplkrkqrrsrttfsaqqldelerafertqypdiytreelaqrtklteariqTIFIVRKMRG
Low Complexity Region (SEG)
MCWGDRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKLSDGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG
Disordered region (IsUnstruct)
******LI************************************************************************FERTQYPDIYTREELAQRTKLFPHFLIIIE*******************************************TQYPDIYTREELAQRTKLTEARIQTIFIV*****
Disordered Region (DISOPRED)
*CWGDRLIKEGLCDRGSA*************************************************************************************************************************SAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR*
Disordered Region (DISEMBL)
MCWGDRLIKEGLCDRGSAPSVSAISRLLR************************PGIPLK**********SAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQ***********PGIPLK**********SAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG
Disordered Region (DISPRO)
MCWGDRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSS************************RRSRTTFSAQQLDELERAFERTQYPDIYTREEL***************************************SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRK***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MCWGDRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKLSDGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG
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	187	2.2.26 [Sep-21-2011]
P06601	613	Segmentation protein pair	yes	N/A	0.737	0.225	0.459	7e-32
Q645N4	484	Paired box protein Pax-3-	N/A	N/A	0.748	0.289	0.456	2e-31
Q0IH87	483	Paired box protein Pax-3-	N/A	N/A	0.748	0.289	0.456	5e-31
P24610	479	Paired box protein Pax-3	yes	N/A	0.743	0.290	0.456	6e-31
P23760	479	Paired box protein Pax-3	no	N/A	0.743	0.290	0.456	8e-31
P47239	503	Paired box protein Pax-7	no	N/A	0.705	0.262	0.475	8e-31
P23759	520	Paired box protein Pax-7	no	N/A	0.518	0.186	0.549	9e-26
Q28DP6	461	Paired box protein Pax-3	no	N/A	0.390	0.158	0.780	1e-25
P09083	449	Protein gooseberry-neuro	no	N/A	0.502	0.209	0.590	1e-24
P09082	427	Protein gooseberry OS=Dro	no	N/A	0.513	0.224	0.590	2e-22

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

 Score =  136 bits (343), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 85/185 (45%), Positives = 101/185 (54%), Gaps = 47/185 (25%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRGHEG---DDTSSEKKLSDGEGSDCDSEPGIPLKRK 61
           ++LI+EG+CDR +APSVSAISRL+RG +    +D SS      G+G+   S  G  +   
Sbjct: 127 EKLIREGVCDRSTAPSVSAISRLVRGRDAPLDNDMSSASGSPAGDGTKASSSCGSDVSGG 186

Query: 62  QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCD 121
              +                                             + S  + SDC+
Sbjct: 187 HHNN--------------------------------------------GKPSDEDISDCE 202

Query: 122 SEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI 181
           SEPGI LKRKQRR RTTFSA QLDELERAFERTQYPDIYTREELAQRT LTEARIQ  F 
Sbjct: 203 SEPGIALKRKQRRCRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFS 262

Query: 182 VRKMR 186
            R+ R
Sbjct: 263 NRRAR 267

Pair-rule protein expressed in a segmentally repeating pattern to define the polarity of embryonic segments. Capable of sequence-specific DNA-binding.
Drosophila melanogaster (taxid: 7227)

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

 Score =  134 bits (338), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 83/182 (45%), Positives = 105/182 (57%), Gaps = 42/182 (23%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKLSDGEGSDCDSEPGIPLKRKQRR 64
           D+L+K+G+CDR + PSVS+ISR+LR           K   G+  D +      L RK++ 
Sbjct: 135 DKLLKDGVCDRNTVPSVSSISRILR----------SKFGKGDEEDME------LDRKEQE 178

Query: 65  SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEP 124
                +   +D +                 L +R  + P          S EGSD DSEP
Sbjct: 179 ESEKRAKHSIDGI-----------------LRERAPVSPE---------SEEGSDIDSEP 212

Query: 125 GIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRK 184
            +PLKRKQRRSRTTF+A+QL+ELERAFERT YPDIYTREELAQR KLTEAR+Q  F  R+
Sbjct: 213 DLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRR 272

Query: 185 MR 186
            R
Sbjct: 273 AR 274

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

Xenopus laevis (taxid: 8355)

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

 Score =  133 bits (335), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 83/182 (45%), Positives = 104/182 (57%), Gaps = 42/182 (23%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKLSDGEGSDCDSEPGIPLKRKQRR 64
           D+L+K+G+CDR + PSVS+ISR+LR           K   G+  D +      L RK++ 
Sbjct: 134 DKLLKDGVCDRNTVPSVSSISRILR----------SKFGKGDEEDME------LDRKEQE 177

Query: 65  SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEP 124
                +   +D +                 L +R    P          S EGSD DSEP
Sbjct: 178 ESEKRAKHSIDGI-----------------LRERAPASPE---------SEEGSDIDSEP 211

Query: 125 GIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRK 184
            +PLKRKQRRSRTTF+A+QL+ELERAFERT YPDIYTREELAQR KLTEAR+Q  F  R+
Sbjct: 212 DLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRR 271

Query: 185 MR 186
            R
Sbjct: 272 AR 273

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

Xenopus laevis (taxid: 8355)

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

 Score =  133 bits (335), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 83/182 (45%), Positives = 102/182 (56%), Gaps = 43/182 (23%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKLSDGEGSDCDSEPGIPLKRKQRR 64
           D+L+K+ +CDR + PSVS+ISR+LR           K   GE  + D      L+RK+  
Sbjct: 135 DKLLKDAVCDRNTVPSVSSISRILR----------SKFGKGEEEEAD------LERKEAE 178

Query: 65  SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEP 124
                +   +D +    ER   P                          S EGSD DSEP
Sbjct: 179 ESEKKAKHSIDGI--LSERASAPQ-------------------------SDEGSDIDSEP 211

Query: 125 GIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRK 184
            +PLKRKQRRSRTTF+A+QL+ELERAFERT YPDIYTREELAQR KLTEAR+Q  F  R+
Sbjct: 212 DLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRR 271

Query: 185 MR 186
            R
Sbjct: 272 AR 273

Probable transcription factor associated with development of alveolar rhabdomyosarcoma.

Mus musculus (taxid: 10090)

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

 Score =  133 bits (334), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 83/182 (45%), Positives = 102/182 (56%), Gaps = 43/182 (23%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKLSDGEGSDCDSEPGIPLKRKQRR 64
           D+L+K+ +CDR + PSVS+ISR+LR           K   GE  + D      L+RK+  
Sbjct: 135 DKLLKDAVCDRNTVPSVSSISRILR----------SKFGKGEEEEAD------LERKEAE 178

Query: 65  SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEP 124
                +   +D +    ER   P                          S EGSD DSEP
Sbjct: 179 ESEKKAKHSIDGI--LSERASAPQ-------------------------SDEGSDIDSEP 211

Query: 125 GIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRK 184
            +PLKRKQRRSRTTF+A+QL+ELERAFERT YPDIYTREELAQR KLTEAR+Q  F  R+
Sbjct: 212 DLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRR 271

Query: 185 MR 186
            R
Sbjct: 272 AR 273

Probable transcription factor associated with development of alveolar rhabdomyosarcoma.

Homo sapiens (taxid: 9606)

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

 Score =  133 bits (334), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 88/185 (47%), Positives = 103/185 (55%), Gaps = 53/185 (28%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLR---GHEGDDTSSEKKLSDGEGSDCDSEPGIPLKRK 61
           DRL+K+G CDR + PSVS+ISR+LR   G + DD   +KK  DGE     S  GI L  K
Sbjct: 135 DRLLKDGHCDRSTVPSVSSISRVLRIKFGKKEDDEEGDKKEEDGEKKAKHSIDGI-LGDK 193

Query: 62  QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCD 121
             R         LDE                                        GSD +
Sbjct: 194 GNR---------LDE----------------------------------------GSDVE 204

Query: 122 SEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI 181
           SEP +PLKRKQRRSRTTF+A+QL+ELE+AFERT YPDIYTREELAQRTKLTEAR+Q  F 
Sbjct: 205 SEPDLPLKRKQRRSRTTFTAEQLEELEKAFERTHYPDIYTREELAQRTKLTEARVQVWFS 264

Query: 182 VRKMR 186
            R+ R
Sbjct: 265 NRRAR 269

Probable transcription factor. May have a role in myogenesis.

Mus musculus (taxid: 10090)

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

 Score =  116 bits (290), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 67/122 (54%), Positives = 79/122 (64%), Gaps = 25/122 (20%)

Query: 5   DRLIKEGLCDRGSAPS--VSAISRLLR-----------------------GHEGDDTSSE 39
           DRL+K+G CDR + PS  VS+ISR+LR                        H  D    +
Sbjct: 135 DRLLKDGHCDRSTVPSGLVSSISRVLRIKFGKKEEEDEADKKEDDGEKKAKHSIDGILGD 194

Query: 40  KKLSDGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRT 99
           K     EGSD +SEP +PLKRKQRRSRTTF+A+QL+ELE+AFERT YPDIYTREELAQRT
Sbjct: 195 KGNRLDEGSDVESEPDLPLKRKQRRSRTTFTAEQLEELEKAFERTHYPDIYTREELAQRT 254

Query: 100 KL 101
           KL
Sbjct: 255 KL 256

Probable transcription factor. May have a role in myogenesis.

Homo sapiens (taxid: 9606)

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

 Score =  116 bits (290), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 57/73 (78%), Positives = 63/73 (86%)

Query: 114 SGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTE 173
           S EGSD DSEP +PLKRKQRRSRTTF+A+QL+ELERAFERT YPDIYTREELAQR KLTE
Sbjct: 178 SEEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTE 237

Query: 174 ARIQTIFIVRKMR 186
           AR+Q  F  R+ R
Sbjct: 238 ARVQVWFSNRRAR 250

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

Xenopus tropicalis (taxid: 8364)

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

 Score =  112 bits (280), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 62/105 (59%), Positives = 73/105 (69%), Gaps = 11/105 (10%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKLS--------DGEGSDCDSEPGI 56
           ++LIKEG  D    PS S+ISRLLRG +       K  +        D + SD +SEPGI
Sbjct: 120 EKLIKEGFAD---PPSTSSISRLLRGSDRGSEDGRKDYTINGILGGRDSDISDTESEPGI 176

Query: 57  PLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           PLKRKQRRSRTTF+A+QL+ LERAF RTQYPD+YTREELAQ T L
Sbjct: 177 PLKRKQRRSRTTFTAEQLEALERAFSRTQYPDVYTREELAQTTAL 221

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

Drosophila melanogaster (taxid: 7227)

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

 Score =  105 bits (262), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 62/105 (59%), Positives = 74/105 (70%), Gaps = 9/105 (8%)

Query: 6   RLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSS--EKKLSDGEGS-------DCDSEPGI 56
           +LI+ G+CD+ +APSVS+ISRLLRG  G  TS   +  L  G GS       + D+EP +
Sbjct: 120 KLIEAGVCDKQNAPSVSSISRLLRGSSGSGTSHSIDGILGGGAGSVGSEDESEDDAEPSV 179

Query: 57  PLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
            LKRKQRRSRTTFS  Q+D LER F RTQYPD+YTREELAQ T L
Sbjct: 180 QLKRKQRRSRTTFSNDQIDALERIFARTQYPDVYTREELAQSTGL 224

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

Drosophila melanogaster (taxid: 7227)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	187
328719097	574	PREDICTED: paired box protein Pax-3-B-li	0.513	0.167	0.868	6e-43
307180596	516	Segmentation protein paired [Camponotus	0.802	0.290	0.543	6e-38
328782878	531	PREDICTED: paired box protein Pax-3-B [A	0.502	0.177	0.83	1e-37
383854529	483	PREDICTED: paired box protein Pax-3-B-li	0.502	0.194	0.82	2e-37
350397864	522	PREDICTED: LOW QUALITY PROTEIN: protein	0.502	0.180	0.81	2e-36
340724544	502	PREDICTED: LOW QUALITY PROTEIN: segmenta	0.502	0.187	0.794	4e-36
270009304	447	paired [Tribolium castaneum]	0.502	0.210	0.795	1e-35
242007394	439	Paired box protein Pax-7, putative [Pedi	0.502	0.214	0.772	1e-35
307197090	481	Segmentation protein paired [Harpegnatho	0.518	0.201	0.731	7e-35
322794106	486	hypothetical protein SINV_02934 [Solenop	0.502	0.193	0.77	9e-35

>gi|328719097|ref|XP_001949018.2| PREDICTED: paired box protein Pax-3-B-like [Acyrthosiphon pisum]

 Score =  179 bits (453), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 86/99 (86%), Positives = 95/99 (95%), Gaps = 3/99 (3%)

Query: 6   RLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKLSDG---EGSDCDSEPGIPLKRKQ 62
           RLI+EGLCDRGSAPS+SAISRLLRGH+GDD++SEKK+SDG   +GSDCDSEPGIPLKRKQ
Sbjct: 134 RLIREGLCDRGSAPSISAISRLLRGHDGDDSASEKKVSDGKTSDGSDCDSEPGIPLKRKQ 193

Query: 63  RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           RRSRTTF+A QLDELE+AFERTQYPDIYTREELAQRTKL
Sbjct: 194 RRSRTTFTALQLDELEKAFERTQYPDIYTREELAQRTKL 232

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307180596|gb|EFN68551.1| Segmentation protein paired [Camponotus floridanus]

 Score =  162 bits (410), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 99/182 (54%), Positives = 118/182 (64%), Gaps = 32/182 (17%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKLSDGEGSDCDSEPGIPLKRKQRR 64
           DRLIKEG+CDR SAPSVSAISRLLRG + +D   + KL  G+GSD  S            
Sbjct: 119 DRLIKEGICDRTSAPSVSAISRLLRGRDPED---DVKL--GDGSDYPS------------ 161

Query: 65  SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEP 124
              T+       +E   +R+ Y D+ T + +       PH      ++ +  GSDCDSEP
Sbjct: 162 ---TYELLWRHIVEAISDRSSYVDMGTIKPVG------PH------RRKTSSGSDCDSEP 206

Query: 125 GIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRK 184
           GI LKRKQRRSRTTF+A QLDELERAFERTQYPDIYTREELAQRT+L+EARIQ  F  R+
Sbjct: 207 GIQLKRKQRRSRTTFTAHQLDELERAFERTQYPDIYTREELAQRTRLSEARIQVWFSNRR 266

Query: 185 MR 186
            R
Sbjct: 267 AR 268

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328782878|ref|XP_003250208.1| PREDICTED: paired box protein Pax-3-B [Apis mellifera]

 Score =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 83/100 (83%), Positives = 88/100 (88%), Gaps = 6/100 (6%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKLSDGE---GSDCDSEPGIPLKRK 61
           DRLIKEG+CDR SAPSVSAISRLLRG + +D   E KL DG+   GSDCDSEPGIPLKRK
Sbjct: 160 DRLIKEGICDRTSAPSVSAISRLLRGRDPED---EAKLGDGKTSSGSDCDSEPGIPLKRK 216

Query: 62  QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           QRRSRTTF+A QLDELERAFERTQYPDIYTREELAQRTKL
Sbjct: 217 QRRSRTTFTAHQLDELERAFERTQYPDIYTREELAQRTKL 256

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383854529|ref|XP_003702773.1| PREDICTED: paired box protein Pax-3-B-like [Megachile rotundata]

 Score =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 82/100 (82%), Positives = 88/100 (88%), Gaps = 6/100 (6%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKLSDGE---GSDCDSEPGIPLKRK 61
           DRLIKEG+CDR SAPSVSAISRLLRG + +D   E KL DG+   GSDC+SEPGIPLKRK
Sbjct: 112 DRLIKEGICDRTSAPSVSAISRLLRGRDPED---EAKLGDGKTSSGSDCESEPGIPLKRK 168

Query: 62  QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           QRRSRTTF+A QLDELERAFERTQYPDIYTREELAQRTKL
Sbjct: 169 QRRSRTTFTAHQLDELERAFERTQYPDIYTREELAQRTKL 208

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350397864|ref|XP_003485014.1| PREDICTED: LOW QUALITY PROTEIN: protein gooseberry-like [Bombus impatiens]

 Score =  157 bits (397), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 81/100 (81%), Positives = 86/100 (86%), Gaps = 6/100 (6%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKLSD---GEGSDCDSEPGIPLKRK 61
           DRLIKEG+CDR SAPSVSAISRLLRG + +D   E KL D     GSDC+SEPGIPLKRK
Sbjct: 157 DRLIKEGICDRTSAPSVSAISRLLRGRDPED---ETKLGDRKTSSGSDCESEPGIPLKRK 213

Query: 62  QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           QRRSRTTF+A QLDELERAFERTQYPDIYTREELAQRTKL
Sbjct: 214 QRRSRTTFTAHQLDELERAFERTQYPDIYTREELAQRTKL 253

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340724544|ref|XP_003400641.1| PREDICTED: LOW QUALITY PROTEIN: segmentation protein paired-like [Bombus terrestris]

 Score =  156 bits (394), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 81/102 (79%), Positives = 86/102 (84%), Gaps = 8/102 (7%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKLSD-----GEGSDCDSEPGIPLK 59
           DRLIKEG+CDR SAPSVSAISRLLRG + +D   E KL D       GSDC+SEPGIPLK
Sbjct: 132 DRLIKEGICDRTSAPSVSAISRLLRGRDPED---ETKLGDRDGKTSSGSDCESEPGIPLK 188

Query: 60  RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           RKQRRSRTTF+A QLDELERAFERTQYPDIYTREELAQRTKL
Sbjct: 189 RKQRRSRTTFTAHQLDELERAFERTQYPDIYTREELAQRTKL 230

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270009304|gb|EFA05752.1| paired [Tribolium castaneum]

 Score =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 78/98 (79%), Positives = 86/98 (87%), Gaps = 4/98 (4%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKLSDGEG-SDCDSEPGIPLKRKQR 63
           DRL+KEG+CDR +APSVSAISRLLRG  G+    + K +D EG SDCDSEPGIPLKRKQR
Sbjct: 121 DRLVKEGICDRSTAPSVSAISRLLRGKGGE---CDDKSTDNEGVSDCDSEPGIPLKRKQR 177

Query: 64  RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           RSRTTF+A QLDELE+AFERTQYPDIYTREELAQRTKL
Sbjct: 178 RSRTTFTAHQLDELEKAFERTQYPDIYTREELAQRTKL 215

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242007394|ref|XP_002424525.1| Paired box protein Pax-7, putative [Pediculus humanus corporis] gi|212507958|gb|EEB11787.1| Paired box protein Pax-7, putative [Pediculus humanus corporis]

 Score =  154 bits (390), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 78/101 (77%), Positives = 89/101 (88%), Gaps = 7/101 (6%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKLSDG----EGSDCDSEPGIPLKR 60
           DRLIKEG+CDR S PSVSAISRLLRG +G+D   ++K++DG    + SDC+SEPGIPLKR
Sbjct: 123 DRLIKEGICDRSSVPSVSAISRLLRGRDGED---DRKINDGCKNSDNSDCESEPGIPLKR 179

Query: 61  KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           KQRRSRTTF+A QLDELE+AFERTQYPDIYTREELAQRTKL
Sbjct: 180 KQRRSRTTFTALQLDELEKAFERTQYPDIYTREELAQRTKL 220

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307197090|gb|EFN78458.1| Segmentation protein paired [Harpegnathos saltator]

 Score =  152 bits (383), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 71/97 (73%), Positives = 84/97 (86%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKLSDGEGSDCDSEPGIPLKRKQRR 64
           DRL+KEG+C++ +APSVSAISRL+RG + +D +   ++    GSDCDSEPGI LKRKQRR
Sbjct: 73  DRLVKEGICEKANAPSVSAISRLIRGRDNEDDARIGEVKTSSGSDCDSEPGITLKRKQRR 132

Query: 65  SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           SRTTF+A QLDELE+AFERTQYPDIYTREELAQRTKL
Sbjct: 133 SRTTFTAHQLDELEKAFERTQYPDIYTREELAQRTKL 169

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322794106|gb|EFZ17315.1| hypothetical protein SINV_02934 [Solenopsis invicta]

 Score =  151 bits (382), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 77/100 (77%), Positives = 86/100 (86%), Gaps = 6/100 (6%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKLSDGE---GSDCDSEPGIPLKRK 61
           DRLIKEG+CDR SAPSVSAISRLLRG + +D   + KL DG+   GSDC+SEPGI LKRK
Sbjct: 120 DRLIKEGICDRTSAPSVSAISRLLRGRDSED---DVKLGDGKTSSGSDCESEPGITLKRK 176

Query: 62  QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           QRRSRTTF+A QLDELERAFE+TQYPDIY REELAQRT+L
Sbjct: 177 QRRSRTTFTAHQLDELERAFEKTQYPDIYVREELAQRTRL 216

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	187
ZFIN|ZDB-GENE-980526-52	509	pax3a "paired box gene 3a" [Da	0.529	0.194	0.617	8.6e-35
FB|FBgn0003145	613	prd "paired" [Drosophila melan	0.368	0.112	0.840	1.5e-34
UNIPROTKB|P23760	479	PAX3 "Paired box protein Pax-3	0.508	0.198	0.64	1.2e-25
MGI|MGI:97487	479	Pax3 "paired box gene 3" [Mus	0.508	0.198	0.64	1.2e-25
UNIPROTKB|F1MTX0	484	PAX3 "Uncharacterized protein"	0.508	0.196	0.64	1.3e-25
UNIPROTKB|E2QX72	485	PAX3 "Uncharacterized protein"	0.508	0.195	0.64	1.3e-25
UNIPROTKB|F1LMV3	487	Pax3 "Protein Pax3" [Rattus no	0.508	0.195	0.64	1.4e-25
UNIPROTKB|I3LAG7	483	PAX3 "Uncharacterized protein"	0.502	0.194	0.623	2.8e-25
ZFIN|ZDB-GENE-080917-53	480	pax3b "paired box gene 3b" [Da	0.737	0.287	0.496	6e-25
UNIPROTKB|Q28DP6	461	pax3 "Paired box protein Pax-3	0.390	0.158	0.780	6.1e-25

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

 Score = 299 (110.3 bits), Expect = 8.6e-35, Sum P(2) = 8.6e-35
 Identities = 63/102 (61%), Positives = 77/102 (75%)

Query:    88 DIYTREELAQRTKLFPHFL--IIIEQQS-SGEGSDCDSEPGIPLKRKQRRSRTTFSAQQL 144
             D   + E+ +  +   H +  I+ ++ S S EGSD DSEPG+PLKRKQRRSRTTF+A+QL
Sbjct:   173 DEVEKREIEENERRAKHSIDGILGDRSSHSDEGSDVDSEPGLPLKRKQRRSRTTFTAEQL 232

Query:   145 DELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
             +ELERAFERT YPDIYTREELAQR KLTEAR+Q  F  R+ R
Sbjct:   233 EELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRAR 274

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

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

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

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;IDA

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

GO:0048066 "developmental pigmentation" evidence=IMP

GO:0050936 "xanthophore differentiation" evidence=IMP

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

GO:0007275 "multicellular organismal development" evidence=IEA

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

FB|FBgn0003145 prd "paired" [Drosophila melanogaster (taxid:7227)]

 Score = 287 (106.1 bits), Expect = 1.5e-34, Sum P(2) = 1.5e-34
 Identities = 58/69 (84%), Positives = 60/69 (86%)

Query:   118 SDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQ 177
             SDC+SEPGI LKRKQRR RTTFSA QLDELERAFERTQYPDIYTREELAQRT LTEARIQ
Sbjct:   199 SDCESEPGIALKRKQRRCRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQ 258

Query:   178 TIFIVRKMR 186
               F  R+ R
Sbjct:   259 VWFSNRRAR 267

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

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

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

GO:0005667 "transcription factor complex" evidence=ISS

GO:0007366 "periodic partitioning by pair rule gene" evidence=NAS;TAS

GO:0003677 "DNA binding" evidence=NAS

GO:0005634 "nucleus" evidence=NAS

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

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

UNIPROTKB|P23760 PAX3 "Paired box protein Pax-3" [Homo sapiens (taxid:9606)]

 Score = 294 (108.6 bits), Expect = 1.2e-25, P = 1.2e-25
 Identities = 64/100 (64%), Positives = 75/100 (75%)

Query:    92 REELAQRTKLFPHFL--IIIEQQS---SGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDE 146
             R+E  +  K   H +  I+ E+ S   S EGSD DSEP +PLKRKQRRSRTTF+A+QL+E
Sbjct:   174 RKEAEESEKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEE 233

Query:   147 LERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
             LERAFERT YPDIYTREELAQR KLTEAR+Q  F  R+ R
Sbjct:   234 LERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRAR 273

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0007605 "sensory perception of sound" evidence=TAS

GO:0006915 "apoptotic process" evidence=TAS

GO:0009887 "organ morphogenesis" evidence=TAS

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

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

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

GO:0005515 "protein binding" evidence=IPI

MGI|MGI:97487 Pax3 "paired box gene 3" [Mus musculus (taxid:10090)]

 Score = 294 (108.6 bits), Expect = 1.2e-25, P = 1.2e-25
 Identities = 64/100 (64%), Positives = 75/100 (75%)

Query:    92 REELAQRTKLFPHFL--IIIEQQS---SGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDE 146
             R+E  +  K   H +  I+ E+ S   S EGSD DSEP +PLKRKQRRSRTTF+A+QL+E
Sbjct:   174 RKEAEESEKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEE 233

Query:   147 LERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
             LERAFERT YPDIYTREELAQR KLTEAR+Q  F  R+ R
Sbjct:   234 LERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRAR 273

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

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

GO:0001843 "neural tube closure" evidence=IMP

GO:0003677 "DNA binding" evidence=IEA

GO:0003682 "chromatin binding" evidence=IDA

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005667 "transcription factor complex" evidence=TAS

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007507 "heart development" evidence=IMP

GO:0007517 "muscle organ development" evidence=IMP

GO:0008283 "cell proliferation" evidence=IMP

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

GO:0016477 "cell migration" evidence=IMP

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

GO:0021915 "neural tube development" evidence=IGI

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

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

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

GO:0048066 "developmental pigmentation" evidence=IMP

GO:0048663 "neuron fate commitment" evidence=IGI

GO:0060594 "mammary gland specification" evidence=IMP

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

 Score = 294 (108.6 bits), Expect = 1.3e-25, P = 1.3e-25
 Identities = 64/100 (64%), Positives = 75/100 (75%)

Query:    92 REELAQRTKLFPHFL--IIIEQQS---SGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDE 146
             R+E  +  K   H +  I+ E+ S   S EGSD DSEP +PLKRKQRRSRTTF+A+QL+E
Sbjct:   174 RKEAEESEKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEE 233

Query:   147 LERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
             LERAFERT YPDIYTREELAQR KLTEAR+Q  F  R+ R
Sbjct:   234 LERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRAR 273

GO:0005634 "nucleus" evidence=IEA

GO:0060594 "mammary gland specification" evidence=IEA

GO:0048663 "neuron fate commitment" evidence=IEA

GO:0048066 "developmental pigmentation" evidence=IEA

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

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

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

GO:0008283 "cell proliferation" evidence=IEA

GO:0007517 "muscle organ development" evidence=IEA

GO:0007507 "heart development" evidence=IEA

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

GO:0003682 "chromatin binding" evidence=IEA

GO:0001843 "neural tube closure" evidence=IEA

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

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

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

 Score = 294 (108.6 bits), Expect = 1.3e-25, P = 1.3e-25
 Identities = 64/100 (64%), Positives = 75/100 (75%)

Query:    92 REELAQRTKLFPHFL--IIIEQQS---SGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDE 146
             R+E  +  K   H +  I+ E+ S   S EGSD DSEP +PLKRKQRRSRTTF+A+QL+E
Sbjct:   175 RKEAEESEKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEE 234

Query:   147 LERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
             LERAFERT YPDIYTREELAQR KLTEAR+Q  F  R+ R
Sbjct:   235 LERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRAR 274

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

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

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

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

UNIPROTKB|F1LMV3 Pax3 "Protein Pax3" [Rattus norvegicus (taxid:10116)]

 Score = 294 (108.6 bits), Expect = 1.4e-25, P = 1.4e-25
 Identities = 64/100 (64%), Positives = 75/100 (75%)

Query:    92 REELAQRTKLFPHFL--IIIEQQS---SGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDE 146
             R+E  +  K   H +  I+ E+ S   S EGSD DSEP +PLKRKQRRSRTTF+A+QL+E
Sbjct:   177 RKEAEESEKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEE 236

Query:   147 LERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
             LERAFERT YPDIYTREELAQR KLTEAR+Q  F  R+ R
Sbjct:   237 LERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRAR 276

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

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

GO:0001843 "neural tube closure" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0007507 "heart development" evidence=IEA

GO:0007517 "muscle organ development" evidence=IEA

GO:0008283 "cell proliferation" evidence=IEA

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

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

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

GO:0048066 "developmental pigmentation" evidence=IEA

GO:0048663 "neuron fate commitment" evidence=IEA

GO:0060594 "mammary gland specification" evidence=IEA

GO:0071837 "HMG box domain binding" evidence=IPI

UNIPROTKB|I3LAG7 PAX3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 291 (107.5 bits), Expect = 2.8e-25, P = 2.8e-25
 Identities = 63/101 (62%), Positives = 77/101 (76%)

Query:    92 REELAQRTKLFPHFL--IIIEQQS---SGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDE 146
             R+E  +  K   H +  I+ E+ S   S EGSD DSEP +PLKRKQRRSRTTF+A+QL+E
Sbjct:   172 RKEAEESEKKTKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEE 231

Query:   147 LERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG 187
             LERAFERT YPDIYTREELAQR KLTEAR+Q +++   +RG
Sbjct:   232 LERAFERTHYPDIYTREELAQRAKLTEARVQRLWL--SLRG 270

GO:0005634 "nucleus" evidence=IEA

GO:0060594 "mammary gland specification" evidence=IEA

GO:0048663 "neuron fate commitment" evidence=IEA

GO:0048066 "developmental pigmentation" evidence=IEA

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

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

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

GO:0008283 "cell proliferation" evidence=IEA

GO:0007517 "muscle organ development" evidence=IEA

GO:0007507 "heart development" evidence=IEA

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

GO:0003682 "chromatin binding" evidence=IEA

GO:0001843 "neural tube closure" evidence=IEA

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

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

ZFIN|ZDB-GENE-080917-53 pax3b "paired box gene 3b" [Danio rerio (taxid:7955)]

 Score = 288 (106.4 bits), Expect = 6.0e-25, P = 6.0e-25
 Identities = 77/155 (49%), Positives = 98/155 (63%)

Query:    39 EKKLSDGEGSDCDSEPGIP-LKRKQR-RSRTTFSAQQLDELERAFERTQYPDIYTREELA 96
             +K L +G   D ++ P +  + R  R RS T    ++ +E E   ER +      REE A
Sbjct:   139 DKLLKEGI-CDRNNVPTVSSISRIMRGRSGTRADEEEEEEDEEDIERRE------REENA 191

Query:    97 QRTKLFPHFL--IIIEQQS---SGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAF 151
              R     H +  I+ ++ S   S EGS+ +SEP +PLKRKQRRSRTTF+A QL+ELERAF
Sbjct:   192 HRGA---HSIEGILADRFSASPSDEGSEVESEPDLPLKRKQRRSRTTFTADQLEELERAF 248

Query:   152 ERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
             ERT YPDIYTREELAQR KLTEAR+Q  F  R+ R
Sbjct:   249 ERTHYPDIYTREELAQRAKLTEARVQVWFSNRRAR 283

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

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

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

UNIPROTKB|Q28DP6 pax3 "Paired box protein Pax-3" [Xenopus (Silurana) tropicalis (taxid:8364)]

 Score = 287 (106.1 bits), Expect = 6.1e-25, P = 6.1e-25
 Identities = 57/73 (78%), Positives = 63/73 (86%)

Query:   114 SGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTE 173
             S EGSD DSEP +PLKRKQRRSRTTF+A+QL+ELERAFERT YPDIYTREELAQR KLTE
Sbjct:   178 SEEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTE 237

Query:   174 ARIQTIFIVRKMR 186
             AR+Q  F  R+ R
Sbjct:   238 ARVQVWFSNRRAR 250

GO:0005634 "nucleus" evidence=ISS

GO:0008543 "fibroblast growth factor receptor signaling pathway" evidence=ISS

GO:0014029 "neural crest formation" evidence=ISS

GO:0014034 "neural crest cell fate commitment" evidence=ISS

GO:0016055 "Wnt receptor signaling pathway" evidence=ISS

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

GO:0048785 "hatching gland development" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	187
pfam00046	57	pfam00046, Homeobox, Homeobox domain	3e-16
smart00389	57	smart00389, HOX, Homeodomain	2e-14
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	5e-14
pfam00046	57	pfam00046, Homeobox, Homeobox domain	4e-12
smart00389	57	smart00389, HOX, Homeodomain	3e-10
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	7e-10
cd00131	128	cd00131, PAX, Paired Box domain	2e-06
smart00351	125	smart00351, PAX, Paired Box domain	5e-06
pfam00292	125	pfam00292, PAX, 'Paired box' domain	1e-05
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	5e-04
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	0.004

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

 Score = 68.7 bits (169), Expect = 3e-16
 Identities = 25/54 (46%), Positives = 38/54 (70%)

Query: 133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           RR RTTF+ +QL+ELE+ FE+ +YP    REELA++  LTE +++  F  R+ +
Sbjct: 1   RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAK 54

Length = 57

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 63.8 bits (156), Expect = 2e-14
 Identities = 22/55 (40%), Positives = 38/55 (69%)

Query: 132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           +RR RT+F+ +QL+ELE+ F++  YP    REELA++  L+E +++  F  R+ +
Sbjct: 1   KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAK 55

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

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

 Score = 63.4 bits (155), Expect = 5e-14
 Identities = 24/54 (44%), Positives = 35/54 (64%)

Query: 133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           RR RT F+ +QL+ELE+ FE+  YP    REELA+   LTE +++  F  R+ +
Sbjct: 1   RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAK 54

Length = 59

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

 Score = 58.3 bits (142), Expect = 4e-12
 Identities = 21/39 (53%), Positives = 29/39 (74%)

Query: 63  RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           RR RTTF+ +QL+ELE+ FE+ +YP    REELA++  L
Sbjct: 1   RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGL 39

Length = 57

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 53.4 bits (129), Expect = 3e-10
 Identities = 19/40 (47%), Positives = 29/40 (72%)

Query: 62  QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           +RR RT+F+ +QL+ELE+ F++  YP    REELA++  L
Sbjct: 1   KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGL 40

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

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

 Score = 52.2 bits (126), Expect = 7e-10
 Identities = 20/39 (51%), Positives = 26/39 (66%)

Query: 63  RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           RR RT F+ +QL+ELE+ FE+  YP    REELA+   L
Sbjct: 1   RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGL 39

Length = 59

>gnl|CDD|238076 cd00131, PAX, Paired Box domain

 Score = 44.7 bits (106), Expect = 2e-06
 Identities = 15/26 (57%), Positives = 23/26 (88%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRG 30
           DRL++EG+CD+ + PSVS+I+R+LR 
Sbjct: 101 DRLLQEGVCDKSNVPSVSSINRILRN 126

Length = 128

>gnl|CDD|128645 smart00351, PAX, Paired Box domain

 Score = 43.5 bits (103), Expect = 5e-06
 Identities = 15/25 (60%), Positives = 22/25 (88%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLR 29
           DRL+ EG+CD+ + PSVS+I+R+LR
Sbjct: 101 DRLLSEGVCDKDNVPSVSSINRILR 125

Length = 125

>gnl|CDD|109353 pfam00292, PAX, 'Paired box' domain

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 16/25 (64%), Positives = 21/25 (84%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLR 29
           DRL+ EG+CD  + PSVS+ISR+LR
Sbjct: 101 DRLLAEGVCDNDNVPSVSSISRILR 125

Length = 125

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

 Score = 38.6 bits (90), Expect = 5e-04
 Identities = 15/51 (29%), Positives = 22/51 (43%)

Query: 130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIF 180
              +  R   + +QL  LER FE   YP   TR +L+    +    +Q  F
Sbjct: 49  SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWF 99

Length = 156

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

 Score = 35.9 bits (83), Expect = 0.004
 Identities = 21/85 (24%), Positives = 30/85 (35%), Gaps = 10/85 (11%)

Query: 19  PSVSAISRLLRGHEGDDTSSEKKLSDGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELE 78
           P +  I       E +   SE KL   +                +  R   + +QL  LE
Sbjct: 18  PQIRTIKTTKNKREVEAADSEMKLERKQDGS----------SPPKSKRRRTTDEQLMVLE 67

Query: 79  RAFERTQYPDIYTREELAQRTKLFP 103
           R FE   YP   TR +L+    + P
Sbjct: 68  REFEINPYPSSITRIKLSLLLNMPP 92

Length = 156

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	187
KOG0484|consensus	125		99.86
KOG0849|consensus	354		99.84
KOG0490|consensus	235		99.76
KOG0843|consensus	197		99.75
KOG2251|consensus	228		99.74
KOG0850|consensus	245		99.72
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.72
KOG0488|consensus	309		99.72
KOG0484|consensus	125		99.71
KOG0842|consensus	307		99.71
KOG0489|consensus	261		99.7
KOG0494|consensus	332		99.69
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.69
KOG0492|consensus	246		99.67
KOG0487|consensus	308		99.66
KOG0485|consensus	268		99.65
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.62
KOG0493|consensus	342		99.62
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.57
KOG0848|consensus	317		99.54
KOG0491|consensus	194		99.53
KOG0486|consensus	351		99.52
KOG3862|consensus	327		99.49
KOG3802|consensus	398		99.49
KOG0844|consensus	408		99.49
KOG3517|consensus	334		99.47
KOG2251|consensus	228		99.46
COG5576	156	Homeodomain-containing transcription factor [Trans	99.45
KOG0494|consensus	332		99.44
KOG0850|consensus	245		99.44
KOG0842|consensus	307		99.43
KOG0483|consensus	198		99.41
KOG0843|consensus	197		99.41
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.39
KOG4577|consensus	383		99.37
KOG0488|consensus	309		99.36
KOG0490|consensus	235		99.31
KOG0489|consensus	261		99.3
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.24
KOG0485|consensus	268		99.24
KOG0847|consensus	288		99.23
KOG0492|consensus	246		99.23
KOG0486|consensus	351		99.16
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.09
KOG0493|consensus	342		99.06
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	98.99
COG5576	156	Homeodomain-containing transcription factor [Trans	98.97
KOG0844|consensus	408		98.95
KOG0487|consensus	308		98.95
KOG0848|consensus	317		98.89
KOG0849|consensus	354		98.88
KOG0775|consensus	304		98.85
KOG0491|consensus	194		98.82
KOG1168|consensus	385		98.74
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.72
KOG2252|consensus	558		98.54
KOG0847|consensus	288		98.48
KOG0483|consensus	198		98.39
KOG4577|consensus	383		98.36
KOG3802|consensus	398		98.26
KOG0774|consensus	334		98.19
KOG1146|consensus	1406		97.8
KOG2252|consensus	558		97.64
KOG3623|consensus	1007		97.58
KOG0775|consensus	304		97.45
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	97.42
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	97.34
KOG0773|consensus	342		96.63
KOG1168|consensus	385		96.53
KOG0774|consensus	334		96.1
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	95.8
KOG3623|consensus	1007		95.57
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	95.2
KOG1146|consensus	1406		95.1
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	93.58
PF13551	112	HTH_29: Winged helix-turn helix	87.57
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	85.68
COG3413	215	Predicted DNA binding protein [General function pr	83.97
KOG0773|consensus	342		82.69
PF10668	60	Phage_terminase: Phage terminase small subunit; In	82.54

>KOG0484|consensus

Probab=99.86  E-value=1.2e-22  Score=129.58  Aligned_cols=63  Identities=59%  Similarity=0.874  Sum_probs=59.3

Q ss_pred             CCCcccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        124 PGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       124 ~~~~~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+...++|++|.||+||..||.+||++|...+||++..|++||.+++|++.+|||||||||+|
T Consensus         9 ~~l~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAK   71 (125)
T KOG0484|consen    9 LGLTEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAK   71 (125)
T ss_pred             CChhHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHH
Confidence            344567899999999999999999999999999999999999999999999999999999987

>KOG0849|consensus

Probab=99.84  E-value=4.4e-21  Score=152.58  Aligned_cols=135  Identities=38%  Similarity=0.578  Sum_probs=95.2

Q ss_pred             Ccc--ccchhhcCCCCCCCCCccchhhhcccCCCCCCCCcccccCCCCCCCCCCCCCCCcccCCCCCCCCcCHHHHHHHH
Q psy15514          1 MCW--GDRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKLSDGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELE   78 (187)
Q Consensus         1 ~~~--rdrll~e~vc~~~~vPSvsSinrilr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~rt~ft~~ql~~Le   78 (187)
                      |+|  ||+|+.+++|+++++|||++|||++++........   .                +....               
T Consensus        94 ~~~~ir~~l~~~~~~~~~t~Ps~ssi~r~~r~~~~~~d~~---~----------------~~~~~---------------  139 (354)
T KOG0849|consen   94 FAWEIRDQLLHEGLCTQATLPSVSSINRVLRNGALGKDQG---L----------------PSQQV---------------  139 (354)
T ss_pred             cchhhhhcccCcccccCCCCCChhhhhHHhhccccccccc---c----------------ccccc---------------
Confidence            789  99999999999999999999999999876543220   0                00000               


Q ss_pred             HHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHHhhhcCCCC
Q psy15514         79 RAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPD  158 (187)
Q Consensus        79 ~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~  158 (187)
                        +....++.       ...++..       .. ......+....++....++.+|.||+|+..|+..|+..|++++||+
T Consensus       140 --~~~~~~~~-------~~~~gs~-------~~-~s~~~~~~~~~p~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~  202 (354)
T KOG0849|consen  140 --TKEKSPSI-------SGALGSQ-------AG-ASLLSADDEEPPGYALQRGGRRNRTSFSPSQLEALEECFQRTPYPD  202 (354)
T ss_pred             --cccccCCc-------ccccCCc-------cc-cccccCCccccccccccccccccccccccchHHHHHHHhcCCCCCc
Confidence              00000000       0000000       11 1122223333444455677888899999999999999999999999


Q ss_pred             HHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        159 IYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       159 ~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ...|+.||.++++++..|++||+|||+|
T Consensus       203 i~~Re~La~~i~l~e~riqvwf~nrra~  230 (354)
T KOG0849|consen  203 IVGRETLAKETGLPEPRVQVWFQNRRAK  230 (354)
T ss_pred             hhhHHHHhhhccCCchHHHHHHhhhhhh
Confidence            9999999999999999999999999986

>KOG0490|consensus

Probab=99.76  E-value=7.6e-19  Score=133.45  Aligned_cols=128  Identities=37%  Similarity=0.435  Sum_probs=110.1

Q ss_pred             ccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCCCC----------C------
Q psy15514         59 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCD----------S------  122 (187)
Q Consensus        59 ~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~----------~------  122 (187)
                      ..++++.|+.|+..|+++|++.|+..|||+.+.++.||..+++++..|++||+|++...-...          .      
T Consensus        57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~~~~~~~~~~~~~~~~~  136 (235)
T KOG0490|consen   57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEERPLPEGENLPDLSGTAP  136 (235)
T ss_pred             hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhccccccccCCCCCCCCC
Confidence            457889999999999999999999999999999999999999999999999998765332111          0      


Q ss_pred             -------CCCCcccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        123 -------EPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       123 -------~~~~~~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                             ........+.++.|+.+...|+..|...|..+++|+...++.|+..+|++...|++||+|+|++
T Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~  207 (235)
T KOG0490|consen  137 PSASRDKLDKGPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAK  207 (235)
T ss_pred             ccccccccccCCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHH
Confidence                   0011223566778899999999999999999999999999999999999999999999999865

>KOG0843|consensus

Probab=99.75  E-value=8.2e-19  Score=123.06  Aligned_cols=56  Identities=38%  Similarity=0.547  Sum_probs=54.5

Q ss_pred             cccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       131 ~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +.+|.||.||.+||..||..|+.++|..-.+|+.||+.|+|++.||+|||||||+|
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk  156 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTK  156 (197)
T ss_pred             CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHH
Confidence            77889999999999999999999999999999999999999999999999999987

>KOG2251|consensus

Probab=99.74  E-value=1.7e-18  Score=125.45  Aligned_cols=59  Identities=51%  Similarity=0.783  Sum_probs=57.0

Q ss_pred             ccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        128 LKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       128 ~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ..++.+|.||+|+..|+++||..|.+.+||++..+++||.+|+|++.+|+|||+|||+|
T Consensus        33 ~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK   91 (228)
T KOG2251|consen   33 GPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAK   91 (228)
T ss_pred             cchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccch
Confidence            45788999999999999999999999999999999999999999999999999999997

>KOG0850|consensus

Probab=99.72  E-value=2.3e-18  Score=125.30  Aligned_cols=58  Identities=36%  Similarity=0.560  Sum_probs=55.4

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+|.|+.||.|+..||..|.+.|++++|+-..+|.+||..|||+.+||||||||||.|
T Consensus       119 ~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK  176 (245)
T KOG0850|consen  119 GKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSK  176 (245)
T ss_pred             cccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHH
Confidence            4677888999999999999999999999999999999999999999999999999987

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.72  E-value=1.2e-17  Score=97.89  Aligned_cols=52  Identities=19%  Similarity=0.261  Sum_probs=50.5

Q ss_pred             cccCCCCCHHHHHHHHHHhhhcCC----CCHHHHHHHHHHcCCChhhhhhhhcccC
Q psy15514        133 RRSRTTFSAQQLDELERAFERTQY----PDIYTREELAQRTKLTEARIQTIFIVRK  184 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f~~~~~----p~~~~~~~la~~~~l~~~~v~~WF~nrR  184 (187)
                      +|.||.||.+|+..|+..|+.++|    |+..++++||..+||++.+|+|||||.+
T Consensus         2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            688999999999999999999999    9999999999999999999999999976

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.

>KOG0488|consensus

Probab=99.72  E-value=6.3e-18  Score=131.85  Aligned_cols=58  Identities=43%  Similarity=0.641  Sum_probs=56.1

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+|.++.||.||..|+.+||+.|++..|.+..+|++||..|||+..||++||||||+|
T Consensus       169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtK  226 (309)
T KOG0488|consen  169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTK  226 (309)
T ss_pred             CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHH
Confidence            3788889999999999999999999999999999999999999999999999999997

>KOG0484|consensus

Probab=99.71  E-value=2.8e-18  Score=109.57  Aligned_cols=59  Identities=51%  Similarity=0.693  Sum_probs=55.5

Q ss_pred             CcccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         57 PLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        57 ~~~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      .-.+++||.||+||..||.+||++|..+||||+++|++||.++.|++..|++||||++.
T Consensus        12 ~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRA   70 (125)
T KOG0484|consen   12 TEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRA   70 (125)
T ss_pred             hHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHH
Confidence            34568999999999999999999999999999999999999999999999999998764

>KOG0842|consensus

Probab=99.71  E-value=6.6e-18  Score=129.75  Aligned_cols=58  Identities=38%  Similarity=0.581  Sum_probs=55.1

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ..++||.|..||..|+.+||+.|...+|.+..||++||..|.||++||||||||||.|
T Consensus       150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK  207 (307)
T KOG0842|consen  150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYK  207 (307)
T ss_pred             cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhh
Confidence            4567778899999999999999999999999999999999999999999999999987

>KOG0489|consensus

Probab=99.70  E-value=3.2e-18  Score=131.36  Aligned_cols=57  Identities=39%  Similarity=0.525  Sum_probs=54.9

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+.+|.||.||..|+.+||+.|..|+|.+...|.+||..|.|+|.||||||||||||
T Consensus       157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK  213 (261)
T KOG0489|consen  157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMK  213 (261)
T ss_pred             CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHH
Confidence            457889999999999999999999999999999999999999999999999999997

>KOG0494|consensus

Probab=99.69  E-value=1.6e-17  Score=122.68  Aligned_cols=55  Identities=49%  Similarity=0.821  Sum_probs=52.0

Q ss_pred             ccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       132 ~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .|+.||.||..|+++||+.|...+||+...|+.||.++.|++.+|+|||||||+|
T Consensus       141 RRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAK  195 (332)
T KOG0494|consen  141 RRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAK  195 (332)
T ss_pred             cccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHH
Confidence            3334999999999999999999999999999999999999999999999999997

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.69  E-value=1.8e-17  Score=98.55  Aligned_cols=54  Identities=39%  Similarity=0.613  Sum_probs=51.7

Q ss_pred             cccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ++.|+.||.+|+..|+..|..++||+..+++.||..+||+..+|++||+|+|++
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k   54 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRK   54 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHH
Confidence            467899999999999999999999999999999999999999999999999975

; 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 ....

>KOG0492|consensus

Probab=99.67  E-value=2.4e-17  Score=118.07  Aligned_cols=58  Identities=36%  Similarity=0.582  Sum_probs=54.9

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG  187 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~  187 (187)
                      +..|+.||.||..||..||+.|...+|.++.++.+++..|.|++.||++||||||+|+
T Consensus       142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKa  199 (246)
T KOG0492|consen  142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKA  199 (246)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHH
Confidence            4457789999999999999999999999999999999999999999999999999986

>KOG0487|consensus

Probab=99.66  E-value=6.8e-17  Score=124.24  Aligned_cols=58  Identities=31%  Similarity=0.457  Sum_probs=55.5

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+..|++|..+|..|+.+||+.|-.|.|++...|.+|++.|+|+++||+|||||||+|
T Consensus       232 ~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK  289 (308)
T KOG0487|consen  232 ARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMK  289 (308)
T ss_pred             ccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhH
Confidence            4667888999999999999999999999999999999999999999999999999998

>KOG0485|consensus

Probab=99.65  E-value=8.6e-17  Score=116.03  Aligned_cols=58  Identities=31%  Similarity=0.482  Sum_probs=54.9

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ..++++.||+|+..|+..||..|+...|.+..+|..||..|.|++.||++||||||.|
T Consensus       101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnK  158 (268)
T KOG0485|consen  101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNK  158 (268)
T ss_pred             ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHH
Confidence            3466778999999999999999999999999999999999999999999999999986

>smart00389 HOX Homeodomain

Probab=99.62  E-value=6.2e-16  Score=91.53  Aligned_cols=53  Identities=40%  Similarity=0.712  Sum_probs=50.7

Q ss_pred             ccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        134 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       134 r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +.|+.|+.+|+..|+..|..++||+..++..||..+||+..+|++||+|||++
T Consensus         2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~   54 (56)
T smart00389        2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAK   54 (56)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhc
Confidence            46778999999999999999999999999999999999999999999999986

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

>KOG0493|consensus

Probab=99.62  E-value=4.5e-16  Score=115.25  Aligned_cols=55  Identities=35%  Similarity=0.581  Sum_probs=53.0

Q ss_pred             ccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       132 ~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+|.||.||.+||..|+..|+.+.|.....|++||.+|+|.+.||++||||+|+|
T Consensus       246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAK  300 (342)
T KOG0493|consen  246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAK  300 (342)
T ss_pred             hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhh
Confidence            4678999999999999999999999999999999999999999999999999987

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

Probab=99.57  E-value=3e-15  Score=89.52  Aligned_cols=53  Identities=43%  Similarity=0.712  Sum_probs=50.5

Q ss_pred             ccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        134 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       134 r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +.++.|+.+|+..|+..|..++||+..++..||..+||+..+|++||+|+|.+
T Consensus         2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~   54 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAK   54 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            45788999999999999999999999999999999999999999999999975

>KOG0848|consensus

Probab=99.54  E-value=1.3e-15  Score=113.28  Aligned_cols=54  Identities=28%  Similarity=0.465  Sum_probs=51.4

Q ss_pred             cccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      -+.|.++|+.|..+||+.|..++|.++..+.+||..|||+|+||+|||||||+|
T Consensus       200 DKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAK  253 (317)
T KOG0848|consen  200 DKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAK  253 (317)
T ss_pred             cceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHH
Confidence            346789999999999999999999999999999999999999999999999997

>KOG0491|consensus

Probab=99.53  E-value=1.1e-15  Score=105.75  Aligned_cols=57  Identities=40%  Similarity=0.652  Sum_probs=53.9

Q ss_pred             cccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCCC
Q psy15514        131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG  187 (187)
Q Consensus       131 ~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~  187 (187)
                      +.++.||+|+..|+..|++.|+...|.+..++.+||..|+|++.||+.||||||+|.
T Consensus        99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~  155 (194)
T KOG0491|consen   99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKH  155 (194)
T ss_pred             HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Confidence            456679999999999999999999999999999999999999999999999999983

>KOG0486|consensus

Probab=99.52  E-value=8.4e-15  Score=111.26  Aligned_cols=56  Identities=55%  Similarity=0.842  Sum_probs=54.7

Q ss_pred             cccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       131 ~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      |++|.||.||..|+.+||..|+++.||+...|++||.-++|++.+|+|||.|||+|
T Consensus       111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrak  166 (351)
T KOG0486|consen  111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAK  166 (351)
T ss_pred             hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhh
Confidence            78889999999999999999999999999999999999999999999999999987

>KOG3862|consensus

Probab=99.49  E-value=5.3e-15  Score=110.16  Aligned_cols=31  Identities=45%  Similarity=0.967  Sum_probs=29.5

Q ss_pred             Ccc--ccchhhcCCCCCCCCCccchhhhcccCC
Q psy15514          1 MCW--GDRLIKEGLCDRGSAPSVSAISRLLRGH   31 (187)
Q Consensus         1 ~~~--rdrll~e~vc~~~~vPSvsSinrilr~~   31 (187)
                      |||  ||+|++|+|||+|+||||||||||||++
T Consensus       103 faweiR~~l~~~~ic~~d~vpsVssinri~r~~  135 (327)
T KOG3862|consen  103 FAWEIRDRLLAEPICDNDTVPSVSSINRIIRTK  135 (327)
T ss_pred             hhhhhhhhhhcccccCCCCCchHHHHHHHHHHh
Confidence            899  9999999999999999999999999953

>KOG3802|consensus

Probab=99.49  E-value=3.6e-14  Score=111.55  Aligned_cols=128  Identities=18%  Similarity=0.227  Sum_probs=85.3

Q ss_pred             cccCCCCCCCCcCHHHHHH-HHHH----hhhcCCCChhhhHHHHHh-hcCCchhhHhHhhccCC--CCCCCCCCCCCccc
Q psy15514         58 LKRKQRRSRTTFSAQQLDE-LERA----FERTQYPDIYTREELAQR-TKLFPHFLIIIEQQSSG--EGSDCDSEPGIPLK  129 (187)
Q Consensus        58 ~~~~~~r~rt~ft~~ql~~-Le~~----F~~~~yp~~~~r~~la~~-~~l~~~~v~~wfq~~~~--~~~~~~~~~~~~~~  129 (187)
                      +..|+||..-.||..++.. |...    |.++. ++.++--.|.-+ +.--.--++.|..+...  ..............
T Consensus       213 K~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTT-IcRFEALqLSFKNMCKLKPLL~KWLeEAes~~~~~~~~~~e~i~a~  291 (398)
T KOG3802|consen  213 KTFKQRRIKLGFTQADVGLALGALYGNVFSQTT-ICRFEALQLSFKNMCKLKPLLEKWLEEAESRESTGSPNSIEKIGAQ  291 (398)
T ss_pred             HHHHhheeccccchhHHHHHHHhhhCcccchhh-hhHhHhhccCHHHHhhhHHHHHHHHHHHhcccccCCCCCHHHhhcc
Confidence            4448888888999888874 3322    22222 222221112111 11011125778765444  22222222222233


Q ss_pred             ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .++|++||.|.......||++|.+|+.|+..++..||.+|+|....|+|||.|||.|
T Consensus       292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQk  348 (398)
T KOG3802|consen  292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQK  348 (398)
T ss_pred             ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccc
Confidence            477889999999999999999999999999999999999999999999999999987

>KOG0844|consensus

Probab=99.49  E-value=1.3e-14  Score=109.83  Aligned_cols=59  Identities=36%  Similarity=0.510  Sum_probs=56.0

Q ss_pred             ccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        128 LKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       128 ~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .....||.||.||.+|+..||+.|-+..|-+...|-+||..|+|++..|+|||||||+|
T Consensus       177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMK  235 (408)
T KOG0844|consen  177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMK  235 (408)
T ss_pred             ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhh
Confidence            34567999999999999999999999999999999999999999999999999999998

>KOG3517|consensus

Probab=99.47  E-value=6.3e-15  Score=108.60  Aligned_cols=32  Identities=50%  Similarity=1.007  Sum_probs=30.8

Q ss_pred             Ccc--ccchhhcCCCCCCCCCccchhhhcccCCC
Q psy15514          1 MCW--GDRLIKEGLCDRGSAPSVSAISRLLRGHE   32 (187)
Q Consensus         1 ~~~--rdrll~e~vc~~~~vPSvsSinrilr~~~   32 (187)
                      |||  |||||++||||+-||||||||.|||||+-
T Consensus        98 FAWEIRDRLlsdgiCDk~NvPSVSSISRILRNKi  131 (334)
T KOG3517|consen   98 FAWEIRDRLLSDGICDKYNVPSVSSISRILRNKI  131 (334)
T ss_pred             eeehhhhhhhhcccccccCCcchHHHHHHHHhhh
Confidence            899  99999999999999999999999999874

>KOG2251|consensus

Probab=99.46  E-value=5.5e-14  Score=102.17  Aligned_cols=62  Identities=40%  Similarity=0.562  Sum_probs=58.5

Q ss_pred             CcccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCC
Q psy15514         57 PLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGS  118 (187)
Q Consensus        57 ~~~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~  118 (187)
                      ..++++||.||+|+..|+++||..|.+++|||+..+++||.+++|.+..|++||.|++.+..
T Consensus        32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r   93 (228)
T KOG2251|consen   32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCR   93 (228)
T ss_pred             ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhh
Confidence            46779999999999999999999999999999999999999999999999999999987664

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.45  E-value=5.2e-14  Score=99.29  Aligned_cols=57  Identities=26%  Similarity=0.379  Sum_probs=52.8

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ...++.|.+.|.+|+.+|++.|..++||+..++..|+..++|++.-|++||||+|++
T Consensus        49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~  105 (156)
T COG5576          49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAK  105 (156)
T ss_pred             CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHH
Confidence            345667778899999999999999999999999999999999999999999999986

>KOG0494|consensus

Probab=99.44  E-value=2.2e-13  Score=100.98  Aligned_cols=56  Identities=41%  Similarity=0.651  Sum_probs=51.8

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      +.|+.||.||..|+++||+.|...||||++.|+-||.++.|.++.|++||||++..
T Consensus       140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAK  195 (332)
T KOG0494|consen  140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAK  195 (332)
T ss_pred             ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHH
Confidence            44455999999999999999999999999999999999999999999999998754

>KOG0850|consensus

Probab=99.44  E-value=6.6e-14  Score=102.22  Aligned_cols=60  Identities=33%  Similarity=0.375  Sum_probs=55.5

Q ss_pred             cccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514         58 LKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG  117 (187)
Q Consensus        58 ~~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~  117 (187)
                      ..+|.|..||.|+..||..|.+.|++++|+-..+|.+||..+||+..+|+|||||++++-
T Consensus       118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~  177 (245)
T KOG0850|consen  118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKF  177 (245)
T ss_pred             CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHH
Confidence            345778899999999999999999999999999999999999999999999999998643

>KOG0842|consensus

Probab=99.43  E-value=1e-13  Score=106.86  Aligned_cols=63  Identities=35%  Similarity=0.423  Sum_probs=57.8

Q ss_pred             ccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCCCC
Q psy15514         59 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCD  121 (187)
Q Consensus        59 ~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~  121 (187)
                      +.++|+.|-.||..|+-+||+.|..+.|++..+|++||..++||++||+|||||++.+.+...
T Consensus       150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~  212 (307)
T KOG0842|consen  150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQ  212 (307)
T ss_pred             cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhh
Confidence            457778889999999999999999999999999999999999999999999999998776443

>KOG0483|consensus

Probab=99.41  E-value=2.2e-13  Score=99.31  Aligned_cols=52  Identities=21%  Similarity=0.364  Sum_probs=49.3

Q ss_pred             cCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        135 SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       135 ~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ++.+|+.+|+..||..|+.+.+.....+..||..|||.+.||.|||||||||
T Consensus        53 kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRAR  104 (198)
T KOG0483|consen   53 KKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRAR  104 (198)
T ss_pred             ccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhcccc
Confidence            3456899999999999999999999999999999999999999999999997

>KOG0843|consensus

Probab=99.41  E-value=1.8e-13  Score=96.30  Aligned_cols=58  Identities=33%  Similarity=0.358  Sum_probs=54.8

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGS  118 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~  118 (187)
                      +.+|.||.||.+|+..||..|+.++|..-.+|+.||..++|++.+|++||||++..-.
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~k  158 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHK  158 (197)
T ss_pred             CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHH
Confidence            7789999999999999999999999999999999999999999999999999986543

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.39  E-value=4.1e-13  Score=78.67  Aligned_cols=52  Identities=15%  Similarity=0.247  Sum_probs=49.8

Q ss_pred             CCCCCCcCHHHHHHHHHHhhhcCC----CChhhhHHHHHhhcCCchhhHhHhhccC
Q psy15514         63 RRSRTTFSAQQLDELERAFERTQY----PDIYTREELAQRTKLFPHFLIIIEQQSS  114 (187)
Q Consensus        63 ~r~rt~ft~~ql~~Le~~F~~~~y----p~~~~r~~la~~~~l~~~~v~~wfq~~~  114 (187)
                      +|.||.||.+|+..|+..|+..+|    |+...+++||..+||++..|++||+|..
T Consensus         2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            688999999999999999999999    9999999999999999999999999853

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.

>KOG4577|consensus

Probab=99.37  E-value=3.2e-13  Score=101.62  Aligned_cols=58  Identities=31%  Similarity=0.481  Sum_probs=55.0

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ....+|.||++|..||+.|+.+|...+.|....|+.|+.++||.-+.|||||||||+|
T Consensus       164 d~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAK  221 (383)
T KOG4577|consen  164 DASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAK  221 (383)
T ss_pred             ccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHH
Confidence            3456889999999999999999999999999999999999999999999999999997

>KOG0488|consensus

Probab=99.36  E-value=8.2e-13  Score=103.32  Aligned_cols=61  Identities=34%  Similarity=0.382  Sum_probs=56.7

Q ss_pred             cccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCC
Q psy15514         58 LKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGS  118 (187)
Q Consensus        58 ~~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~  118 (187)
                      .++|.|+.||.||..|+.+||+.|+.+.|....+|.+||..+||+..||+.||||++.+..
T Consensus       168 ~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWK  228 (309)
T KOG0488|consen  168 TPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWK  228 (309)
T ss_pred             CCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHH
Confidence            4478888999999999999999999999999999999999999999999999999886654

>KOG0490|consensus

Probab=99.31  E-value=6.8e-13  Score=100.74  Aligned_cols=58  Identities=41%  Similarity=0.512  Sum_probs=55.6

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ..+.++.|+.|+..|+++|+++|+..+||+...++.||..+++++..|++||||||+|
T Consensus        57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak  114 (235)
T KOG0490|consen   57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAK  114 (235)
T ss_pred             hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHh
Confidence            5678899999999999999999999999999999999999999999999999999986

>KOG0489|consensus

Probab=99.30  E-value=1.5e-12  Score=100.14  Aligned_cols=59  Identities=31%  Similarity=0.303  Sum_probs=55.1

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGS  118 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~  118 (187)
                      .+.+|.||.||..|+.+||+.|+.+.|+....|.+||..+.|++.+|+|||||++.+..
T Consensus       157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~K  215 (261)
T KOG0489|consen  157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWK  215 (261)
T ss_pred             CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHH
Confidence            45789999999999999999999999999999999999999999999999999986543

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.24  E-value=1.1e-11  Score=73.37  Aligned_cols=52  Identities=35%  Similarity=0.431  Sum_probs=49.3

Q ss_pred             CCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccC
Q psy15514         63 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSS  114 (187)
Q Consensus        63 ~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~  114 (187)
                      ++.|+.||..|+..|+..|..++||+...++.||..+||+..+|..||+|++
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR   52 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRR   52 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhH
Confidence            4678999999999999999999999999999999999999999999999865

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

>KOG0485|consensus

Probab=99.24  E-value=1.1e-11  Score=89.81  Aligned_cols=59  Identities=27%  Similarity=0.316  Sum_probs=54.7

Q ss_pred             ccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514         59 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG  117 (187)
Q Consensus        59 ~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~  117 (187)
                      ..++++.||+|+..|+..||..|+...|.+..+|..||..+.|++.||++||||++.+.
T Consensus       101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKw  159 (268)
T KOG0485|consen  101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKW  159 (268)
T ss_pred             ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHH
Confidence            34677889999999999999999999999999999999999999999999999998654

>KOG0847|consensus

Probab=99.23  E-value=3.7e-12  Score=92.38  Aligned_cols=57  Identities=35%  Similarity=0.579  Sum_probs=53.0

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+++-.|.+|+-.|+..||..|+..+|+--.++.+||..+|+++.+|+|||||||+|
T Consensus       165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTK  221 (288)
T KOG0847|consen  165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTK  221 (288)
T ss_pred             ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhh
Confidence            445556889999999999999999999999999999999999999999999999987

>KOG0492|consensus

Probab=99.23  E-value=7.4e-12  Score=90.14  Aligned_cols=56  Identities=34%  Similarity=0.431  Sum_probs=52.7

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      ..|.+||.||..||..||+.|...+|.++.+|.+++..+.|++.+|++||||++..
T Consensus       143 ~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAK  198 (246)
T KOG0492|consen  143 PNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAK  198 (246)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHH
Confidence            45678999999999999999999999999999999999999999999999999854

>KOG0486|consensus

Probab=99.16  E-value=4.3e-11  Score=91.31  Aligned_cols=61  Identities=41%  Similarity=0.536  Sum_probs=56.2

Q ss_pred             CcccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514         57 PLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG  117 (187)
Q Consensus        57 ~~~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~  117 (187)
                      .+..|++|.||.||.+|+.+||..|.++.||++.+|++||.-++|++..|.+||.+++.+.
T Consensus       107 kki~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakw  167 (351)
T KOG0486|consen  107 KKISKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKW  167 (351)
T ss_pred             chhhhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhh
Confidence            3445899999999999999999999999999999999999999999999999999887553

>smart00389 HOX Homeodomain

Probab=99.09  E-value=2.1e-10  Score=67.59  Aligned_cols=52  Identities=37%  Similarity=0.561  Sum_probs=48.9

Q ss_pred             CCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         64 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        64 r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      +.|+.|+..|+..|+..|..++||+..++..||..+|++..+|..||++++.
T Consensus         2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~   53 (56)
T smart00389        2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRA   53 (56)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhh
Confidence            4567899999999999999999999999999999999999999999998874

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

>KOG0493|consensus

Probab=99.06  E-value=1.2e-10  Score=86.71  Aligned_cols=56  Identities=32%  Similarity=0.401  Sum_probs=52.8

Q ss_pred             CCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCC
Q psy15514         63 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGS  118 (187)
Q Consensus        63 ~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~  118 (187)
                      +|+||.||.+||..|...|+.+.|+.-..|.+||..++|.+.+|++||||.+..-.
T Consensus       247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiK  302 (342)
T KOG0493|consen  247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIK  302 (342)
T ss_pred             cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhh
Confidence            57899999999999999999999999999999999999999999999999986644

>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=98.99  E-value=8e-10  Score=65.71  Aligned_cols=53  Identities=40%  Similarity=0.565  Sum_probs=49.1

Q ss_pred             CCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         64 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        64 r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      +.++.|+..|+..|+..|..++||+..++..||..+||+..+|..||++++..
T Consensus         2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~   54 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAK   54 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            35678999999999999999999999999999999999999999999987643

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=98.97  E-value=5.6e-10  Score=78.91  Aligned_cols=56  Identities=29%  Similarity=0.340  Sum_probs=50.9

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      ..++.|+.-|..|+..|++.|..++||+..++.+|+..+++++..|++||||++..
T Consensus        50 ~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~  105 (156)
T COG5576          50 PPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAK  105 (156)
T ss_pred             cCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHH
Confidence            45566677899999999999999999999999999999999999999999998743

>KOG0844|consensus

Probab=98.95  E-value=5.2e-10  Score=85.11  Aligned_cols=63  Identities=27%  Similarity=0.281  Sum_probs=57.6

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCCCCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCDS  122 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~  122 (187)
                      ...||.||.||.+|+..||+.|-+..|.+...|-+||..++|.+..|++||||++.+++....
T Consensus       179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl  241 (408)
T KOG0844|consen  179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL  241 (408)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence            357899999999999999999999999999999999999999999999999999987654433

>KOG0487|consensus

Probab=98.95  E-value=6.8e-10  Score=85.88  Aligned_cols=65  Identities=23%  Similarity=0.230  Sum_probs=57.2

Q ss_pred             CCCcccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCC
Q psy15514         55 GIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSD  119 (187)
Q Consensus        55 ~~~~~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~  119 (187)
                      .+...++.|..|-.||-.|+.+||+.|-.+.|+...-|-+|+..++|+++||+|||||++.+.+.
T Consensus       228 ~~~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK  292 (308)
T KOG0487|consen  228 NASSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKK  292 (308)
T ss_pred             ccccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhh
Confidence            34444566677788999999999999999999999999999999999999999999999977543

>KOG0848|consensus

Probab=98.89  E-value=5.3e-10  Score=83.64  Aligned_cols=54  Identities=26%  Similarity=0.319  Sum_probs=50.4

Q ss_pred             CCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514         64 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG  117 (187)
Q Consensus        64 r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~  117 (187)
                      ..|.+||..|.-+||+.|+-..|+.+....+||..++|++++|++||||++.++
T Consensus       201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKE  254 (317)
T KOG0848|consen  201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKE  254 (317)
T ss_pred             ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHH
Confidence            457789999999999999999999999999999999999999999999998654

>KOG0849|consensus

Probab=98.88  E-value=3.5e-09  Score=84.79  Aligned_cols=63  Identities=44%  Similarity=0.634  Sum_probs=57.3

Q ss_pred             CCCCCcccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         53 EPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        53 ~~~~~~~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      .++....++.+|.||.|++.|+..|+..|+.++||+++.|+.||..+++++..|++||++++.
T Consensus       167 ~p~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra  229 (354)
T KOG0849|consen  167 PPGYALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRA  229 (354)
T ss_pred             cccccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhh
Confidence            344555667888899999999999999999999999999999999999999999999999775

>KOG0775|consensus

Probab=98.85  E-value=2.5e-09  Score=80.32  Aligned_cols=48  Identities=27%  Similarity=0.406  Sum_probs=43.8

Q ss_pred             CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        139 FSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       139 ~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      |...-...|..+|..++||+..++.+||+.+||+..||-+||+|||.+
T Consensus       183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQR  230 (304)
T KOG0775|consen  183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQR  230 (304)
T ss_pred             hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhh
Confidence            444556799999999999999999999999999999999999999975

>KOG0491|consensus

Probab=98.82  E-value=9.3e-10  Score=76.62  Aligned_cols=57  Identities=33%  Similarity=0.408  Sum_probs=52.8

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG  117 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~  117 (187)
                      +.+..||+|+..|+..|++.|+.+.|.+..++.+||..++|++.+|+.||||++...
T Consensus        99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~  155 (194)
T KOG0491|consen   99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKH  155 (194)
T ss_pred             HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Confidence            456679999999999999999999999999999999999999999999999987543

>KOG1168|consensus

Probab=98.74  E-value=1.6e-09  Score=82.03  Aligned_cols=58  Identities=19%  Similarity=0.296  Sum_probs=54.1

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ...++|+||.+-......||..|...+.|+.+.+..+|++|+|....|+|||.|.|.|
T Consensus       306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQK  363 (385)
T KOG1168|consen  306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQK  363 (385)
T ss_pred             ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHH
Confidence            4556788999999999999999999999999999999999999999999999999976

>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=98.72  E-value=2.8e-09  Score=57.89  Aligned_cols=34  Identities=35%  Similarity=0.554  Sum_probs=28.4

Q ss_pred             hcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        153 RTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       153 ~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .++||+..+++.||..+||+..||..||-|.|.+
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            4789999999999999999999999999998853

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

>KOG2252|consensus

Probab=98.54  E-value=1.1e-07  Score=78.06  Aligned_cols=59  Identities=19%  Similarity=0.336  Sum_probs=54.2

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG  187 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~  187 (187)
                      ....++.|.+||+.|...|..+|+.+++|+.+..+.|+..|+|....|.+||.|-|.|+
T Consensus       417 ~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  417 MLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             cccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            34556679999999999999999999999999999999999999999999999988763

>KOG0847|consensus

Probab=98.48  E-value=9.8e-08  Score=69.68  Aligned_cols=58  Identities=29%  Similarity=0.379  Sum_probs=53.3

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG  117 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~  117 (187)
                      .+.+..|.+|+..|+..|+..|+.++|+--.++.+||..+++++.+|++||||++...
T Consensus       165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKW  222 (288)
T KOG0847|consen  165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKW  222 (288)
T ss_pred             ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhh
Confidence            4556678899999999999999999999999999999999999999999999998654

>KOG0483|consensus

Probab=98.39  E-value=4.2e-07  Score=66.62  Aligned_cols=54  Identities=19%  Similarity=0.228  Sum_probs=49.2

Q ss_pred             CCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCCC
Q psy15514         67 TTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDC  120 (187)
Q Consensus        67 t~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~  120 (187)
                      -.|+.+|+..||..|+..+|.....+..||..+||.+.+|.+||||++......
T Consensus        55 ~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~k  108 (198)
T KOG0483|consen   55 RRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTK  108 (198)
T ss_pred             ccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccch
Confidence            458999999999999999999999999999999999999999999998665433

>KOG4577|consensus

Probab=98.36  E-value=2.5e-07  Score=70.25  Aligned_cols=60  Identities=27%  Similarity=0.364  Sum_probs=55.0

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDC  120 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~  120 (187)
                      ..+|+||++|+.||+.|...+...+-|....|+.|+..+||.-+.|++||||++..+..-
T Consensus       166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRL  225 (383)
T KOG4577|consen  166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRL  225 (383)
T ss_pred             ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhh
Confidence            456889999999999999999999999999999999999999999999999998776543

>KOG3802|consensus

Probab=98.26  E-value=1.1e-06  Score=69.83  Aligned_cols=62  Identities=15%  Similarity=0.192  Sum_probs=58.1

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCCCCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCDS  122 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~  122 (187)
                      ++|+.||.+.......||..|..++-|+..+...||..++|....|++||+|++-.++....
T Consensus       293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            67778899999999999999999999999999999999999999999999999988877665

>KOG0774|consensus

Probab=98.19  E-value=1.6e-06  Score=65.00  Aligned_cols=54  Identities=30%  Similarity=0.487  Sum_probs=49.2

Q ss_pred             ccccCCCCCHHHHHHHHHHhh---hcCCCCHHHHHHHHHHcCCChhhhhhhhcccCC
Q psy15514        132 QRRSRTTFSAQQLDELERAFE---RTQYPDIYTREELAQRTKLTEARIQTIFIVRKM  185 (187)
Q Consensus       132 ~~r~r~~~t~~q~~~Le~~f~---~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~  185 (187)
                      .+|+|..|+..-.++|..+|-   .++||+..++++||++.+++..||-.||.|.|-
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrI  244 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRI  244 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhcccccccee
Confidence            467788899999999999994   578999999999999999999999999999874

>KOG1146|consensus

Probab=97.80  E-value=2.2e-05  Score=70.75  Aligned_cols=59  Identities=24%  Similarity=0.258  Sum_probs=55.0

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG  187 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~  187 (187)
                      .-..++.|+.++..||..|...|....||...+.+.|...++++...|++||||-|.|+
T Consensus       900 ~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s  958 (1406)
T KOG1146|consen  900 GMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKS  958 (1406)
T ss_pred             hhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhh
Confidence            34567789999999999999999999999999999999999999999999999999875

>KOG2252|consensus

Probab=97.64  E-value=9e-05  Score=61.41  Aligned_cols=55  Identities=18%  Similarity=0.247  Sum_probs=51.1

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      ..+++|.+||..|...|...|..+++|+....+.|+..++|....|..||.|.+.
T Consensus       419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRR  473 (558)
T KOG2252|consen  419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARR  473 (558)
T ss_pred             cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhh
Confidence            5566799999999999999999999999999999999999999999999998653

>KOG3623|consensus

Probab=97.58  E-value=0.00015  Score=62.05  Aligned_cols=113  Identities=14%  Similarity=0.135  Sum_probs=82.6

Q ss_pred             HHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHHhhh
Q psy15514         74 LDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFER  153 (187)
Q Consensus        74 l~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~f~~  153 (187)
                      +..|...|..+..|..++...++...|++-..|+.||++.....-+..-.+..+....+-+.++....++-..|..+++.
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            67788899999999999999999999999999999999877654433333333333344445566666666667777776


Q ss_pred             cCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        154 TQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       154 ~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +.-+.-.+--..+.++...+..|.+||++|+..
T Consensus       648 q~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsst  680 (1007)
T KOG3623|consen  648 QASPSNDEFPLIATRLQNDPPVVEVWDHSRSST  680 (1007)
T ss_pred             ccCccCcccchhhhhccCCCcchhhcccCCCCC
Confidence            665554444444555777788889999999864

>KOG0775|consensus

Probab=97.45  E-value=0.00022  Score=54.22  Aligned_cols=57  Identities=23%  Similarity=0.219  Sum_probs=47.7

Q ss_pred             ccCCCCCCCC---------cCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         59 KRKQRRSRTT---------FSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        59 ~~~~~r~rt~---------ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      .+|-.-+||.         |-+.....|...|..++||...+..+||..+||+..+|..||.|++-
T Consensus       164 RrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQ  229 (304)
T KOG0775|consen  164 RRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQ  229 (304)
T ss_pred             eccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhh
Confidence            3455556776         45566678999999999999999999999999999999999998763

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

Probab=97.42  E-value=0.00011  Score=42.43  Aligned_cols=41  Identities=15%  Similarity=0.292  Sum_probs=31.0

Q ss_pred             HHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccC
Q psy15514        144 LDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRK  184 (187)
Q Consensus       144 ~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR  184 (187)
                      +..|+..|...+++.......|..+.+|+..+|+.||-.+.
T Consensus        10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~   50 (56)
T PF11569_consen   10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM   50 (56)
T ss_dssp             -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred             hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence            35599999999999999999999999999999999997664

>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=97.34  E-value=9.7e-05  Score=40.03  Aligned_cols=32  Identities=25%  Similarity=0.242  Sum_probs=26.0

Q ss_pred             hcCCCChhhhHHHHHhhcCCchhhHhHhhccC
Q psy15514         83 RTQYPDIYTREELAQRTKLFPHFLIIIEQQSS  114 (187)
Q Consensus        83 ~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~  114 (187)
                      .++||+..+++.|+..+|++..+|..||-|.+
T Consensus         7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaR   38 (40)
T PF05920_consen    7 HNPYPSKEEKEELAKQTGLSRKQISNWFINAR   38 (40)
T ss_dssp             TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhH
Confidence            36799999999999999999999999998753

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

>KOG0773|consensus

Probab=96.63  E-value=0.0016  Score=52.44  Aligned_cols=54  Identities=20%  Similarity=0.309  Sum_probs=45.2

Q ss_pred             cccCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        133 RRSRTTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f~~---~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+....+......+|+.+...   .+||+..++..|+.++||+..||.+||.|.|-+
T Consensus       240 ~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R  296 (342)
T KOG0773|consen  240 WRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVR  296 (342)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccc
Confidence            344457888888888877433   579999999999999999999999999999865

>KOG1168|consensus

Probab=96.53  E-value=0.00069  Score=51.96  Aligned_cols=56  Identities=18%  Similarity=0.208  Sum_probs=49.8

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      -++|.||..-.-....||..|..++-|+..-...+|.+++|....|.+||.|.+..
T Consensus       308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQK  363 (385)
T KOG1168|consen  308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQK  363 (385)
T ss_pred             ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHH
Confidence            45567788888888999999999999999999999999999999999999987743

>KOG0774|consensus

Probab=96.10  E-value=0.0054  Score=46.49  Aligned_cols=54  Identities=26%  Similarity=0.280  Sum_probs=47.1

Q ss_pred             CCCCCCCcCHHHHHHHHHHhhh---cCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         62 QRRSRTTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        62 ~~r~rt~ft~~ql~~Le~~F~~---~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      .+|.|-.|+-.--+.|...|..   ++||+-.+.++||+.-+++..+|..||.+.+-
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrI  244 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRI  244 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhcccccccee
Confidence            4566677999999999999954   68999999999999999999999999987653

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

Probab=95.80  E-value=0.022  Score=32.80  Aligned_cols=46  Identities=15%  Similarity=0.376  Sum_probs=35.6

Q ss_pred             cccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhccc
Q psy15514        133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVR  183 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nr  183 (187)
                      ++.|..+|.++...+-..++.+.     ....||..+|++..+|..|..|+
T Consensus         1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k   46 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK   46 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred             CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence            46788999999888888888876     57789999999999999999886

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

>KOG3623|consensus

Probab=95.57  E-value=0.014  Score=50.40  Aligned_cols=43  Identities=16%  Similarity=0.142  Sum_probs=40.2

Q ss_pred             HHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        144 LDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       144 ~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +..|...|..|..|...+...+|..+||+...|+.||.+++++
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~  610 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAE  610 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhh
Confidence            6788999999999999999999999999999999999998764

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

Probab=95.20  E-value=0.03  Score=32.43  Aligned_cols=43  Identities=9%  Similarity=0.061  Sum_probs=31.1

Q ss_pred             HHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         73 QLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        73 ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      .+..|+..|...+++.-.....|..+.+|+..+|+.||..+..
T Consensus         9 d~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~   51 (56)
T PF11569_consen    9 DIQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ   51 (56)
T ss_dssp             --HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred             chHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence            4567999999999999999999999999999999999976543

>KOG1146|consensus

Probab=95.10  E-value=0.029  Score=51.52  Aligned_cols=57  Identities=21%  Similarity=0.225  Sum_probs=52.4

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG  117 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~  117 (187)
                      .+++.||.++..||..|...|....||...+.+.|...+++..+.|++||+|.+...
T Consensus       902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s  958 (1406)
T KOG1146|consen  902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKS  958 (1406)
T ss_pred             hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhh
Confidence            466789999999999999999999999999999999999999999999999877544

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

Probab=93.58  E-value=0.12  Score=29.65  Aligned_cols=39  Identities=26%  Similarity=0.416  Sum_probs=33.3

Q ss_pred             CCHHHHHHHHHHhhhcCC--CCHHHHHHHHHHcCCChhhhh
Q psy15514        139 FSAQQLDELERAFERTQY--PDIYTREELAQRTKLTEARIQ  177 (187)
Q Consensus       139 ~t~~q~~~Le~~f~~~~~--p~~~~~~~la~~~~l~~~~v~  177 (187)
                      +|+.|.+.|..+++..-|  |-.....+||..+|++..-+.
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~   41 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVS   41 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHH
Confidence            588999999999999886  666777899999999987654

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

>PF13551 HTH_29: Winged helix-turn helix

Probab=87.57  E-value=1.6  Score=28.49  Aligned_cols=86  Identities=17%  Similarity=0.171  Sum_probs=52.4

Q ss_pred             hhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcc-cccccccCCCCCHHHHHHHHHHhhhcCC-----CCHHHHHH
Q psy15514         91 TREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPL-KRKQRRSRTTFSAQQLDELERAFERTQY-----PDIYTREE  164 (187)
Q Consensus        91 ~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~-~~~~~r~r~~~t~~q~~~Le~~f~~~~~-----p~~~~~~~  164 (187)
                      +..++|..+|++...|..|...-...+...     ... .....+.+..+++++...|...+..++.     .+......
T Consensus        14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~-----l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~   88 (112)
T PF13551_consen   14 TIAEIARRLGISRRTVYRWLKRYREGGIEG-----LLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAE   88 (112)
T ss_pred             cHHHHHHHHCcCHHHHHHHHHHHHcccHHH-----HHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHH
Confidence            467889999999999999976544333111     111 1112233333899999999999987752     22332222


Q ss_pred             -H-HHH--cCCChhhhhhhhc
Q psy15514        165 -L-AQR--TKLTEARIQTIFI  181 (187)
Q Consensus       165 -l-a~~--~~l~~~~v~~WF~  181 (187)
                       | ...  +.++...|..|++
T Consensus        89 ~l~~~~~~~~~s~~ti~r~L~  109 (112)
T PF13551_consen   89 WLIEEEFGIDVSPSTIRRILK  109 (112)
T ss_pred             HHHHhccCccCCHHHHHHHHH
Confidence             3 222  2577788888774

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

Probab=85.68  E-value=2  Score=26.12  Aligned_cols=43  Identities=16%  Similarity=0.183  Sum_probs=28.4

Q ss_pred             ccCCCCCHHHHHHHHHHh-hhcCCCCHHHHHHHHHHcCCChhhhhhhhc
Q psy15514        134 RSRTTFSAQQLDELERAF-ERTQYPDIYTREELAQRTKLTEARIQTIFI  181 (187)
Q Consensus       134 r~r~~~t~~q~~~Le~~f-~~~~~p~~~~~~~la~~~~l~~~~v~~WF~  181 (187)
                      +.|..||+++...+-..+ ...     .....+|.++||+...|..|-.
T Consensus         2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l~~W~~   45 (76)
T PF01527_consen    2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTLYNWRK   45 (76)
T ss_dssp             -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccccHHHH
Confidence            356789988887776555 333     3677899999999999999964

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

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

Probab=83.97  E-value=1.4  Score=33.05  Aligned_cols=40  Identities=18%  Similarity=0.385  Sum_probs=34.9

Q ss_pred             CCCHHHHHHHHHHhhhcCC--CCHHHHHHHHHHcCCChhhhh
Q psy15514        138 TFSAQQLDELERAFERTQY--PDIYTREELAQRTKLTEARIQ  177 (187)
Q Consensus       138 ~~t~~q~~~Le~~f~~~~~--p~~~~~~~la~~~~l~~~~v~  177 (187)
                      .+|+.|++.|..+|...-|  |-.....+||+.+|++..-+.
T Consensus       155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~  196 (215)
T COG3413         155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLS  196 (215)
T ss_pred             cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHH
Confidence            6999999999999999875  777778899999999987554

>KOG0773|consensus

Probab=82.69  E-value=1.4  Score=35.46  Aligned_cols=55  Identities=15%  Similarity=0.059  Sum_probs=44.5

Q ss_pred             CCCCCCCcCHHHHHHHHHHhhh---cCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         62 QRRSRTTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        62 ~~r~rt~ft~~ql~~Le~~F~~---~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      ..+....+.......|......   .+||...+...|+..+||+..+|..||-|.+..
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R  296 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVR  296 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccc
Confidence            4455667888888888877433   469999999899999999999999999876643

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

Probab=82.54  E-value=1  Score=26.54  Aligned_cols=20  Identities=15%  Similarity=0.290  Sum_probs=17.5

Q ss_pred             HHHHHHHHcCCChhhhhhhh
Q psy15514        161 TREELAQRTKLTEARIQTIF  180 (187)
Q Consensus       161 ~~~~la~~~~l~~~~v~~WF  180 (187)
                      .-.+||.+||+++.+|..|=
T Consensus        24 ~lkdIA~~Lgvs~~tIr~WK   43 (60)
T PF10668_consen   24 KLKDIAEKLGVSESTIRKWK   43 (60)
T ss_pred             cHHHHHHHHCCCHHHHHHHh
Confidence            35688999999999999994

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	187
1fjl_A	81	Homeodomain From The Drosophila Paired Protein Boun		3e-27
3cmy_A	61	Structure Of A Homeodomain In Complex With Dna Leng		2e-18
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		2e-14
2m0c_A	75	Solution Nmr Structure Of Homeobox Domain Of Human		1e-13
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		6e-12
3a02_A	60	Crystal Structure Of Aristaless Homeodomain Length		3e-11
2l7m_P	68	Solution Structure Of The Pitx2 Homeodomain R24h Mu		2e-10
2l7f_P	68	Solution Structure Of The Pitx2 Homeodomain Length		3e-10
2cue_A	80	Solution Structure Of The Homeobox Domain Of The Hu		1e-09
2dms_A	80	Solution Structure Of The Homeobox Domain Of Homeob		3e-09
2dmu_A	70	Solution Structure Of The Homeobox Domain Of Homeob		2e-07
1pdn_C	128	Crystal Structure Of A Paired Domain-Dna Complex At		3e-05
2dmt_A	80	Solution Structure Of The Homeobox Domain Of Homeob		2e-04
2kt0_A	84	Solution Structure Of Human Stem Cell Transcription		5e-04
2m34_A	71	Nmr Structure Of The Homeodomain Transcription Fact		6e-04

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

Iteration: 1
 Score =  117 bits (294), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 59/69 (85%), Positives = 61/69 (88%)
Query: 118 SDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQ 177
           SDC+SEPGI LKRKQRRSRTTFSA QLDELERAFERTQYPDIYTREELAQRT LTEARIQ
Sbjct: 4   SDCESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQ 63
Query: 178 TIFIVRKMR 186
             F  R+ R
Sbjct: 64  VWFQNRRAR 72

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

Iteration: 1
 Score = 88.2 bits (217), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 43/56 (76%), Positives = 48/56 (85%)
Query: 132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG 187
           QRRSRTTF+A+QL+ELERAFERT YPDIYTREELAQR KLTEAR+Q  F  R+ R 
Sbjct: 2   QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARW 57

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

Iteration: 1
 Score = 75.5 bits (184), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 37/59 (62%), Positives = 46/59 (77%)
Query: 129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG 187
           KRKQRR RTTF++ QL+ELE+AF RT YPD++TREELA +  LTEARIQ  F  R+ + 
Sbjct: 3   KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKW 61

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

Iteration: 1
 Score = 72.4 bits (176), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 32/54 (59%), Positives = 44/54 (81%)
Query: 131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRK 184
           K+RR+RTTF++ QL+ELE+ F++T YPD+Y RE+LA RT LTEAR+Q  F  R+
Sbjct: 8   KKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRR 61

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

Iteration: 1
 Score = 67.0 bits (162), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 32/54 (59%), Positives = 41/54 (75%)
Query: 134 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG 187
           R RTTF++ QL+ELE+AF RT YPD++TREELA +  LTEARIQ  F  R+ + 
Sbjct: 1   RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKW 54

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

Iteration: 1
 Score = 64.7 bits (156), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 29/46 (63%), Positives = 36/46 (78%)
Query: 135 SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIF 180
           S  TF++ QL+ELE+AF RT YPD++TREELA +  LTEARIQ  F
Sbjct: 2   SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWF 47

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

Iteration: 1
 Score = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 30/56 (53%), Positives = 39/56 (69%)
Query: 132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG 187
           QRR RT F++QQL ELE  F+R  YPD+ TREE+A  T LTEAR++  F  R+ + 
Sbjct: 3   QRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKW 58

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

Iteration: 1
 Score = 61.2 bits (147), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/56 (53%), Positives = 40/56 (71%)
Query: 132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG 187
           QRR RT F++QQL ELE  F+R +YPD+ TREE+A  T LTEAR++  F  R+ + 
Sbjct: 3   QRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKW 58

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

Iteration: 1
 Score = 59.3 bits (142), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 26/53 (49%), Positives = 38/53 (71%)
Query: 134 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           R+RT+F+ +Q++ LE+ FERT YPD++ RE LA +  L EARIQ  F  R+ +
Sbjct: 9   RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAK 61

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

Iteration: 1
 Score = 57.8 bits (138), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 27/54 (50%), Positives = 37/54 (68%)
Query: 133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           RR RTTF+  QLD LE  F +T+YPDI+ REE+A +  L E+R+Q  F  R+ +
Sbjct: 8   RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAK 61

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 37/54 (68%)
Query: 133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           RR RT F+ +QL+ LE  F+ T+YPD+ TRE+LA++  L E +++  F  R+ +
Sbjct: 8   RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAK 61

>pdb|1PDN|C Chain C, Crystal Structure Of A Paired Domain-Dna Complex At 2.5 Angstroms Resolution Reveals Structural Basis For Pax Developmental Mutations Length = 128

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 19/28 (67%), Positives = 26/28 (92%)
Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRGHE 32
           ++LI+EG+CDR +APSVSAISRL+RG +
Sbjct: 101 EKLIREGVCDRSTAPSVSAISRLVRGRD 128

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/64 (39%), Positives = 39/64 (60%), Gaps = 1/64 (1%)
Query: 123 EPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIV 182
           EPG   K K RRSRT F+  QL  LE+ FE+ +Y     R +LA+   L++ +++T +  
Sbjct: 9   EPGTKAK-KGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQN 67
Query: 183 RKMR 186
           R+M+
Sbjct: 68  RRMK 71

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 110 EQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRT 169
           +Q +S E S    E  +P+K+  +++RT FS+ QL  L   F+R +Y  +   +EL+   
Sbjct: 2   KQPTSAENSVAKKEDKVPVKK--QKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNIL 59
Query: 170 KLTEARIQTIFIVRKMRG 187
            L+  +++T F  ++M+ 
Sbjct: 60  NLSYKQVKTWFQNQRMKS 77

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 34/56 (60%)
Query: 131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           K RR RT F+++QL ELE+ F   +Y  +  R ++A   KL+E +++  F  R+ +
Sbjct: 6   KSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAK 61

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	187
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	5e-31
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	3e-26
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	1e-25
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	6e-21
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	2e-25
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	8e-21
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	3e-25
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	1e-20
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	8e-25
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	5e-20
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	5e-24
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	1e-19
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	7e-23
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	5e-18
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	1e-22
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	1e-17
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	2e-22
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	6e-18
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	1e-21
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	2e-17
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	9e-20
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	5e-16
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	8e-19
1uhs_A	72	HOP, homeodomain only protein; structural genomics	4e-18
1uhs_A	72	HOP, homeodomain only protein; structural genomics	1e-13
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	1e-16
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	2e-13
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	2e-16
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	3e-16
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	5e-15
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	3e-16
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	8e-12
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	5e-15
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	3e-11
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	2e-14
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	2e-11
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	5e-13
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	8e-11
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	4e-12
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	2e-11
1lfb_A	99	Liver transcription factor (LFB1); transcription r	8e-12
1lfb_A	99	Liver transcription factor (LFB1); transcription r	1e-11
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	3e-11
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	4e-09
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	4e-11
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	3e-10
1e3o_C	160	Octamer-binding transcription factor 1; transcript	7e-11
1e3o_C	160	Octamer-binding transcription factor 1; transcript	2e-09
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	1e-10
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	6e-08
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	1e-10
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	3e-07
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	3e-10
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	2e-07
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	4e-10
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	6e-08
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	4e-10
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	5e-07
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	6e-10
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	1e-07
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	1e-09
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	3e-07
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	1e-09
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	2e-07
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	2e-09
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	5e-07
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	2e-09
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	8e-07
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	3e-09
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	5e-07
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	3e-09
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	1e-06
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	5e-09
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	8e-07
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	5e-09
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	4e-06
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	1e-08
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	1e-05
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	6e-08
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	7e-05
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	2e-07
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	3e-05
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	2e-07
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	2e-04
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	2e-07
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	1e-04
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	1e-06
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	6e-04
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	1e-06
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	3e-06
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	3e-06
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	1e-04
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	5e-06
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	1e-05
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	1e-05
2k27_A	159	Paired box protein PAX-8; paired domain, solution	4e-05
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	4e-05
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	6e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-05
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	7e-05
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	8e-05
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	1e-04
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	2e-04
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	5e-04

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

 Score =  107 bits (268), Expect = 5e-31
 Identities = 57/65 (87%), Positives = 59/65 (90%)

Query: 116 EGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEAR 175
           + SDC+SEPGI LKRKQRRSRTTFSA QLDELERAFERTQYPDIYTREELAQRT LTEAR
Sbjct: 2   DISDCESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEAR 61

Query: 176 IQTIF 180
           IQ  F
Sbjct: 62  IQVWF 66

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

 Score = 94.7 bits (236), Expect = 3e-26
 Identities = 50/56 (89%), Positives = 52/56 (92%)

Query: 46  EGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           + SDC+SEPGI LKRKQRRSRTTFSA QLDELERAFERTQYPDIYTREELAQRT L
Sbjct: 2   DISDCESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNL 57

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

 Score = 93.2 bits (232), Expect = 1e-25
 Identities = 25/54 (46%), Positives = 36/54 (66%)

Query: 127 PLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIF 180
                 +R+RT+F+ +Q++ LE+ FERT YPD++ RE LA +  L EARIQ  F
Sbjct: 2   SSGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWF 55

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

 Score = 81.3 bits (201), Expect = 6e-21
 Identities = 19/45 (42%), Positives = 30/45 (66%)

Query: 57  PLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
                 +R+RT+F+ +Q++ LE+ FERT YPD++ RE LA +  L
Sbjct: 2   SSGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDL 46

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

 Score = 92.8 bits (231), Expect = 2e-25
 Identities = 22/52 (42%), Positives = 34/52 (65%)

Query: 129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIF 180
               RR RT F+ +QL+ LE  F+ T+YPD+ TRE+LA++  L E +++  F
Sbjct: 4   GSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWF 55

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

 Score = 80.5 bits (199), Expect = 8e-21
 Identities = 20/43 (46%), Positives = 29/43 (67%)

Query: 59  KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
               RR RT F+ +QL+ LE  F+ T+YPD+ TRE+LA++  L
Sbjct: 4   GSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHL 46

>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 = 92.1 bits (229), Expect = 3e-25
 Identities = 26/52 (50%), Positives = 34/52 (65%)

Query: 129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIF 180
               RR RTTF+  QLD LE  F +T+YPDI+ REE+A +  L E+R+Q  F
Sbjct: 4   GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWF 55

>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 = 80.2 bits (198), Expect = 1e-20
 Identities = 22/43 (51%), Positives = 28/43 (65%)

Query: 59  KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
               RR RTTF+  QLD LE  F +T+YPDI+ REE+A +  L
Sbjct: 4   GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINL 46

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

 Score = 90.8 bits (226), Expect = 8e-25
 Identities = 28/50 (56%), Positives = 37/50 (74%)

Query: 131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIF 180
            QRR RT F++QQL +LE  F+R +YPD+ TREE+A  T LTEAR++  F
Sbjct: 2   SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWF 51

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

 Score = 78.5 bits (194), Expect = 5e-20
 Identities = 23/41 (56%), Positives = 30/41 (73%)

Query: 61  KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
            QRR RT F++QQL +LE  F+R +YPD+ TREE+A  T L
Sbjct: 2   SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNL 42

>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 = 89.1 bits (221), Expect = 5e-24
 Identities = 17/52 (32%), Positives = 26/52 (50%)

Query: 129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIF 180
               +R RT+F   QL  ++  F     PD    ++LAQ+T LT+  +Q  F
Sbjct: 4   GSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWF 55

>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 = 77.9 bits (192), Expect = 1e-19
 Identities = 14/43 (32%), Positives = 21/43 (48%)

Query: 59  KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
               +R RT+F   QL  ++  F     PD    ++LAQ+T L
Sbjct: 4   GSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGL 46

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

 Score = 85.8 bits (213), Expect = 7e-23
 Identities = 21/48 (43%), Positives = 26/48 (54%)

Query: 133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIF 180
           RR RT F+  Q++ LE  F    YP I   E+LAQ+  L   RIQ  F
Sbjct: 2   RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWF 49

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

 Score = 73.5 bits (181), Expect = 5e-18
 Identities = 17/39 (43%), Positives = 22/39 (56%)

Query: 63  RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           RR RT F+  Q++ LE  F    YP I   E+LAQ+  L
Sbjct: 2   RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNL 40

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

 Score = 85.0 bits (211), Expect = 1e-22
 Identities = 29/46 (63%), Positives = 36/46 (78%)

Query: 135 SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIF 180
           S  TF++ QL+ELE+AF RT YPD++TREELA +  LTEARIQ  F
Sbjct: 2   SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWF 47

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

 Score = 71.9 bits (177), Expect = 1e-17
 Identities = 22/37 (59%), Positives = 29/37 (78%)

Query: 65  SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           S  TF++ QL+ELE+AF RT YPD++TREELA +  L
Sbjct: 2   SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGL 38

>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 = 84.7 bits (210), Expect = 2e-22
 Identities = 16/52 (30%), Positives = 21/52 (40%)

Query: 129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIF 180
               R SRT F+  QL  L+  F+   YP     E+L+    L    I   F
Sbjct: 4   GSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWF 55

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

 Score = 73.2 bits (180), Expect = 6e-18
 Identities = 14/43 (32%), Positives = 19/43 (44%)

Query: 59  KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
               R SRT F+  QL  L+  F+   YP     E+L+    L
Sbjct: 4   GSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNL 46

>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 = 82.4 bits (204), Expect = 1e-21
 Identities = 15/50 (30%), Positives = 23/50 (46%)

Query: 131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIF 180
           K  R RT  + +QL  L   +     PD   +E+L + T L+   I+  F
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWF 51

>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 = 71.6 bits (176), Expect = 2e-17
 Identities = 13/41 (31%), Positives = 19/41 (46%)

Query: 61  KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           K  R RT  + +QL  L   +     PD   +E+L + T L
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGL 42

>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 = 78.3 bits (193), Expect = 9e-20
 Identities = 14/63 (22%), Positives = 26/63 (41%)

Query: 118 SDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQ 177
           S      G    ++ +R RTT + +QL+ L + +     P     + +A    L +  +Q
Sbjct: 3   SGSSGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQ 62

Query: 178 TIF 180
             F
Sbjct: 63  VWF 65

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

 Score = 68.7 bits (168), Expect = 5e-16
 Identities = 12/54 (22%), Positives = 22/54 (40%)

Query: 48  SDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           S      G    ++ +R RTT + +QL+ L + +     P     + +A    L
Sbjct: 3   SGSSGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGL 56

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

 Score = 79.1 bits (194), Expect = 8e-19
 Identities = 19/112 (16%), Positives = 33/112 (29%), Gaps = 17/112 (15%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKL-----------------SDGEG 47
              I +      +  + S +S+ L       T     L                 +   G
Sbjct: 41  QHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQKRAALYTWYVRKQREVAQQFTHAGQGG 100

Query: 48  SDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRT 99
              +        +K RR+R  +       L +A+ER + P    RE L +  
Sbjct: 101 LIEEPTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEEC 152

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

 Score = 73.6 bits (181), Expect = 4e-18
 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 133 RRSRTTFSAQQLDELERAFERT-QYPDIYTREELAQRTKLTEARIQTIF 180
                T +  Q++ LE  F +  ++PD  T   +A    LTE + Q  F
Sbjct: 2   SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWF 50

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

 Score = 61.6 bits (150), Expect = 1e-13
 Identities = 10/40 (25%), Positives = 17/40 (42%), Gaps = 1/40 (2%)

Query: 63  RRSRTTFSAQQLDELERAFERT-QYPDIYTREELAQRTKL 101
                T +  Q++ LE  F +  ++PD  T   +A    L
Sbjct: 2   SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGL 41

>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 = 69.7 bits (171), Expect = 1e-16
 Identities = 12/49 (24%), Positives = 22/49 (44%)

Query: 129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQ 177
               +R RT  +  QL  L + F+    P     +E+A ++ L +  I+
Sbjct: 4   GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIK 52

>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 = 61.6 bits (150), Expect = 2e-13
 Identities = 11/43 (25%), Positives = 19/43 (44%)

Query: 59  KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
               +R RT  +  QL  L + F+    P     +E+A ++ L
Sbjct: 4   GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGL 46

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

 Score = 73.1 bits (178), Expect = 2e-16
 Identities = 31/168 (18%), Positives = 57/168 (33%), Gaps = 27/168 (16%)

Query: 8   IKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKLSDGEGSDCDSEPGIPLKRKQRRSRT 67
           I +      +  + S +S+ L                          G P+K ++R +  
Sbjct: 45  IPQREVVDVTGLNQSHLSQHLNK------------------------GTPMKTQKRAALY 80

Query: 68  TFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIP 127
           T+  ++  E+ R F +T      +     + ++    FL     Q S      D     P
Sbjct: 81  TWYVRKQREILRQFNQTVQS---SGNMTDKSSQDQLLFLFPEFSQQSHGPGQSDDACSEP 137

Query: 128 LKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEAR 175
             +K RR+R  +       L +A++R + P    RE L +     E  
Sbjct: 138 TNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECL 185

>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 = 69.7 bits (170), Expect = 3e-16
 Identities = 18/73 (24%), Positives = 27/73 (36%), Gaps = 15/73 (20%)

Query: 129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELA---------------QRTKLTE 173
               R SR T+  + L  +E  F   QYPD   REE+A                  ++T 
Sbjct: 4   GSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTS 63

Query: 174 ARIQTIFIVRKMR 186
            ++   F  R+  
Sbjct: 64  LKVYNWFANRRKE 76

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

 Score = 66.2 bits (161), Expect = 5e-15
 Identities = 15/41 (36%), Positives = 19/41 (46%)

Query: 59 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRT 99
              R SR T+  + L  +E  F   QYPD   REE+A   
Sbjct: 4  GSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANAC 44

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

 Score = 68.6 bits (168), Expect = 3e-16
 Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 1/55 (1%)

Query: 133 RRSRTTFSAQQLDELERAFERT-QYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
            ++ +  +  Q++ LE  F +  ++PD  T   +A    LTE + Q  F  R   
Sbjct: 3   AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAE 57

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

 Score = 57.1 bits (138), Expect = 8e-12
 Identities = 9/40 (22%), Positives = 19/40 (47%), Gaps = 1/40 (2%)

Query: 63  RRSRTTFSAQQLDELERAFERT-QYPDIYTREELAQRTKL 101
            ++ +  +  Q++ LE  F +  ++PD  T   +A    L
Sbjct: 3   AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGL 42

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

 Score = 65.9 bits (161), Expect = 5e-15
 Identities = 13/52 (25%), Positives = 22/52 (42%)

Query: 129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIF 180
                  +   S +QL  L+ +F R Q+P     E L + T L+   ++  F
Sbjct: 5   SSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWF 56

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

 Score = 55.9 bits (135), Expect = 3e-11
 Identities = 12/43 (27%), Positives = 18/43 (41%)

Query: 59  KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
                  +   S +QL  L+ +F R Q+P     E L + T L
Sbjct: 5   SSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGL 47

>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 = 64.0 bits (156), Expect = 2e-14
 Identities = 12/56 (21%), Positives = 24/56 (42%)

Query: 131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
                    + +Q+  L+ +F ++Q+PD      L + T L  + I+  F   + R
Sbjct: 3   HHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYR 58

>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 = 56.3 bits (136), Expect = 2e-11
 Identities = 9/41 (21%), Positives = 18/41 (43%)

Query: 61  KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
                    + +Q+  L+ +F ++Q+PD      L + T L
Sbjct: 3   HHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGL 43

>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 = 62.7 bits (152), Expect = 5e-13
 Identities = 15/68 (22%), Positives = 28/68 (41%)

Query: 110 EQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRT 169
            +  + EG     E       K+R+ RT+F+ Q ++ L   FE+   P      E+A+  
Sbjct: 71  AELRNQEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKEL 130

Query: 170 KLTEARIQ 177
                 ++
Sbjct: 131 NYDREVVR 138

>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 = 56.6 bits (136), Expect = 8e-11
 Identities = 22/118 (18%), Positives = 39/118 (33%), Gaps = 21/118 (17%)

Query: 5   DRLIKEGL--CDRGSAPSVSAISRLLRGHEG-------------------DDTSSEKKLS 43
            R +  GL     G A + +      +                       +   +E +L 
Sbjct: 15  IRRLSLGLTQTQVGQAMTATEGPAYSQSAISRFEKLDITPKSAQKLKPVLEKWLNEAELR 74

Query: 44  DGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           + EG     E       K+R+ RT+F+ Q ++ L   FE+   P      E+A+    
Sbjct: 75  NQEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNY 132

>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 = 60.0 bits (145), Expect = 4e-12
 Identities = 15/70 (21%), Positives = 24/70 (34%)

Query: 111 QQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTK 170
                E         +    ++R+ RTT S    D LER F     P       +A+   
Sbjct: 66  WLEEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELN 125

Query: 171 LTEARIQTIF 180
           L +  ++  F
Sbjct: 126 LEKEVVRVWF 135

>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 = 58.5 bits (141), Expect = 2e-11
 Identities = 24/117 (20%), Positives = 35/117 (29%), Gaps = 24/117 (20%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTS--------------------SEKKLSD 44
            R IK G     +  +V      + G E   T+                      K L +
Sbjct: 14  VRRIKLGY----TQTNVGEALAAVHGSEFSQTTICRFENLQLSFKNACKLKAILSKWLEE 69

Query: 45  GEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
            E         +    ++R+ RTT S    D LER F     P       +A+   L
Sbjct: 70  AEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNL 126

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

 Score = 58.3 bits (140), Expect = 8e-12
 Identities = 13/46 (28%), Positives = 20/46 (43%)

Query: 129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEA 174
            +K RR+R  +       L +A+ER + P    RE L +     E 
Sbjct: 6   TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAEC 51

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

 Score = 57.5 bits (138), Expect = 1e-11
 Identities = 12/41 (29%), Positives = 19/41 (46%)

Query: 59 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRT 99
           +K RR+R  +       L +A+ER + P    RE L +  
Sbjct: 6  TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEEC 46

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

 Score = 58.1 bits (140), Expect = 3e-11
 Identities = 12/70 (17%), Positives = 27/70 (38%)

Query: 111 QQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTK 170
           +++        +   I  + ++R+ RT+        LE  F +   P  +    LA   +
Sbjct: 78  EETDSSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQ 137

Query: 171 LTEARIQTIF 180
           L +  ++  F
Sbjct: 138 LEKEVVRVWF 147

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

 Score = 52.3 bits (125), Expect = 4e-09
 Identities = 14/65 (21%), Positives = 25/65 (38%), Gaps = 2/65 (3%)

Query: 39  EKKLSDGEGS--DCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELA 96
            K L + + S     +   I  + ++R+ RT+        LE  F +   P  +    LA
Sbjct: 74  NKWLEETDSSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLA 133

Query: 97  QRTKL 101
              +L
Sbjct: 134 DSLQL 138

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

 Score = 57.8 bits (139), Expect = 4e-11
 Identities = 13/77 (16%), Positives = 33/77 (42%)

Query: 111 QQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTK 170
           +++    +  +      L + ++R RT+   +    LE  F ++  P +     +A +  
Sbjct: 75  EEADNNENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLG 134

Query: 171 LTEARIQTIFIVRKMRG 187
           L +  ++  F  R+ +G
Sbjct: 135 LEKDVVRVWFSNRRQKG 151

>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 = 55.1 bits (132), Expect = 3e-10
 Identities = 19/115 (16%), Positives = 36/115 (31%), Gaps = 18/115 (15%)

Query: 5   DRLIKEGLCD----------RGSAPSVSAISRLLRGHEGD------DTSSEKKLSDGE-- 46
            + I  G              G   S + ISR                  EK + + +  
Sbjct: 21  QKRITLGYTQADVGLTLGVLFGKVFSQTTISRFEALQLSLKNMSKLRPLLEKWVEEADNN 80

Query: 47  GSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
            +  +      L + ++R RT+   +    LE  F ++  P +     +A +  L
Sbjct: 81  ENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGL 135

>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 = 56.9 bits (137), Expect = 7e-11
 Identities = 15/69 (21%), Positives = 30/69 (43%)

Query: 118 SDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQ 177
               + PGI    ++R+ RT+        LE++F   Q P       +A++  + +  I+
Sbjct: 87  PSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIR 146

Query: 178 TIFIVRKMR 186
             F  R+ +
Sbjct: 147 VWFSNRRQK 155

>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 = 53.4 bits (128), Expect = 2e-09
 Identities = 18/85 (21%), Positives = 34/85 (40%)

Query: 17  SAPSVSAISRLLRGHEGDDTSSEKKLSDGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDE 76
           S  ++S +  LL     D  ++    S        + PGI    ++R+ RT+        
Sbjct: 56  SFKNMSKLKPLLEKWLNDAEANLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVA 115

Query: 77  LERAFERTQYPDIYTREELAQRTKL 101
           LE++F   Q P       +A++  +
Sbjct: 116 LEKSFMENQKPTSEDITLIAEQLNM 140

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

 Score = 54.4 bits (131), Expect = 1e-10
 Identities = 23/76 (30%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query: 110 EQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRT 169
           +Q +S E S    E  +P   K++++RT FS+ QL  L   F+R +Y  +   +EL+   
Sbjct: 2   KQPTSAENSVAKKEDKVP--VKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNIL 59

Query: 170 KLTEARIQTIFIVRKM 185
            L+  +++T F  ++M
Sbjct: 60  NLSYKQVKTWFQNQRM 75

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

 Score = 47.5 bits (113), Expect = 6e-08
 Identities = 14/59 (23%), Positives = 28/59 (47%)

Query: 43  SDGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
                 +  ++    +  K++++RT FS+ QL  L   F+R +Y  +   +EL+    L
Sbjct: 3   QPTSAENSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNL 61

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

 Score = 54.6 bits (131), Expect = 1e-10
 Identities = 14/72 (19%), Positives = 29/72 (40%), Gaps = 5/72 (6%)

Query: 115 GEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEA 174
           G      + P    ++ + ++       Q+  LE +F ++ +P     + L   TKL+  
Sbjct: 1   GSSGSSGAYPDFAPQKFKEKT-----QGQVKILEDSFLKSSFPTQAELDRLRVETKLSRR 55

Query: 175 RIQTIFIVRKMR 186
            I + F  R+  
Sbjct: 56  EIDSWFSERRKL 67

>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 = 45.4 bits (107), Expect = 3e-07
 Identities = 11/57 (19%), Positives = 23/57 (40%), Gaps = 5/57 (8%)

Query: 45  GEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           G      + P    ++ + ++       Q+  LE +F ++ +P     + L   TKL
Sbjct: 1   GSSGSSGAYPDFAPQKFKEKT-----QGQVKILEDSFLKSSFPTQAELDRLRVETKL 52

>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 = 53.0 bits (128), Expect = 3e-10
 Identities = 17/58 (29%), Positives = 32/58 (55%)

Query: 129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           K K  + +++ S Q    LE  F R Q  +   +EE+A++  +T  +++  FI ++MR
Sbjct: 2   KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 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 = 45.3 bits (108), Expect = 2e-07
 Identities = 13/46 (28%), Positives = 23/46 (50%)

Query: 59  KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPH 104
           K K  + +++ S Q    LE  F R Q  +   +EE+A++  + P 
Sbjct: 2   KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPL 47

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

 Score = 52.6 bits (127), Expect = 4e-10
 Identities = 19/54 (35%), Positives = 31/54 (57%)

Query: 132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKM 185
           +R+ R  FS  Q+ ELER F++ +Y     R++LA   KLT  +++  F  R+ 
Sbjct: 2   RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRY 55

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

 Score = 46.5 bits (111), Expect = 6e-08
 Identities = 16/40 (40%), Positives = 24/40 (60%)

Query: 62  QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           +R+ R  FS  Q+ ELER F++ +Y     R++LA   KL
Sbjct: 2   RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKL 41

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

 Score = 52.9 bits (127), Expect = 4e-10
 Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 115 GEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEA 174
           G       EPG    +K RRSRT F+  QL  LE+ FE+ +Y     R +LA+   L++ 
Sbjct: 1   GSSGSSGGEPG-TKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQL 59

Query: 175 RIQTIFIVRKMR 186
           +++T +  R+M+
Sbjct: 60  QVKTWYQNRRMK 71

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

 Score = 44.8 bits (106), Expect = 5e-07
 Identities = 22/57 (38%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 45  GEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           G       EPG    +K RRSRT F+  QL  LE+ FE+ +Y     R +LA+   L
Sbjct: 1   GSSGSSGGEPG-TKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGL 56

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

 Score = 51.9 bits (125), Expect = 6e-10
 Identities = 20/53 (37%), Positives = 28/53 (52%)

Query: 133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKM 185
           R+ RT F+  QL  LER F + QY  I  R E +    LTE +++  F  R+ 
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRA 53

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

 Score = 45.7 bits (109), Expect = 1e-07
 Identities = 16/39 (41%), Positives = 20/39 (51%)

Query: 63  RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           R+ RT F+  QL  LER F + QY  I  R E +    L
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSL 39

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

 Score = 51.1 bits (123), Expect = 1e-09
 Identities = 15/55 (27%), Positives = 31/55 (56%)

Query: 131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKM 185
            +++ RT FS  QL  L+  F++ +Y  +   +EL+    L+  +++T F  ++M
Sbjct: 2   TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRM 56

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

 Score = 44.6 bits (106), Expect = 3e-07
 Identities = 12/41 (29%), Positives = 22/41 (53%)

Query: 61  KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
            +++ RT FS  QL  L+  F++ +Y  +   +EL+    L
Sbjct: 2   TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNL 42

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

 Score = 51.7 bits (124), Expect = 1e-09
 Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 2/64 (3%)

Query: 122 SEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI 181
           +  G+P   K+R+ R  F+  Q  ELER F + +Y     RE LA   +LT  +++  F 
Sbjct: 1   ASDGLP--NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQ 58

Query: 182 VRKM 185
             + 
Sbjct: 59  NHRY 62

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

 Score = 45.5 bits (108), Expect = 2e-07
 Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 52  SEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           +  G+P   K+R+ R  F+  Q  ELER F + +Y     RE LA   +L
Sbjct: 1   ASDGLP--NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRL 48

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

 Score = 50.9 bits (122), Expect = 2e-09
 Identities = 19/57 (33%), Positives = 33/57 (57%)

Query: 130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
              R+ RT +S+ QL  L+R F++TQY  +  R ELA    LT+ +++  F  ++ +
Sbjct: 5   SSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSK 61

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

 Score = 44.3 bits (105), Expect = 5e-07
 Identities = 17/42 (40%), Positives = 24/42 (57%)

Query: 60  RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
              R+ RT +S+ QL  L+R F++TQY  +  R ELA    L
Sbjct: 5   SSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGL 46

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

 Score = 50.8 bits (122), Expect = 2e-09
 Identities = 17/56 (30%), Positives = 26/56 (46%)

Query: 131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
                 +  S  Q+ ELER F   +Y     R  LA+  KLTE +++  F  R+ +
Sbjct: 3   HHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYK 58

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

 Score = 43.9 bits (104), Expect = 8e-07
 Identities = 13/41 (31%), Positives = 17/41 (41%)

Query: 61  KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
                 +  S  Q+ ELER F   +Y     R  LA+  KL
Sbjct: 3   HHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKL 43

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

 Score = 50.4 bits (121), Expect = 3e-09
 Identities = 18/54 (33%), Positives = 28/54 (51%)

Query: 132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKM 185
           +R+ R  FS  Q+ ELER F++ +Y     RE LA    LT  +++  F   + 
Sbjct: 2   RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRY 55

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

 Score = 44.3 bits (105), Expect = 5e-07
 Identities = 16/40 (40%), Positives = 22/40 (55%)

Query: 62  QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           +R+ R  FS  Q+ ELER F++ +Y     RE LA    L
Sbjct: 2   RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHL 41

>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 = 50.6 bits (121), Expect = 3e-09
 Identities = 14/51 (27%), Positives = 19/51 (37%), Gaps = 1/51 (1%)

Query: 131 KQRRSRTTFSAQQLDELERAFERTQ-YPDIYTREELAQRTKLTEARIQTIF 180
              RSRT  S + L  L+        YPD      L+ +  L +  I   F
Sbjct: 6   SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFF 56

>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 = 43.6 bits (103), Expect = 1e-06
 Identities = 12/42 (28%), Positives = 16/42 (38%), Gaps = 1/42 (2%)

Query: 61  KQRRSRTTFSAQQLDELERAFERTQ-YPDIYTREELAQRTKL 101
              RSRT  S + L  L+        YPD      L+ +  L
Sbjct: 6   SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDL 47

>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 = 50.6 bits (120), Expect = 5e-09
 Identities = 16/71 (22%), Positives = 25/71 (35%)

Query: 110 EQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRT 169
                          G   K          + +QL  L+ AF RTQ+P     ++LA+ +
Sbjct: 3   HHHHHHSSGLEVLFQGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKES 62

Query: 170 KLTEARIQTIF 180
            L    I + F
Sbjct: 63  GLARTDIVSWF 73

>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 = 44.4 bits (104), Expect = 8e-07
 Identities = 14/50 (28%), Positives = 22/50 (44%)

Query: 52  SEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
              G   K          + +QL  L+ AF RTQ+P     ++LA+ + L
Sbjct: 15  LFQGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGL 64

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

 Score = 50.2 bits (120), Expect = 5e-09
 Identities = 19/57 (33%), Positives = 36/57 (63%)

Query: 130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
            K+++ RT+F+  Q+ ELE+ F + +Y     R  LA+  K+T+A+++T F  R+ +
Sbjct: 15  PKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTK 71

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

 Score = 42.5 bits (100), Expect = 4e-06
 Identities = 14/42 (33%), Positives = 25/42 (59%)

Query: 60  RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
            K+++ RT+F+  Q+ ELE+ F + +Y     R  LA+  K+
Sbjct: 15  PKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKM 56

>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 = 49.6 bits (118), Expect = 1e-08
 Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 5/70 (7%)

Query: 117 GSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARI 176
           GS   S P    ++ + ++     A+QL  L+ +F  +          L  +TKLT   I
Sbjct: 1   GSSGSSGPDFTPQKFKEKT-----AEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREI 55

Query: 177 QTIFIVRKMR 186
              F  +K  
Sbjct: 56  DAWFTEKKKS 65

>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 = 41.1 bits (96), Expect = 1e-05
 Identities = 13/55 (23%), Positives = 23/55 (41%), Gaps = 5/55 (9%)

Query: 47  GSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           GS   S P    ++ + ++     A+QL  L+ +F  +          L  +TKL
Sbjct: 1   GSSGSSGPDFTPQKFKEKT-----AEQLRVLQASFLNSSVLTDEELNRLRAQTKL 50

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

 Score = 47.0 bits (112), Expect = 6e-08
 Identities = 17/57 (29%), Positives = 30/57 (52%)

Query: 130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
              +  +  FS  Q  ELE+ FE  +Y     R+ LA+  +L+E +++T F  R+ +
Sbjct: 5   SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAK 61

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

 Score = 38.6 bits (90), Expect = 7e-05
 Identities = 13/42 (30%), Positives = 20/42 (47%)

Query: 60  RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
              +  +  FS  Q  ELE+ FE  +Y     R+ LA+  +L
Sbjct: 5   SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQL 46

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

 Score = 47.9 bits (113), Expect = 2e-07
 Identities = 12/68 (17%), Positives = 26/68 (38%)

Query: 119 DCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQT 178
             + E G       ++ R  F+  Q   L   F+  + P    +  ++Q+  L  + +  
Sbjct: 84  RKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSN 143

Query: 179 IFIVRKMR 186
            F+  + R
Sbjct: 144 FFMNARRR 151

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

 Score = 41.4 bits (96), Expect = 3e-05
 Identities = 11/63 (17%), Positives = 21/63 (33%)

Query: 39  EKKLSDGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQR 98
              L        + E G       ++ R  F+  Q   L   F+  + P    +  ++Q+
Sbjct: 74  MSALRLAACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQ 133

Query: 99  TKL 101
             L
Sbjct: 134 LGL 136

>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 = 45.7 bits (108), Expect = 2e-07
 Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 2/57 (3%)

Query: 130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
              +        +QL  LE +F +   P     + L   TK+T   I + F  R+ +
Sbjct: 7   GPTKYKERA--PEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKK 61

>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 = 37.6 bits (87), Expect = 2e-04
 Identities = 9/42 (21%), Positives = 15/42 (35%), Gaps = 2/42 (4%)

Query: 60  RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
              +        +QL  LE +F +   P     + L   TK+
Sbjct: 7   GPTKYKERA--PEQLRALESSFAQNPLPLDEELDRLRSETKM 46

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

 Score = 45.0 bits (107), Expect = 2e-07
 Identities = 19/49 (38%), Positives = 30/49 (61%)

Query: 137 TTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKM 185
           T+FS  Q+ ELER F R +Y     R  LA+  ++T+A+++T F  R+ 
Sbjct: 2   TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRT 50

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

 Score = 37.7 bits (88), Expect = 1e-04
 Identities = 14/35 (40%), Positives = 20/35 (57%)

Query: 67  TTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           T+FS  Q+ ELER F R +Y     R  LA+  ++
Sbjct: 2   TSFSRSQVLELERRFLRQKYLASAERAALAKALRM 36

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

 Score = 43.1 bits (102), Expect = 1e-06
 Identities = 18/55 (32%), Positives = 32/55 (58%)

Query: 132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           ++R RT FS++QL  L+R F   +Y     R++L+    L EA+I+  F  ++ +
Sbjct: 3   EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAK 57

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

 Score = 35.8 bits (83), Expect = 6e-04
 Identities = 14/40 (35%), Positives = 23/40 (57%)

Query: 62  QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           ++R RT FS++QL  L+R F   +Y     R++L+    L
Sbjct: 3   EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGL 42

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

 Score = 43.2 bits (102), Expect = 1e-06
 Identities = 18/55 (32%), Positives = 32/55 (58%)

Query: 132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
            RR+RTTF++ Q+ ELE+ F + +Y       +L+ +  L  A+++  F  R+ R
Sbjct: 2   PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRR 56

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

 Score = 42.0 bits (99), Expect = 3e-06
 Identities = 21/54 (38%), Positives = 29/54 (53%)

Query: 133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           RR RT F+  QL  LE+ F +  Y     R ELA +  L E+ I+  F  R+M+
Sbjct: 2   RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMK 55

>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 = 42.3 bits (99), Expect = 3e-06
 Identities = 12/47 (25%), Positives = 19/47 (40%)

Query: 134 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIF 180
            S    + +QL  L+  F + Q+      ++L Q T L    I   F
Sbjct: 5   SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWF 51

>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 = 38.1 bits (88), Expect = 1e-04
 Identities = 10/38 (26%), Positives = 17/38 (44%)

Query: 64  RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
            S    + +QL  L+  F + Q+      ++L Q T L
Sbjct: 5   SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGL 42

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

 Score = 42.6 bits (100), Expect = 5e-06
 Identities = 19/65 (29%), Positives = 32/65 (49%)

Query: 122 SEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI 181
           ++   P        RT F+ +QL ELE+ F   +Y     R E+A   +L E +++  F 
Sbjct: 24  AKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQ 83

Query: 182 VRKMR 186
            R+M+
Sbjct: 84  NRRMK 88

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

 Score = 40.4 bits (95), Expect = 1e-05
 Identities = 21/56 (37%), Positives = 30/56 (53%)

Query: 131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
             +R+RT ++  QL ELE+ F   +Y     R ELA    LTE  I+  F  R+M+
Sbjct: 2   SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMK 57

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5 Length = 128

 Score = 42.0 bits (98), Expect = 1e-05
 Identities = 19/28 (67%), Positives = 26/28 (92%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRGHE 32
           ++LI+EG+CDR +APSVSAISRL+RG +
Sbjct: 101 EKLIREGVCDRSTAPSVSAISRLVRGRD 128

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens} Length = 159

 Score = 41.4 bits (96), Expect = 4e-05
 Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 2/46 (4%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRG--HEGDDTSSEKKLSDGEGS 48
           DRL+ EG+CD  + PSVS+I+R++R    +  +   +     G   
Sbjct: 109 DRLLAEGVCDNDTVPSVSSINRIIRTKVQQPFNLPMDSGAPGGGSH 154

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

 Score = 39.4 bits (92), Expect = 4e-05
 Identities = 20/57 (35%), Positives = 29/57 (50%)

Query: 130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
             +RR R T++  Q  ELE+ F    Y     R E+A    LTE +I+  F  R+M+
Sbjct: 18  GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMK 74

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

 Score = 39.1 bits (91), Expect = 6e-05
 Identities = 19/56 (33%), Positives = 31/56 (55%)

Query: 131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           + +R RT+++  Q  ELE+ F   +Y     R E+A    LTE +I+  F  R+M+
Sbjct: 27  ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMK 82

>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 = 41.8 bits (97), Expect = 6e-05
 Identities = 19/126 (15%), Positives = 40/126 (31%), Gaps = 16/126 (12%)

Query: 74  LDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSS------GEGSDCDSE---P 124
            D  +    + +   I   ++    T     F  ++ +Q         E    + +    
Sbjct: 39  QDMPKSILSKEEIDHIIMSKDAVSGTLRL--FWTLLSKQEEMVQKFVEEVLRINYKFLMS 96

Query: 125 GIPLKRKQRRSRTTFSAQQLDELERAFER-TQYPDIYTREELAQ--RTKLTEARIQTIFI 181
            I  +++Q    T    +Q D L    +   +Y    +R +     R  L E R     +
Sbjct: 97  PIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYN--VSRLQPYLKLRQALLELRPAKNVL 154

Query: 182 VRKMRG 187
           +  + G
Sbjct: 155 IDGVLG 160

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

 Score = 38.6 bits (90), Expect = 7e-05
 Identities = 19/55 (34%), Positives = 30/55 (54%)

Query: 132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           ++R R T++  Q  ELE+ F   +Y     R E+A    LTE +I+  F  R+M+
Sbjct: 2   RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMK 56

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

 Score = 38.3 bits (89), Expect = 8e-05
 Identities = 14/57 (24%), Positives = 29/57 (50%)

Query: 130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
            + R+ R  ++  QL ELER +   ++     R  ++  T L+E ++   F  R+++
Sbjct: 5   LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVK 61

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

 Score = 37.9 bits (88), Expect = 1e-04
 Identities = 16/57 (28%), Positives = 29/57 (50%)

Query: 130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
              R+ R  +S  QL ELER +   ++     R +++  T L+E +I   F  R+++
Sbjct: 5   SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVK 61

>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A Length = 149

 Score = 39.0 bits (90), Expect = 2e-04
 Identities = 13/29 (44%), Positives = 20/29 (68%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLLRGHEG 33
           DRL+ E +CD  + PSVS+I+R++R    
Sbjct: 116 DRLLAERVCDNDTVPSVSSINRIIRTKVQ 144

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

 Score = 36.4 bits (84), Expect = 5e-04
 Identities = 18/57 (31%), Positives = 29/57 (50%)

Query: 130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           R  R+ R  ++  Q  ELE+ F    Y     R E+A+   LTE +++  F  R+M+
Sbjct: 11  RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMK 67

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	187
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.85
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.85
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.83
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.83
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.83
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.83
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.82
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.82
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.82
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.81
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.81
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.81
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.81
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.81
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.81
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.81
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.8
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.8
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.8
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.8
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.8
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.8
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.8
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.8
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.8
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.8
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.8
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.79
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.79
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.79
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.79
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.79
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.79
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.79
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.79
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.78
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.78
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.78
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.78
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.78
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.78
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.77
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.77
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.77
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.77
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.76
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.76
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.76
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.75
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.75
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.75
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.74
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.74
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.74
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.74
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.74
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.74
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.73
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.73
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.73
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.73
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.73
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.72
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.72
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.72
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.72
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.71
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.71
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.7
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.69
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.68
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.67
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.62
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.6
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.59
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.58
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.57
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.57
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.57
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.56
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.56
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.55
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.55
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.54
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.53
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.51
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.51
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.51
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.51
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.51
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.51
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.5
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.5
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.49
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.49
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.49
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.49
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.48
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.48
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.48
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.48
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.48
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.48
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.47
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.47
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.47
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.46
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.46
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.46
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.46
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.45
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.44
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.44
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.44
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.44
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.42
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.42
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.41
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.4
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.4
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.4
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.38
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.38
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.38
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.38
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.37
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.37
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.37
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.35
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.34
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.34
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.33
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.3
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.3
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.3
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.3
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.3
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.29
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.29
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.28
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.28
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.28
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.27
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.26
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.23
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.23
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.22
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.22
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.18
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.16
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.04
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	98.91
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	98.63
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	98.53
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.37
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	96.48
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	93.27
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	89.09
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	86.42
2k27_A	159	Paired box protein PAX-8; paired domain, solution	85.59
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	85.2
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	83.65

>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=99.85  E-value=1.6e-21  Score=122.62  Aligned_cols=59  Identities=24%  Similarity=0.262  Sum_probs=55.8

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhh----cCCCCHHHHHHHHHHcCCChhhhhhhhcccCCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFER----TQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG  187 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~----~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~  187 (187)
                      ..+.+|.||.||.+|+.+||..|+.    ++||+..++++||..|||++.+|+|||||||+|.
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~   76 (80)
T 1wh5_A           14 GGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSG   76 (80)
T ss_dssp             CCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSS
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCC
Confidence            3567889999999999999999999    9999999999999999999999999999999983

>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=99.85  E-value=2.6e-21  Score=121.38  Aligned_cols=57  Identities=23%  Similarity=0.256  Sum_probs=54.2

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhh-----cCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFER-----TQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~-----~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ..+.+|.||.||.+|+.+|| .|..     ++||+..++++||..+||++.+|+|||||||+|
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k   75 (80)
T 1wh7_A           14 GGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNS   75 (80)
T ss_dssp             CCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCC
T ss_pred             CCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccC
Confidence            45678899999999999999 8999     999999999999999999999999999999998

>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=99.83  E-value=1.4e-21  Score=127.68  Aligned_cols=86  Identities=22%  Similarity=0.249  Sum_probs=58.9

Q ss_pred             hcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhh
Q psy15514         99 TKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQT  178 (187)
Q Consensus        99 ~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~  178 (187)
                      ++.+...+..|+++.+........  ..+.....++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++
T Consensus         3 ~~~~~~~~~~W~~~~r~~~~~~~~--~~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~v   80 (97)
T 1b72_A            3 PNTPTARTFDWMKVKRNPPKTAKV--SEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKI   80 (97)
T ss_dssp             -----CCCCGGGGC----------------------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCcccccccccccCCCCCCCC--CCCCCCCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHH
Confidence            455667788999987755432221  112235677889999999999999999999999999999999999999999999


Q ss_pred             hhcccCCC
Q psy15514        179 IFIVRKMR  186 (187)
Q Consensus       179 WF~nrR~k  186 (187)
                      ||||||+|
T Consensus        81 WFqNRR~k   88 (97)
T 1b72_A           81 WFQNRRMK   88 (97)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHhHH
Confidence            99999986

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

Probab=99.83  E-value=5.6e-21  Score=120.52  Aligned_cols=58  Identities=36%  Similarity=0.566  Sum_probs=55.3

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .++.++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus        14 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k   71 (80)
T 2dmt_A           14 AKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMK   71 (80)
T ss_dssp             CCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHH
Confidence            4567889999999999999999999999999999999999999999999999999986

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

Probab=99.83  E-value=1.1e-20  Score=120.36  Aligned_cols=59  Identities=29%  Similarity=0.478  Sum_probs=56.0

Q ss_pred             ccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        128 LKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       128 ~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ...+.++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus        18 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k   76 (84)
T 2kt0_A           18 VPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMK   76 (84)
T ss_dssp             CCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence            45677889999999999999999999999999999999999999999999999999987

>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=99.83  E-value=3.1e-21  Score=122.05  Aligned_cols=67  Identities=85%  Similarity=1.190  Sum_probs=54.5

Q ss_pred             CCCCCCCcccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        120 CDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       120 ~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +.+.++....++.++.|+.||.+|+..||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         6 ~~~~~~~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k   72 (81)
T 1fjl_A            6 CESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRAR   72 (81)
T ss_dssp             -----------CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             cCCCCCCcccCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhh
Confidence            3444455556778899999999999999999999999999999999999999999999999999986

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

Probab=99.82  E-value=1.2e-20  Score=116.09  Aligned_cols=57  Identities=28%  Similarity=0.476  Sum_probs=54.5

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+.++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k   61 (70)
T 2cra_A            5 SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVK   61 (70)
T ss_dssp             CCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHH
Confidence            456788999999999999999999999999999999999999999999999999987

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

Probab=99.82  E-value=7.8e-21  Score=114.12  Aligned_cols=56  Identities=27%  Similarity=0.462  Sum_probs=49.4

Q ss_pred             cccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       131 ~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +.++.|+.||.+|+.+||..|..++||+..++.+||..+||++.+|++||||||+|
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k   57 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMK   57 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcc
Confidence            45778999999999999999999999999999999999999999999999999987

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

Probab=99.82  E-value=7.6e-21  Score=120.06  Aligned_cols=59  Identities=22%  Similarity=0.309  Sum_probs=55.6

Q ss_pred             ccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        128 LKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       128 ~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ...+.++.|+.||.+|+.+||..|..++||+..++++||..+||++.+|++||||||+|
T Consensus        13 ~~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   71 (80)
T 2da3_A           13 EPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRAR   71 (80)
T ss_dssp             CCCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHh
Confidence            34667889999999999999999999999999999999999999999999999999986

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

Probab=99.81  E-value=7.6e-21  Score=113.78  Aligned_cols=55  Identities=33%  Similarity=0.568  Sum_probs=50.1

Q ss_pred             ccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       132 ~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .++.|+.||.+|+..||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   57 (61)
T 2hdd_A            3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAK   57 (61)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhccc
Confidence            4678999999999999999999999999999999999999999999999999986

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

Probab=99.81  E-value=9.4e-21  Score=114.09  Aligned_cols=56  Identities=38%  Similarity=0.492  Sum_probs=51.8

Q ss_pred             cccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       131 ~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +.++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k   57 (63)
T 2h1k_A            2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMK   57 (63)
T ss_dssp             ---CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhh
Confidence            35778999999999999999999999999999999999999999999999999986

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

Probab=99.81  E-value=1.8e-20  Score=115.17  Aligned_cols=57  Identities=33%  Similarity=0.531  Sum_probs=54.5

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+.++.|+.||.+|+.+||..|..++||+..+++.||..+||++.+|++||||||+|
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   61 (70)
T 2djn_A            5 SSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSK   61 (70)
T ss_dssp             CCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhh
Confidence            456788999999999999999999999999999999999999999999999999987

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

Probab=99.81  E-value=1.3e-20  Score=111.68  Aligned_cols=54  Identities=37%  Similarity=0.586  Sum_probs=52.0

Q ss_pred             cccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   54 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAK   54 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhh
Confidence            467899999999999999999999999999999999999999999999999986

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

Probab=99.81  E-value=1.8e-20  Score=115.22  Aligned_cols=57  Identities=40%  Similarity=0.713  Sum_probs=54.2

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+.++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k   61 (70)
T 2dmu_A            5 SSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAK   61 (70)
T ss_dssp             TSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehcccccccc
Confidence            456788999999999999999999999999999999999999999999999999976

>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=99.81  E-value=2.4e-20  Score=116.71  Aligned_cols=58  Identities=31%  Similarity=0.480  Sum_probs=54.7

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ..+.++.|+.||..|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         6 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k   63 (77)
T 1nk2_P            6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYK   63 (77)
T ss_dssp             SCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcc
Confidence            3466788999999999999999999999999999999999999999999999999986

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

Probab=99.81  E-value=2.1e-20  Score=114.97  Aligned_cols=57  Identities=28%  Similarity=0.348  Sum_probs=54.4

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+.++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k   61 (70)
T 2da2_A            5 SSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQK   61 (70)
T ss_dssp             CCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHH
Confidence            456788999999999999999999999999999999999999999999999999976

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

Probab=99.80  E-value=1.9e-20  Score=113.84  Aligned_cols=56  Identities=27%  Similarity=0.439  Sum_probs=53.5

Q ss_pred             cccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       131 ~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +.++.|+.||.+|+..||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   57 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCK   57 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHH
Confidence            35788999999999999999999999999999999999999999999999999986

>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=99.80  E-value=4e-20  Score=115.75  Aligned_cols=58  Identities=31%  Similarity=0.430  Sum_probs=55.0

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .++.++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus        10 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k   67 (77)
T 1puf_A           10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMK   67 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            4567789999999999999999999999999999999999999999999999999986

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

Probab=99.80  E-value=3.4e-20  Score=109.66  Aligned_cols=56  Identities=25%  Similarity=0.315  Sum_probs=53.5

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhh-cCCCCHHHHHHHHHHcCCChhhhhhhhcccCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFER-TQYPDIYTREELAQRTKLTEARIQTIFIVRKM  185 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~-~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~  185 (187)
                      +..+|.||.|+.+|+..|+..|+. ++||+...++.||..+||++.+|++||||+|.
T Consensus         5 ~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~   61 (71)
T 1wi3_A            5 SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRY   61 (71)
T ss_dssp             CCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhcccee
Confidence            467889999999999999999999 99999999999999999999999999999984

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

Probab=99.80  E-value=1.6e-20  Score=112.46  Aligned_cols=57  Identities=28%  Similarity=0.446  Sum_probs=47.3

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+.++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||+|||+|
T Consensus         3 ~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k   59 (61)
T 1akh_A            3 EKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR   59 (61)
T ss_dssp             ---------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhc
Confidence            456788999999999999999999999999999999999999999999999999986

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

Probab=99.80  E-value=3.5e-20  Score=116.88  Aligned_cols=57  Identities=47%  Similarity=0.763  Sum_probs=54.7

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+.++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k   61 (80)
T 2dms_A            5 SSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAK   61 (80)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHH
Confidence            467889999999999999999999999999999999999999999999999999986

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

Probab=99.80  E-value=2.3e-20  Score=111.29  Aligned_cols=54  Identities=39%  Similarity=0.569  Sum_probs=51.6

Q ss_pred             cccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ++.|+.||.+|+..||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   55 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMK   55 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHhH
Confidence            578999999999999999999999999999999999999999999999999986

>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=99.80  E-value=1.8e-20  Score=115.23  Aligned_cols=57  Identities=23%  Similarity=0.335  Sum_probs=54.4

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+.++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k   61 (70)
T 2da1_A            5 SSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFK   61 (70)
T ss_dssp             CCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHH
Confidence            456789999999999999999999999999999999999999999999999999976

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

Probab=99.80  E-value=2.6e-20  Score=113.82  Aligned_cols=55  Identities=33%  Similarity=0.505  Sum_probs=53.0

Q ss_pred             ccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       132 ~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k   56 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRR   56 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHH
Confidence            5778999999999999999999999999999999999999999999999999986

>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=99.80  E-value=2.7e-20  Score=114.56  Aligned_cols=52  Identities=23%  Similarity=0.178  Sum_probs=49.8

Q ss_pred             cCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        135 SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       135 ~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .|+.||.+|+.+|+..|..++||+..++++||..+||++.+|++||||||+|
T Consensus         6 ~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k   57 (76)
T 2ecc_A            6 SGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYA   57 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHH
Confidence            4677999999999999999999999999999999999999999999999975

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

Probab=99.80  E-value=3.3e-20  Score=109.97  Aligned_cols=55  Identities=35%  Similarity=0.553  Sum_probs=52.6

Q ss_pred             ccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       132 ~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .++.|+.||.+|+..||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         2 ~rr~Rt~~t~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   56 (58)
T 3rkq_A            2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYK   56 (58)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             cCCCCCCcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhhcc
Confidence            3578999999999999999999999999999999999999999999999999986

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

Probab=99.80  E-value=3.7e-20  Score=116.76  Aligned_cols=57  Identities=46%  Similarity=0.823  Sum_probs=54.3

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ...++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k   61 (80)
T 2cue_A            5 SSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAK   61 (80)
T ss_dssp             CSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHH
Confidence            456788999999999999999999999999999999999999999999999999986

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

Probab=99.79  E-value=4.1e-20  Score=114.48  Aligned_cols=57  Identities=25%  Similarity=0.471  Sum_probs=54.1

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+.++.|+.||.+|+..||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k   61 (73)
T 2l7z_A            5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVK   61 (73)
T ss_dssp             SCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHH
Confidence            456788999999999999999999999999999999999999999999999999976

>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=99.79  E-value=5.1e-20  Score=113.19  Aligned_cols=56  Identities=30%  Similarity=0.452  Sum_probs=53.3

Q ss_pred             cccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       131 ~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ..++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         6 ~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   61 (70)
T 2e1o_A            6 SGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAK   61 (70)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhh
Confidence            45678899999999999999999999999999999999999999999999999986

>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=99.79  E-value=2.5e-20  Score=113.82  Aligned_cols=55  Identities=35%  Similarity=0.492  Sum_probs=52.7

Q ss_pred             ccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       132 ~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .++.|+.||.+|+..||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k   56 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMK   56 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhH
Confidence            3678999999999999999999999999999999999999999999999999986

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

Probab=99.79  E-value=7.2e-20  Score=118.47  Aligned_cols=58  Identities=33%  Similarity=0.558  Sum_probs=55.0

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ..+.++.|+.||.+|+..||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k   71 (93)
T 3a01_A           14 PPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTK   71 (93)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhh
Confidence            4567788999999999999999999999999999999999999999999999999986

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

Probab=99.79  E-value=5.1e-20  Score=112.49  Aligned_cols=55  Identities=33%  Similarity=0.508  Sum_probs=52.8

Q ss_pred             ccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       132 ~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .++.|+.||.+|+..||..|..++||+..++..||..+||++.+|++||+|||+|
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k   56 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYK   56 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhh
Confidence            4678999999999999999999999999999999999999999999999999976

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

Probab=99.79  E-value=5.7e-20  Score=115.96  Aligned_cols=57  Identities=30%  Similarity=0.428  Sum_probs=54.3

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+.++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   61 (80)
T 2dmq_A            5 SSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAK   61 (80)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHH
Confidence            456788999999999999999999999999999999999999999999999999986

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

Probab=99.79  E-value=2.3e-20  Score=117.72  Aligned_cols=58  Identities=17%  Similarity=0.166  Sum_probs=54.9

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhhc----CCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFERT----QYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~~----~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ..+.++.|+.||.+|+.+||..|..+    +||+..++++||..+||++.+|+|||||||+|
T Consensus         5 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k   66 (80)
T 2da4_A            5 SSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRK   66 (80)
T ss_dssp             CCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHH
Confidence            35678899999999999999999999    99999999999999999999999999999986

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

Probab=99.79  E-value=8.2e-20  Score=113.90  Aligned_cols=58  Identities=57%  Similarity=0.928  Sum_probs=55.0

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .++.++.|+.||.+|+..||..|..++||+..++..||..+||++.+|++||+|||+|
T Consensus         6 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   63 (75)
T 2m0c_A            6 KGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAK   63 (75)
T ss_dssp             CSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHH
Confidence            4567888999999999999999999999999999999999999999999999999986

>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=99.78  E-value=2.3e-20  Score=114.05  Aligned_cols=56  Identities=52%  Similarity=0.812  Sum_probs=53.6

Q ss_pred             cccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       131 ~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +.++.|+.||.+|+..||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   57 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAK   57 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHH
Confidence            46788999999999999999999999999999999999999999999999999986

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

Probab=99.78  E-value=1e-19  Score=114.90  Aligned_cols=57  Identities=35%  Similarity=0.484  Sum_probs=50.2

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+.++.|+.||.+|+.+||..|..++||+..++.+||..+||++.+|++||||||+|
T Consensus        18 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k   74 (81)
T 1b8i_A           18 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMK   74 (81)
T ss_dssp             ------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhh
Confidence            456788999999999999999999999999999999999999999999999999986

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

Probab=99.78  E-value=7.7e-20  Score=109.02  Aligned_cols=52  Identities=58%  Similarity=0.875  Sum_probs=48.1

Q ss_pred             cCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        135 SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       135 ~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .|+.||.+|+..||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   53 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAK   53 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhh
Confidence            4789999999999999999999999999999999999999999999999986

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

Probab=99.78  E-value=1e-19  Score=110.92  Aligned_cols=54  Identities=41%  Similarity=0.605  Sum_probs=52.2

Q ss_pred             cccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   55 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAK   55 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHH
Confidence            578999999999999999999999999999999999999999999999999976

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

Probab=99.78  E-value=1e-19  Score=116.77  Aligned_cols=58  Identities=33%  Similarity=0.471  Sum_probs=51.1

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ..+.++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus        25 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k   82 (88)
T 2r5y_A           25 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMK   82 (88)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHH
Confidence            3456788999999999999999999999999999999999999999999999999986

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

Probab=99.78  E-value=9.8e-20  Score=106.97  Aligned_cols=50  Identities=38%  Similarity=0.555  Sum_probs=47.2

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        137 TTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       137 ~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      |.||.+|+..||..|..++||+..++.+||..+||++.+|++||||||+|
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k   51 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTK   51 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhh
Confidence            67999999999999999999999999999999999999999999999986

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

Probab=99.77  E-value=1.8e-19  Score=112.43  Aligned_cols=55  Identities=25%  Similarity=0.349  Sum_probs=51.8

Q ss_pred             ccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       132 ~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +...|+.||.+|+.+||..|..++||+..++.+||..+||++.+|++||||||+|
T Consensus         8 ~~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k   62 (76)
T 2dn0_A            8 ASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYH   62 (76)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHH
Confidence            3446899999999999999999999999999999999999999999999999976

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

Probab=99.77  E-value=2e-19  Score=111.36  Aligned_cols=54  Identities=26%  Similarity=0.278  Sum_probs=51.3

Q ss_pred             cccCCCCCHHHHHHHHHHhhh-cCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        133 RRSRTTFSAQQLDELERAFER-TQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f~~-~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+.|+.||.+|+.+||..|.. ++||+..++..||..+||++.+|++||||||+|
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k   57 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAE   57 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            467899999999999999995 999999999999999999999999999999976

>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=99.77  E-value=5.1e-19  Score=110.02  Aligned_cols=53  Identities=25%  Similarity=0.325  Sum_probs=50.4

Q ss_pred             ccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        134 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       134 r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         9 ~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k   61 (75)
T 2da5_A            9 TKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKK   61 (75)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTH
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHH
Confidence            45677999999999999999999999999999999999999999999999986

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

Probab=99.77  E-value=2.1e-19  Score=110.99  Aligned_cols=54  Identities=28%  Similarity=0.325  Sum_probs=51.2

Q ss_pred             cccCCCCCHHHHHHHHHHhhh-cCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        133 RRSRTTFSAQQLDELERAFER-TQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f~~-~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+.|+.||.+|+.+||..|.. ++||+..++..||..+||++.+|++||||||+|
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k   56 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAE   56 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHH
Confidence            357899999999999999996 999999999999999999999999999999986

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

Probab=99.76  E-value=3.7e-19  Score=110.57  Aligned_cols=55  Identities=24%  Similarity=0.276  Sum_probs=52.6

Q ss_pred             ccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       132 ~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .++.|+.||.+|+..||..|..++||+..++++||..+||++.+|++||||||+|
T Consensus         6 ~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   60 (74)
T 2ly9_A            6 SFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYN   60 (74)
T ss_dssp             CCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHH
Confidence            4678899999999999999999999999999999999999999999999999976

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

Probab=99.76  E-value=5.4e-19  Score=106.71  Aligned_cols=55  Identities=22%  Similarity=0.350  Sum_probs=52.7

Q ss_pred             ccccCCCCCHHHHHHHHHHh---hhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        132 QRRSRTTFSAQQLDELERAF---ERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       132 ~~r~r~~~t~~q~~~Le~~f---~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .++.|+.|+.+|+.+|+..|   ..++||+..++..||..+||++.+|++||+|||+|
T Consensus         3 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r   60 (64)
T 1du6_A            3 GHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR   60 (64)
T ss_dssp             CCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTT
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            46788999999999999999   99999999999999999999999999999999987

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

Probab=99.76  E-value=3.5e-19  Score=116.02  Aligned_cols=58  Identities=26%  Similarity=0.302  Sum_probs=51.7

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ....++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus        22 ~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k   79 (96)
T 3nar_A           22 KSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYA   79 (96)
T ss_dssp             -----CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhH
Confidence            3456678999999999999999999999999999999999999999999999999985

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

Probab=99.75  E-value=3.4e-19  Score=126.79  Aligned_cols=124  Identities=16%  Similarity=0.180  Sum_probs=72.9

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCch-------hhHhHhhccCCCCCCCCCCCCCccccccc
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPH-------FLIIIEQQSSGEGSDCDSEPGIPLKRKQR  133 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~-------~v~~wfq~~~~~~~~~~~~~~~~~~~~~~  133 (187)
                      +.+|....||+.++.........+.|.-..- . ....+.++..       -+..|.....................+.+
T Consensus        23 k~~ri~lg~tQ~~vg~alg~l~g~~~Sqtti-~-rFE~l~ls~kn~~klkPlL~~wl~eae~~~~~~~~~~~~~~~~~~r  100 (164)
T 2xsd_C           23 KQRRIKLGFTQADVGLALGTLYGNVFSQTTI-C-RFEALQLSFKNMCKLKPLLNKWLEETDSSSGSPTNLDKIAAQGRKR  100 (164)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHSCCCCHHHH-H-HHHTTCSBHHHHHHHHHHHHHHHHHHCC------------------
T ss_pred             HHHHhhcCCcccccccccccccCCCcCcchh-h-hhhccCCCHHHHHHcchhHHHHHhhhccccCCCcccccccccccCC
Confidence            5566667788888775544444444431111 0 0112222211       15677766554433222222233456778


Q ss_pred             ccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        134 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       134 r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +.|+.||..|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus       101 r~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k  153 (164)
T 2xsd_C          101 KKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQK  153 (164)
T ss_dssp             -----CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHH
Confidence            89999999999999999999999999999999999999999999999999986

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

Probab=99.75  E-value=8.3e-20  Score=132.54  Aligned_cols=59  Identities=29%  Similarity=0.425  Sum_probs=51.9

Q ss_pred             ccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcC---------------------CChhhhhhhhcccCCC
Q psy15514        128 LKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTK---------------------LTEARIQTIFIVRKMR  186 (187)
Q Consensus       128 ~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~---------------------l~~~~v~~WF~nrR~k  186 (187)
                      ..++.+|.|+.|+..|+.+|+..|..++||+..+|++||..++                     |++.+|++||||||+|
T Consensus       111 ~~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~  190 (194)
T 1ic8_A          111 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE  190 (194)
T ss_dssp             ------CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHH
T ss_pred             ccccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhh
Confidence            3467788999999999999999999999999999999999999                     9999999999999986

>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=99.75  E-value=9.7e-19  Score=108.33  Aligned_cols=57  Identities=18%  Similarity=0.304  Sum_probs=53.6

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~---~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+.++.|+.|+.+|+.+|+..|..   ++||+..+++.||..+||++.+|++||+|||+|
T Consensus         5 ~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r   64 (73)
T 1x2n_A            5 SSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRR   64 (73)
T ss_dssp             SSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhh
Confidence            456778999999999999999987   999999999999999999999999999999976

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

Probab=99.74  E-value=8.6e-19  Score=114.06  Aligned_cols=59  Identities=29%  Similarity=0.410  Sum_probs=50.0

Q ss_pred             ccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHH------------------cC---CChhhhhhhhcccCCC
Q psy15514        128 LKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQR------------------TK---LTEARIQTIFIVRKMR  186 (187)
Q Consensus       128 ~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~------------------~~---l~~~~v~~WF~nrR~k  186 (187)
                      ..++.++.|+.|+.+|+.+||..|..++||+..++++||..                  +|   |++.+|++||||||+|
T Consensus         5 ~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k   84 (99)
T 1lfb_A            5 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE   84 (99)
T ss_dssp             --------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHH
Confidence            34677889999999999999999999999999999999999                  88   9999999999999986

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

Probab=99.74  E-value=6.6e-19  Score=104.62  Aligned_cols=48  Identities=25%  Similarity=0.365  Sum_probs=46.2

Q ss_pred             CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        139 FSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       139 ~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      -|.+|+.+||..|..++||+..++.+||..+||++.+|++||||||+|
T Consensus        11 ~~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k   58 (66)
T 3nau_A           11 KTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYR   58 (66)
T ss_dssp             CCHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhh
Confidence            478999999999999999999999999999999999999999999975

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

Probab=99.74  E-value=1e-18  Score=108.19  Aligned_cols=54  Identities=30%  Similarity=0.504  Sum_probs=51.9

Q ss_pred             cccCCCCCHHHHHHHHHHh---hhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        133 RRSRTTFSAQQLDELERAF---ERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f---~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ++.|+.||.+|+.+|+..|   ..++||+..++..||..+||++.+|++||+|||+|
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r   58 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR   58 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence            6788999999999999999   99999999999999999999999999999999975

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

Probab=99.74  E-value=1.3e-18  Score=104.56  Aligned_cols=50  Identities=12%  Similarity=0.079  Sum_probs=47.5

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        137 TTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       137 ~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ..++.+|+..||..|..++||+..++.+||..+||++.+|++||||||+|
T Consensus         8 ~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak   57 (64)
T 2e19_A            8 QPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAG   57 (64)
T ss_dssp             CCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCC
Confidence            34578999999999999999999999999999999999999999999987

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

Probab=99.74  E-value=9.3e-19  Score=113.83  Aligned_cols=57  Identities=32%  Similarity=0.461  Sum_probs=54.6

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcC---------------CChhhhhhhhcccCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTK---------------LTEARIQTIFIVRKMR  186 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~---------------l~~~~v~~WF~nrR~k  186 (187)
                      .+.++.|+.|+.+|+.+||..|+.++||+..+++.||..++               |++.+|++||||||+|
T Consensus         5 ~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k   76 (95)
T 2cuf_A            5 SSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKE   76 (95)
T ss_dssp             SCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHH
Confidence            56788999999999999999999999999999999999999               9999999999999986

>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=99.74  E-value=1.2e-18  Score=103.78  Aligned_cols=51  Identities=24%  Similarity=0.350  Sum_probs=49.4

Q ss_pred             CCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        136 RTTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       136 r~~~t~~q~~~Le~~f~~---~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ++.||.+|+.+||..|..   ++||+..++..||..+||++.+|++||+|||+|
T Consensus         2 r~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r   55 (60)
T 1k61_A            2 GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRK   55 (60)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             cCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHcc
Confidence            688999999999999999   999999999999999999999999999999976

>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=99.73  E-value=1.7e-18  Score=112.14  Aligned_cols=57  Identities=25%  Similarity=0.373  Sum_probs=54.2

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHc---------------------CCChhhhhhhhcccCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRT---------------------KLTEARIQTIFIVRKMR  186 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~---------------------~l~~~~v~~WF~nrR~k  186 (187)
                      ++.+|.|+.|++.|+.+||..|+.++||+..++++||..+                     +|++.+|++||||||+|
T Consensus         4 ~~~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k   81 (102)
T 2da6_A            4 GSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKE   81 (102)
T ss_dssp             CCSCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHH
Confidence            4678899999999999999999999999999999999999                     89999999999999975

>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=99.73  E-value=3.2e-18  Score=109.79  Aligned_cols=50  Identities=24%  Similarity=0.342  Sum_probs=48.0

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        137 TTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       137 ~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ..||.+|+.+||..|..++||+..+++.||..+||++.+|++||||||+|
T Consensus        18 k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k   67 (89)
T 2dmp_A           18 KEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKL   67 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHH
Confidence            45999999999999999999999999999999999999999999999976

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

Probab=99.73  E-value=2.9e-18  Score=109.15  Aligned_cols=49  Identities=27%  Similarity=0.259  Sum_probs=47.8

Q ss_pred             CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .||.+|+.+||..|..++||+..++.+||..+||++.+|+|||||||+|
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k   65 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKS   65 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchH
Confidence            7999999999999999999999999999999999999999999999975

>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=99.73  E-value=2.2e-18  Score=120.41  Aligned_cols=79  Identities=23%  Similarity=0.319  Sum_probs=58.3

Q ss_pred             hHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCC
Q psy15514        106 LIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKM  185 (187)
Q Consensus       106 v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~  185 (187)
                      +..|..............  .....+.++.|+.||..|+..||..|..++||+..++..||..+||++.+|++||||||+
T Consensus        63 L~~wl~e~e~~~~~~~~~--~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~  140 (146)
T 1au7_A           63 LSKWLEEAEQVGALYNEK--VGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQ  140 (146)
T ss_dssp             HHHHHHHCCC------------------CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhcccCccCcc--cCCCCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhh
Confidence            467777665443322221  223456778899999999999999999999999999999999999999999999999998


Q ss_pred             C
Q psy15514        186 R  186 (187)
Q Consensus       186 k  186 (187)
                      |
T Consensus       141 k  141 (146)
T 1au7_A          141 R  141 (146)
T ss_dssp             H
T ss_pred             h
Confidence            6

>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=99.73  E-value=3e-18  Score=109.64  Aligned_cols=58  Identities=22%  Similarity=0.318  Sum_probs=54.0

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~---~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ..+.++.|+.|+.+|+.+|+..|..   ++||+..++..||..+||++.+|++||+|||+|
T Consensus        24 ~~~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r   84 (87)
T 1mnm_C           24 KSTKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRK   84 (87)
T ss_dssp             EESSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence            3456667899999999999999999   999999999999999999999999999999976

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

Probab=99.72  E-value=9.3e-19  Score=107.73  Aligned_cols=54  Identities=24%  Similarity=0.346  Sum_probs=49.9

Q ss_pred             cccCCCCCHHHHHHHHHHh-hhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        133 RRSRTTFSAQQLDELERAF-ERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f-~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+.+..++.+|+.+||..| ..++||+..++.+||..+||++.+|++||||||+|
T Consensus         9 ~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k   63 (72)
T 2cqx_A            9 IKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQ   63 (72)
T ss_dssp             CCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccC
Confidence            3455678889999999999 99999999999999999999999999999999986

>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=99.72  E-value=2.4e-18  Score=122.14  Aligned_cols=58  Identities=21%  Similarity=0.317  Sum_probs=51.1

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ..+.++.|+.||..|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus        98 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k  155 (160)
T 1e3o_C           98 LSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQK  155 (160)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhh
Confidence            3567889999999999999999999999999999999999999999999999999986

>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=99.72  E-value=3e-18  Score=109.70  Aligned_cols=54  Identities=30%  Similarity=0.504  Sum_probs=51.3

Q ss_pred             cccCCCCCHHHHHHHHHHh---hhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        133 RRSRTTFSAQQLDELERAF---ERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f---~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ++.|+.|+.+|+.+|+..|   ..++||+..++..||..+||++.+|++||+|||+|
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r   58 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR   58 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            5788999999999999999   99999999999999999999999999999999976

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

Probab=99.72  E-value=3.5e-18  Score=103.90  Aligned_cols=50  Identities=34%  Similarity=0.495  Sum_probs=48.2

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        137 TTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       137 ~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ..+|..|+.+||..|..++||+..++.+||..+||++.+|++||||||+|
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak   58 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYK   58 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhh
Confidence            56899999999999999999999999999999999999999999999986

>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=99.71  E-value=6.2e-18  Score=107.08  Aligned_cols=57  Identities=19%  Similarity=0.352  Sum_probs=53.0

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~---~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+.++.|+.|+.+|+.+|+.+|..   ++||+..+++.||..+||++.||++||||||+|
T Consensus         5 ~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r   64 (83)
T 2dmn_A            5 SSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRR   64 (83)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhh
Confidence            356778899999999999999987   599999999999999999999999999999986

>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=99.71  E-value=5.7e-18  Score=107.32  Aligned_cols=53  Identities=23%  Similarity=0.351  Sum_probs=49.6

Q ss_pred             ccCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        134 RSRTTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       134 r~r~~~t~~q~~~Le~~f~~---~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +.|+.|+.+|+.+|+..|..   ++||+..++..||..+||++.+|++||||||+|
T Consensus         4 krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r   59 (83)
T 1le8_B            4 YRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAK   59 (83)
T ss_dssp             -CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHcc
Confidence            45567999999999999999   999999999999999999999999999999975

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

Probab=99.70  E-value=2.8e-18  Score=121.15  Aligned_cols=124  Identities=15%  Similarity=0.163  Sum_probs=79.5

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCch-------hhHhHhhccCCCCCCCCCCCCCccccccc
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPH-------FLIIIEQQSSGEGSDCDSEPGIPLKRKQR  133 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~-------~v~~wfq~~~~~~~~~~~~~~~~~~~~~~  133 (187)
                      +++|..-.||..++...-.......|. ..+... .+.+.|+..       .++.|.....................+.+
T Consensus        20 k~~ri~lg~tq~~vg~al~~l~G~~~S-qtti~r-fE~l~ls~~nm~kLkPlL~~Wl~eae~~~~~~~~~~~~~~~~~~r   97 (155)
T 3l1p_A           20 KQKRITLGYTQADVGLTLGVLFGKVFS-QTTISR-FEALQLSLKNMSKLRPLLEKWVEEADNNENLQEISKSETLVQARK   97 (155)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHSCCCC-HHHHHH-HHTTCSCHHHHHHHHHHHHHHHHHHTTCHHHHHSSCC---CCCSC
T ss_pred             HhhhheecccHHHHHHHHHhhcCcccc-cccccc-cccccCChhhHhhcchHHHHHhhhhhcccCccccccccccccCCC
Confidence            344555567877777543333222221 111111 133444332       24567765443221111111111124667


Q ss_pred             ccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        134 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       134 r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +.|+.|+..|+..||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus        98 r~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k  150 (155)
T 3l1p_A           98 RKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQK  150 (155)
T ss_dssp             CCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeecccccccc
Confidence            78999999999999999999999999999999999999999999999999986

>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=99.69  E-value=6.2e-18  Score=100.66  Aligned_cols=46  Identities=30%  Similarity=0.306  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHh-hhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        141 AQQLDELERAF-ERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       141 ~~q~~~Le~~f-~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +.|+.+||..| ..++||+..++.+||..+||++.||++||||||+|
T Consensus         9 ~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k   55 (64)
T 1x2m_A            9 AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQ   55 (64)
T ss_dssp             SCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence            45799999999 67999999999999999999999999999999976

>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=99.68  E-value=1.5e-17  Score=117.07  Aligned_cols=57  Identities=25%  Similarity=0.424  Sum_probs=54.5

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+.++.|+.|+.+|+..||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus        91 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k  147 (151)
T 3d1n_I           91 SKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQT  147 (151)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhc
Confidence            467788999999999999999999999999999999999999999999999999986

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

Probab=99.67  E-value=2.5e-17  Score=117.54  Aligned_cols=58  Identities=17%  Similarity=0.303  Sum_probs=51.3

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ..+.++.|+.||.+|+..|+..|..++||+..++..||..+||++.+|++||||||+|
T Consensus        94 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r  151 (164)
T 2d5v_A           94 GNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRR  151 (164)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhcc
Confidence            4567889999999999999999999999999999999999999999999999999987

>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=99.62  E-value=2.1e-16  Score=95.87  Aligned_cols=50  Identities=24%  Similarity=0.301  Sum_probs=45.9

Q ss_pred             CCCCHHHHHHHHHHhh---hcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        137 TTFSAQQLDELERAFE---RTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       137 ~~~t~~q~~~Le~~f~---~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ..|+.+|+.+|+..|.   .++||+..++..||..+||++.+|++||+|||+|
T Consensus         3 g~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r   55 (67)
T 3k2a_A            3 GIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRR   55 (67)
T ss_dssp             ---CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHH
Confidence            3689999999999999   9999999999999999999999999999999975

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

Probab=99.60  E-value=5.4e-16  Score=113.59  Aligned_cols=60  Identities=28%  Similarity=0.472  Sum_probs=53.1

Q ss_pred             cccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcC---------------------CChhhhhhhhcccCC
Q psy15514        127 PLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTK---------------------LTEARIQTIFIVRKM  185 (187)
Q Consensus       127 ~~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~---------------------l~~~~v~~WF~nrR~  185 (187)
                      +..++.+|.|+.|++.|+.+|+..|..++||+..+|++||..++                     |++.+|++||+|||+
T Consensus       137 ~~~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~  216 (221)
T 2h8r_A          137 PTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRK  216 (221)
T ss_dssp             -----CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHT
T ss_pred             cccCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhh
Confidence            34567889999999999999999999999999999999999987                     899999999999998


Q ss_pred             C
Q psy15514        186 R  186 (187)
Q Consensus       186 k  186 (187)
                      +
T Consensus       217 ~  217 (221)
T 2h8r_A          217 E  217 (221)
T ss_dssp             T
T ss_pred             h
Confidence            6

>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=99.59  E-value=7.5e-15  Score=91.88  Aligned_cols=58  Identities=26%  Similarity=0.316  Sum_probs=53.8

Q ss_pred             ccCCCCCCCCcCHHHHHHHHHHhhh-----cCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514         59 KRKQRRSRTTFSAQQLDELERAFER-----TQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG  117 (187)
Q Consensus        59 ~~~~~r~rt~ft~~ql~~Le~~F~~-----~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~  117 (187)
                      ..+.+|.||.||..|+..|+ .|..     ++||+..++++||..++|++.+|++||||++...
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~   76 (80)
T 1wh7_A           14 GGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSG   76 (80)
T ss_dssp             CCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCS
T ss_pred             CCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCC
Confidence            34678899999999999999 8999     9999999999999999999999999999998664

>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=99.58  E-value=7.6e-15  Score=92.00  Aligned_cols=58  Identities=24%  Similarity=0.263  Sum_probs=54.5

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhh----cCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFER----TQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG  117 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~----~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~  117 (187)
                      .+.+|.||.||..|+..|+..|+.    ++||+..++++||..++|++.+|++||||++...
T Consensus        15 ~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~   76 (80)
T 1wh5_A           15 GIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSG   76 (80)
T ss_dssp             CCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSS
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCC
Confidence            467889999999999999999999    9999999999999999999999999999998654

>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=99.57  E-value=2.2e-15  Score=94.98  Aligned_cols=66  Identities=74%  Similarity=1.020  Sum_probs=52.9

Q ss_pred             CCCCCCCCcccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         50 CDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        50 ~~~~~~~~~~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      |.+.++....++.++.||.||..|+..|+..|..++||+...+..||..+||++.+|++||+|++.
T Consensus         6 ~~~~~~~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~   71 (81)
T 1fjl_A            6 CESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRA   71 (81)
T ss_dssp             -----------CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCCCCCcccCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhh
Confidence            344455555678889999999999999999999999999999999999999999999999999763

>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=99.57  E-value=4.9e-15  Score=93.14  Aligned_cols=58  Identities=33%  Similarity=0.357  Sum_probs=54.2

Q ss_pred             ccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         59 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        59 ~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      .++.++.||.||..|+..||..|..++||+..++.+||..++|++.+|++||+|++..
T Consensus        14 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k   71 (80)
T 2dmt_A           14 AKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMK   71 (80)
T ss_dssp             CCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHH
Confidence            4567889999999999999999999999999999999999999999999999998744

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

Probab=99.57  E-value=8e-15  Score=93.05  Aligned_cols=61  Identities=25%  Similarity=0.283  Sum_probs=56.0

Q ss_pred             CcccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514         57 PLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG  117 (187)
Q Consensus        57 ~~~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~  117 (187)
                      ....+.++.||.||..|+..||..|..++||+...+..||..+||++.+|++||+|++...
T Consensus        17 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~   77 (84)
T 2kt0_A           17 KVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKS   77 (84)
T ss_dssp             CCCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence            3455778899999999999999999999999999999999999999999999999987553

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

Probab=99.56  E-value=3.6e-15  Score=88.21  Aligned_cols=56  Identities=27%  Similarity=0.257  Sum_probs=53.2

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhh-cCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFER-TQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~-~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      +..+|.||.|+.+|+..|+..|+. ++||+...++.||..+||+++.|++||||++.
T Consensus         5 ~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~   61 (71)
T 1wi3_A            5 SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRY   61 (71)
T ss_dssp             CCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhcccee
Confidence            467899999999999999999999 99999999999999999999999999999874

>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=99.56  E-value=7e-15  Score=90.05  Aligned_cols=59  Identities=24%  Similarity=0.309  Sum_probs=54.6

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGS  118 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~  118 (187)
                      .+.++.||.||..|+..||..|..++||+..++.+||..++|++.+|++||+|++....
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~k   63 (70)
T 2cra_A            5 SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK   63 (70)
T ss_dssp             CCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhc
Confidence            35678899999999999999999999999999999999999999999999999886543

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

Probab=99.55  E-value=7.7e-15  Score=89.88  Aligned_cols=59  Identities=32%  Similarity=0.373  Sum_probs=54.6

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGS  118 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~  118 (187)
                      .+.++.||.||..|+..||..|..++||+..++++||..++|++.+|++||+|++....
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~k   63 (70)
T 2djn_A            5 SSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIK   63 (70)
T ss_dssp             CCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhc
Confidence            36678899999999999999999999999999999999999999999999999886543

>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=2.5e-15  Score=89.60  Aligned_cols=45  Identities=13%  Similarity=0.186  Sum_probs=43.4

Q ss_pred             HHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCC
Q psy15514        141 AQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKM  185 (187)
Q Consensus       141 ~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~  185 (187)
                      .+|+..|+.+|..+++|+..++..||..+||+...|++||+|||+
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa   58 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKV   58 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhccc
Confidence            578999999999999999999999999999999999999999996

>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=99.54  E-value=1e-14  Score=91.75  Aligned_cols=58  Identities=19%  Similarity=0.259  Sum_probs=54.0

Q ss_pred             ccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         59 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        59 ~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      +.+.++.||.||..|+..|+..|..++||+..++++||..++|++.+|++||+|++..
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   71 (80)
T 2da3_A           14 PQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRAR   71 (80)
T ss_dssp             CCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHh
Confidence            4577889999999999999999999999999999999999999999999999998643

>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=99.53  E-value=1.5e-14  Score=90.26  Aligned_cols=57  Identities=33%  Similarity=0.398  Sum_probs=53.4

Q ss_pred             ccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         59 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        59 ~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      +.+.++.||.||..|+..||..|..++||+...+.+||..++|++.+|++||+|++.
T Consensus         6 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~   62 (77)
T 1nk2_P            6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRY   62 (77)
T ss_dssp             SCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhc
Confidence            456788899999999999999999999999999999999999999999999999864

>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=99.51  E-value=1.1e-14  Score=86.78  Aligned_cols=54  Identities=28%  Similarity=0.415  Sum_probs=48.3

Q ss_pred             CCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         62 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        62 ~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      .++.||.||..|+..||..|..++||+..++.+||..+||++.+|++||+|++.
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~   56 (61)
T 2hdd_A            3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRA   56 (61)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcc
Confidence            567899999999999999999999999999999999999999999999999763

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

Probab=99.51  E-value=1.2e-14  Score=87.09  Aligned_cols=55  Identities=31%  Similarity=0.318  Sum_probs=50.0

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      +.++.||.||..|+..||..|..++||+...+.+||..+||++.+|++||+|++.
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~   56 (63)
T 2h1k_A            2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRM   56 (63)
T ss_dssp             ---CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhh
Confidence            4567899999999999999999999999999999999999999999999999763

>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=99.51  E-value=1.9e-14  Score=88.10  Aligned_cols=57  Identities=26%  Similarity=0.348  Sum_probs=53.3

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      .+.++.||.||..|+..||..|..++||+..++..||..++|++.+|++||+|++..
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k   61 (70)
T 2da2_A            5 SSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQK   61 (70)
T ss_dssp             CCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHH
Confidence            367788999999999999999999999999999999999999999999999998743

>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=99.51  E-value=1.8e-14  Score=88.24  Aligned_cols=57  Identities=19%  Similarity=0.218  Sum_probs=53.2

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      .+.++.||.||..|+..|+..|..++||+..++..||..++|++.+|++||+|++..
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k   61 (70)
T 2da1_A            5 SSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFK   61 (70)
T ss_dssp             CCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHH
Confidence            367788999999999999999999999999999999999999999999999998643

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

Probab=99.51  E-value=2.1e-14  Score=87.97  Aligned_cols=55  Identities=36%  Similarity=0.565  Sum_probs=52.2

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      +.++.||.||..|+..||..|..++||+..++.+||..++|++.+|++||+|++.
T Consensus         6 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~   60 (70)
T 2dmu_A            6 SGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRA   60 (70)
T ss_dssp             SSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccc
Confidence            5678899999999999999999999999999999999999999999999999864

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

Probab=99.51  E-value=1.2e-14  Score=86.91  Aligned_cols=56  Identities=23%  Similarity=0.268  Sum_probs=48.2

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      +.++.||.||..|+..||..|..++||+..++.+||..+||++.+|++||+|++..
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k   57 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMK   57 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcc
Confidence            45778999999999999999999999999999999999999999999999998754

>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=99.50  E-value=2.2e-14  Score=86.82  Aligned_cols=56  Identities=27%  Similarity=0.401  Sum_probs=52.5

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      +.++.||.||..|+..|+..|..++||+..++..||..+||++.+|++||+|++..
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   57 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCK   57 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHH
Confidence            45788999999999999999999999999999999999999999999999998754

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

Probab=99.50  E-value=2.3e-14  Score=84.46  Aligned_cols=52  Identities=35%  Similarity=0.434  Sum_probs=49.7

Q ss_pred             CCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccC
Q psy15514         63 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSS  114 (187)
Q Consensus        63 ~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~  114 (187)
                      ++.||.||..|+..|+..|..++||+..++.+||..+||++.+|++||+|++
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR   52 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRR   52 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhh
Confidence            4678999999999999999999999999999999999999999999999976

>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=99.49  E-value=4.5e-14  Score=88.03  Aligned_cols=57  Identities=26%  Similarity=0.241  Sum_probs=53.2

Q ss_pred             ccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         59 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        59 ~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      .++.++.||.||..|+..||..|..++||+..++.+||..+||++.+|++||+|++.
T Consensus        10 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~   66 (77)
T 1puf_A           10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRM   66 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            346778899999999999999999999999999999999999999999999999763

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

Probab=99.49  E-value=3.8e-14  Score=89.03  Aligned_cols=55  Identities=35%  Similarity=0.629  Sum_probs=52.2

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      +.++.||.||..|+..||..|..++||+..++.+||..++|++.+|++||+|++.
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~   60 (80)
T 2cue_A            6 SGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRA   60 (80)
T ss_dssp             SSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHH
Confidence            5678899999999999999999999999999999999999999999999998763

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

Probab=99.49  E-value=3e-14  Score=86.68  Aligned_cols=54  Identities=28%  Similarity=0.344  Sum_probs=51.2

Q ss_pred             CCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         62 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        62 ~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      +++.||.||..|+..|+..|..++||+...+..||..+||++.+|++||+|++.
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~   55 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRR   55 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHH
Confidence            467899999999999999999999999999999999999999999999999763

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

Probab=99.49  E-value=3.9e-14  Score=88.98  Aligned_cols=57  Identities=39%  Similarity=0.574  Sum_probs=53.4

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      ++.++.||.||..|+..||..|..++||+..++.+||..++|++.+|++||+|++..
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k   61 (80)
T 2dms_A            5 SSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAK   61 (80)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHH
Confidence            467888999999999999999999999999999999999999999999999998753

>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=99.48  E-value=2.5e-14  Score=87.09  Aligned_cols=55  Identities=42%  Similarity=0.611  Sum_probs=52.1

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      +.++.||.||..|+..|+..|..++||+..++.+||..+||++.+|++||+|++.
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~   56 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRA   56 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhH
Confidence            5678899999999999999999999999999999999999999999999999763

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

Probab=99.48  E-value=5.7e-14  Score=90.65  Aligned_cols=58  Identities=26%  Similarity=0.348  Sum_probs=53.8

Q ss_pred             ccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         59 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        59 ~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      +++.++.||.||..|+..||..|..++||+...+.+||..+||++.+|++||+|++..
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k   71 (93)
T 3a01_A           14 PPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTK   71 (93)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhh
Confidence            4467788999999999999999999999999999999999999999999999998743

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

Probab=99.48  E-value=4.8e-14  Score=86.95  Aligned_cols=57  Identities=23%  Similarity=0.318  Sum_probs=53.3

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      .+.++.|+.||..|+..||..|..++||+..++.+||..+||++.+|++||+|++..
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k   61 (73)
T 2l7z_A            5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVK   61 (73)
T ss_dssp             SCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHH
Confidence            456788999999999999999999999999999999999999999999999998743

>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=99.48  E-value=2.2e-14  Score=85.45  Aligned_cols=55  Identities=22%  Similarity=0.270  Sum_probs=45.1

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSS  114 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~  114 (187)
                      .+.++.|+.||..|+..|+..|..++||+..++..||..+||++.+|++||+|++
T Consensus         3 ~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR   57 (61)
T 1akh_A            3 EKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKR   57 (61)
T ss_dssp             ---------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4567889999999999999999999999999999999999999999999999975

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

Probab=99.48  E-value=3.2e-14  Score=84.43  Aligned_cols=53  Identities=32%  Similarity=0.362  Sum_probs=49.8

Q ss_pred             CCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         63 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        63 ~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      ++.||.||..|+..|+..|..++||+..++.+||..+||++.+|++||+|++.
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~   54 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRM   54 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHh
Confidence            57789999999999999999999999999999999999999999999999763

>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=99.48  E-value=3.6e-14  Score=86.32  Aligned_cols=54  Identities=28%  Similarity=0.294  Sum_probs=51.0

Q ss_pred             CCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         62 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        62 ~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      .++.||.||..|+..||..|..++||+...+.+||..+||++.+|++||+|++.
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~   55 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRM   55 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHh
Confidence            357889999999999999999999999999999999999999999999999864

>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=99.47  E-value=6.5e-14  Score=85.70  Aligned_cols=55  Identities=25%  Similarity=0.267  Sum_probs=51.6

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      +.++.|+.||..|+..||..|..++||+..++.+||..++|++.+|++||+|++.
T Consensus         6 ~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~   60 (70)
T 2e1o_A            6 SGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRA   60 (70)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHh
Confidence            4567889999999999999999999999999999999999999999999999864

>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=99.47  E-value=6.5e-14  Score=87.99  Aligned_cols=56  Identities=29%  Similarity=0.379  Sum_probs=52.5

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      .+.++.||.||..|+..|+..|..++||+..++..||..++|++.+|++||+|++.
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~   60 (80)
T 2dmq_A            5 SSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARA   60 (80)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHH
Confidence            35678899999999999999999999999999999999999999999999998763

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

Probab=99.47  E-value=3e-14  Score=89.51  Aligned_cols=56  Identities=14%  Similarity=0.075  Sum_probs=53.0

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhhc----CCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFERT----QYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~~----~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      ++.++.||.||..|+..|+..|..+    +||+..++++||..++|++.+|++||+|++.
T Consensus         6 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~   65 (80)
T 2da4_A            6 SGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRR   65 (80)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHH
Confidence            4678899999999999999999999    9999999999999999999999999999874

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

Probab=99.46  E-value=8.8e-14  Score=86.32  Aligned_cols=58  Identities=47%  Similarity=0.732  Sum_probs=53.8

Q ss_pred             ccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         59 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        59 ~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      .++.++.||.||..|+..|+..|..++||+..++.+||..+||++.+|++||+|++..
T Consensus         6 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   63 (75)
T 2m0c_A            6 KGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAK   63 (75)
T ss_dssp             CSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHH
Confidence            3467788999999999999999999999999999999999999999999999998743

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

Probab=99.46  E-value=6.4e-14  Score=85.21  Aligned_cols=54  Identities=35%  Similarity=0.422  Sum_probs=51.0

Q ss_pred             CCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         62 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        62 ~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      .++.||.||..|+..||..|..++||+...+.+||..+||++.+|++||+|++.
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~   55 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRY   55 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhh
Confidence            467889999999999999999999999999999999999999999999999764

>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=99.46  E-value=7e-14  Score=85.89  Aligned_cols=52  Identities=21%  Similarity=0.074  Sum_probs=48.6

Q ss_pred             CCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         64 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        64 r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      ..++.||.+|+..|+..|..++||+..++++||..+||++.+|++||+|++.
T Consensus         5 ~~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~   56 (76)
T 2ecc_A            5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRY   56 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHH
Confidence            3457799999999999999999999999999999999999999999999874

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

Probab=99.46  E-value=7.1e-14  Score=82.38  Aligned_cols=53  Identities=34%  Similarity=0.426  Sum_probs=50.3

Q ss_pred             CCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccC
Q psy15514         62 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSS  114 (187)
Q Consensus        62 ~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~  114 (187)
                      .++.|+.|+..|+..|+..|..++||+..++.+||..+||++.+|++||+|++
T Consensus         2 ~rr~Rt~~t~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR   54 (58)
T 3rkq_A            2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRR   54 (58)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             cCCCCCCcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhh
Confidence            45778999999999999999999999999999999999999999999999975

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

Probab=99.45  E-value=3.1e-14  Score=89.89  Aligned_cols=50  Identities=20%  Similarity=0.309  Sum_probs=47.2

Q ss_pred             CCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        137 TTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       137 ~~~t~~q~~~Le~~f~~---~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ..|+.+++.+|+.+|..   ++||+..++.+||..+||++.||++||+|+|+|
T Consensus        10 ~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R   62 (89)
T 2lk2_A           10 HMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRR   62 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            46899999999999987   999999999999999999999999999999975

>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=99.44  E-value=1.1e-13  Score=87.10  Aligned_cols=56  Identities=29%  Similarity=0.293  Sum_probs=48.6

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      +..++.||.||..|+..||..|..++||+...+.+||..+||++.+|++||+|++.
T Consensus        18 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~   73 (81)
T 1b8i_A           18 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRM   73 (81)
T ss_dssp             ------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhh
Confidence            35678899999999999999999999999999999999999999999999999864

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

Probab=99.44  E-value=1.6e-13  Score=85.34  Aligned_cols=56  Identities=21%  Similarity=0.144  Sum_probs=51.4

Q ss_pred             CCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514         62 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG  117 (187)
Q Consensus        62 ~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~  117 (187)
                      +...|+.||..|+..||..|..++||+..++.+||..++|++.+|++||+|++...
T Consensus         8 ~~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~   63 (76)
T 2dn0_A            8 ASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHC   63 (76)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHS
T ss_pred             CCCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHH
Confidence            34458999999999999999999999999999999999999999999999987544

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

Probab=99.44  E-value=1.1e-13  Score=84.00  Aligned_cols=54  Identities=35%  Similarity=0.463  Sum_probs=51.0

Q ss_pred             CCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         63 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        63 ~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      ++.||.||..|+..|+..|..++||+..++..||..+||++.+|++||+|++..
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   55 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAK   55 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHH
Confidence            578899999999999999999999999999999999999999999999998643

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

Probab=99.44  E-value=7.9e-14  Score=89.14  Aligned_cols=56  Identities=27%  Similarity=0.284  Sum_probs=49.4

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      ++.++.||.||..|+..||..|..++||+..++.+||..++|++.+|++||+|++.
T Consensus        26 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~   81 (88)
T 2r5y_A           26 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRM   81 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHH
Confidence            45778899999999999999999999999999999999999999999999999864

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

Probab=99.42  E-value=1.2e-13  Score=81.87  Aligned_cols=51  Identities=45%  Similarity=0.662  Sum_probs=46.6

Q ss_pred             CCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         65 SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        65 ~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      .||.||..|+..|+..|..++||+...+.+||..+||++.+|++||+|++.
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~   52 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRA   52 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhh
Confidence            478999999999999999999999999999999999999999999999864

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

Probab=99.42  E-value=1.5e-13  Score=89.18  Aligned_cols=58  Identities=22%  Similarity=0.204  Sum_probs=50.6

Q ss_pred             ccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         59 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        59 ~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      ....++.|+.||..|+..|+..|..++||+..++++||..++|++.+|++||+|++..
T Consensus        22 ~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k   79 (96)
T 3nar_A           22 KSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYA   79 (96)
T ss_dssp             -----CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhH
Confidence            3456678999999999999999999999999999999999999999999999998743

>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=99.41  E-value=1.6e-13  Score=89.33  Aligned_cols=56  Identities=29%  Similarity=0.287  Sum_probs=49.4

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      .+.++.||.||..|+..||..|..++||+...+.+||..++|++.+|++||+|++.
T Consensus        32 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~   87 (97)
T 1b72_A           32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRM   87 (97)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhH
Confidence            46778899999999999999999999999999999999999999999999999863

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

Probab=99.40  E-value=2.9e-14  Score=104.47  Aligned_cols=62  Identities=21%  Similarity=0.255  Sum_probs=52.5

Q ss_pred             CCcccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhc---------------------CCchhhHhHhhccC
Q psy15514         56 IPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTK---------------------LFPHFLIIIEQQSS  114 (187)
Q Consensus        56 ~~~~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~---------------------l~~~~v~~wfq~~~  114 (187)
                      .+..++.+|.|+.|+..|+..|+..|..++||+..+|++||..++                     +++.+|++||+|++
T Consensus       136 ~~~~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR  215 (221)
T 2h8r_A          136 EPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRR  215 (221)
T ss_dssp             ------CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHH
T ss_pred             ccccCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhh
Confidence            345668899999999999999999999999999999999999877                     78999999999988


Q ss_pred             CCC
Q psy15514        115 GEG  117 (187)
Q Consensus       115 ~~~  117 (187)
                      ...
T Consensus       216 ~~~  218 (221)
T 2h8r_A          216 KEE  218 (221)
T ss_dssp             TTC
T ss_pred             hhh
Confidence            653

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

Probab=99.40  E-value=2e-13  Score=79.75  Aligned_cols=49  Identities=31%  Similarity=0.310  Sum_probs=45.5

Q ss_pred             CCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         67 TTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        67 t~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      |.||..|+..||..|..++||+...+.+||..+||++.+|++||+|++.
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~   50 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRT   50 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhh
Confidence            7899999999999999999999999999999999999999999999763

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

Probab=99.40  E-value=3.5e-13  Score=83.33  Aligned_cols=58  Identities=17%  Similarity=0.091  Sum_probs=53.1

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGS  118 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~  118 (187)
                      ..++.|+.||..|+..|+..|..++||+..++++||..++|++.+|++||+|++....
T Consensus         5 ~~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~k   62 (74)
T 2ly9_A            5 DSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQR   62 (74)
T ss_dssp             CCCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHH
Confidence            3467789999999999999999999999999999999999999999999999875543

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

Probab=99.38  E-value=4.4e-13  Score=82.65  Aligned_cols=53  Identities=19%  Similarity=0.112  Sum_probs=49.3

Q ss_pred             CCCCCCcCHHHHHHHHHHhhh-cCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         63 RRSRTTFSAQQLDELERAFER-TQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        63 ~r~rt~ft~~ql~~Le~~F~~-~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      .+.||.||..|+..||..|.. ++||+...+.+||..+||++.+|++||+|++.
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~   56 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLA   56 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            356799999999999999995 99999999999999999999999999999864

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

Probab=99.38  E-value=2.9e-13  Score=87.92  Aligned_cols=60  Identities=22%  Similarity=0.210  Sum_probs=49.6

Q ss_pred             cccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHh------------------hc---CCchhhHhHhhccCCC
Q psy15514         58 LKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQR------------------TK---LFPHFLIIIEQQSSGE  116 (187)
Q Consensus        58 ~~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~------------------~~---l~~~~v~~wfq~~~~~  116 (187)
                      ..++.++.|+.|+..|+..||..|..++||+...+++||..                  +|   |++.+|++||+|++..
T Consensus         5 ~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k   84 (99)
T 1lfb_A            5 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE   84 (99)
T ss_dssp             --------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHH
Confidence            35578899999999999999999999999999999999999                  88   9999999999999864


Q ss_pred             C
Q psy15514        117 G  117 (187)
Q Consensus       117 ~  117 (187)
                      .
T Consensus        85 ~   85 (99)
T 1lfb_A           85 E   85 (99)
T ss_dssp             T
T ss_pred             H
Confidence            3

>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=99.38  E-value=7.8e-13  Score=81.89  Aligned_cols=53  Identities=17%  Similarity=0.101  Sum_probs=49.2

Q ss_pred             CCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514         65 SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG  117 (187)
Q Consensus        65 ~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~  117 (187)
                      .|+.||..|+..||..|..++||+..++.+||..++|++.+|++||+|++...
T Consensus        10 kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~   62 (75)
T 2da5_A           10 KYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKV   62 (75)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHH
T ss_pred             CCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHH
Confidence            45679999999999999999999999999999999999999999999988543

>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=99.38  E-value=7.3e-13  Score=81.66  Aligned_cols=56  Identities=11%  Similarity=0.094  Sum_probs=51.8

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhh---cCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~---~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      ++.++.|+.|+..|+..|+..|..   ++||+..+++.||..+||++.+|++||+|++.
T Consensus         5 ~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~   63 (73)
T 1x2n_A            5 SSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARR   63 (73)
T ss_dssp             SSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHh
Confidence            356788999999999999999987   99999999999999999999999999999763

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

Probab=99.37  E-value=5.4e-13  Score=80.12  Aligned_cols=56  Identities=16%  Similarity=0.119  Sum_probs=52.1

Q ss_pred             CCCCCCCCcCHHHHHHHHHHh---hhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAF---ERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F---~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      +.++.|+.|+..|+..|+..|   ..++||+..++..||..+||++.+|++||+|++..
T Consensus         2 ~~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r   60 (64)
T 1du6_A            2 SGHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR   60 (64)
T ss_dssp             CCCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTT
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            356788999999999999999   89999999999999999999999999999998754

>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=99.37  E-value=4.9e-13  Score=82.20  Aligned_cols=52  Identities=21%  Similarity=0.165  Sum_probs=48.9

Q ss_pred             CCCCCcCHHHHHHHHHHhhh-cCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         64 RSRTTFSAQQLDELERAFER-TQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        64 r~rt~ft~~ql~~Le~~F~~-~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      +.|+.||..|+..||..|.. ++||+...+..||..+||++.+|++||+|++.
T Consensus         3 k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~   55 (72)
T 1uhs_A            3 EGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLA   55 (72)
T ss_dssp             CCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHH
Confidence            46799999999999999996 99999999999999999999999999999864

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

Probab=99.37  E-value=5.7e-13  Score=86.32  Aligned_cols=56  Identities=27%  Similarity=0.291  Sum_probs=52.9

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhc---------------CCchhhHhHhhccCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTK---------------LFPHFLIIIEQQSSG  115 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~---------------l~~~~v~~wfq~~~~  115 (187)
                      .+.++.|+.|+..|+..||..|..++||+...+++||..++               |++.+|++||+|++.
T Consensus         5 ~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~   75 (95)
T 2cuf_A            5 SSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRK   75 (95)
T ss_dssp             SCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHH
Confidence            46788999999999999999999999999999999999999               999999999998764

>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=99.35  E-value=1.1e-12  Score=84.89  Aligned_cols=56  Identities=16%  Similarity=0.156  Sum_probs=52.3

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhh---------------------cCCchhhHhHhhccCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRT---------------------KLFPHFLIIIEQQSSG  115 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~---------------------~l~~~~v~~wfq~~~~  115 (187)
                      ++.++.||.|+..|+..|+..|+.++||+..++++||..+                     .+++.+|++||+|++.
T Consensus         4 ~~~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~   80 (102)
T 2da6_A            4 GSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRK   80 (102)
T ss_dssp             CCSCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHH
Confidence            4678899999999999999999999999999999999999                     6899999999999873

>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding cooperativity, maltose binding protein, MBP, sugar binding, DNA binding protein; 2.10A {Escherichia coli} SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A

Probab=99.34  E-value=4.1e-13  Score=108.61  Aligned_cols=56  Identities=29%  Similarity=0.415  Sum_probs=52.6

Q ss_pred             ccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCCC
Q psy15514        132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG  187 (187)
Q Consensus       132 ~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~  187 (187)
                      .++.++.|+..|+..|++.|+.++||+..+|++||..+||++.||++||||||+|.
T Consensus       365 ~~~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~  420 (421)
T 1mh3_A          365 QTAAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS  420 (421)
T ss_dssp             HHHHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCC
T ss_pred             hhhhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhccccc
Confidence            45567889999999999999999999999999999999999999999999999983

>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=99.34  E-value=1.2e-12  Score=80.69  Aligned_cols=53  Identities=25%  Similarity=0.273  Sum_probs=50.2

Q ss_pred             CCCCCCcCHHHHHHHHHHh---hhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         63 RRSRTTFSAQQLDELERAF---ERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        63 ~r~rt~ft~~ql~~Le~~F---~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      ++.|+.|+..|+..|+..|   ..++||+..++..||..+||++.+|++||+|++.
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~   57 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRI   57 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHh
Confidence            5778999999999999999   8999999999999999999999999999999864

>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=99.33  E-value=8.1e-13  Score=93.59  Aligned_cols=57  Identities=16%  Similarity=0.197  Sum_probs=49.6

Q ss_pred             ccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         59 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        59 ~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      ..+.++.||.||..|+..||..|..++||+...+..||..++|++.+|++||+|++.
T Consensus        98 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~  154 (160)
T 1e3o_C           98 LSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQ  154 (160)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhh
Confidence            457788999999999999999999999999999999999999999999999999864

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

Probab=99.30  E-value=7.4e-13  Score=81.21  Aligned_cols=55  Identities=16%  Similarity=0.194  Sum_probs=49.4

Q ss_pred             CCCCCCcCHHHHHHHHHHh-hhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514         63 RRSRTTFSAQQLDELERAF-ERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG  117 (187)
Q Consensus        63 ~r~rt~ft~~ql~~Le~~F-~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~  117 (187)
                      .+.+..++..|+..||..| ..++||+...+.+||..++|++.+|++||+|++...
T Consensus         9 ~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~   64 (72)
T 2cqx_A            9 IKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQD   64 (72)
T ss_dssp             CCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCC
Confidence            3455678889999999999 999999999999999999999999999999987544

>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=99.30  E-value=2.3e-12  Score=76.34  Aligned_cols=49  Identities=20%  Similarity=0.194  Sum_probs=47.1

Q ss_pred             CCCcCHHHHHHHHHHhhh---cCCCChhhhHHHHHhhcCCchhhHhHhhccC
Q psy15514         66 RTTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLFPHFLIIIEQQSS  114 (187)
Q Consensus        66 rt~ft~~ql~~Le~~F~~---~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~  114 (187)
                      ++.|+..|+..|+..|..   ++||+..++..||..+||++.+|++||+|++
T Consensus         2 r~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR   53 (60)
T 1k61_A            2 GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR   53 (60)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_pred             cCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence            578999999999999999   9999999999999999999999999999976

>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=99.30  E-value=2.2e-12  Score=89.96  Aligned_cols=58  Identities=22%  Similarity=0.256  Sum_probs=50.8

Q ss_pred             ccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         59 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        59 ~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      .++.++.||.||..|+..||..|..++||+...+..||..++|++.+|++||+|++..
T Consensus        84 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k  141 (146)
T 1au7_A           84 NERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQR  141 (146)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhh
Confidence            4567788999999999999999999999999999999999999999999999998743

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

Probab=99.30  E-value=4.2e-12  Score=80.63  Aligned_cols=47  Identities=19%  Similarity=0.077  Sum_probs=45.9

Q ss_pred             CcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccC
Q psy15514         68 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSS  114 (187)
Q Consensus        68 ~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~  114 (187)
                      .||..|+.+||..|..++||+..++.+||..+||++.+|++||+|++
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR   63 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKK   63 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccc
Confidence            79999999999999999999999999999999999999999999986

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

Probab=99.30  E-value=1.6e-12  Score=92.27  Aligned_cols=59  Identities=17%  Similarity=0.178  Sum_probs=46.3

Q ss_pred             cccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         58 LKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        58 ~~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      ...+.++.||.||..|+..||..|..++||+...+.+||..++|++.+|++||+|++..
T Consensus        95 ~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k  153 (164)
T 2xsd_C           95 AQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQK  153 (164)
T ss_dssp             -----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             ccccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHH
Confidence            34577889999999999999999999999999999999999999999999999998744

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

Probab=99.29  E-value=1.9e-12  Score=76.78  Aligned_cols=45  Identities=20%  Similarity=0.192  Sum_probs=43.5

Q ss_pred             CHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccC
Q psy15514         70 SAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSS  114 (187)
Q Consensus        70 t~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~  114 (187)
                      |..|+.+|+..|..++||+..++++||..+||++.+|++||+|++
T Consensus        12 ~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR   56 (66)
T 3nau_A           12 TKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHR   56 (66)
T ss_dssp             CHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccch
Confidence            578999999999999999999999999999999999999999986

>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=99.29  E-value=3.4e-12  Score=81.33  Aligned_cols=55  Identities=18%  Similarity=0.164  Sum_probs=51.1

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhh---cCCCChhhhHHHHHhhcCCchhhHhHhhccC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLFPHFLIIIEQQSS  114 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~---~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~  114 (187)
                      .+.++.|+.|+..|+..|+..|..   ++||+..++..||..+||++.+|++||+|++
T Consensus        25 ~~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR   82 (87)
T 1mnm_C           25 STKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR   82 (87)
T ss_dssp             ESSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence            345666899999999999999999   9999999999999999999999999999976

>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=99.28  E-value=3e-12  Score=81.62  Aligned_cols=53  Identities=25%  Similarity=0.273  Sum_probs=49.5

Q ss_pred             CCCCCCcCHHHHHHHHHHh---hhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         63 RRSRTTFSAQQLDELERAF---ERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        63 ~r~rt~ft~~ql~~Le~~F---~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      ++.|+.|+..|+..|+..|   ..++||+..++..||..+||++.+|++||+|++.
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~   57 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRI   57 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            5778999999999999999   8999999999999999999999999999998764

>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=99.28  E-value=5.3e-12  Score=79.61  Aligned_cols=55  Identities=13%  Similarity=0.159  Sum_probs=50.8

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhh---cCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~---~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      +.++.|+.|+..|+..|+..|..   ++||+..+++.||..++|++.+|++||+|++.
T Consensus         6 ~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~   63 (83)
T 2dmn_A            6 SGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARR   63 (83)
T ss_dssp             CCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHh
Confidence            56678899999999999999987   59999999999999999999999999999763

>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=99.28  E-value=6.8e-12  Score=80.15  Aligned_cols=48  Identities=19%  Similarity=0.158  Sum_probs=45.9

Q ss_pred             CcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         68 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        68 ~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      .||..|+..||..|..++||+..++++||..++|++.+|++||+|++.
T Consensus        19 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~   66 (89)
T 2dmp_A           19 EKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRK   66 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHH
Confidence            499999999999999999999999999999999999999999999763

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

Probab=99.27  E-value=7e-12  Score=75.00  Aligned_cols=51  Identities=10%  Similarity=0.002  Sum_probs=47.2

Q ss_pred             CCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514         67 TTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG  117 (187)
Q Consensus        67 t~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~  117 (187)
                      ..++..|+..||..|..++||+..++.+||..++|++.+|++||+|++...
T Consensus         8 ~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~   58 (64)
T 2e19_A            8 QPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQ   58 (64)
T ss_dssp             CCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTC
T ss_pred             CCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCC
Confidence            456789999999999999999999999999999999999999999987654

>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=99.26  E-value=5.5e-12  Score=88.51  Aligned_cols=57  Identities=21%  Similarity=0.310  Sum_probs=53.3

Q ss_pred             ccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         59 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        59 ~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      +++.++.||.|+..|+..|+..|..++||+..++..||..++|++.+|++||+|++.
T Consensus        90 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~  146 (151)
T 3d1n_I           90 PSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQ  146 (151)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHh
Confidence            346778899999999999999999999999999999999999999999999999863

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

Probab=99.23  E-value=6.3e-12  Score=89.47  Aligned_cols=60  Identities=13%  Similarity=0.120  Sum_probs=51.3

Q ss_pred             ccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCC
Q psy15514         59 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGS  118 (187)
Q Consensus        59 ~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~  118 (187)
                      ..+.++.||.||..|+..|+..|..++||+...+..||..++|++.+|++||+|++....
T Consensus        94 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k  153 (164)
T 2d5v_A           94 GNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSL  153 (164)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSS
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhcccc
Confidence            346788999999999999999999999999999999999999999999999999876544

>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=99.23  E-value=8.5e-12  Score=78.72  Aligned_cols=51  Identities=20%  Similarity=0.180  Sum_probs=47.7

Q ss_pred             CCCCcCHHHHHHHHHHhhh---cCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         65 SRTTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        65 ~rt~ft~~ql~~Le~~F~~---~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      .++.|+..|+..|+..|..   ++||+..++..||..+||++.+|++||+|++.
T Consensus         5 rr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~   58 (83)
T 1le8_B            5 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRA   58 (83)
T ss_dssp             CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHc
Confidence            3466999999999999999   99999999999999999999999999999873

>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=99.22  E-value=5.8e-12  Score=74.80  Aligned_cols=49  Identities=22%  Similarity=0.131  Sum_probs=43.7

Q ss_pred             HHHHHHHHHHh-hhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCC
Q psy15514         71 AQQLDELERAF-ERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSD  119 (187)
Q Consensus        71 ~~ql~~Le~~F-~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~  119 (187)
                      ..|+.+||..| ..++||+...+.+||..++|++.+|++||+|++.....
T Consensus         9 ~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~   58 (64)
T 1x2m_A            9 AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   58 (64)
T ss_dssp             SCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             chHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCC
Confidence            35799999999 67999999999999999999999999999999865443

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

Probab=99.22  E-value=9.9e-12  Score=75.29  Aligned_cols=51  Identities=29%  Similarity=0.279  Sum_probs=47.5

Q ss_pred             CCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514         67 TTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG  117 (187)
Q Consensus        67 t~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~  117 (187)
                      ..+|..|+.+||..|..++||+...+.+||..++|++.+|++||+|++...
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~   59 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKT   59 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHS
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhh
Confidence            457899999999999999999999999999999999999999999987543

>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=99.18  E-value=1.5e-11  Score=86.61  Aligned_cols=56  Identities=16%  Similarity=0.202  Sum_probs=52.7

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      .++++.||.|+..|+..|+..|..++||+...+..||..++|++.+|++||+|++.
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~  149 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQ  149 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             cCCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccc
Confidence            46778899999999999999999999999999999999999999999999999863

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

Probab=99.16  E-value=1.6e-11  Score=89.08  Aligned_cols=112  Identities=18%  Similarity=0.149  Sum_probs=75.1

Q ss_pred             ccchhhcCCCCC----CCCCccchhhhcccCCCCCCCCcccc----------------cCCCCC-CCCCCCCCCCcccCC
Q psy15514          4 GDRLIKEGLCDR----GSAPSVSAISRLLRGHEGDDTSSEKK----------------LSDGEG-SDCDSEPGIPLKRKQ   62 (187)
Q Consensus         4 rdrll~e~vc~~----~~vPSvsSinrilr~~~~~~~~~~~~----------------~~~~~~-~~~~~~~~~~~~~~~   62 (187)
                      ++.|...|+|..    ...+|+|+|++++++...........                ...+.+ ...+.....+..++.
T Consensus        36 k~~l~~~gitQ~~lA~~~GiSqs~ISr~l~~~~~~~~~kraaly~W~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~k~  115 (194)
T 1ic8_A           36 KSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQKRAALYTWYVRKQREVAQQFTHAGQGGLIEEPTGDELPTKKG  115 (194)
T ss_dssp             HHHHHHTTCCHHHHHHHHCCCHHHHHHHHHSBCCCCHHHHHHHHHHHHHHTTTTHHHHCCC-------------------
T ss_pred             HHHHHHcCCCHHHHHHHhCCChHHHHHHHhcCccccccccccchhhHHHhhhhhhccccCCCCCCCCCCCcccccccccC
Confidence            788888888755    34599999999998653322110000                000000 011111222344678


Q ss_pred             CCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhc---------------------CCchhhHhHhhccCC
Q psy15514         63 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTK---------------------LFPHFLIIIEQQSSG  115 (187)
Q Consensus        63 ~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~---------------------l~~~~v~~wfq~~~~  115 (187)
                      +|.|+.|+..|+..|+..|..++||+...|++||..++                     +++.+|++||+|++.
T Consensus       116 rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~  189 (194)
T 1ic8_A          116 RRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRK  189 (194)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHH
T ss_pred             CCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhh
Confidence            89999999999999999999999999999999999999                     999999999999874

>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=99.04  E-value=1.8e-10  Score=69.51  Aligned_cols=49  Identities=16%  Similarity=0.059  Sum_probs=44.3

Q ss_pred             CCcCHHHHHHHHHHhh---hcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         67 TTFSAQQLDELERAFE---RTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        67 t~ft~~ql~~Le~~F~---~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      ..|+..|+..|+..|.   .++||+..++.+||..+||++.+|++||+|++.
T Consensus         3 g~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~   54 (67)
T 3k2a_A            3 GIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARR   54 (67)
T ss_dssp             ---CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHH
Confidence            4799999999999999   999999999999999999999999999999864

>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=98.91  E-value=9.1e-10  Score=65.61  Aligned_cols=45  Identities=11%  Similarity=0.054  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         71 AQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        71 ~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      ..|+..|+..|..+++|+..++..||..+||+...|++||+|++.
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa   58 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKV   58 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhccc
Confidence            468999999999999999999999999999999999999999873

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

Probab=98.63  E-value=2.4e-08  Score=62.89  Aligned_cols=48  Identities=15%  Similarity=0.113  Sum_probs=44.7

Q ss_pred             CCcCHHHHHHHHHHhhh---cCCCChhhhHHHHHhhcCCchhhHhHhhccC
Q psy15514         67 TTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLFPHFLIIIEQQSS  114 (187)
Q Consensus        67 t~ft~~ql~~Le~~F~~---~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~  114 (187)
                      .-|+..+...|+..|..   ++||+..++..||..+||++.+|.+||+|++
T Consensus        10 ~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR   60 (89)
T 2lk2_A           10 HMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINAR   60 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence            45889999999999987   8999999999999999999999999999875

>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=98.53  E-value=5.8e-08  Score=78.27  Aligned_cols=55  Identities=22%  Similarity=0.208  Sum_probs=50.6

Q ss_pred             CCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         62 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        62 ~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      .++.++.|+..|+..|++.|+.++||+...|++||..++|++.+|++||+|++..
T Consensus       365 ~~~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~  419 (421)
T 1mh3_A          365 QTAAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR  419 (421)
T ss_dssp             HHHHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCC
T ss_pred             hhhhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccc
Confidence            3456788999999999999999999999999999999999999999999998754

>2nzz_A Penetratin conjugated GAS (374-394) peptide; conformational analysis, G protein, GAS subunit, A2A adenosine receptor, cell-penetrating peptides; NMR {Synthetic} PDB: 2o00_A

Probab=98.37  E-value=2.5e-08  Score=52.06  Aligned_cols=13  Identities=31%  Similarity=0.547  Sum_probs=11.7

Q ss_pred             hhhhhhhcccCCC
Q psy15514        174 ARIQTIFIVRKMR  186 (187)
Q Consensus       174 ~~v~~WF~nrR~k  186 (187)
                      .||+|||||||+|
T Consensus         1 rQVkIWFQNRRaK   13 (37)
T 2nzz_A            1 RQIKIWFQNRRMK   13 (37)
T ss_dssp             CCTTTTTTCSHHH
T ss_pred             CCceeccHHHHHH
Confidence            4899999999986

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

Probab=96.48  E-value=0.003  Score=37.34  Aligned_cols=40  Identities=23%  Similarity=0.279  Sum_probs=36.6

Q ss_pred             HHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhccc
Q psy15514        144 LDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVR  183 (187)
Q Consensus       144 ~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nr  183 (187)
                      .+.|+..|...+.+.....+.|+.+.+|+..+|+.||-.|
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            3679999999999999999999999999999999999544

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

Probab=93.27  E-value=0.28  Score=28.93  Aligned_cols=44  Identities=16%  Similarity=0.095  Sum_probs=39.0

Q ss_pred             HHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514         74 LDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG  117 (187)
Q Consensus        74 l~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~  117 (187)
                      .+.|+..|...+.+.-...+.|+.+.+++..+|+.||-.+....
T Consensus        18 ~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~k~~E~   61 (70)
T 2ys9_A           18 IQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSRLPQP   61 (70)
T ss_dssp             CHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHHHSCCS
T ss_pred             chHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHhccccc
Confidence            47899999999999999999999999999999999997655443

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=89.09  E-value=0.55  Score=26.40  Aligned_cols=45  Identities=11%  Similarity=0.130  Sum_probs=31.6

Q ss_pred             CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhc
Q psy15514        136 RTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI  181 (187)
Q Consensus       136 r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~  181 (187)
                      +..||.+....+...+... ........++|..+|++...|..|..
T Consensus         3 r~~ys~efK~~~~~~~~~g-~s~~~~~~~vA~~~gIs~~tl~~W~~   47 (59)
T 2glo_A            3 RRIFTPHFKLQVLESYRND-NDCKGNQRATARKYNIHRRQIQKWLQ   47 (59)
T ss_dssp             CCCCCHHHHHHHHHHHHHC-TTTTTCHHHHHHHTTSCHHHHHHHHT
T ss_pred             CCcCCHHHHHHHHHHHHcC-CCcchHHHHHHHHHCcCHHHHHHHHH
Confidence            4578988877775444433 22112256899999999999999975

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=86.42  E-value=3.1  Score=25.24  Aligned_cols=45  Identities=7%  Similarity=0.105  Sum_probs=32.6

Q ss_pred             ccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhc
Q psy15514        132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI  181 (187)
Q Consensus       132 ~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~  181 (187)
                      .++.+..|+.++....-..+... .    ...++|..+|++...|..|..
T Consensus        16 ~~~~~~~ys~e~k~~~v~~~~~g-~----s~~~iA~~~gIs~sTl~rW~k   60 (87)
T 2elh_A           16 GKRPLRSLTPRDKIHAIQRIHDG-E----SKASVARDIGVPESTLRGWCK   60 (87)
T ss_dssp             CSSCCSSCCHHHHHHHHHHHHHT-C----CHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHCC-C----CHHHHHHHHCcCHHHHHHHHH
Confidence            34456789998866555556432 2    256889999999999999974

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens}

Probab=85.59  E-value=6.4  Score=26.57  Aligned_cols=106  Identities=8%  Similarity=0.020  Sum_probs=63.3

Q ss_pred             CcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHH
Q psy15514         68 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDEL  147 (187)
Q Consensus        68 ~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~L  147 (187)
                      .++.++...+...+...     ....++|..++++...|..|...-...+..   .   + .....+....++.++...+
T Consensus        25 ~~s~e~r~~ii~l~~~G-----~s~~~IA~~lgis~~TV~rwl~r~~~~G~~---~---~-~~r~gr~~~~~~~~~~~~I   92 (159)
T 2k27_A           25 PLPEVVRQRIVDLAHQG-----VRPCDISRQLRVSHGCVSKILGRYYETGSI---R---P-GVIGGSKPKVATPKVVEKI   92 (159)
T ss_dssp             SSCHHHHHHHHHHHHHT-----CCHHHHHHHHTCCSHHHHHHHCCSSTTSCC---C---C-CCCCCCCCCCCCTTHHHHH
T ss_pred             CCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHhcCCc---c---C-CCCCCCCCCCCCHHHHHHH
Confidence            57777666555555432     245678999999999999998654332211   0   0 1111122345777777888


Q ss_pred             HHHhhhcCCCCHHHHHH-HHHH------cCCChhhhhhhhcccCC
Q psy15514        148 ERAFERTQYPDIYTREE-LAQR------TKLTEARIQTIFIVRKM  185 (187)
Q Consensus       148 e~~f~~~~~p~~~~~~~-la~~------~~l~~~~v~~WF~nrR~  185 (187)
                      ......++..+..+... |...      ..++...|..|+...+.
T Consensus        93 ~~~~~~~~~~s~~~i~~~l~~~~~~~~~~~~S~sTV~r~L~~~~~  137 (159)
T 2k27_A           93 GDYKRQNPTMFAWEIRDRLLAEGVCDNDTVPSVSSINRIIRTKVQ  137 (159)
T ss_dssp             HHHHHHCSSSCHHHHHHHHHHHTCSCTTTSCCHHHHHHHHHHHSC
T ss_pred             HHHHHHCccchHHHHHHHHHHhcccccCCccCHHHHHHHHHHHhC
Confidence            77777665555544332 3222      24788999999866543

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=85.20  E-value=2.1  Score=22.15  Aligned_cols=42  Identities=10%  Similarity=0.060  Sum_probs=30.1

Q ss_pred             CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccC
Q psy15514        138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRK  184 (187)
Q Consensus       138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR  184 (187)
                      .++.++...+...+... +    ...++|..+|++...|..|...-+
T Consensus         5 ~l~~~~~~~i~~~~~~g-~----s~~~IA~~lgis~~Tv~~~~~~~~   46 (51)
T 1tc3_C            5 ALSDTERAQLDVMKLLN-V----SLHEMSRKISRSRHCIRVYLKDPV   46 (51)
T ss_dssp             CCCHHHHHHHHHHHHTT-C----CHHHHHHHHTCCHHHHHHHHHCST
T ss_pred             CCCHHHHHHHHHHHHcC-C----CHHHHHHHHCcCHHHHHHHHhhHH
Confidence            46777765555555433 2    356889999999999999986544

>1hlv_A CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} SCOP: a.4.1.7 a.4.1.7 PDB: 1bw6_A

Probab=83.65  E-value=2.2  Score=27.87  Aligned_cols=46  Identities=15%  Similarity=0.270  Sum_probs=35.5

Q ss_pred             cCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhccc
Q psy15514        135 SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVR  183 (187)
Q Consensus       135 ~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nr  183 (187)
                      .|..||.++...+-..+..+....   ..++|..+|++...|..|..++
T Consensus         4 ~r~~~t~e~K~~iv~~~~~~g~~~---~~~~A~~~gvs~stl~~~~~~~   49 (131)
T 1hlv_A            4 KRRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNK   49 (131)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTH
T ss_pred             cceeCCHHHHHHHHHHHHHCCCCc---HHHHHHHhCCCHHHHHHHHhch
Confidence            567899999988877775554443   2368999999999999998664

---

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	187
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	2e-14
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	3e-10
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	1e-13
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	4e-09
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	3e-13
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	1e-09
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	4e-13
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	2e-08
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	8e-13
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	2e-08
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	8e-13
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	4e-08
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	1e-12
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	1e-08
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	2e-12
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	6e-10
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	2e-12
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	8e-08
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	7e-12
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	3e-07
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	2e-11
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	3e-07
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	2e-11
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	3e-07
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	3e-11
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	4e-07
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	4e-11
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	6e-10
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	5e-11
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	1e-07
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	5e-11
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	6e-08
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	8e-11
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	1e-07
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	1e-10
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	3e-07
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	1e-10
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	7e-06
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	3e-10
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	2e-06
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	3e-10
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	5e-06
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	4e-10
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	3e-06
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	5e-10
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	3e-06
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	8e-10
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	2e-05
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	1e-09
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	2e-06
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	3e-09
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	5e-05
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	4e-09
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	2e-05
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	6e-09
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	1e-04
d1k78a2	61	a.4.1.5 (A:82-142) Pax-5 {Human (Homo sapiens) [Ta	3e-08
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	4e-08
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	1e-04
d6paxa2	65	a.4.1.5 (A:69-133) Pax-6 {Human (Homo sapiens) [Ta	8e-08
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	5e-07
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	3e-06
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	2e-05
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	4e-04
d1pdnc_	123	a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Dros	8e-04

>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 = 63.3 bits (154), Expect = 2e-14
 Identities = 18/57 (31%), Positives = 29/57 (50%)

Query: 130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           R  R+ R  ++  Q  ELE+ F    Y     R E+A+   LTE +++  F  R+M+
Sbjct: 11  RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMK 67

>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 = 52.1 bits (125), Expect = 3e-10
 Identities = 13/42 (30%), Positives = 19/42 (45%)

Query: 60  RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           R  R+ R  ++  Q  ELE+ F    Y     R E+A+   L
Sbjct: 11  RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNL 52

>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 = 60.6 bits (147), Expect = 1e-13
 Identities = 26/54 (48%), Positives = 39/54 (72%)

Query: 133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           +R+RT+F+ +Q++ LE+ FERT YPD++ RE LA +  L EARIQ  F  R+ +
Sbjct: 2   QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAK 55

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.0 bits (117), Expect = 4e-09
 Identities = 19/39 (48%), Positives = 30/39 (76%)

Query: 63  RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           +R+RT+F+ +Q++ LE+ FERT YPD++ RE LA +  L
Sbjct: 2   QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDL 40

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 65

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 59.5 bits (144), Expect = 3e-13
 Identities = 48/56 (85%), Positives = 49/56 (87%)

Query: 131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           KQRRSRTTFSA QLDELERAFERTQYPDIYTREELAQRT LTEARIQ  F  R+ R
Sbjct: 1   KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRAR 56

>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 = 50.3 bits (120), Expect = 1e-09
 Identities = 39/41 (95%), Positives = 39/41 (95%)

Query: 61  KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           KQRRSRTTFSA QLDELERAFERTQYPDIYTREELAQRT L
Sbjct: 1   KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNL 41

>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 = 59.0 bits (143), Expect = 4e-13
 Identities = 18/51 (35%), Positives = 27/51 (52%)

Query: 136 RTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           R T++  Q  ELE+ F   +Y     R E+A    LTE +I+  F  R+M+
Sbjct: 1   RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMK 51

>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 = 46.7 bits (111), Expect = 2e-08
 Identities = 12/36 (33%), Positives = 17/36 (47%)

Query: 66  RTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           R T++  Q  ELE+ F   +Y     R E+A    L
Sbjct: 1   RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSL 36

>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 = 58.3 bits (141), Expect = 8e-13
 Identities = 17/54 (31%), Positives = 30/54 (55%)

Query: 133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           +  +  FS  Q  ELE+ FE  +Y     R+ LA+  +L+E +++T F  R+ +
Sbjct: 1   KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAK 54

>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 = 46.7 bits (111), Expect = 2e-08
 Identities = 13/39 (33%), Positives = 20/39 (51%)

Query: 63  RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           +  +  FS  Q  ELE+ FE  +Y     R+ LA+  +L
Sbjct: 1   KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQL 39

>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 = 58.3 bits (141), Expect = 8e-13
 Identities = 18/53 (33%), Positives = 29/53 (54%)

Query: 134 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           R RT FS++QL  L+R F   +Y     R++L+    L EA+I+  F   + +
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 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 = 45.6 bits (108), Expect = 4e-08
 Identities = 14/38 (36%), Positives = 21/38 (55%)

Query: 64  RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           R RT FS++QL  L+R F   +Y     R++L+    L
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGL 38

>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 = 58.3 bits (141), Expect = 1e-12
 Identities = 15/56 (26%), Positives = 26/56 (46%)

Query: 131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           K  R RT  + +QL  L   +     PD   +E+L + T L+   I+  F  ++ +
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCK 57

>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 = 47.5 bits (113), Expect = 1e-08
 Identities = 13/41 (31%), Positives = 19/41 (46%)

Query: 61  KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           K  R RT  + +QL  L   +     PD   +E+L + T L
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGL 42

>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 = 57.7 bits (139), Expect = 2e-12
 Identities = 29/55 (52%), Positives = 40/55 (72%)

Query: 132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           QRR RT F++QQL +LE  F+R +YPD+ TREE+A  T LTEAR++  F  R+ +
Sbjct: 1   QRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAK 55

>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 = 50.7 bits (121), Expect = 6e-10
 Identities = 23/40 (57%), Positives = 30/40 (75%)

Query: 62  QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           QRR RT F++QQL +LE  F+R +YPD+ TREE+A  T L
Sbjct: 1   QRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNL 40

>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 = 57.2 bits (138), Expect = 2e-12
 Identities = 16/54 (29%), Positives = 29/54 (53%)

Query: 133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           R+ R  +S  QL ELER +   ++     R +++  T L+E +I   F  R+++
Sbjct: 2   RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVK 55

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.2 bits (107), Expect = 8e-08
 Identities = 12/39 (30%), Positives = 20/39 (51%)

Query: 63  RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           R+ R  +S  QL ELER +   ++     R +++  T L
Sbjct: 2   RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSL 40

>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 = 56.9 bits (137), Expect = 7e-12
 Identities = 19/65 (29%), Positives = 32/65 (49%)

Query: 122 SEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI 181
           ++   P        RT F+ +QL ELE+ F   +Y     R E+A   +L E +++  F 
Sbjct: 17  AKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQ 76

Query: 182 VRKMR 186
            R+M+
Sbjct: 77  NRRMK 81

>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 = 44.2 bits (104), Expect = 3e-07
 Identities = 15/50 (30%), Positives = 23/50 (46%)

Query: 52  SEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           ++   P        RT F+ +QL ELE+ F   +Y     R E+A   +L
Sbjct: 17  AKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLEL 66

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 53

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 54.5 bits (131), Expect = 2e-11
 Identities = 15/51 (29%), Positives = 30/51 (58%)

Query: 136 RTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           +++ S Q    LE+ F R Q  +   +EE+A++  +T  +++  FI ++MR
Sbjct: 1   KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 51

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 53

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 43.3 bits (102), Expect = 3e-07
 Identities = 10/34 (29%), Positives = 19/34 (55%)

Query: 66 RTTFSAQQLDELERAFERTQYPDIYTREELAQRT 99
          +++ S Q    LE+ F R Q  +   +EE+A++ 
Sbjct: 1  KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKC 34

>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 = 54.5 bits (131), Expect = 2e-11
 Identities = 20/53 (37%), Positives = 28/53 (52%)

Query: 134 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           R RT F+  QL  LE+ F +  Y     R ELA +  L E+ I+  F  R+M+
Sbjct: 1   RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMK 53

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 43.4 bits (102), Expect = 3e-07
 Identities = 15/38 (39%), Positives = 19/38 (50%)

Query: 64  RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           R RT F+  QL  LE+ F +  Y     R ELA +  L
Sbjct: 1   RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNL 38

>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 = 54.2 bits (130), Expect = 3e-11
 Identities = 20/54 (37%), Positives = 29/54 (53%)

Query: 133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           R+ RT F+  QL  LER F + QY  I  R E +    LTE +++  F  R+ +
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAK 54

>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 = 43.4 bits (102), Expect = 4e-07
 Identities = 16/39 (41%), Positives = 20/39 (51%)

Query: 63  RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           R+ RT F+  QL  LER F + QY  I  R E +    L
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSL 39

>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 = 54.7 bits (131), Expect = 4e-11
 Identities = 18/69 (26%), Positives = 27/69 (39%), Gaps = 15/69 (21%)

Query: 133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELA---------------QRTKLTEARIQ 177
           R SR T+  + L  +E  F   QYPD   REE+A                  ++T  ++ 
Sbjct: 1   RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVY 60

Query: 178 TIFIVRKMR 186
             F  R+  
Sbjct: 61  NWFANRRKE 69

>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 = 51.6 bits (123), Expect = 6e-10
 Identities = 15/53 (28%), Positives = 19/53 (35%)

Query: 63  RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG 115
           R SR T+  + L  +E  F   QYPD   REE+A                   
Sbjct: 1   RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLER 53

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 50

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.3 bits (128), Expect = 5e-11
 Identities = 9/45 (20%), Positives = 18/45 (40%)

Query: 136 RTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIF 180
           R  F+  Q   L   F+  + P    +  ++Q+  L  + +   F
Sbjct: 2   RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFF 46

>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 = 44.5 bits (105), Expect = 1e-07
 Identities = 8/36 (22%), Positives = 15/36 (41%)

Query: 66  RTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           R  F+  Q   L   F+  + P    +  ++Q+  L
Sbjct: 2   RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGL 37

>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 = 53.9 bits (129), Expect = 5e-11
 Identities = 12/59 (20%), Positives = 26/59 (44%)

Query: 128 LKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           L + ++R RT+   +    LE  F +   P +     +A +  L +  ++  F  R+ +
Sbjct: 4   LVQARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQK 62

>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 = 45.8 bits (108), Expect = 6e-08
 Identities = 10/46 (21%), Positives = 19/46 (41%)

Query: 58  LKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFP 103
           L + ++R RT+   +    LE  F +   P +     +A +  L  
Sbjct: 4   LVQARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEK 49

>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 = 53.5 bits (128), Expect = 8e-11
 Identities = 19/59 (32%), Positives = 30/59 (50%)

Query: 128 LKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           L  K+R+ R  F+  Q  ELER F + +Y     RE LA   +LT  +++  F   + +
Sbjct: 5   LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYK 63

>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 = 45.0 bits (106), Expect = 1e-07
 Identities = 17/44 (38%), Positives = 23/44 (52%)

Query: 58  LKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           L  K+R+ R  F+  Q  ELER F + +Y     RE LA   +L
Sbjct: 5   LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRL 48

>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 = 52.6 bits (126), Expect = 1e-10
 Identities = 15/53 (28%), Positives = 22/53 (41%)

Query: 134 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           + RTT S    D LER F     P       +A+   L +  ++  F  R+ R
Sbjct: 1   KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQR 53

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 43.4 bits (102), Expect = 3e-07
 Identities = 12/40 (30%), Positives = 15/40 (37%)

Query: 64  RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFP 103
           + RTT S    D LER F     P       +A+   L  
Sbjct: 1   KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEK 40

>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 = 52.4 bits (126), Expect = 1e-10
 Identities = 10/57 (17%), Positives = 22/57 (38%), Gaps = 3/57 (5%)

Query: 133 RRSRTTFSAQQLDELERAFERTQ---YPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           +  R        + +     +     YP    ++++A +T LT  ++   FI  + R
Sbjct: 3   KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRR 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 = 39.7 bits (93), Expect = 7e-06
 Identities = 6/42 (14%), Positives = 15/42 (35%), Gaps = 3/42 (7%)

Query: 63  RRSRTTFSAQQLDELERAFERTQ---YPDIYTREELAQRTKL 101
           +  R        + +     +     YP    ++++A +T L
Sbjct: 3   KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNL 44

>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 = 51.9 bits (124), Expect = 3e-10
 Identities = 18/54 (33%), Positives = 32/54 (59%)

Query: 133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           RR+RTTF++ Q+ ELE+ F + +Y       +L+ +  L  A+++  F  R+ R
Sbjct: 2   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRR 55

>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 = 41.8 bits (98), Expect = 2e-06
 Identities = 14/39 (35%), Positives = 24/39 (61%)

Query: 63  RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           RR+RTTF++ Q+ ELE+ F + +Y       +L+ +  L
Sbjct: 2   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLAL 40

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 80

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 52.3 bits (125), Expect = 3e-10
 Identities = 19/79 (24%), Positives = 30/79 (37%), Gaps = 9/79 (11%)

Query: 113 SSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFER----TQYPDIYTREELAQR 168
           S   GS+  S  G       +R RT F+A+Q +++    ER     Q  D    E+    
Sbjct: 3   SGSSGSNPSSSGG-----TTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAE 57

Query: 169 TKLTEARIQTIFIVRKMRG 187
           T +    ++      K  G
Sbjct: 58  TGVRRQVLKIWMHNNKNSG 76

>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 = 40.8 bits (95), Expect = 5e-06
 Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 9/63 (14%)

Query: 43  SDGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFER----TQYPDIYTREELAQR 98
           S   GS+  S  G       +R RT F+A+Q +++    ER     Q  D    E+    
Sbjct: 3   SGSSGSNPSSSGG-----TTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAE 57

Query: 99  TKL 101
           T +
Sbjct: 58  TGV 60

>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 = 51.5 bits (123), Expect = 4e-10
 Identities = 18/55 (32%), Positives = 29/55 (52%)

Query: 132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           +R+ R  FS  Q+ ELER F++ +Y     RE LA    LT  +++  F   + +
Sbjct: 2   RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYK 56

>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 = 41.1 bits (96), Expect = 3e-06
 Identities = 16/40 (40%), Positives = 22/40 (55%)

Query: 62  QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           +R+ R  FS  Q+ ELER F++ +Y     RE LA    L
Sbjct: 2   RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHL 41

>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 = 50.9 bits (122), Expect = 5e-10
 Identities = 13/54 (24%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 134 RSRTTFSAQQLDELERAFER-TQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           +       +  D LE+ F   T+YPD    + L+++   +  +IQ  F  R+ +
Sbjct: 3   KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQ 56

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 59

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: LAG1 longevity assurance homolog 5, LASS5
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.5 bits (95), Expect = 3e-06
 Identities = 9/39 (23%), Positives = 17/39 (43%), Gaps = 1/39 (2%)

Query: 64  RSRTTFSAQQLDELERAFER-TQYPDIYTREELAQRTKL 101
           +       +  D LE+ F   T+YPD    + L+++   
Sbjct: 3   KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDW 41

>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 = 8e-10
 Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 3/57 (5%)

Query: 133 RRSRTTFSAQQLDELERAFE---RTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           RR R  F+ Q  + L   F       YP    +EELA++  +T +++   F  +++R
Sbjct: 2   RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR 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 = 39.2 bits (91), Expect = 2e-05
 Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 3/42 (7%)

Query: 63  RRSRTTFSAQQLDELERAFE---RTQYPDIYTREELAQRTKL 101
           RR R  F+ Q  + L   F       YP    +EELA++  +
Sbjct: 2   RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGI 43

>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 = 50.4 bits (120), Expect = 1e-09
 Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 1/55 (1%)

Query: 133 RRSRTTFSAQQLDELERAFERT-QYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
                T +  Q++ LE  F +  ++PD  T   +A    LTE + Q  F  R   
Sbjct: 2   SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAE 56

>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 = 41.5 bits (97), Expect = 2e-06
 Identities = 10/40 (25%), Positives = 17/40 (42%), Gaps = 1/40 (2%)

Query: 63  RRSRTTFSAQQLDELERAFERT-QYPDIYTREELAQRTKL 101
                T +  Q++ LE  F +  ++PD  T   +A    L
Sbjct: 2   SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGL 41

>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 = 48.6 bits (116), Expect = 3e-09
 Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 140 SAQQLDELERAF-ERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           +AQ    LE+ F   T++PD    E L+++       IQ  F  R+ +
Sbjct: 1   TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQ 48

>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 = 37.4 bits (87), Expect = 5e-05
 Identities = 10/33 (30%), Positives = 17/33 (51%), Gaps = 1/33 (3%)

Query: 70  SAQQLDELERAF-ERTQYPDIYTREELAQRTKL 101
           +AQ    LE+ F   T++PD    E L+++   
Sbjct: 1   TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDW 33

>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 = 48.4 bits (115), Expect = 4e-09
 Identities = 11/51 (21%), Positives = 22/51 (43%)

Query: 136 RTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           RT+        LE++F   Q P       +A++  + +  I+  F  R+ +
Sbjct: 2   RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQK 52

>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 = 38.8 bits (90), Expect = 2e-05
 Identities = 8/36 (22%), Positives = 15/36 (41%)

Query: 66  RTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 101
           RT+        LE++F   Q P       +A++  +
Sbjct: 2   RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNM 37

>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 = 48.2 bits (115), Expect = 6e-09
 Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 5/57 (8%)

Query: 133 RRSRTTFSAQQLDELERAFERTQ---YPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
           R  R  F+ + +  LE  F +     Y D    E L + T L+  +I+     R+ +
Sbjct: 1   RGHR--FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRK 55

>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 = 36.7 bits (85), Expect = 1e-04
 Identities = 12/42 (28%), Positives = 17/42 (40%), Gaps = 5/42 (11%)

Query: 63  RRSRTTFSAQQLDELERAFERTQ---YPDIYTREELAQRTKL 101
           R  R  F+ + +  LE  F +     Y D    E L + T L
Sbjct: 1   RGHR--FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSL 40

>d1k78a2 a.4.1.5 (A:82-142) Pax-5 {Human (Homo sapiens) [TaxId: 9606]} Length = 61

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.1 bits (110), Expect = 3e-08
 Identities = 13/25 (52%), Positives = 20/25 (80%)

Query: 5  DRLIKEGLCDRGSAPSVSAISRLLR 29
          DRL+ E +CD  + PSVS+I+R++R
Sbjct: 35 DRLLAERVCDNDTVPSVSSINRIIR 59

>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 = 46.2 bits (109), Expect = 4e-08
 Identities = 14/57 (24%), Positives = 21/57 (36%), Gaps = 1/57 (1%)

Query: 131 KQRRSRTTFSAQQLDELERAFERT-QYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
              RSRT  S + L  L+        YPD      L+ +  L +  I   F  ++  
Sbjct: 6   SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYH 62

>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 = 37.0 bits (85), Expect = 1e-04
 Identities = 12/42 (28%), Positives = 16/42 (38%), Gaps = 1/42 (2%)

Query: 61  KQRRSRTTFSAQQLDELERAFERT-QYPDIYTREELAQRTKL 101
              RSRT  S + L  L+        YPD      L+ +  L
Sbjct: 6   SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDL 47

>d6paxa2 a.4.1.5 (A:69-133) Pax-6 {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-6
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.0 bits (107), Expect = 8e-08
 Identities = 14/30 (46%), Positives = 21/30 (70%)

Query: 5  DRLIKEGLCDRGSAPSVSAISRLLRGHEGD 34
          DRL+ EG+C   + PSVS+I+R+LR    +
Sbjct: 33 DRLLSEGVCTNDNIPSVSSINRVLRNLASE 62

>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 = 43.6 bits (102), Expect = 5e-07
 Identities = 10/44 (22%), Positives = 17/44 (38%)

Query: 136 RTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTI 179
           R  +       L +A+ER + P    RE L +     E   + +
Sbjct: 1   RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGV 44

>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 = 41.3 bits (96), Expect = 3e-06
 Identities = 9/34 (26%), Positives = 14/34 (41%)

Query: 66 RTTFSAQQLDELERAFERTQYPDIYTREELAQRT 99
          R  +       L +A+ER + P    RE L +  
Sbjct: 1  RFKWGPASQQILFQAYERQKNPSKEERETLVEEC 34

>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 = 38.9 bits (90), Expect = 2e-05
 Identities = 13/54 (24%), Positives = 21/54 (38%)

Query: 133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
            +     +A+QL  L+ +F  +          L  +TKLT   I   F  +K  
Sbjct: 5   PQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKS 58

>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 = 35.5 bits (81), Expect = 4e-04
 Identities = 12/54 (22%), Positives = 20/54 (37%)

Query: 133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186
             S    + +QL  L+  F + Q+      ++L Q T L    I   F   +  
Sbjct: 4   GSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYA 57

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 123

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Paired protein (prd)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 35.7 bits (82), Expect = 8e-04
 Identities = 17/24 (70%), Positives = 23/24 (95%)

Query: 5   DRLIKEGLCDRGSAPSVSAISRLL 28
           ++LI+EG+CDR +APSVSAISRL+
Sbjct: 100 EKLIREGVCDRSTAPSVSAISRLV 123

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	187
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.88
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.87
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.86
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.86
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.85
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.85
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.85
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.85
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.85
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.84
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.83
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.83
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.82
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.82
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.82
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.82
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.82
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.82
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.81
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.81
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.8
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.78
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.78
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.77
d1k78a2	61	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	99.75
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.73
d6paxa2	65	Pax-6 {Human (Homo sapiens) [TaxId: 9606]}	99.72
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.71
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.7
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.7
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.69
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.65
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.65
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.64
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.63
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.63
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.62
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.61
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.6
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.59
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.58
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.58
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.57
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.57
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.57
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.56
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.56
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.56
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.54
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.53
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.52
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.5
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.49
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.48
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.46
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.45
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.43
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.38
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.26
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.25
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.23
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.22
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.13
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.07
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.07
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.01
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	93.54
d1hlva1	66	DNA-binding domain of centromere binding protein B	92.94

>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=99.88  E-value=8.1e-24  Score=121.01  Aligned_cols=53  Identities=34%  Similarity=0.543  Sum_probs=51.5

Q ss_pred             ccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        134 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       134 r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      |.|+.||++|+..||..|+.++||+..++.+||..+||++.+|++||||||+|
T Consensus         1 R~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~lgL~~~qV~vWFqNrRaK   53 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK   53 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             CCCccCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChHHhhhcccccCCC
Confidence            46899999999999999999999999999999999999999999999999987

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=2.3e-23  Score=120.86  Aligned_cols=55  Identities=29%  Similarity=0.495  Sum_probs=52.6

Q ss_pred             cccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCCC
Q psy15514        133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG  187 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~  187 (187)
                      ++.|+.||.+|+.+||..|..++||+..++++||..+||++.+|++||||||+|.
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~   56 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKE   56 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhc
Confidence            5678999999999999999999999999999999999999999999999999873

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.86  E-value=6.8e-23  Score=119.38  Aligned_cols=54  Identities=37%  Similarity=0.586  Sum_probs=52.0

Q ss_pred             cccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ++.|+.||++|+.+||..|+.++||+..++++||..+||++.+|++||||||+|
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k   54 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAK   54 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhH
Confidence            467899999999999999999999999999999999999999999999999986

>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=99.86  E-value=1.1e-22  Score=117.92  Aligned_cols=53  Identities=38%  Similarity=0.550  Sum_probs=51.4

Q ss_pred             ccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        134 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       134 r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      |.|+.||++|+.+||..|..++||+..++++||..+||++.+|++||||||+|
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k   53 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMK   53 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhh
Confidence            57899999999999999999999999999999999999999999999999986

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Antennapedia Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.85  E-value=1e-22  Score=116.89  Aligned_cols=51  Identities=35%  Similarity=0.470  Sum_probs=49.9

Q ss_pred             CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        136 RTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       136 r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ||.||.+|+..||..|..++||+..++.+||..+||++.+|++||||||+|
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak   51 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMK   51 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhh
Confidence            789999999999999999999999999999999999999999999999986

>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=99.85  E-value=1.8e-22  Score=117.02  Aligned_cols=54  Identities=31%  Similarity=0.474  Sum_probs=51.8

Q ss_pred             cccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ++.|+.||++|+.+||..|+.++||+..+++.||..+||++.+|++||||||+|
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k   54 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAK   54 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhh
Confidence            467899999999999999999999999999999999999999999999999986

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.85  E-value=1.9e-22  Score=120.69  Aligned_cols=55  Identities=33%  Similarity=0.505  Sum_probs=52.6

Q ss_pred             ccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       132 ~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +++.|+.||.+|+.+||..|+.++||+..++..||..|||++.+|++||||||+|
T Consensus         1 Prr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k   55 (67)
T d1zq3p1           1 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRR   55 (67)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHh
Confidence            3577999999999999999999999999999999999999999999999999985

>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=99.85  E-value=5.3e-22  Score=121.83  Aligned_cols=58  Identities=31%  Similarity=0.477  Sum_probs=54.8

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG  187 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~  187 (187)
                      .+.++.|+.||.+|+.+||.+|+.++||+..+++.||..+||++.+|++||||||+|.
T Consensus         7 ~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~   64 (77)
T d1vnda_           7 NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKT   64 (77)
T ss_dssp             SSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHH
Confidence            4567789999999999999999999999999999999999999999999999999873

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-a9
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.85  E-value=4.6e-22  Score=121.90  Aligned_cols=58  Identities=31%  Similarity=0.430  Sum_probs=54.5

Q ss_pred             cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+..++.|+.||.+|+.+||.+|..++||+..+++.||..+||++.+|++||||||+|
T Consensus        10 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k   67 (77)
T d1pufa_          10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMK   67 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             cCcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHH
Confidence            3455778999999999999999999999999999999999999999999999999986

>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=99.84  E-value=5.7e-22  Score=117.93  Aligned_cols=56  Identities=86%  Similarity=1.124  Sum_probs=53.5

Q ss_pred             cccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       131 ~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +.++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||||+|+|
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k   56 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRAR   56 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHH
Confidence            35778999999999999999999999999999999999999999999999999986

>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=99.83  E-value=8.3e-22  Score=118.07  Aligned_cols=55  Identities=33%  Similarity=0.508  Sum_probs=52.6

Q ss_pred             ccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       132 ~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .++.|+.||+.|+.+|+..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k   56 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYK   56 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHH
Confidence            3678999999999999999999999999999999999999999999999999976

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.2e-21  Score=117.52  Aligned_cols=54  Identities=48%  Similarity=0.875  Sum_probs=52.1

Q ss_pred             cccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +|.||.||.+|+.+||..|..++||+..+++.||..+||++.+|++||||+|+|
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k   55 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAK   55 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHH
Confidence            567899999999999999999999999999999999999999999999999976

>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=99.82  E-value=2.4e-21  Score=110.51  Aligned_cols=52  Identities=29%  Similarity=0.460  Sum_probs=50.3

Q ss_pred             CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCCC
Q psy15514        136 RTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG  187 (187)
Q Consensus       136 r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~  187 (187)
                      |+.||++|+.+|+..|..++||+..++..||..+||++.+|++||||||+|.
T Consensus         1 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~   52 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS   52 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhcc
Confidence            6899999999999999999999999999999999999999999999999873

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.82  E-value=2e-21  Score=115.76  Aligned_cols=56  Identities=27%  Similarity=0.439  Sum_probs=53.6

Q ss_pred             cccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       131 ~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +.+|.|+.||.+|+.+|+..|..++||+..+++.||.++||++.+|++||||||+|
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k   57 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCK   57 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHH
Confidence            45788999999999999999999999999999999999999999999999999976

>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=99.82  E-value=1.6e-21  Score=122.45  Aligned_cols=57  Identities=32%  Similarity=0.484  Sum_probs=51.1

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .++++.|+.||.+|+.+||..|+.++||+..++++||..|||++.+|+|||||||+|
T Consensus        25 ~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k   81 (88)
T d1b72a_          25 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMK   81 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHH
Confidence            455788999999999999999999999999999999999999999999999999986

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=6.2e-22  Score=116.05  Aligned_cols=54  Identities=52%  Similarity=0.825  Sum_probs=52.3

Q ss_pred             cccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ++.|+.||++|+.+|+..|..++||+..+++.||..+||++.+|++||+|+|+|
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k   55 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAK   55 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHH
Confidence            678999999999999999999999999999999999999999999999999986

>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=99.82  E-value=2.5e-21  Score=116.84  Aligned_cols=54  Identities=28%  Similarity=0.325  Sum_probs=51.1

Q ss_pred             cccCCCCCHHHHHHHHHHhhh-cCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        133 RRSRTTFSAQQLDELERAFER-TQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f~~-~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ++.|+.||.+|+.+||..|.. ++||+...++.||..+||++.+|++||||||+|
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak   56 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAE   56 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            467899999999999999986 789999999999999999999999999999986

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-3 POU Homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=6.3e-21  Score=113.74  Aligned_cols=57  Identities=21%  Similarity=0.346  Sum_probs=53.8

Q ss_pred             cccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCCC
Q psy15514        131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG  187 (187)
Q Consensus       131 ~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~  187 (187)
                      ..++.|+.|+.+|+..|+.+|..++||+..+++.||..+||++.+|++||||+|+|.
T Consensus         7 ~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~   63 (67)
T d1ocpa_           7 ARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKG   63 (67)
T ss_dssp             CSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSS
T ss_pred             ccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHH
Confidence            346789999999999999999999999999999999999999999999999999873

>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=99.81  E-value=2.4e-20  Score=115.37  Aligned_cols=58  Identities=24%  Similarity=0.257  Sum_probs=53.5

Q ss_pred             ccccccCCCCCHHHHHHHHHHhhh----cCCCCHHHHHHHHHHcCCChhhhhhhhcccCCCC
Q psy15514        130 RKQRRSRTTFSAQQLDELERAFER----TQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG  187 (187)
Q Consensus       130 ~~~~r~r~~~t~~q~~~Le~~f~~----~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~  187 (187)
                      .+.+|.||.||.+|++.|+.+|+.    ++||+..++++||.+|||++.+|+|||||+|+++
T Consensus        15 ~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~   76 (80)
T d1wh7a_          15 GTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSG   76 (80)
T ss_dssp             CCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCS
T ss_pred             cCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCC
Confidence            456778999999999999998886    7899999999999999999999999999999864

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.81  E-value=6.5e-21  Score=110.71  Aligned_cols=53  Identities=28%  Similarity=0.383  Sum_probs=51.2

Q ss_pred             ccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        134 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       134 r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      |.||.|+.+|+.+||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k   53 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQR   53 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHH
Confidence            46899999999999999999999999999999999999999999999999986

>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=99.80  E-value=1.1e-20  Score=106.65  Aligned_cols=50  Identities=18%  Similarity=0.301  Sum_probs=48.8

Q ss_pred             cCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccC
Q psy15514        135 SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRK  184 (187)
Q Consensus       135 ~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR  184 (187)
                      .|+.||++|+..||..|..++||+..++..||..+||++.+|++||||||
T Consensus         1 PRt~ft~~Q~~~Le~~F~~n~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1           1 PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             CCSCCCHHHHHHHHHHTTSSCSSTHHHHHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhhcCCcCc
Confidence            47999999999999999999999999999999999999999999999998

>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=99.78  E-value=4.8e-20  Score=111.63  Aligned_cols=56  Identities=25%  Similarity=0.310  Sum_probs=52.1

Q ss_pred             cccccCCCCCHHHHHHHHHHhh-hcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        131 KQRRSRTTFSAQQLDELERAFE-RTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       131 ~~~r~r~~~t~~q~~~Le~~f~-~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ..++.|+.||++|+.+|+.+|. .++||+..+++.||..+||+..+|++||||+|+|
T Consensus         6 ~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k   62 (71)
T d1wi3a_           6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYH   62 (71)
T ss_dssp             CCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhh
Confidence            3467889999999999999997 4899999999999999999999999999999986

>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=99.78  E-value=3e-20  Score=115.54  Aligned_cols=54  Identities=33%  Similarity=0.493  Sum_probs=51.1

Q ss_pred             cccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcC---------------CChhhhhhhhcccCCC
Q psy15514        133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTK---------------LTEARIQTIFIVRKMR  186 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~---------------l~~~~v~~WF~nrR~k  186 (187)
                      ++.|+.||++|+.+||.+|+.++||+..++++||..+|               |++.+|++||||||+|
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k   69 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKE   69 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHH
Confidence            57899999999999999999999999999999999875               9999999999999976

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=6.2e-20  Score=106.05  Aligned_cols=52  Identities=21%  Similarity=0.294  Sum_probs=50.3

Q ss_pred             cCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        135 SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       135 ~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .||.|+.+|+..||..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         1 kRT~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k   52 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQK   52 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            4799999999999999999999999999999999999999999999999975

>d1k78a2 a.4.1.5 (A:82-142) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=6.4e-20  Score=103.60  Aligned_cols=31  Identities=45%  Similarity=0.963  Sum_probs=29.9

Q ss_pred             Ccc--ccchhhcCCCCCCCCCccchhhhcccCC
Q psy15514          1 MCW--GDRLIKEGLCDRGSAPSVSAISRLLRGH   31 (187)
Q Consensus         1 ~~~--rdrll~e~vc~~~~vPSvsSinrilr~~   31 (187)
                      |||  ||+||+|||||.+|||||||||||||++
T Consensus        29 FaWEIRd~Li~egiC~~~nvPSvSsInRilR~k   61 (61)
T d1k78a2          29 FAWEIRDRLLAERVCDNDTVPSVSSINRIIRTK   61 (61)
T ss_dssp             CHHHHHHHHHHTTSSCTTTSCCHHHHHHHHHCC
T ss_pred             cHHHHHHHHHHcCCCCCCCCCchHHHHHHhhcC
Confidence            899  9999999999999999999999999974

>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=99.73  E-value=9.7e-19  Score=107.11  Aligned_cols=49  Identities=27%  Similarity=0.259  Sum_probs=47.0

Q ss_pred             CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+|.+|+.+|+..|..++||+..+++.||..+||++.+|++||||||+|
T Consensus        10 ~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r   58 (76)
T d2ecba1          10 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKS   58 (76)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHH
Confidence            4599999999999999999999999999999999999999999999975

>d6paxa2 a.4.1.5 (A:69-133) Pax-6 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=2.1e-19  Score=102.56  Aligned_cols=33  Identities=45%  Similarity=0.920  Sum_probs=30.9

Q ss_pred             Ccc--ccchhhcCCCCCCCCCccchhhhcccCCCC
Q psy15514          1 MCW--GDRLIKEGLCDRGSAPSVSAISRLLRGHEG   33 (187)
Q Consensus         1 ~~~--rdrll~e~vc~~~~vPSvsSinrilr~~~~   33 (187)
                      |||  ||+||+||||+.+|||||||||||||++.+
T Consensus        27 FaWEIRd~Li~egiC~~~~vPSvSsInRilR~~~~   61 (65)
T d6paxa2          27 FAWEIRDRLLSEGVCTNDNIPSVSSINRVLRNLAS   61 (65)
T ss_dssp             CHHHHHHHHHHTTSSCTTTCCCHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHcCCCCCCCCCchHHHHHHHHHhhh
Confidence            899  999999999999999999999999997643

>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=99.71  E-value=2.5e-18  Score=105.11  Aligned_cols=52  Identities=27%  Similarity=0.394  Sum_probs=49.1

Q ss_pred             CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcC---------------------CChhhhhhhhcccCCCC
Q psy15514        136 RTTFSAQQLDELERAFERTQYPDIYTREELAQRTK---------------------LTEARIQTIFIVRKMRG  187 (187)
Q Consensus       136 r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~---------------------l~~~~v~~WF~nrR~k~  187 (187)
                      |++||++|+.+||..|+.++||+..+++.||.+++                     |++.+|++||+|||+|.
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~   73 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEE   73 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTT
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHH
Confidence            67899999999999999999999999999999994                     99999999999999874

>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=99.70  E-value=3.3e-18  Score=103.98  Aligned_cols=54  Identities=30%  Similarity=0.505  Sum_probs=50.5

Q ss_pred             cccCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        133 RRSRTTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f~~---~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ++.|+.|+.+|+.+|+.+|..   ++||+..+++.||..+||+..+|++||+|+|+|
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r   58 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR   58 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHH
Confidence            567899999999999999974   889999999999999999999999999999975

>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=99.70  E-value=4.1e-18  Score=104.32  Aligned_cols=52  Identities=23%  Similarity=0.178  Sum_probs=48.8

Q ss_pred             cCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        135 SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       135 ~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      .+..+|.+|+.+|+..|..++||+..+++.||..+||++.+|++||+|+|+|
T Consensus         6 ~~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k   57 (76)
T d2ecca1           6 SGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYA   57 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            3456899999999999999999999999999999999999999999999974

>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=99.69  E-value=2.6e-18  Score=97.13  Aligned_cols=47  Identities=30%  Similarity=0.322  Sum_probs=44.0

Q ss_pred             CHHHHHHHHHHhhh-cCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        140 SAQQLDELERAFER-TQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       140 t~~q~~~Le~~f~~-~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      |.+|..+||..|.. ++||+..+++.||..+||++.+|++||||||+|
T Consensus         1 T~~q~~iLE~~F~~~~~~P~~~~~~~LA~~~~ls~~qV~~WFqNrR~k   48 (52)
T d1x2ma1           1 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQ   48 (52)
T ss_dssp             SSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHH
T ss_pred             ChhHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcc
Confidence            45789999999987 789999999999999999999999999999986

>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=99.65  E-value=6.3e-18  Score=98.03  Aligned_cols=53  Identities=25%  Similarity=0.365  Sum_probs=48.1

Q ss_pred             ccCCCCCHHHHHHHHHHhhh-cCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        134 RSRTTFSAQQLDELERAFER-TQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       134 r~r~~~t~~q~~~Le~~f~~-~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      +.++.++.++..+||..|.. ++||+..+++.||..+||++.+|++||||||++
T Consensus         3 k~~~~~k~~~~~iLE~~F~~~~~yPs~~~~~~LA~~lgls~~qV~~WFqNrR~k   56 (59)
T d2cqxa1           3 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQ   56 (59)
T ss_dssp             CCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCccccHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcc
Confidence            34567888888999999986 689999999999999999999999999999976

>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=99.65  E-value=4.4e-17  Score=95.51  Aligned_cols=54  Identities=19%  Similarity=0.327  Sum_probs=50.0

Q ss_pred             cccCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        133 RRSRTTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       133 ~r~r~~~t~~q~~~Le~~f~~---~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ++.|+.|+.+++.+|+.+|..   ++||+..++..||..+||+..+|++||+|+|+|
T Consensus         3 krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R   59 (62)
T d1x2na1           3 KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRR   59 (62)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHH
Confidence            456789999999999999985   789999999999999999999999999999975

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.64  E-value=6.5e-17  Score=94.27  Aligned_cols=50  Identities=24%  Similarity=0.363  Sum_probs=46.3

Q ss_pred             CCCCHHHHHHHHHHhhhc---CCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514        137 TTFSAQQLDELERAFERT---QYPDIYTREELAQRTKLTEARIQTIFIVRKMR  186 (187)
Q Consensus       137 ~~~t~~q~~~Le~~f~~~---~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k  186 (187)
                      ..|+.+|+.+|+.+|..+   +||+..+++.||..+||+..+|++||+|+|+|
T Consensus         3 ~Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r   55 (60)
T d1k61a_           3 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRK   55 (60)
T ss_dssp             CSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhccc
Confidence            349999999999999765   69999999999999999999999999999975

>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=99.63  E-value=4.9e-16  Score=94.85  Aligned_cols=61  Identities=31%  Similarity=0.372  Sum_probs=56.2

Q ss_pred             ccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCC
Q psy15514         59 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSD  119 (187)
Q Consensus        59 ~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~  119 (187)
                      +.+.++.||+||..|+..|+..|+.++||+...++.||..+||++.+|++||+|++.....
T Consensus         6 p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   66 (77)
T d1vnda_           6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR   66 (77)
T ss_dssp             SSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHH
Confidence            4567788999999999999999999999999999999999999999999999999976543

>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=99.63  E-value=1.4e-16  Score=90.51  Aligned_cols=51  Identities=31%  Similarity=0.422  Sum_probs=49.0

Q ss_pred             CCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccC
Q psy15514         64 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSS  114 (187)
Q Consensus        64 r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~  114 (187)
                      |.||.||..|+..||..|..++||+..++.+||..+||++.+|++||||++
T Consensus         1 R~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~lgL~~~qV~vWFqNrR   51 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNAR   51 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChHHhhhcccccC
Confidence            468999999999999999999999999999999999999999999999975

>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=99.62  E-value=2.1e-16  Score=91.11  Aligned_cols=54  Identities=26%  Similarity=0.348  Sum_probs=50.9

Q ss_pred             CCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         63 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        63 ~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      ++.||.||..|+.+||..|..++||+...+++||..+||++.+|++||||++..
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k   55 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVK   55 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhh
Confidence            567899999999999999999999999999999999999999999999998743

>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=99.61  E-value=2.9e-16  Score=90.90  Aligned_cols=53  Identities=34%  Similarity=0.429  Sum_probs=50.2

Q ss_pred             CCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         63 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        63 ~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      ++.|+.||+.|+.+|+..|+.++||+...+++||..+||++.+|++||+|++.
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~   53 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRA   53 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHh
Confidence            46789999999999999999999999999999999999999999999999763

>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=99.60  E-value=4.3e-16  Score=89.70  Aligned_cols=52  Identities=31%  Similarity=0.339  Sum_probs=49.6

Q ss_pred             CCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         64 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        64 r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      |.||.||+.|+..||..|..++||+...+++||..+||++.+|++||+|++.
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~   52 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRM   52 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhh
Confidence            5689999999999999999999999999999999999999999999999763

>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=99.59  E-value=6.1e-16  Score=91.94  Aligned_cols=54  Identities=28%  Similarity=0.344  Sum_probs=50.9

Q ss_pred             CCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         62 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        62 ~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      +++.||.||..|+.+|+..|..++||+...+..||..+||++.+|++||+|++.
T Consensus         1 Prr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~   54 (67)
T d1zq3p1           1 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRR   54 (67)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHH
Confidence            356789999999999999999999999999999999999999999999999874

>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=99.58  E-value=9.1e-16  Score=91.47  Aligned_cols=53  Identities=36%  Similarity=0.659  Sum_probs=50.3

Q ss_pred             CCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         63 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        63 ~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      +|.||.||..|+..|+..|..++||+..+++.||..+||++.+|++||+|++.
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~   54 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRA   54 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhH
Confidence            56789999999999999999999999999999999999999999999998763

>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=99.58  E-value=7.4e-16  Score=87.90  Aligned_cols=50  Identities=28%  Similarity=0.256  Sum_probs=48.2

Q ss_pred             CCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         66 RTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        66 rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      ||.||..|+..||..|..++||+...+.+||..+||++.+|++||||++.
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRa   50 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRM   50 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchh
Confidence            68999999999999999999999999999999999999999999999863

>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=99.57  E-value=1.9e-15  Score=92.06  Aligned_cols=56  Identities=27%  Similarity=0.247  Sum_probs=52.3

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      +..++.||.||..|+.+|+..|..++||+...++.||..+||++.+|++||+|++.
T Consensus        11 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~   66 (77)
T d1pufa_          11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRM   66 (77)
T ss_dssp             CTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHH
Confidence            35567899999999999999999999999999999999999999999999999863

>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=99.57  E-value=1e-15  Score=88.06  Aligned_cols=52  Identities=27%  Similarity=0.285  Sum_probs=49.5

Q ss_pred             CCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccC
Q psy15514         63 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSS  114 (187)
Q Consensus        63 ~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~  114 (187)
                      ++.|+.||+.|+..|+..|+.++||+...++.||..+||++.+|++||+|++
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR   52 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRR   52 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhh
Confidence            3578999999999999999999999999999999999999999999999976

>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=99.57  E-value=9.3e-16  Score=89.30  Aligned_cols=53  Identities=43%  Similarity=0.631  Sum_probs=50.7

Q ss_pred             CCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccC
Q psy15514         62 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSS  114 (187)
Q Consensus        62 ~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~  114 (187)
                      +++.||.||..|+..|+..|..++||+..++..||..+||++.+|++||+|++
T Consensus         1 Qrr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR   53 (60)
T d1yz8p1           1 QRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRR   53 (60)
T ss_dssp             SSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHH
Confidence            46789999999999999999999999999999999999999999999999976

>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=99.56  E-value=1.3e-15  Score=90.70  Aligned_cols=54  Identities=35%  Similarity=0.422  Sum_probs=51.1

Q ss_pred             CCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         62 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        62 ~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      +++.||.||+.|+.+|+..|..++||+...+..||..+||++.+|++||+|++.
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~   55 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRY   55 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHH
Confidence            357889999999999999999999999999999999999999999999999874

>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=99.56  E-value=1.4e-15  Score=89.85  Aligned_cols=55  Identities=73%  Similarity=0.919  Sum_probs=51.9

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      ++++.||.||..|+..|+..|..++||+..++..||..+||++.+|++||+|++.
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~   55 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRA   55 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHH
Confidence            4577899999999999999999999999999999999999999999999999763

>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=99.56  E-value=2.2e-15  Score=84.55  Aligned_cols=50  Identities=16%  Similarity=0.129  Sum_probs=48.2

Q ss_pred             CCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccC
Q psy15514         65 SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSS  114 (187)
Q Consensus        65 ~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~  114 (187)
                      +||.||..|+..|+..|..++||+...+..||..+||++.+|++||+|++
T Consensus         1 PRt~ft~~Q~~~Le~~F~~n~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1           1 PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             CCSCCCHHHHHHHHHHTTSSCSSTHHHHHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhhcCCcCc
Confidence            47999999999999999999999999999999999999999999999975

>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=99.54  E-value=2.1e-14  Score=88.25  Aligned_cols=57  Identities=26%  Similarity=0.295  Sum_probs=52.3

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhh----cCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFER----TQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG  117 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~----~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~  117 (187)
                      +.+|.||.||..|+..|+..|+.    ++||+..++++||..+||++.+|++||+|.+...
T Consensus        16 ~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~   76 (80)
T d1wh7a_          16 TTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSG   76 (80)
T ss_dssp             CSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCS
T ss_pred             CCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCC
Confidence            56688999999999999988886    7999999999999999999999999999988654

>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=99.53  E-value=2.9e-15  Score=93.56  Aligned_cols=56  Identities=29%  Similarity=0.287  Sum_probs=49.4

Q ss_pred             cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      .++++.|+.||..|+..|+..|..++||+..++++||..+||++.+|++||||++.
T Consensus        25 ~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~   80 (88)
T d1b72a_          25 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRM   80 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHH
Confidence            35567899999999999999999999999999999999999999999999999863

>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=99.52  E-value=6e-15  Score=87.32  Aligned_cols=56  Identities=27%  Similarity=0.401  Sum_probs=52.6

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      +.+|.||.||..|+..|+..|..++||+..+++.||..+||++.+|++||+|++..
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k   57 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCK   57 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHH
Confidence            45788999999999999999999999999999999999999999999999998744

>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=99.50  E-value=1.6e-14  Score=85.59  Aligned_cols=57  Identities=18%  Similarity=0.209  Sum_probs=53.0

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG  117 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~  117 (187)
                      .+++.||.|+..|+..|+..|..++||+..++++||..+||++.+|++||+|++...
T Consensus         7 ~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~   63 (67)
T d1ocpa_           7 ARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKG   63 (67)
T ss_dssp             CSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSS
T ss_pred             ccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHH
Confidence            456788999999999999999999999999999999999999999999999987653

>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=99.49  E-value=1.3e-14  Score=87.05  Aligned_cols=53  Identities=21%  Similarity=0.160  Sum_probs=49.4

Q ss_pred             CCCCCCcCHHHHHHHHHHhhh-cCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         63 RRSRTTFSAQQLDELERAFER-TQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        63 ~r~rt~ft~~ql~~Le~~F~~-~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      ++.|+.||..|+..|+..|.. +.||+...++.||..+||++.+|++||+|++.
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRa   55 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLA   55 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            467899999999999999986 67999999999999999999999999999874

>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=99.48  E-value=1.7e-14  Score=81.67  Aligned_cols=50  Identities=22%  Similarity=0.240  Sum_probs=48.0

Q ss_pred             CCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         66 RTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        66 rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      ||.||++|+..|+..|..++||+..++..||..+||++.+|++||+|++.
T Consensus         1 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~   50 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRM   50 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhh
Confidence            68999999999999999999999999999999999999999999999764

>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=99.46  E-value=3e-14  Score=85.69  Aligned_cols=57  Identities=26%  Similarity=0.237  Sum_probs=51.8

Q ss_pred             CCCCCCCCcCHHHHHHHHHHhhh-cCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514         61 KQRRSRTTFSAQQLDELERAFER-TQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG  117 (187)
Q Consensus        61 ~~~r~rt~ft~~ql~~Le~~F~~-~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~  117 (187)
                      +.++.|+.||.+|+..|+..|+. ++||+..++++||..+||+..+|++||+|++...
T Consensus         6 ~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~   63 (71)
T d1wi3a_           6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHV   63 (71)
T ss_dssp             CCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHC
T ss_pred             CCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhh
Confidence            45677899999999999999974 8999999999999999999999999999987554

>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=99.45  E-value=3.5e-14  Score=81.84  Aligned_cols=53  Identities=23%  Similarity=0.216  Sum_probs=49.8

Q ss_pred             CCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         64 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        64 r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      +.||.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|++..
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k   53 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQR   53 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHH
Confidence            45899999999999999999999999999999999999999999999998643

>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=99.43  E-value=4.4e-14  Score=87.24  Aligned_cols=53  Identities=28%  Similarity=0.314  Sum_probs=49.1

Q ss_pred             CCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhc---------------CCchhhHhHhhccCC
Q psy15514         63 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTK---------------LFPHFLIIIEQQSSG  115 (187)
Q Consensus        63 ~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~---------------l~~~~v~~wfq~~~~  115 (187)
                      |+.|+.||+.|+.+||..|+.++||+...+++||..+|               +++.+|++||+|++.
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~   68 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRK   68 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHH
Confidence            57889999999999999999999999999999999765               899999999999874

>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=99.38  E-value=2e-13  Score=78.24  Aligned_cols=50  Identities=16%  Similarity=0.161  Sum_probs=48.1

Q ss_pred             CCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         66 RTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        66 rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      ||.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|++.
T Consensus         2 RT~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~   51 (57)
T d1e3oc1           2 RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQ   51 (57)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            79999999999999999999999999999999999999999999999763

>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=99.26  E-value=3.3e-12  Score=77.51  Aligned_cols=47  Identities=19%  Similarity=0.070  Sum_probs=45.1

Q ss_pred             cCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         69 FSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        69 ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      +|.+|+..|+..|..++||+..++++||..+||++.+|++||+|++.
T Consensus        11 ~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~   57 (76)
T d2ecba1          11 KTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKK   57 (76)
T ss_dssp             CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHH
Confidence            58999999999999999999999999999999999999999999874

>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=99.25  E-value=3.9e-12  Score=77.26  Aligned_cols=50  Identities=20%  Similarity=0.064  Sum_probs=47.0

Q ss_pred             CCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         66 RTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        66 rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      +..||.+|+..|+..|..++||+..+++.||..++|++.+|++||+|++.
T Consensus         7 ~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~   56 (76)
T d2ecca1           7 GKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRY   56 (76)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            35689999999999999999999999999999999999999999999874

>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=99.23  E-value=4.7e-12  Score=76.27  Aligned_cols=53  Identities=25%  Similarity=0.274  Sum_probs=48.7

Q ss_pred             CCCCCCcCHHHHHHHHHHhhh---cCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         63 RRSRTTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        63 ~r~rt~ft~~ql~~Le~~F~~---~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      ++.|+.|+..|+..|+..|..   ++||+..+++.||..+||++.+|++||+|.+.
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~   57 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRI   57 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHH
Confidence            456789999999999999975   77999999999999999999999999999764

>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=99.22  E-value=3.7e-12  Score=77.32  Aligned_cols=52  Identities=19%  Similarity=0.176  Sum_probs=47.7

Q ss_pred             CCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhc---------------------CCchhhHhHhhccCCCC
Q psy15514         66 RTTFSAQQLDELERAFERTQYPDIYTREELAQRTK---------------------LFPHFLIIIEQQSSGEG  117 (187)
Q Consensus        66 rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~---------------------l~~~~v~~wfq~~~~~~  117 (187)
                      |+.||+.|+..|+..|+.++||+...++.||..++                     +++.+|++||+|++...
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~   73 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEE   73 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTT
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999999999985                     78889999999987553

>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=99.13  E-value=9.9e-12  Score=69.57  Aligned_cols=47  Identities=23%  Similarity=0.169  Sum_probs=42.7

Q ss_pred             CHHHHHHHHHHhhh-cCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514         70 SAQQLDELERAFER-TQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE  116 (187)
Q Consensus        70 t~~ql~~Le~~F~~-~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~  116 (187)
                      |.+|+..||..|.. ++||+...+++||..+||++.+|++||+|++..
T Consensus         1 T~~q~~iLE~~F~~~~~~P~~~~~~~LA~~~~ls~~qV~~WFqNrR~k   48 (52)
T d1x2ma1           1 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQ   48 (52)
T ss_dssp             SSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHH
T ss_pred             ChhHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcc
Confidence            45789999999976 789999999999999999999999999998643

>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=99.07  E-value=1.7e-11  Score=70.40  Aligned_cols=51  Identities=18%  Similarity=0.193  Sum_probs=46.0

Q ss_pred             CCCCcCHHHHHHHHHHhhh-cCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514         65 SRTTFSAQQLDELERAFER-TQYPDIYTREELAQRTKLFPHFLIIIEQQSSG  115 (187)
Q Consensus        65 ~rt~ft~~ql~~Le~~F~~-~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~  115 (187)
                      .++.++.++...||..|.. ++||+...+++||..+||++.+|++||+|++.
T Consensus         4 ~~~~~k~~~~~iLE~~F~~~~~yPs~~~~~~LA~~lgls~~qV~~WFqNrR~   55 (59)
T d2cqxa1           4 DSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRN   55 (59)
T ss_dssp             CCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCccccHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhc
Confidence            4567888888999999976 68999999999999999999999999999763

>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=99.07  E-value=9.3e-11  Score=68.03  Aligned_cols=52  Identities=12%  Similarity=0.115  Sum_probs=47.4

Q ss_pred             CCCCCCcCHHHHHHHHHHhhh---cCCCChhhhHHHHHhhcCCchhhHhHhhccC
Q psy15514         63 RRSRTTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLFPHFLIIIEQQSS  114 (187)
Q Consensus        63 ~r~rt~ft~~ql~~Le~~F~~---~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~  114 (187)
                      ++.|+.|+.+++..|+..|..   ++||+..++..||..+||+..+|.+||+|.+
T Consensus         3 krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R   57 (62)
T d1x2na1           3 KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINAR   57 (62)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHH
Confidence            345678999999999999985   7899999999999999999999999999865

>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=99.01  E-value=1.6e-10  Score=66.58  Aligned_cols=47  Identities=21%  Similarity=0.211  Sum_probs=43.9

Q ss_pred             CcCHHHHHHHHHHhhhc---CCCChhhhHHHHHhhcCCchhhHhHhhccC
Q psy15514         68 TFSAQQLDELERAFERT---QYPDIYTREELAQRTKLFPHFLIIIEQQSS  114 (187)
Q Consensus        68 ~ft~~ql~~Le~~F~~~---~yp~~~~r~~la~~~~l~~~~v~~wfq~~~  114 (187)
                      .|+.+|+..|+..|..+   +||+..+++.||..+||++.+|++||+|.+
T Consensus         4 Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R   53 (60)
T d1k61a_           4 RFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR   53 (60)
T ss_dssp             SCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhc
Confidence            49999999999999765   699999999999999999999999999876

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=93.54  E-value=0.067  Score=27.82  Aligned_cols=40  Identities=18%  Similarity=0.354  Sum_probs=34.8

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhc
Q psy15514        137 TTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI  181 (187)
Q Consensus       137 ~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~  181 (187)
                      ..+|++|+..+.+.+.... +    ..++|..+||+...|-.||.
T Consensus         4 ~~lt~~q~~~a~~l~~~G~-s----~~~iA~~~gVSr~TiYry~p   43 (47)
T d1ijwc_           4 RAINKHEQEQISRLLEKGH-P----RQQLAIIFGIGVSTLYRYFP   43 (47)
T ss_dssp             CSSCHHHHHHHHHHHHTTC-C----HHHHHHHHTCCHHHHHHHSC
T ss_pred             CcCCHHHHHHHHHHHHCCC-C----HHHHHHHHCcCHHHHHhhCC
Confidence            5789999999999998664 3    77899999999999999984

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.94  E-value=0.13  Score=28.72  Aligned_cols=46  Identities=15%  Similarity=0.270  Sum_probs=37.7

Q ss_pred             cCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhccc
Q psy15514        135 SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVR  183 (187)
Q Consensus       135 ~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nr  183 (187)
                      .|..+|.++...+-..++.++-..   ..++|..+||+...|..|..|+
T Consensus         4 kRk~LT~~eK~~ii~~~e~g~k~s---q~eIA~~fGv~~STvs~IlKnK   49 (66)
T d1hlva1           4 KRRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNK   49 (66)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTH
T ss_pred             ccccCCHHHHHHHHHHHHcCCcch---HHHHHHHhCCChhHHHHHHHHH
Confidence            345689888888888888886433   4579999999999999999886