Psyllid ID: psy2123

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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---
Protein Sequence
MEYDWMLTLRCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHRNLDAPTSEQPLPPCTNATPLSSAPPSSSHSFDFCAMPHSQCNSTCTFTSP
Secondary Structure (PSIPRED)
cccccccccccccccccHHHcccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHccccccccHHHcccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
meydwmltlrcdgedddydyerrkpkprrnrttfnsHQLNALEKVFErthypdafVREELAKKVCLSEARVQVWFQNRRAKfrrnernfishrnldaptseqplppctnatplssappssshsfdfcamphsqcnstctftsp
Flexible Loop (DISEMBL)
meydwmltlrcdgedddydyerrkpkprrnrttfnshqlnALEKVFERTHYPDAFVREELAKkvclsearvqvwfqnrrakfrrnernfishrnldaptseqPLPPCTNATPLSSAPPSSSHSFDFCAMPHSQCNSTCTFTSP
Low Complexity Region (SEG)
MEYDWMLTLRCDGedddydyerrkpkprrnrttFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHRNLDAPTSEQPLPPCTNATplssappssshsFDFCAMPHSQCNSTCTFTSP
Disordered region (IsUnstruct)
****WMLTLRC***************************LNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR************************************************************
Disordered Region (DISOPRED)
********************************TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK**************************************************************
Disordered Region (DISEMBL)
MEYDWMLTLRCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHRNLDAPTSEQPLPPCTNAT***********SFDFCAMPHSQ**********
Disordered Region (DISPRO)
******L***********************RTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN*******************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEYDWMLTLRCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHRNLDAPTSEQPLPPCTNATPLSSAPPSSSHSFDFCAMPHSQCNSTCTFTSP
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	143	2.2.26 [Sep-21-2011]
Q90963	165	Paired mesoderm homeobox	yes	N/A	0.524	0.454	0.682	3e-25
Q99811	253	Paired mesoderm homeobox	yes	N/A	0.643	0.363	0.572	3e-25
P63014	245	Paired mesoderm homeobox	yes	N/A	0.524	0.306	0.650	4e-25
P63013	245	Paired mesoderm homeobox	yes	N/A	0.524	0.306	0.650	4e-25
P54821	245	Paired mesoderm homeobox	no	N/A	0.524	0.306	0.650	4e-25
Q05437	245	Paired mesoderm homeobox	no	N/A	0.524	0.306	0.650	5e-25
Q06348	247	Paired mesoderm homeobox	no	N/A	0.524	0.303	0.682	1e-24
Q9I9D5	334	Retinal homeobox protein	N/A	N/A	0.699	0.299	0.549	1e-21
Q4LAL6	397	Homeobox protein aristale	no	N/A	0.482	0.173	0.666	2e-21
Q9PVX0	317	Retinal homeobox protein	no	N/A	0.615	0.277	0.561	2e-21

>sp|Q90963|PRRX2_CHICK Paired mesoderm homeobox protein 2 (Fragment) OS=Gallus gallus GN=PRRX2 PE=2 SV=1

 Score =  114 bits (284), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 56/82 (68%), Positives = 64/82 (78%), Gaps = 7/82 (8%)

Query: 32  TTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFIS 91
           TTFNS QL ALE+VFERTHYPDAFVREELA++V LSEARVQVWFQNRRAKFRRNER  ++
Sbjct: 21  TTFNSSQLQALERVFERTHYPDAFVREELARRVNLSEARVQVWFQNRRAKFRRNERAMLA 80

Query: 92  HRNLDAPTS-------EQPLPP 106
           +R+     S       EQP+ P
Sbjct: 81  NRSASLLKSYSQEAAIEQPMAP 102

May play a role in development of the heart.
Gallus gallus (taxid: 9031)

>sp|Q99811|PRRX2_HUMAN Paired mesoderm homeobox protein 2 OS=Homo sapiens GN=PRRX2 PE=2 SV=2

 Score =  113 bits (283), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 63/110 (57%), Positives = 73/110 (66%), Gaps = 18/110 (16%)

Query: 32  TTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFIS 91
           TTFNS QL ALE+VFERTHYPDAFVREELA++V LSEARVQVWFQNRRAKFRRNER  ++
Sbjct: 109 TTFNSSQLQALERVFERTHYPDAFVREELARRVNLSEARVQVWFQNRRAKFRRNERAMLA 168

Query: 92  HRNLDAPTS-------EQPLPP-----------CTNATPLSSAPPSSSHS 123
            R+     S       EQP+ P            T ++P S+ PP S  S
Sbjct: 169 SRSASLLKSYSQEAAIEQPVAPRPTALSPDYLSWTASSPYSTVPPYSPGS 218

May play a role in the scarless healing of cutaneous wounds during the first two trimesters of development.

Homo sapiens (taxid: 9606)

>sp|P63014|PRRX1_RAT Paired mesoderm homeobox protein 1 OS=Rattus norvegicus GN=Prrx1 PE=2 SV=1

 Score =  113 bits (282), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 54/83 (65%), Positives = 64/83 (77%), Gaps = 8/83 (9%)

Query: 32  TTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFIS 91
           TTFNS QL ALE+VFERTHYPDAFVRE+LA++V L+EARVQVWFQNRRAKFRRNER  ++
Sbjct: 99  TTFNSSQLQALERVFERTHYPDAFVREDLARRVNLTEARVQVWFQNRRAKFRRNERAMLA 158

Query: 92  HRNL--------DAPTSEQPLPP 106
           ++N         D    EQP+ P
Sbjct: 159 NKNASLLKSYSGDVTAVEQPIVP 181

Acts as a transcriptional regulator of muscle creatine kinase (MCK) and so has a role in the establishment of diverse mesodermal muscle types. The protein binds to an A/T-rich element in the muscle creatine enhancer.

Rattus norvegicus (taxid: 10116)

>sp|P63013|PRRX1_MOUSE Paired mesoderm homeobox protein 1 OS=Mus musculus GN=Prrx1 PE=2 SV=1

 Score =  113 bits (282), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 54/83 (65%), Positives = 64/83 (77%), Gaps = 8/83 (9%)

Query: 32  TTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFIS 91
           TTFNS QL ALE+VFERTHYPDAFVRE+LA++V L+EARVQVWFQNRRAKFRRNER  ++
Sbjct: 99  TTFNSSQLQALERVFERTHYPDAFVREDLARRVNLTEARVQVWFQNRRAKFRRNERAMLA 158

Query: 92  HRNL--------DAPTSEQPLPP 106
           ++N         D    EQP+ P
Sbjct: 159 NKNASLLKSYSGDVTAVEQPIVP 181

Acts as a transcriptional regulator of muscle creatine kinase (MCK) and so has a role in the establishment of diverse mesodermal muscle types. The protein binds to an A/T-rich element in the muscle creatine enhancer.

Mus musculus (taxid: 10090)

>sp|P54821|PRRX1_HUMAN Paired mesoderm homeobox protein 1 OS=Homo sapiens GN=PRRX1 PE=1 SV=2

 Score =  113 bits (282), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 54/83 (65%), Positives = 64/83 (77%), Gaps = 8/83 (9%)

Query: 32  TTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFIS 91
           TTFNS QL ALE+VFERTHYPDAFVRE+LA++V L+EARVQVWFQNRRAKFRRNER  ++
Sbjct: 99  TTFNSSQLQALERVFERTHYPDAFVREDLARRVNLTEARVQVWFQNRRAKFRRNERAMLA 158

Query: 92  HRNL--------DAPTSEQPLPP 106
           ++N         D    EQP+ P
Sbjct: 159 NKNASLLKSYSGDVTAVEQPIVP 181

Acts as a transcriptional regulator of muscle creatine kinase (MCK) and so has a role in the establishment of diverse mesodermal muscle types. The protein binds to an A/T-rich element in the muscle creatine enhancer.

Homo sapiens (taxid: 9606)

>sp|Q05437|PRRX1_CHICK Paired mesoderm homeobox protein 1 OS=Gallus gallus GN=PRRX1 PE=1 SV=2

 Score =  112 bits (281), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 54/83 (65%), Positives = 63/83 (75%), Gaps = 8/83 (9%)

Query: 32  TTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFIS 91
           TTFNS QL ALE+VFERTHYPDAFVRE+LA++V L+EARVQVWFQNRRAKFRRNER  ++
Sbjct: 99  TTFNSSQLQALERVFERTHYPDAFVREDLARRVNLTEARVQVWFQNRRAKFRRNERAMLA 158

Query: 92  HRNL--------DAPTSEQPLPP 106
            +N         D    EQP+ P
Sbjct: 159 SKNASLLKSYSGDVTAVEQPIVP 181

May participate in maintenance of mesenchymal cell lineages derived from both mesoderm and the neural crest and in patterning of the limbs and the face.

Gallus gallus (taxid: 9031)

>sp|Q06348|PRRX2_MOUSE Paired mesoderm homeobox protein 2 OS=Mus musculus GN=Prrx2 PE=2 SV=2

 Score =  111 bits (277), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 56/82 (68%), Positives = 63/82 (76%), Gaps = 7/82 (8%)

Query: 32  TTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFIS 91
           TTFNS QL ALE+VFERTHYPDAFVREELA++V LSEARVQVWFQNRRAKFRRNER  ++
Sbjct: 103 TTFNSSQLQALERVFERTHYPDAFVREELARRVNLSEARVQVWFQNRRAKFRRNERAMLA 162

Query: 92  HRNLDAPTS-------EQPLPP 106
            R+     S       EQP+ P
Sbjct: 163 TRSASLLKSYGQEAAIEQPVAP 184

Mus musculus (taxid: 10090)

>sp|Q9I9D5|RX1_ASTFA Retinal homeobox protein Rx1 OS=Astyanax fasciatus GN=rx1 PE=2 SV=1

 Score =  102 bits (253), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 56/102 (54%), Positives = 70/102 (68%), Gaps = 2/102 (1%)

Query: 19  DYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNR 78
           D E+ K K RRNRTTF ++QL+ LE+ FE++HYPD + REELA KV L E RVQVWFQNR
Sbjct: 134 DEEQPKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQVWFQNR 193

Query: 79  RAKFRRNERNFISHRNL-DAPTSEQPLPPC-TNATPLSSAPP 118
           RAK+RR E+   S   L D+P      PP  TN  P+S++ P
Sbjct: 194 RAKWRRQEKMDASAVKLHDSPMLSFNRPPMHTNVGPMSNSLP 235

Plays a critical role in eye formation by regulating the initial specification of retinal cells and/or their subsequent proliferation.

Astyanax fasciatus (taxid: 223369)

>sp|Q4LAL6|ALX4_BOVIN Homeobox protein aristaless-like 4 OS=Bos taurus GN=ALX4 PE=2 SV=1

 Score =  101 bits (251), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 46/69 (66%), Positives = 55/69 (79%)

Query: 19  DYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNR 78
           D E  K K RRNRTTF S+QL  LEKVF++THYPD + RE+LA +  L+EARVQVWFQNR
Sbjct: 192 DSESNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNR 251

Query: 79  RAKFRRNER 87
           RAK+R+ ER
Sbjct: 252 RAKWRKRER 260

Transcription factor involved in skull and limb development.

Bos taurus (taxid: 9913)

>sp|Q9PVX0|RX2_CHICK Retinal homeobox protein Rx2 OS=Gallus gallus GN=RX2 PE=2 SV=1

 Score =  101 bits (251), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 50/89 (56%), Positives = 63/89 (70%), Gaps = 1/89 (1%)

Query: 12  DGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARV 71
            G+    D E+ K K RRNRTTF ++QL+ LE+ FE++HYPD + REELA KV L E RV
Sbjct: 107 GGDGKPSDEEQPKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRV 166

Query: 72  QVWFQNRRAKFRRNERNFISHRNL-DAPT 99
           QVWFQNRRAK+RR E+  +S   L D+P 
Sbjct: 167 QVWFQNRRAKWRRQEKLEVSSMKLQDSPI 195

Plays a critical role in eye formation by regulating the initial specification of retinal cells and/or their subsequent proliferation.

Gallus gallus (taxid: 9031)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	143
328717151	244	PREDICTED: paired mesoderm homeobox prot	0.713	0.418	0.645	1e-29
242020400	270	Ultrabithorax, putative [Pediculus human	0.552	0.292	0.790	2e-27
443703131	195	hypothetical protein CAPTEDRAFT_171492 [	0.783	0.574	0.528	3e-27
195429318	288	GK19597 [Drosophila willistoni] gi|19415	0.657	0.326	0.656	1e-26
195489018	286	GE11607 [Drosophila yakuba] gi|194178660	0.587	0.293	0.761	2e-26
195380555	288	GJ20984 [Drosophila virilis] gi|19414383	0.762	0.378	0.601	2e-26
24659086	275	CG9876 [Drosophila melanogaster] gi|2162	0.587	0.305	0.75	5e-26
33589354	275	RE60081p [Drosophila melanogaster]	0.587	0.305	0.75	5e-26
269784949	242	paired mesoderm homeobox 2-like protein	0.713	0.421	0.592	6e-26
195346972	273	GM15584 [Drosophila sechellia] gi|194135	0.587	0.307	0.75	7e-26

>gi|328717151|ref|XP_003246132.1| PREDICTED: paired mesoderm homeobox protein 1-like [Acyrthosiphon pisum]

 Score =  134 bits (338), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 71/110 (64%), Positives = 83/110 (75%), Gaps = 8/110 (7%)

Query: 22  RRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81
           +RK KPRRNRTTF+S QL ALEKVFERTHYPDAFVREELA++VCLSEARVQVWFQNRRAK
Sbjct: 41  QRKSKPRRNRTTFSSCQLRALEKVFERTHYPDAFVREELARRVCLSEARVQVWFQNRRAK 100

Query: 82  FRRNERNFISHRN--------LDAPTSEQPLPPCTNATPLSSAPPSSSHS 123
           FRRNER+ +S  N          +P  EQPL P +N   + + PP ++ S
Sbjct: 101 FRRNERSSLSRNNPTLSTVPDCRSPNVEQPLLPRSNTNVVHAEPPFTAGS 150

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242020400|ref|XP_002430643.1| Ultrabithorax, putative [Pediculus humanus corporis] gi|212515815|gb|EEB17905.1| Ultrabithorax, putative [Pediculus humanus corporis]

 Score =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 64/81 (79%), Positives = 70/81 (86%), Gaps = 2/81 (2%)

Query: 14  EDDDY-DYERRK-PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARV 71
           E DDY D E  K  KPRRNRTTF + QL+ALE+VFE+THYPDAFVREELAK+V LSEARV
Sbjct: 71  EKDDYVDGENGKMKKPRRNRTTFTTIQLSALERVFEKTHYPDAFVREELAKRVGLSEARV 130

Query: 72  QVWFQNRRAKFRRNERNFISH 92
           QVWFQNRRAKFRRNER+ ISH
Sbjct: 131 QVWFQNRRAKFRRNERSLISH 151

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443703131|gb|ELU00842.1| hypothetical protein CAPTEDRAFT_171492 [Capitella teleta]

 Score =  126 bits (316), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 73/138 (52%), Positives = 84/138 (60%), Gaps = 26/138 (18%)

Query: 22  RRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81
           ++K K RRNRTTFNS QL ALE+VFERTHYPDAFVREELA++V LSEARVQVWFQNRRAK
Sbjct: 27  KKKQKQRRNRTTFNSQQLAALERVFERTHYPDAFVREELARRVNLSEARVQVWFQNRRAK 86

Query: 82  FRRNERNFISHRNL----------------DAPTSEQPLPPCTNAT-PLSSAPPSSSHSF 124
           FRRNERN ++ R+                    T EQPL    NAT PL        H  
Sbjct: 87  FRRNERNVLAQRSTMYGSGGAVGAVRPAESGCGTGEQPLSVRPNATQPL--------HGG 138

Query: 125 DFCAMPHSQCNSTCTFTS 142
           D+ +  +S   S C    
Sbjct: 139 DYASW-NSPAGSPCALAG 155

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|195429318|ref|XP_002062710.1| GK19597 [Drosophila willistoni] gi|194158795|gb|EDW73696.1| GK19597 [Drosophila willistoni]

 Score =  124 bits (311), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 65/99 (65%), Positives = 72/99 (72%), Gaps = 5/99 (5%)

Query: 26  KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
           KPRRNRTTF+S QL ALEKVFERTHYPDAFVREELA KV LSEARVQVWFQNRRAKFRRN
Sbjct: 112 KPRRNRTTFSSAQLTALEKVFERTHYPDAFVREELATKVHLSEARVQVWFQNRRAKFRRN 171

Query: 86  ERNFISHRNLDAPTSEQPLPPCTNATPLSSAPPSSSHSF 124
           ER+    R L      Q +P      P+S+A   + H +
Sbjct: 172 ERSVSGSRPLMDHAGSQLVP-----APISTASTGNMHKY 205

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195489018|ref|XP_002092559.1| GE11607 [Drosophila yakuba] gi|194178660|gb|EDW92271.1| GE11607 [Drosophila yakuba]

 Score =  124 bits (310), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 64/84 (76%), Positives = 66/84 (78%)

Query: 26  KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
           KPRRNRTTF+S QL ALEKVFERTHYPDAFVREELA KV LSEARVQVWFQNRRAKFRRN
Sbjct: 126 KPRRNRTTFSSAQLTALEKVFERTHYPDAFVREELATKVHLSEARVQVWFQNRRAKFRRN 185

Query: 86  ERNFISHRNLDAPTSEQPLPPCTN 109
           ER+  S   LDA     P P   N
Sbjct: 186 ERSVGSRPLLDAAPQLVPAPISNN 209

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195380555|ref|XP_002049036.1| GJ20984 [Drosophila virilis] gi|194143833|gb|EDW60229.1| GJ20984 [Drosophila virilis]

 Score =  123 bits (309), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 68/113 (60%), Positives = 77/113 (68%), Gaps = 4/113 (3%)

Query: 26  KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
           KPRRNRTTF+S QL ALEKVFERTHYPDAFVREELA KV LSEARVQVWFQNRRAKFRRN
Sbjct: 133 KPRRNRTTFSSAQLTALEKVFERTHYPDAFVREELATKVHLSEARVQVWFQNRRAKFRRN 192

Query: 86  ERNF-ISHRNLDAPTSEQPLPPCTNATP---LSSAPPSSSHSFDFCAMPHSQC 134
           ER+  I    LD  T   P P   N      L+ + P  +++ +F  +    C
Sbjct: 193 ERSVSIGRPLLDTATQLVPAPMPNNIHKYPNLTHSAPPGAYALNFAPLELRSC 245

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|24659086|ref|NP_611756.1| CG9876 [Drosophila melanogaster] gi|21626590|gb|AAF46956.2| CG9876 [Drosophila melanogaster] gi|94400579|gb|ABF17914.1| FI01017p [Drosophila melanogaster]

 Score =  122 bits (306), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 63/84 (75%), Positives = 65/84 (77%)

Query: 26  KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
           KPRRNRTTF+S QL ALEKVFERTHYPDAFVREELA KV LSEARVQVWFQNRRAKFRRN
Sbjct: 116 KPRRNRTTFSSAQLTALEKVFERTHYPDAFVREELATKVHLSEARVQVWFQNRRAKFRRN 175

Query: 86  ERNFISHRNLDAPTSEQPLPPCTN 109
           ER+  S   LD      P P   N
Sbjct: 176 ERSVGSRTLLDTAPQLVPAPISNN 199

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|33589354|gb|AAQ22444.1| RE60081p [Drosophila melanogaster]

 Score =  122 bits (306), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 63/84 (75%), Positives = 65/84 (77%)

Query: 26  KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
           KPRRNRTTF+S QL ALEKVFERTHYPDAFVREELA KV LSEARVQVWFQNRRAKFRRN
Sbjct: 116 KPRRNRTTFSSAQLTALEKVFERTHYPDAFVREELATKVHLSEARVQVWFQNRRAKFRRN 175

Query: 86  ERNFISHRNLDAPTSEQPLPPCTN 109
           ER+  S   LD      P P   N
Sbjct: 176 ERSVGSRTLLDTAPQLVPAPISNN 199

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|269784949|ref|NP_001161626.1| paired mesoderm homeobox 2-like protein [Saccoglossus kowalevskii] gi|268054257|gb|ACY92615.1| paired mesoderm homeobox 2-like protein [Saccoglossus kowalevskii]

 Score =  122 bits (305), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 67/113 (59%), Positives = 80/113 (70%), Gaps = 11/113 (9%)

Query: 22  RRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81
           ++  K RR+RTTF ++QL ALEKVFERTHYPDAFVREELAKKV LSEARVQVWFQNRRAK
Sbjct: 94  KKAKKQRRSRTTFTTNQLGALEKVFERTHYPDAFVREELAKKVDLSEARVQVWFQNRRAK 153

Query: 82  FRRNERNFISHRNLDAPT--------SEQPL-PPCTNATP--LSSAPPSSSHS 123
           +RRNERN ++ R    P          + PL  P T A+P  L+   P++SH 
Sbjct: 154 YRRNERNVLAARQKLYPAPIADNNILEQSPLTAPSTLASPDYLTWTNPANSHG 206

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|195346972|ref|XP_002040028.1| GM15584 [Drosophila sechellia] gi|194135377|gb|EDW56893.1| GM15584 [Drosophila sechellia]

 Score =  122 bits (305), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 63/84 (75%), Positives = 65/84 (77%)

Query: 26  KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
           KPRRNRTTF+S QL ALEKVFERTHYPDAFVREELA KV LSEARVQVWFQNRRAKFRRN
Sbjct: 116 KPRRNRTTFSSAQLTALEKVFERTHYPDAFVREELATKVHLSEARVQVWFQNRRAKFRRN 175

Query: 86  ERNFISHRNLDAPTSEQPLPPCTN 109
           ER+  S   LD      P P   N
Sbjct: 176 ERSVGSRPLLDTAPQLVPAPISNN 199

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	143
FB|FBgn0034821	275	CG9876 [Drosophila melanogaste	0.517	0.269	0.740	2.6e-22
UNIPROTKB|F1NZI9	165	PRRX2 "Paired mesoderm homeobo	0.510	0.442	0.675	3.4e-22
UNIPROTKB|Q90963	165	PRRX2 "Paired mesoderm homeobo	0.510	0.442	0.675	3.4e-22
UNIPROTKB|E1BF87	166	PRRX2 "Uncharacterized protein	0.510	0.439	0.675	4.3e-22
UNIPROTKB|F1RQG1	211	PRRX2 "Uncharacterized protein	0.510	0.345	0.675	4.3e-22
UNIPROTKB|F1PD53	234	PRRX2 "Uncharacterized protein	0.426	0.260	0.803	5.5e-22
UNIPROTKB|J9P7P0	234	PRRX2 "Uncharacterized protein	0.426	0.260	0.803	5.5e-22
UNIPROTKB|A2VE85	245	PRRX1 "Paired related homeobox	0.510	0.297	0.641	7e-22
UNIPROTKB|E2RGD6	245	PRRX1 "Uncharacterized protein	0.510	0.297	0.641	7e-22
UNIPROTKB|J9P9S0	217	PRRX1 "Uncharacterized protein	0.510	0.336	0.641	7e-22

FB|FBgn0034821 CG9876 [Drosophila melanogaster (taxid:7227)]

 Score = 259 (96.2 bits), Expect = 2.6e-22, P = 2.6e-22
 Identities = 57/77 (74%), Positives = 62/77 (80%)

Query:    34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHR 93
             F+S QL ALEKVFERTHYPDAFVREELA KV LSEARVQVWFQNRRAKFRRNER+  S  
Sbjct:   124 FSSAQLTALEKVFERTHYPDAFVREELATKVHLSEARVQVWFQNRRAKFRRNERSVGSRT 183

Query:    94 NLDAPTSEQPLP-PCTN 109
              LD  T+ Q +P P +N
Sbjct:   184 LLD--TAPQLVPAPISN 198

GO:0005634 "nucleus" evidence=ISS

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

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

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

UNIPROTKB|F1NZI9 PRRX2 "Paired mesoderm homeobox protein 2" [Gallus gallus (taxid:9031)]

 Score = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 54/80 (67%), Positives = 62/80 (77%)

Query:    34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHR 93
             FNS QL ALE+VFERTHYPDAFVREELA++V LSEARVQVWFQNRRAKFRRNER  +++R
Sbjct:    23 FNSSQLQALERVFERTHYPDAFVREELARRVNLSEARVQVWFQNRRAKFRRNERAMLANR 82

Query:    94 NLDAPTS-------EQPLPP 106
             +     S       EQP+ P
Sbjct:    83 SASLLKSYSQEAAIEQPMAP 102

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0002053 "positive regulation of mesenchymal cell proliferation" evidence=IEA

GO:0030326 "embryonic limb morphogenesis" evidence=IEA

GO:0042472 "inner ear morphogenesis" evidence=IEA

GO:0042474 "middle ear morphogenesis" evidence=IEA

GO:0045880 "positive regulation of smoothened signaling pathway" evidence=IEA

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

GO:0048844 "artery morphogenesis" evidence=IEA

GO:0051216 "cartilage development" evidence=IEA

UNIPROTKB|Q90963 PRRX2 "Paired mesoderm homeobox protein 2" [Gallus gallus (taxid:9031)]

 Score = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 54/80 (67%), Positives = 62/80 (77%)

Query:    34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHR 93
             FNS QL ALE+VFERTHYPDAFVREELA++V LSEARVQVWFQNRRAKFRRNER  +++R
Sbjct:    23 FNSSQLQALERVFERTHYPDAFVREELARRVNLSEARVQVWFQNRRAKFRRNERAMLANR 82

Query:    94 NLDAPTS-------EQPLPP 106
             +     S       EQP+ P
Sbjct:    83 SASLLKSYSQEAAIEQPMAP 102

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|E1BF87 PRRX2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 257 (95.5 bits), Expect = 4.3e-22, P = 4.3e-22
 Identities = 54/80 (67%), Positives = 62/80 (77%)

Query:    34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHR 93
             FNS QL ALE+VFERTHYPDAFVREELA++V LSEARVQVWFQNRRAKFRRNER  +++R
Sbjct:    24 FNSSQLQALERVFERTHYPDAFVREELARRVNLSEARVQVWFQNRRAKFRRNERAMLANR 83

Query:    94 NLDAPTS-------EQPLPP 106
             +     S       EQP+ P
Sbjct:    84 SASLLKSYSQEAAIEQPVAP 103

GO:0005634 "nucleus" evidence=IEA

GO:0051216 "cartilage development" evidence=IEA

GO:0048844 "artery morphogenesis" evidence=IEA

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

GO:0045880 "positive regulation of smoothened signaling pathway" evidence=IEA

GO:0042474 "middle ear morphogenesis" evidence=IEA

GO:0042472 "inner ear morphogenesis" evidence=IEA

GO:0030326 "embryonic limb morphogenesis" evidence=IEA

GO:0002053 "positive regulation of mesenchymal cell proliferation" evidence=IEA

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

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

UNIPROTKB|F1RQG1 PRRX2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 257 (95.5 bits), Expect = 4.3e-22, P = 4.3e-22
 Identities = 54/80 (67%), Positives = 62/80 (77%)

Query:    34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHR 93
             FNS QL ALE+VFERTHYPDAFVREELA++V LSEARVQVWFQNRRAKFRRNER  +++R
Sbjct:    69 FNSSQLQALERVFERTHYPDAFVREELARRVNLSEARVQVWFQNRRAKFRRNERAMLANR 128

Query:    94 NLDAPTS-------EQPLPP 106
             +     S       EQP+ P
Sbjct:   129 SASLLKSYSQEAAIEQPVAP 148

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

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

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

UNIPROTKB|F1PD53 PRRX2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 256 (95.2 bits), Expect = 5.5e-22, P = 5.5e-22
 Identities = 49/61 (80%), Positives = 56/61 (91%)

Query:    34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHR 93
             FNS QL ALE+VFERTHYPDAFVREELA++V LSEARVQVWFQNRRAKFRRNER  +++R
Sbjct:    92 FNSSQLQALERVFERTHYPDAFVREELARRVNLSEARVQVWFQNRRAKFRRNERAMLANR 151

Query:    94 N 94
             +
Sbjct:   152 S 152

GO:0005634 "nucleus" evidence=IEA

GO:0051216 "cartilage development" evidence=IEA

GO:0048844 "artery morphogenesis" evidence=IEA

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

GO:0045880 "positive regulation of smoothened signaling pathway" evidence=IEA

GO:0042474 "middle ear morphogenesis" evidence=IEA

GO:0042472 "inner ear morphogenesis" evidence=IEA

GO:0030326 "embryonic limb morphogenesis" evidence=IEA

GO:0002053 "positive regulation of mesenchymal cell proliferation" evidence=IEA

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

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

UNIPROTKB|J9P7P0 PRRX2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 256 (95.2 bits), Expect = 5.5e-22, P = 5.5e-22
 Identities = 49/61 (80%), Positives = 56/61 (91%)

Query:    34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHR 93
             FNS QL ALE+VFERTHYPDAFVREELA++V LSEARVQVWFQNRRAKFRRNER  +++R
Sbjct:    92 FNSSQLQALERVFERTHYPDAFVREELARRVNLSEARVQVWFQNRRAKFRRNERAMLANR 151

Query:    94 N 94
             +
Sbjct:   152 S 152

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

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

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

UNIPROTKB|A2VE85 PRRX1 "Paired related homeobox 1" [Bos taurus (taxid:9913)]

 Score = 255 (94.8 bits), Expect = 7.0e-22, P = 7.0e-22
 Identities = 52/81 (64%), Positives = 62/81 (76%)

Query:    34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHR 93
             FNS QL ALE+VFERTHYPDAFVRE+LA++V L+EARVQVWFQNRRAKFRRNER  ++++
Sbjct:   101 FNSSQLQALERVFERTHYPDAFVREDLARRVNLTEARVQVWFQNRRAKFRRNERAMLANK 160

Query:    94 NL--------DAPTSEQPLPP 106
             N         D    EQP+ P
Sbjct:   161 NASLLKSYSGDVTAVEQPIVP 181

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

GO:0060021 "palate development" evidence=IEA

GO:0051216 "cartilage development" evidence=IEA

GO:0048844 "artery morphogenesis" evidence=IEA

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

GO:0045880 "positive regulation of smoothened signaling pathway" evidence=IEA

GO:0042474 "middle ear morphogenesis" evidence=IEA

GO:0042472 "inner ear morphogenesis" evidence=IEA

GO:0030326 "embryonic limb morphogenesis" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0002053 "positive regulation of mesenchymal cell proliferation" evidence=IEA

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

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

UNIPROTKB|E2RGD6 PRRX1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 255 (94.8 bits), Expect = 7.0e-22, P = 7.0e-22
 Identities = 52/81 (64%), Positives = 62/81 (76%)

Query:    34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHR 93
             FNS QL ALE+VFERTHYPDAFVRE+LA++V L+EARVQVWFQNRRAKFRRNER  ++++
Sbjct:   101 FNSSQLQALERVFERTHYPDAFVREDLARRVNLTEARVQVWFQNRRAKFRRNERAMLANK 160

Query:    94 NL--------DAPTSEQPLPP 106
             N         D    EQP+ P
Sbjct:   161 NASLLKSYSGDVTAVEQPIVP 181

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

GO:0060021 "palate development" evidence=IEA

GO:0051216 "cartilage development" evidence=IEA

GO:0048844 "artery morphogenesis" evidence=IEA

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

GO:0045880 "positive regulation of smoothened signaling pathway" evidence=IEA

GO:0042474 "middle ear morphogenesis" evidence=IEA

GO:0042472 "inner ear morphogenesis" evidence=IEA

GO:0030326 "embryonic limb morphogenesis" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0002053 "positive regulation of mesenchymal cell proliferation" evidence=IEA

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

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

UNIPROTKB|J9P9S0 PRRX1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 255 (94.8 bits), Expect = 7.0e-22, P = 7.0e-22
 Identities = 52/81 (64%), Positives = 62/81 (76%)

Query:    34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHR 93
             FNS QL ALE+VFERTHYPDAFVRE+LA++V L+EARVQVWFQNRRAKFRRNER  ++++
Sbjct:   101 FNSSQLQALERVFERTHYPDAFVREDLARRVNLTEARVQVWFQNRRAKFRRNERAMLANK 160

Query:    94 NL--------DAPTSEQPLPP 106
             N         D    EQP+ P
Sbjct:   161 NASLLKSYSGDVTAVEQPIVP 181

GO:0005634 "nucleus" evidence=IEA

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

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P63014	PRRX1_RAT	No assigned EC number	0.6506	0.5244	0.3061	yes	N/A
P63013	PRRX1_MOUSE	No assigned EC number	0.6506	0.5244	0.3061	yes	N/A
Q99811	PRRX2_HUMAN	No assigned EC number	0.5727	0.6433	0.3636	yes	N/A
Q90963	PRRX2_CHICK	No assigned EC number	0.6829	0.5244	0.4545	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	143
pfam00046	57	pfam00046, Homeobox, Homeobox domain	2e-27
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	8e-23
smart00389	57	smart00389, HOX, Homeodomain	8e-22
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	1e-12

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

 Score = 96.4 bits (241), Expect = 2e-27
 Identities = 36/57 (63%), Positives = 43/57 (75%)

Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
          RR RTTF   QL  LEK FE+  YP A  REELAKK+ L+E +V+VWFQNRRAK++R
Sbjct: 1  RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57

Length = 57

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

 Score = 84.6 bits (210), Expect = 8e-23
 Identities = 33/59 (55%), Positives = 42/59 (71%)

Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
          RR RT F   QL  LEK FE+  YP    REELAK++ L+E +V++WFQNRRAK +R+E
Sbjct: 1  RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59

Length = 59

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 81.9 bits (203), Expect = 8e-22
 Identities = 33/57 (57%), Positives = 41/57 (71%)

Query: 27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
           RR RT+F   QL  LEK F++  YP    REELAKK+ LSE +V+VWFQNRRAK++
Sbjct: 1  KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

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

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

 Score = 60.9 bits (148), Expect = 1e-12
 Identities = 25/66 (37%), Positives = 36/66 (54%), Gaps = 2/66 (3%)

Query: 19  DYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNR 78
                 PK +R RTT    QL  LE+ FE   YP +  R +L+  + +    VQ+WFQN+
Sbjct: 45  QDGSSPPKSKRRRTT--DEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNK 102

Query: 79  RAKFRR 84
           RAK ++
Sbjct: 103 RAKEKK 108

Length = 156

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	143
KOG0489|consensus	261		99.86
KOG0850|consensus	245		99.86
KOG0484|consensus	125		99.83
KOG0848|consensus	317		99.81
KOG0843|consensus	197		99.8
KOG0488|consensus	309		99.8
KOG2251|consensus	228		99.78
KOG0487|consensus	308		99.76
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.76
KOG0842|consensus	307		99.75
KOG0485|consensus	268		99.75
KOG3802|consensus	398		99.75
KOG0492|consensus	246		99.74
KOG0494|consensus	332		99.73
KOG0493|consensus	342		99.68
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.65
KOG0491|consensus	194		99.65
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.65
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.64
KOG0486|consensus	351		99.62
COG5576	156	Homeodomain-containing transcription factor [Trans	99.59
KOG4577|consensus	383		99.57
KOG0844|consensus	408		99.56
KOG0483|consensus	198		99.53
KOG0847|consensus	288		99.42
KOG0775|consensus	304		99.42
KOG1168|consensus	385		99.38
KOG0490|consensus	235		99.29
KOG0849|consensus	354		99.28
KOG0774|consensus	334		99.12
KOG2252|consensus	558		98.89
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.83
KOG0490|consensus	235		98.33
KOG1146|consensus	1406		98.09
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	97.6
KOG3623|consensus	1007		96.96
KOG0773|consensus	342		96.95
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	95.57
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	91.57
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	86.76
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	86.65
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	85.7
KOG1146|consensus	1406		83.56
PF13565	77	HTH_32: Homeodomain-like domain	83.03
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	81.7
PF10668	60	Phage_terminase: Phage terminase small subunit; In	81.52
PRK03975	141	tfx putative transcriptional regulator; Provisiona	80.72
KOG3755|consensus	769		80.42

>KOG0489|consensus

Probab=99.86  E-value=1.2e-21  Score=150.19  Aligned_cols=86  Identities=33%  Similarity=0.504  Sum_probs=71.6

Q ss_pred             CcccccccccCCCCCCcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123           2 EYDWMLTLRCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK   81 (143)
Q Consensus         2 ~~~w~~~~~~~~~~~~~~~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k   81 (143)
                      .|+||.......     .......+.||.||.||..|+..||+.|..|+|.+...|.+||..|.|+++||+|||||||+|
T Consensus       139 ~~p~~~~~~~~~-----~~~~~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK  213 (261)
T KOG0489|consen  139 IYPWMKSTANYL-----SSSETGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMK  213 (261)
T ss_pred             cccchhhhhccc-----ccccccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHH
Confidence            588888766431     111222346788999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhhhccc
Q psy2123          82 FRRNERNFISH   92 (143)
Q Consensus        82 ~rk~~~~~~~~   92 (143)
                      |||.++.....
T Consensus       214 ~Kk~~k~~~~~  224 (261)
T KOG0489|consen  214 WKKENKAKSSQ  224 (261)
T ss_pred             HHHhhcccccc
Confidence            99988765444

>KOG0850|consensus

Probab=99.86  E-value=3.7e-21  Score=141.80  Aligned_cols=79  Identities=34%  Similarity=0.547  Sum_probs=71.4

Q ss_pred             CCCCcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhhccc
Q psy2123          14 EDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISH   92 (143)
Q Consensus        14 ~~~~~~~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~~~~   92 (143)
                      |.++....++++|.||.||.++.-||..|+..|++++|+...||.+||..|||+.+||+|||||||.|.||..+.....
T Consensus       109 E~~e~~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~~  187 (245)
T KOG0850|consen  109 EPSERRPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSGP  187 (245)
T ss_pred             CcceeccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCCc
Confidence            4455566778899999999999999999999999999999999999999999999999999999999999998854433

>KOG0484|consensus

Probab=99.83  E-value=2.2e-20  Score=122.15  Aligned_cols=75  Identities=60%  Similarity=0.905  Sum_probs=67.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhhcccCCCCCC
Q psy2123          24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHRNLDAP   98 (143)
Q Consensus        24 ~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~~~~~~~~~~   98 (143)
                      ++|.||-||.|+..||..||..|-...||++-.+++||..+.|++..|||||||||+|.||+++..........+
T Consensus        14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~~~~~~~   88 (125)
T KOG0484|consen   14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAKMAAKSS   88 (125)
T ss_pred             HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHHhhhhcc
Confidence            456788999999999999999999999999999999999999999999999999999999999876655444433

>KOG0848|consensus

Probab=99.81  E-value=4.7e-20  Score=138.54  Aligned_cols=83  Identities=35%  Similarity=0.568  Sum_probs=68.8

Q ss_pred             cccccccccCCCCCCcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHH
Q psy2123           3 YDWMLTLRCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKF   82 (143)
Q Consensus         3 ~~w~~~~~~~~~~~~~~~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~   82 (143)
                      ||||..---.+.+    ...+.+.+-|-|.++++.|..+||+.|.-++|++++.+.+||.-|||+++||+|||||||+|+
T Consensus       179 ~dwmrkpa~~~~g----~~~KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKE  254 (317)
T KOG0848|consen  179 YDWMRKPAQPGTG----QNVKTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKE  254 (317)
T ss_pred             hhhhhcccccCCC----CCceeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHH
Confidence            7898753221111    223334455779999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhhh
Q psy2123          83 RRNERNF   89 (143)
Q Consensus        83 rk~~~~~   89 (143)
                      ||..++.
T Consensus       255 RK~nKKk  261 (317)
T KOG0848|consen  255 RKDNKKK  261 (317)
T ss_pred             HHHHHHH
Confidence            9988876

>KOG0843|consensus

Probab=99.80  E-value=9.8e-20  Score=129.83  Aligned_cols=87  Identities=38%  Similarity=0.698  Sum_probs=71.2

Q ss_pred             CcccccccccC--CCCCCcc----cccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHH
Q psy2123           2 EYDWMLTLRCD--GEDDDYD----YERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWF   75 (143)
Q Consensus         2 ~~~w~~~~~~~--~~~~~~~----~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WF   75 (143)
                      +|+|+......  +.++...    ..-...+.+|.||.|+.+|+..||..|+.++|....+|++||..|+|++.||+|||
T Consensus        71 ~~p~~~~~~~~~~~~~~~~~~~l~~~~~~~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWF  150 (197)
T KOG0843|consen   71 QYPWLIRIYSRHGGKDTMLEGFLLLPLRSMRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWF  150 (197)
T ss_pred             cCCcceeeeecccccchhhhhhccccccccCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhh
Confidence            68898876532  3222211    12223367899999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHhhhh
Q psy2123          76 QNRRAKFRRNERN   88 (143)
Q Consensus        76 qNrR~k~rk~~~~   88 (143)
                      ||||.|.||....
T Consensus       151 QNRRtk~kr~~~e  163 (197)
T KOG0843|consen  151 QNRRTKHKRMQQE  163 (197)
T ss_pred             hhhhHHHHHHHHH
Confidence            9999999987654

>KOG0488|consensus

Probab=99.80  E-value=1.6e-19  Score=141.03  Aligned_cols=69  Identities=42%  Similarity=0.652  Sum_probs=63.9

Q ss_pred             ccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123          21 ERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF   89 (143)
Q Consensus        21 ~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~   89 (143)
                      ...++|.|+.||+|+..|+..||..|++.+|.+..+|.+||..|||+..||++||||||+||||.....
T Consensus       166 ~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g  234 (309)
T KOG0488|consen  166 RSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEG  234 (309)
T ss_pred             cCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhh
Confidence            344577888999999999999999999999999999999999999999999999999999999977663

>KOG2251|consensus

Probab=99.78  E-value=1.4e-18  Score=127.53  Aligned_cols=70  Identities=56%  Similarity=0.904  Sum_probs=65.4

Q ss_pred             cccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123          20 YERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF   89 (143)
Q Consensus        20 ~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~   89 (143)
                      +....+|.||+||.|+-.|+++||..|.+.+||+...+++||.+|+|.+.+|+|||+|||+|+|+.++..
T Consensus        30 ~~~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   30 YSSGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             cCccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            4466788999999999999999999999999999999999999999999999999999999999987754

>KOG0487|consensus

Probab=99.76  E-value=3.7e-19  Score=137.56  Aligned_cols=65  Identities=35%  Similarity=0.538  Sum_probs=61.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123          25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF   89 (143)
Q Consensus        25 ~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~   89 (143)
                      ++.||+|-.+|+.|+..||+.|..|.|++++.|.+|+..|+|+++||+|||||||+|+||..+..
T Consensus       233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~  297 (308)
T KOG0487|consen  233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN  297 (308)
T ss_pred             cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence            56788899999999999999999999999999999999999999999999999999999988643

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.76  E-value=3.3e-18  Score=102.33  Aligned_cols=57  Identities=47%  Similarity=0.778  Sum_probs=54.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123          28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR   84 (143)
Q Consensus        28 rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk   84 (143)
                      |+.|+.|+.+|+.+|+..|..++||+..+++.||..+||+..+|++||+|+|+++||
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence            467899999999999999999999999999999999999999999999999999886

; 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 ....

>KOG0842|consensus

Probab=99.75  E-value=6.7e-19  Score=136.09  Aligned_cols=66  Identities=38%  Similarity=0.628  Sum_probs=61.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123          24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF   89 (143)
Q Consensus        24 ~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~   89 (143)
                      ..++||.|..|+..|+.+||..|.+.+|++..||++||..|.|+.+||+|||||||-|.||.++..
T Consensus       150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk  215 (307)
T KOG0842|consen  150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDK  215 (307)
T ss_pred             cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhh
Confidence            456778899999999999999999999999999999999999999999999999999999987764

>KOG0485|consensus

Probab=99.75  E-value=7.2e-18  Score=123.56  Aligned_cols=64  Identities=36%  Similarity=0.620  Sum_probs=60.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        25 ~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      .++||.||+|+..|+-.||..|+..+|.+..+|.-||.+|.|++.||+|||||||.||||+...
T Consensus       102 ~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa  165 (268)
T KOG0485|consen  102 DRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA  165 (268)
T ss_pred             cccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence            3577899999999999999999999999999999999999999999999999999999997654

>KOG3802|consensus

Probab=99.75  E-value=1.1e-18  Score=137.79  Aligned_cols=84  Identities=26%  Similarity=0.428  Sum_probs=73.8

Q ss_pred             ccccccccC---CCCCCcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHH
Q psy2123           4 DWMLTLRCD---GEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRA   80 (143)
Q Consensus         4 ~w~~~~~~~---~~~~~~~~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~   80 (143)
                      -|+++++..   ++-...+......|+||+||.|....+..||.+|.+|++|+..|+..||.+|+|.+.+|+|||||||+
T Consensus       268 KWLeEAes~~~~~~~~~~e~i~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQ  347 (398)
T KOG3802|consen  268 KWLEEAESRESTGSPNSIEKIGAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQ  347 (398)
T ss_pred             HHHHHHhcccccCCCCCHHHhhccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeecccc
Confidence            499999852   34444555566668899999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhh
Q psy2123          81 KFRRNER   87 (143)
Q Consensus        81 k~rk~~~   87 (143)
                      |+||...
T Consensus       348 keKR~~~  354 (398)
T KOG3802|consen  348 KEKRITP  354 (398)
T ss_pred             ccccCCC
Confidence            9999765

>KOG0492|consensus

Probab=99.74  E-value=5e-18  Score=123.57  Aligned_cols=65  Identities=38%  Similarity=0.611  Sum_probs=60.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123          25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF   89 (143)
Q Consensus        25 ~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~   89 (143)
                      +-.|+.||.|+..||..||..|...+|.++.++.+++..|.|+++||+|||||||+|.||.+...
T Consensus       142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae  206 (246)
T KOG0492|consen  142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAE  206 (246)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHH
Confidence            33577899999999999999999999999999999999999999999999999999999977654

>KOG0494|consensus

Probab=99.73  E-value=7.4e-18  Score=126.36  Aligned_cols=63  Identities=56%  Similarity=0.920  Sum_probs=58.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123          27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF   89 (143)
Q Consensus        27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~   89 (143)
                      +|+.||.||..|+..||+.|+...||+...|+.||..++|.+.+|+|||||||+||||.++.-
T Consensus       141 RRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w  203 (332)
T KOG0494|consen  141 RRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW  203 (332)
T ss_pred             cccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence            344599999999999999999999999999999999999999999999999999999988753

>KOG0493|consensus

Probab=99.68  E-value=7e-17  Score=121.29  Aligned_cols=59  Identities=37%  Similarity=0.731  Sum_probs=56.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123          27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN   85 (143)
Q Consensus        27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~   85 (143)
                      -+|.||.|+.+||+.|...|+.|+|.+...|.+||.+|||.+.||+|||||+|+|.||.
T Consensus       246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs  304 (342)
T KOG0493|consen  246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS  304 (342)
T ss_pred             hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence            36789999999999999999999999999999999999999999999999999999984

>smart00389 HOX Homeodomain

Probab=99.65  E-value=4.3e-16  Score=92.54  Aligned_cols=55  Identities=56%  Similarity=0.898  Sum_probs=51.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHH
Q psy2123          29 RNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR   83 (143)
Q Consensus        29 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~r   83 (143)
                      +.|+.|+..++.+|+..|..++||+..++..||..+||+..+|++||+|+|.+.+
T Consensus         2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~   56 (56)
T smart00389        2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK   56 (56)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence            5678899999999999999999999999999999999999999999999998753

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

>KOG0491|consensus

Probab=99.65  E-value=2.2e-16  Score=111.31  Aligned_cols=64  Identities=47%  Similarity=0.733  Sum_probs=60.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhhc
Q psy2123          27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFI   90 (143)
Q Consensus        27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~~   90 (143)
                      ++|-|++|+..|+..|++.|+..+|.+..++.+||..|+|++.||+.||||||+|.||..++..
T Consensus       100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~  163 (194)
T KOG0491|consen  100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ  163 (194)
T ss_pred             hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence            5678999999999999999999999999999999999999999999999999999999887654

>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=99.65  E-value=8.3e-16  Score=92.07  Aligned_cols=57  Identities=54%  Similarity=0.894  Sum_probs=53.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123          29 RNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN   85 (143)
Q Consensus        29 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~   85 (143)
                      +.|..++..++.+|+.+|..++||+..++..||.++||+..+|++||+|+|.+.++.
T Consensus         2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~   58 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS   58 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence            467889999999999999999999999999999999999999999999999998763

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.64  E-value=2.2e-16  Score=94.38  Aligned_cols=52  Identities=19%  Similarity=0.418  Sum_probs=50.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCC----CCHHHHHHHHHHcCCChhHHHHHHhhHH
Q psy2123          28 RRNRTTFNSHQLNALEKVFERTHY----PDAFVREELAKKVCLSEARVQVWFQNRR   79 (143)
Q Consensus        28 rr~R~~~~~~q~~~L~~~f~~~~~----p~~~~~~~La~~lgl~~~~V~~WFqNrR   79 (143)
                      +|.||.|+.+|+..|+..|..++|    |+..++++||..+||++.+|+|||||.+
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    9999999999999999999999999964

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

>KOG0486|consensus

Probab=99.62  E-value=3.5e-16  Score=120.07  Aligned_cols=65  Identities=57%  Similarity=0.880  Sum_probs=62.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhhc
Q psy2123          26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFI   90 (143)
Q Consensus        26 ~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~~   90 (143)
                      |+||.|+.|+..|+..||..|+++.||+...+++||..++|++..|+|||.|||+||||+++...
T Consensus       111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~  175 (351)
T KOG0486|consen  111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ  175 (351)
T ss_pred             hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence            67899999999999999999999999999999999999999999999999999999999998765

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.59  E-value=2.9e-15  Score=106.53  Aligned_cols=64  Identities=33%  Similarity=0.583  Sum_probs=58.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        25 ~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      ...+++|++.+..|+.+|+..|..++||+...+..|+..|+|+++.|+|||||+|++.|+....
T Consensus        49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~  112 (156)
T COG5576          49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG  112 (156)
T ss_pred             CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence            3456778889999999999999999999999999999999999999999999999999986654

>KOG4577|consensus

Probab=99.57  E-value=1.6e-15  Score=115.38  Aligned_cols=63  Identities=40%  Similarity=0.627  Sum_probs=59.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123          27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF   89 (143)
Q Consensus        27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~   89 (143)
                      .+|+||.|++.||+.|..+|+..+.|....|++|+.++||.-++|||||||||+|+||.++..
T Consensus       167 nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDA  229 (383)
T KOG4577|consen  167 NKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDA  229 (383)
T ss_pred             cCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhc
Confidence            578999999999999999999999999999999999999999999999999999999877654

>KOG0844|consensus

Probab=99.56  E-value=1.1e-15  Score=117.02  Aligned_cols=64  Identities=42%  Similarity=0.594  Sum_probs=59.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        25 ~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      ...||-||.|+.+|+..||+.|-+..|.+...|.+||..|+|.+..|+|||||||+|+||+...
T Consensus       179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla  242 (408)
T KOG0844|consen  179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA  242 (408)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence            4568899999999999999999999999999999999999999999999999999999987643

>KOG0483|consensus

Probab=99.53  E-value=8.6e-15  Score=107.52  Aligned_cols=58  Identities=34%  Similarity=0.583  Sum_probs=53.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123          29 RNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE   86 (143)
Q Consensus        29 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~   86 (143)
                      +++.+|+.+|+..||..|+.+.+.....+..||..|||..+||.||||||||+||.++
T Consensus        52 ~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq  109 (198)
T KOG0483|consen   52 GKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ  109 (198)
T ss_pred             cccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence            3345699999999999999999999999999999999999999999999999999644

>KOG0847|consensus

Probab=99.42  E-value=3.3e-13  Score=99.38  Aligned_cols=63  Identities=40%  Similarity=0.749  Sum_probs=58.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        26 ~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      +++..|..|+..|+..|+..|+..+|+-..++.+||..+|+++.+|+|||||||.||||+...
T Consensus       166 ~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa  228 (288)
T KOG0847|consen  166 QRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA  228 (288)
T ss_pred             cccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence            345678889999999999999999999999999999999999999999999999999997654

>KOG0775|consensus

Probab=99.42  E-value=1.3e-12  Score=98.85  Aligned_cols=63  Identities=27%  Similarity=0.415  Sum_probs=52.9

Q ss_pred             CCCCCCCCCCCH---------HHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          25 PKPRRNRTTFNS---------HQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        25 ~~~rr~R~~~~~---------~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      +|-.-+||.+..         .-..+|.++|..++||+..++.+||+++||+..||-+||+|||+++|-...
T Consensus       165 rKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~a  236 (304)
T KOG0775|consen  165 RKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAAA  236 (304)
T ss_pred             ccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhccc
Confidence            344445776444         456799999999999999999999999999999999999999999995443

>KOG1168|consensus

Probab=99.38  E-value=7.5e-14  Score=106.44  Aligned_cols=85  Identities=25%  Similarity=0.366  Sum_probs=68.6

Q ss_pred             ccccccccCC----CCCCcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHH
Q psy2123           4 DWMLTLRCDG----EDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRR   79 (143)
Q Consensus         4 ~w~~~~~~~~----~~~~~~~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR   79 (143)
                      -|+++++..-    ...+...---...++|+||.+...+...||++|...+.|+.+.+..||++|+|.+.+|+|||||.|
T Consensus       282 aWLEeAE~a~keK~~~pd~~~l~~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQR  361 (385)
T KOG1168|consen  282 AWLEEAEAAMKEKDTKPDINELLPGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQR  361 (385)
T ss_pred             HHHHHHHHHHHhhccCCchhhccCccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccH
Confidence            3888887321    222222222234467889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhh
Q psy2123          80 AKFRRNERN   88 (143)
Q Consensus        80 ~k~rk~~~~   88 (143)
                      +|.||....
T Consensus       362 QKQKRm~~S  370 (385)
T KOG1168|consen  362 QKQKRMKRS  370 (385)
T ss_pred             HHHHHhhhh
Confidence            999997654

>KOG0490|consensus

Probab=99.29  E-value=2.1e-12  Score=96.73  Aligned_cols=64  Identities=50%  Similarity=0.649  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        24 ~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      ..++++.|+.|+..|+++|+..|+...||+...++.||..+++++..|++||||||+|+++.++
T Consensus        57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~  120 (235)
T KOG0490|consen   57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER  120 (235)
T ss_pred             hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence            4567889999999999999999999999999999999999999999999999999999998775

>KOG0849|consensus

Probab=99.28  E-value=3e-11  Score=96.38  Aligned_cols=67  Identities=58%  Similarity=0.885  Sum_probs=61.6

Q ss_pred             cCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          22 RRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        22 ~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      ...++.+|.|+.|+..|+..|++.|+.++||+...+++||.++++++..|++||+|||++++|....
T Consensus       171 ~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~  237 (354)
T KOG0849|consen  171 ALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD  237 (354)
T ss_pred             cccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence            3455677889999999999999999999999999999999999999999999999999999998743

>KOG0774|consensus

Probab=99.12  E-value=9.9e-11  Score=88.35  Aligned_cols=63  Identities=30%  Similarity=0.592  Sum_probs=56.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHH---hcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123          27 PRRNRTTFNSHQLNALEKVFE---RTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF   89 (143)
Q Consensus        27 ~rr~R~~~~~~q~~~L~~~f~---~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~   89 (143)
                      .+|+|..|+....++|+.+|.   .++||+.+++++||.++|++..||.+||.|.|-+.+|.....
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~  253 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKN  253 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhh
Confidence            356788899999999999994   788999999999999999999999999999999998865443

>KOG2252|consensus

Probab=98.89  E-value=9.3e-09  Score=84.64  Aligned_cols=57  Identities=21%  Similarity=0.402  Sum_probs=53.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHH
Q psy2123          26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKF   82 (143)
Q Consensus        26 ~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~   82 (143)
                      +.+|.|.+|++.|...|...|+.+++|+.++.+.|+.+|+|....|.+||.|-|.+.
T Consensus       419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            456779999999999999999999999999999999999999999999999998874

>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=98.83  E-value=4.9e-09  Score=58.14  Aligned_cols=34  Identities=38%  Similarity=0.655  Sum_probs=29.1

Q ss_pred             hcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123          48 RTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK   81 (143)
Q Consensus        48 ~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k   81 (143)
                      .++||+.++++.||.++||+..||..||-|.|.+
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            5789999999999999999999999999999875

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

>KOG0490|consensus

Probab=98.33  E-value=7.9e-07  Score=66.51  Aligned_cols=66  Identities=56%  Similarity=0.816  Sum_probs=60.2

Q ss_pred             cCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          22 RRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        22 ~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      ....+.++.|+.+...|+..|...|....+|+...++.|+..+|+....|++||+|+|++.++...
T Consensus       148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  148 PSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             CCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            334567788999999999999999999999999999999999999999999999999999998654

>KOG1146|consensus

Probab=98.09  E-value=4.9e-06  Score=74.66  Aligned_cols=61  Identities=31%  Similarity=0.439  Sum_probs=57.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      .++.|+.++..||.+|...|....+|..++.+.|...+++..++|++||||.|+|.++...
T Consensus       903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~  963 (1406)
T KOG1146|consen  903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL  963 (1406)
T ss_pred             hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence            4678999999999999999999999999999999999999999999999999999998765

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

Probab=97.60  E-value=9.4e-05  Score=43.63  Aligned_cols=42  Identities=24%  Similarity=0.363  Sum_probs=31.5

Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHH
Q psy2123          39 LNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRA   80 (143)
Q Consensus        39 ~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~   80 (143)
                      +..|+++|...+++.......|..+.+|+..+|+.||..+..
T Consensus        10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~   51 (56)
T PF11569_consen   10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ   51 (56)
T ss_dssp             -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred             hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence            466999999999999999999999999999999999986644

>KOG3623|consensus

Probab=96.96  E-value=0.0017  Score=55.93  Aligned_cols=49  Identities=24%  Similarity=0.348  Sum_probs=46.0

Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          39 LNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        39 ~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      +..|..+|..|..|+..+...+|.+.||....|+.||.+++++....++
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~r  616 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVER  616 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhcc
Confidence            7889999999999999999999999999999999999999999887664

>KOG0773|consensus

Probab=96.95  E-value=0.00051  Score=54.68  Aligned_cols=61  Identities=23%  Similarity=0.301  Sum_probs=49.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHH---hcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          27 PRRNRTTFNSHQLNALEKVFE---RTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        27 ~rr~R~~~~~~q~~~L~~~f~---~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      ..|.+..+......+|+.+..   ..+||+..++..||.++||+..||.+||-|.|.+..+-..
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~  302 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI  302 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence            344455788888999998743   3479999999999999999999999999999988665443

>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=95.57  E-value=0.052  Score=31.57  Aligned_cols=47  Identities=17%  Similarity=0.337  Sum_probs=34.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHH
Q psy2123          28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRR   79 (143)
Q Consensus        28 rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR   79 (143)
                      +|+|..++-++...+-..++...     ....||..+|+...+|..|..|+.
T Consensus         1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~   47 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD   47 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred             CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence            46788899988777777777665     577899999999999999999854

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

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

Probab=91.57  E-value=0.9  Score=25.53  Aligned_cols=46  Identities=15%  Similarity=0.262  Sum_probs=34.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHH
Q psy2123          33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR   83 (143)
Q Consensus        33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~r   83 (143)
                      .+++.+..+|...|...     ....++|..+|++...|+.+...-..|.|
T Consensus         4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~kLR   49 (50)
T PF04545_consen    4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKKLR   49 (50)
T ss_dssp             TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence            36788899999998322     34678999999999999998876655544

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

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

Probab=86.76  E-value=3.2  Score=23.45  Aligned_cols=43  Identities=19%  Similarity=0.213  Sum_probs=28.4

Q ss_pred             CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123          34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK   81 (143)
Q Consensus        34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k   81 (143)
                      +++.+..++...|-..     -...++|..+|++...|+.|.+.-|.+
T Consensus        11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~~~   53 (54)
T PF08281_consen   11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRARKK   53 (54)
T ss_dssp             S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence            4566666666655433     457789999999999999999865543

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

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

Probab=86.65  E-value=3.1  Score=24.20  Aligned_cols=42  Identities=24%  Similarity=0.388  Sum_probs=33.2

Q ss_pred             CCHHHHHHHHHHHHhcCC--CCHHHHHHHHHHcCCChhHHHHHH
Q psy2123          34 FNSHQLNALEKVFERTHY--PDAFVREELAKKVCLSEARVQVWF   75 (143)
Q Consensus        34 ~~~~q~~~L~~~f~~~~~--p~~~~~~~La~~lgl~~~~V~~WF   75 (143)
                      +|+.|..+|..+|..--|  |-......||..+|++...|..=.
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~L   44 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHL   44 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHH
Confidence            478899999999975543  656677899999999998765533

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

>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs)

Probab=85.70  E-value=3  Score=22.60  Aligned_cols=43  Identities=16%  Similarity=0.203  Sum_probs=31.5

Q ss_pred             CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123          34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK   81 (143)
Q Consensus        34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k   81 (143)
                      +++.+..++...|...     .....+|..+|++...|..|...-+.+
T Consensus        11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~   53 (55)
T cd06171          11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK   53 (55)
T ss_pred             CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            5677777777776422     245678999999999999998765443

A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas

>KOG1146|consensus

Probab=83.56  E-value=2.2  Score=39.82  Aligned_cols=63  Identities=21%  Similarity=0.348  Sum_probs=56.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123          24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE   86 (143)
Q Consensus        24 ~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~   86 (143)
                      ..+.+.-+..+-.+++.+|-.+|-.+.-|+...+.-|....+.+.+++.+||+|-+.+.++..
T Consensus       702 ~~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~  764 (1406)
T KOG1146|consen  702 SPRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ  764 (1406)
T ss_pred             CcccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence            344566788888899999999999999999999999999999999999999999999988754

>PF13565 HTH_32: Homeodomain-like domain

Probab=83.03  E-value=6.2  Score=23.88  Aligned_cols=39  Identities=15%  Similarity=0.079  Sum_probs=26.8

Q ss_pred             CHHHHHHHHHHHHhcCCCCHHHHHH-HHHHcCC----ChhHHHH
Q psy2123          35 NSHQLNALEKVFERTHYPDAFVREE-LAKKVCL----SEARVQV   73 (143)
Q Consensus        35 ~~~q~~~L~~~f~~~~~p~~~~~~~-La~~lgl----~~~~V~~   73 (143)
                      +.++...|.+.+..++..+..+... |..++|+    +...|.-
T Consensus        32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R   75 (77)
T PF13565_consen   32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYR   75 (77)
T ss_pred             cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHH
Confidence            6777788888888888777666655 5666664    4455543

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

Probab=81.70  E-value=1.5  Score=26.65  Aligned_cols=47  Identities=15%  Similarity=0.232  Sum_probs=29.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHH
Q psy2123          29 RNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRR   79 (143)
Q Consensus        29 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR   79 (143)
                      +.|..|++++...+-..+...    ......+|.++||+...+..|-.--+
T Consensus         2 ~~r~~ys~e~K~~~v~~~~~~----g~sv~~va~~~gi~~~~l~~W~~~~~   48 (76)
T PF01527_consen    2 RKRRRYSPEFKLQAVREYLES----GESVSEVAREYGISPSTLYNWRKQYR   48 (76)
T ss_dssp             -SS----HHHHHHHHHHHHHH----HCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHC----CCceEeeecccccccccccHHHHHHh
Confidence            346679998866665555222    24677899999999999999986433

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.

>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=81.52  E-value=1.5  Score=26.27  Aligned_cols=21  Identities=24%  Similarity=0.507  Sum_probs=18.0

Q ss_pred             HHHHHHHHcCCChhHHHHHHh
Q psy2123          56 VREELAKKVCLSEARVQVWFQ   76 (143)
Q Consensus        56 ~~~~La~~lgl~~~~V~~WFq   76 (143)
                      ....||.+||+++.+|+.|=.
T Consensus        24 ~lkdIA~~Lgvs~~tIr~WK~   44 (60)
T PF10668_consen   24 KLKDIAEKLGVSESTIRKWKS   44 (60)
T ss_pred             cHHHHHHHHCCCHHHHHHHhh
Confidence            456789999999999999964

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 [].

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=80.72  E-value=9.2  Score=26.83  Aligned_cols=51  Identities=16%  Similarity=0.190  Sum_probs=39.3

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          32 TTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        32 ~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      ..+++.|..+|...+  ..    ....++|..+|++...|..|..+.+.+.++....
T Consensus         5 ~~Lt~rqreVL~lr~--~G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t   55 (141)
T PRK03975          5 SFLTERQIEVLRLRE--RG----LTQQEIADILGTSRANVSSIEKRARENIEKARET   55 (141)
T ss_pred             cCCCHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            468899999997743  22    2356899999999999999999888877765443

>KOG3755|consensus

Probab=80.42  E-value=2.3  Score=36.64  Aligned_cols=20  Identities=35%  Similarity=0.655  Sum_probs=15.1

Q ss_pred             ChhHHHHHHhhHHHHHHHhh
Q psy2123          67 SEARVQVWFQNRRAKFRRNE   86 (143)
Q Consensus        67 ~~~~V~~WFqNrR~k~rk~~   86 (143)
                      ....|+.||.|||.++++.+
T Consensus       739 ~~kn~~~~fk~~~ee~~~~k  758 (769)
T KOG3755|consen  739 ESKNVQFWFKVRREEEKRLK  758 (769)
T ss_pred             hhcchHHHHHHHHHHHhhhh
Confidence            44568888888888888754

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	143
3a02_A	60	Crystal Structure Of Aristaless Homeodomain Length		3e-17
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		7e-17
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		7e-17
2m0c_A	75	Solution Nmr Structure Of Homeobox Domain Of Human		1e-16
2cue_A	80	Solution Structure Of The Homeobox Domain Of The Hu		2e-16
1fjl_A	81	Homeodomain From The Drosophila Paired Protein Boun		1e-14
3cmy_A	61	Structure Of A Homeodomain In Complex With Dna Leng		1e-14
2dmu_A	70	Solution Structure Of The Homeobox Domain Of Homeob		3e-12
2l7m_P	68	Solution Structure Of The Pitx2 Homeodomain R24h Mu		5e-12
2dms_A	80	Solution Structure Of The Homeobox Domain Of Homeob		5e-12
2l7f_P	68	Solution Structure Of The Pitx2 Homeodomain Length		4e-11
2dmq_A	80	Solution Structure Of The Homeobox Domain Of LimHOM		1e-08
2k40_A	67	Nmr Structure Of Hesx-1 Homeodomain Double Mutant R		3e-08
2djn_A	70	The Solution Structure Of The Homeobox Domain Of Hu		6e-07
2e1o_A	70	Solution Structure Of Rsgi Ruh-028, A Homeobox Doma		2e-06
1ig7_A	58	Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58		4e-06
2m34_A	71	Nmr Structure Of The Homeodomain Transcription Fact		6e-06
2dmt_A	80	Solution Structure Of The Homeobox Domain Of Homeob		1e-05
1ztr_A	61	Solution Structure Of Engrailed Homeodomain L16a Mu		1e-05
3hdd_A	60	Engrailed Homeodomain Dna Complex Length = 60		2e-05
1hdd_C	61	Crystal Structure Of An Engrailed Homeodomain-Dna C		2e-05
1b72_A	97	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		2e-05
3a03_A	56	Crystal Structure Of Hox11l1 Homeodomain Length = 5		3e-05
1enh_A	54	Structural Studies Of The Engrailed Homeodomain Len		3e-05
1p7j_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		4e-05
3a01_A	93	Crystal Structure Of Aristaless And Clawless Homeod		6e-05
2hdd_A	61	Engrailed Homeodomain Q50k Variant Dna Complex Leng		6e-05
1p7i_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		6e-05
1du0_A	57	Engrailed Homeodomain Q50a Variant Dna Complex Leng		1e-04
1b8i_A	81	Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX		1e-04
2l9r_A	69	Solution Nmr Structure Of Homeobox Domain Of Homeob		1e-04
2hos_A	63	Phage-selected Homeodomain Bound To Unmodified Dna		3e-04
1jgg_A	60	Even-Skipped Homeodomain Complexed To At-Rich Dna L		4e-04
1hom_A	68	Determination Of The Three-Dimensional Structure Of		4e-04
1nk2_P	77	VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES		4e-04
1ftt_A	68	Thyroid Transcription Factor 1 Homeodomain (Rattus		5e-04
1bw5_A	66	The Nmr Solution Structure Of The Homeodomain Of Th		7e-04
3rkq_A	58	Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Lengt		7e-04

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

Iteration: 1
 Score = 83.6 bits (205), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 37/54 (68%), Positives = 43/54 (79%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
          F S QL  LEK F RTHYPD F REELA K+ L+EAR+QVWFQNRRAK+R+ E+
Sbjct: 6  FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 59

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

Iteration: 1
 Score = 82.4 bits (202), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 37/54 (68%), Positives = 43/54 (79%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
          F S QL  LEK F RTHYPD F REELA K+ L+EAR+QVWFQNRRAK+R+ E+
Sbjct: 13 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 66

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

Iteration: 1
 Score = 82.4 bits (202), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 37/53 (69%), Positives = 42/53 (79%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
          F S QL  LEK F RTHYPD F REELA K+ L+EAR+QVWFQNRRAK+R+ E
Sbjct: 6  FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58

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

Iteration: 1
 Score = 81.6 bits (200), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 36/54 (66%), Positives = 45/54 (83%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
          F S+QL  LEKVF++THYPD + RE+LA +  L+EARVQVWFQNRRAK+R+ ER
Sbjct: 16 FTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRER 69

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

Iteration: 1
 Score = 81.3 bits (199), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 39/67 (58%), Positives = 46/67 (68%), Gaps = 1/67 (1%)
Query: 34  FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHR 93
           F   Q+ ALEK FERTHYPD F RE LA K+ L EAR+QVWF NRRAK+RR E+   + R
Sbjct: 14  FTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK-LRNQR 72
Query: 94  NLDAPTS 100
               P+S
Sbjct: 73  RQSGPSS 79

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

Iteration: 1
 Score = 75.1 bits (183), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 31/52 (59%), Positives = 42/52 (80%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          F++ QL+ LE+ FERT YPD + REELA++  L+EAR+QVWFQNRRA+ R+ 
Sbjct: 25 FSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 76

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

Iteration: 1
 Score = 75.1 bits (183), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 32/52 (61%), Positives = 41/52 (78%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          F + QL  LE+ FERTHYPD + REELA++  L+EARVQVWF NRRA++R+ 
Sbjct: 9  FTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60

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

Iteration: 1
 Score = 67.4 bits (163), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 30/52 (57%), Positives = 39/52 (75%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          F   QL ALE +F+ T YPD   RE+LA+KV L E +V+VWF+NRRAK+RR+
Sbjct: 14 FTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRS 65

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 31/53 (58%), Positives = 38/53 (71%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
          F S QL  LE  F+R HYPD   REE+A    L+EARV+VWF+NRRAK+R+ E
Sbjct: 10 FTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62

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

Iteration: 1
 Score = 66.2 bits (160), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 30/50 (60%), Positives = 38/50 (76%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
          F   QL+ LE +F +T YPD F+REE+A K+ L E+RVQVWF+NRRAK R
Sbjct: 14 FTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63

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

Iteration: 1
 Score = 63.5 bits (153), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 30/53 (56%), Positives = 37/53 (69%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
          F S QL  LE  F+R  YPD   REE+A    L+EARV+VWF+NRRAK+R+ E
Sbjct: 10 FTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 26/52 (50%), Positives = 34/52 (65%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          F  HQL  ++  F   H PDA   ++LA+K  L++  +QVWFQN RAKFRRN
Sbjct: 14 FKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRN 65

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 35/54 (64%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
          F  +Q+  LE VF    YP   + E+LA+K+ L   R+Q+WFQNRRAK +R+ R
Sbjct: 8  FTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 20/52 (38%), Positives = 37/52 (71%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          ++S QL AL++ F++T Y     R ELA  + L++ +V++WFQN+R+K +++
Sbjct: 14 YSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKS 65

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/52 (50%), Positives = 34/52 (65%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          F++ Q   LEK FE   Y     R+ LAK + LSE +V+ WFQNRRAK+RR+
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRS 65

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 22/51 (43%), Positives = 32/51 (62%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
          F + QL ALE+ F +  Y     R E +  + L+E +V++WFQNRRAK +R
Sbjct: 7  FTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 25/58 (43%), Positives = 35/58 (60%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFIS 91
          F S QL  LEK F    Y     R ++A  + LSE +V++WFQNRRAK++R +   +S
Sbjct: 14 FTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKRIKAGNVS 71

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 33/52 (63%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          F   QL  LEK FE+  Y     R +LA+ + LS+ +V+ W+QNRR K++++
Sbjct: 24 FTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKS 75

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 20/52 (38%), Positives = 35/52 (67%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          F+S QL   ++ F    Y     R++L+ ++ L+EA++++WFQN+RAK RR+
Sbjct: 10 FSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRRS 61

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 19/52 (36%), Positives = 36/52 (69%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          F+S QL  L++ F    Y     R++L+ ++ L+EA++++WFQN+RAK +++
Sbjct: 8  FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 59

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 19/52 (36%), Positives = 36/52 (69%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          F+S QL  L++ F    Y     R++L+ ++ L+EA++++WFQN+RAK +++
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 61

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 32/54 (59%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
          F + QL  LEK F    Y     R E+A  + L+E +V++WFQNRR K ++ ER
Sbjct: 41 FTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER 94

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 33/52 (63%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          F+  Q+  LE+ F R  Y  +  R  LAK + +++A+V+ WFQNRR K+RR 
Sbjct: 4  FSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 33/49 (67%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKF 82
          F+S QL  L++ F    Y     R++L+ ++ L+EA++++WFQN+RAK 
Sbjct: 6  FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKI 54

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 19/52 (36%), Positives = 35/52 (67%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          F+S QL  L++ F    Y     R++L+ ++ L+EA++++WFQN RAK +++
Sbjct: 8  FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKKS 59

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 32/52 (61%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          F   Q+  LEK F +  Y  +  R  LA+ + +++A+V+ WFQNRR K+RR 
Sbjct: 24 FTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQ 75

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 18/52 (34%), Positives = 36/52 (69%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          F+S QL  L++ F    Y     R++L+ ++ L+EA++++WF+N+RAK +++
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKKS 61

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 19/52 (36%), Positives = 35/52 (67%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          F+S QL  L++ F    Y     R++L+ ++ L+EA++++WFQN RAK +++
Sbjct: 8  FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKKS 59

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/52 (34%), Positives = 35/52 (67%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          F+S QL  L++ F    Y     R++L+ ++ L+EA++++WF N+RAK +++
Sbjct: 6  FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKKS 57

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/51 (37%), Positives = 30/51 (58%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
          +  +Q   LEK F   HY     R E+A  + L+E ++++WFQNRR K ++
Sbjct: 27 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKK 77

>pdb|2L9R|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Homeobox Protein Nkx-3.1 From Homo Sapiens, Northeast Structural Genomics Consortium Target Hr6470a Length = 69

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 30/49 (61%)
Query: 38 QLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
          Q+  LE+ F    Y  A  R  LAK + L+E +V++WFQNRR K +R +
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 63

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/52 (36%), Positives = 34/52 (65%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          F+S QL  L++ F    Y     R++L+ ++ L+EA+V+ WF+N RAK +++
Sbjct: 11 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKKS 62

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/51 (45%), Positives = 31/51 (60%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
          F   QL  LEK F + +Y     R ELA ++ L E+ ++VWFQNRR K +R
Sbjct: 8  FTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 58

>pdb|1HOM|A Chain A, Determination Of The Three-Dimensional Structure Of The Antennapedia Homeodomain From Drosophila In Solution By 1h Nuclear Magnetic Resonance Spectroscopy Length = 68

Iteration: 1
 Score = 40.4 bits (93), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 19/51 (37%), Positives = 31/51 (60%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
          +  +Q   LEK F    Y     R E+A  +CL+E ++++WFQNRR K+++
Sbjct: 9  YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 59

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR--NERNFIS 91
          F   Q   LE+ F +  Y  A  RE LA  + L+  +V++WFQN R K +R  NE+ +  
Sbjct: 16 FTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGYEG 75
Query: 92 H 92
          H
Sbjct: 76 H 76

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/55 (36%), Positives = 33/55 (60%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88
          F+  Q+  LE+ F++  Y  A  RE LA  + L+  +V++WFQN R K +R  ++
Sbjct: 9  FSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKD 63

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 18/48 (37%), Positives = 27/48 (56%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81
           N  QL+ L   +     PDA ++E+L +   LS   ++VWFQN+R K
Sbjct: 10 LNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCK 57

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

Iteration: 1
 Score = 39.3 bits (90), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 31/48 (64%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81
          F+  Q+  LE+ F++  Y  A  R++LA  + L+  +V++WFQNRR K
Sbjct: 9  FSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYK 56

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	143
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	2e-38
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	3e-37
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	4e-37
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	9e-37
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	1e-36
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	4e-36
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	6e-36
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	4e-35
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	4e-35
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	3e-34
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	1e-32
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	4e-30
1uhs_A	72	HOP, homeodomain only protein; structural genomics	8e-30
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	2e-27
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	6e-26
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	1e-24
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	7e-24
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	7e-24
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	9e-24
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	1e-22
1e3o_C	160	Octamer-binding transcription factor 1; transcript	2e-21
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	5e-21
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	8e-21
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	4e-20
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	3e-19
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	2e-18
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	2e-18
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	3e-18
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	5e-18
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	5e-18
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	6e-18
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	9e-18
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	1e-17
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	1e-17
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	2e-17
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	2e-17
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	6e-17
1lfb_A	99	Liver transcription factor (LFB1); transcription r	9e-17
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	3e-16
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	4e-16
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	5e-16
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	7e-16
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	3e-15
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	6e-15
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	1e-14
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	1e-14
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	1e-14
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	1e-14
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	5e-14
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	1e-13
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	2e-13
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	4e-13
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	2e-12
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	2e-12
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	5e-12
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	7e-10
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	1e-09
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	2e-07
2e19_A	64	Transcription factor 8; homeobox domain, structura	4e-07
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	2e-06
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	7e-05
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	3e-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 =  124 bits (312), Expect = 2e-38
 Identities = 38/77 (49%), Positives = 53/77 (68%)

Query: 12 DGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARV 71
            + +       K K RR+RTTF++ QL+ LE+ FERT YPD + REELA++  L+EAR+
Sbjct: 3  ISDCESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARI 62

Query: 72 QVWFQNRRAKFRRNERN 88
          QVWFQNRRA+ R+   +
Sbjct: 63 QVWFQNRRARLRKQHTS 79

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

 Score =  121 bits (305), Expect = 3e-37
 Identities = 40/64 (62%), Positives = 47/64 (73%)

Query: 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
              +RNRT+F   Q+ ALEK FERTHYPD F RE LA K+ L EAR+QVWF NRRAK+R
Sbjct: 4  GSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWR 63

Query: 84 RNER 87
          R E+
Sbjct: 64 REEK 67

>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 =  120 bits (304), Expect = 4e-37
 Identities = 35/65 (53%), Positives = 46/65 (70%)

Query: 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
              RR RTTF   QL+ LE +F +T YPD F+REE+A K+ L E+RVQVWF+NRRAK R
Sbjct: 4  GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63

Query: 84 RNERN 88
          + ++ 
Sbjct: 64 QQQQQ 68

>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 =  119 bits (301), Expect = 9e-37
 Identities = 34/65 (52%), Positives = 45/65 (69%)

Query: 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
              RR+RT F   QL ALE +F+ T YPD   RE+LA+KV L E +V+VWF+NRRAK+R
Sbjct: 4  GSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 63

Query: 84 RNERN 88
          R+  +
Sbjct: 64 RSGPS 68

>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 =  119 bits (300), Expect = 1e-36
 Identities = 34/66 (51%), Positives = 43/66 (65%)

Query: 26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
            RR RT F S QL  LE  F+R  YPD   REE+A    L+EARV+VWF+NRRAK+R+ 
Sbjct: 2  SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61

Query: 86 ERNFIS 91
          E   ++
Sbjct: 62 EEFIVT 67

>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 =  118 bits (297), Expect = 4e-36
 Identities = 29/65 (44%), Positives = 39/65 (60%)

Query: 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
              +R RT+F  HQL  ++  F   H PDA   ++LA+K  L++  +QVWFQN RAKFR
Sbjct: 4  GSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFR 63

Query: 84 RNERN 88
          RN   
Sbjct: 64 RNLLR 68

>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 =  117 bits (295), Expect = 6e-36
 Identities = 29/61 (47%), Positives = 39/61 (63%)

Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
          RR RT F  +Q+  LE VF    YP   + E+LA+K+ L   R+Q+WFQNRRAK +R+ R
Sbjct: 2  RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61

Query: 88 N 88
           
Sbjct: 62 E 62

>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 =  115 bits (290), Expect = 4e-35
 Identities = 38/58 (65%), Positives = 45/58 (77%)

Query: 30 NRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
          +  TF S QL  LEK F RTHYPD F REELA K+ L+EAR+QVWFQNRRAK+R+ E+
Sbjct: 2  SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 59

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

 Score =  115 bits (290), Expect = 4e-35
 Identities = 21/65 (32%), Positives = 32/65 (49%)

Query: 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
              R +RT F  +QL  L+  F+   YP     E+L+  + L    + VWFQN R K R
Sbjct: 4  GSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKAR 63

Query: 84 RNERN 88
          ++  +
Sbjct: 64 KSGPS 68

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

 Score =  113 bits (284), Expect = 3e-34
 Identities = 22/62 (35%), Positives = 33/62 (53%)

Query: 26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          K  R RT  N  QL+ L   +     PDA ++E+L +   LS   ++VWFQN+R K ++ 
Sbjct: 2  KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

Query: 86 ER 87
            
Sbjct: 62 SI 63

>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 =  109 bits (275), Expect = 1e-32
 Identities = 21/74 (28%), Positives = 34/74 (45%)

Query: 15 DDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVW 74
                     + +R RTT    QL  L + +     P   + + +A +V L +  VQVW
Sbjct: 5  SSGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVW 64

Query: 75 FQNRRAKFRRNERN 88
          FQN RA+ R++  +
Sbjct: 65 FQNTRARERKSGPS 78

>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70

 Score =  102 bits (257), Expect = 4e-30
 Identities = 17/65 (26%), Positives = 30/65 (46%)

Query: 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
              +R RT     QL  L + F+  + P     +E+A K  L +  ++ WF+N   K R
Sbjct: 4  GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKER 63

Query: 84 RNERN 88
          ++  +
Sbjct: 64 QSGPS 68

>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 =  102 bits (255), Expect = 8e-30
 Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 28 RRNRTTFNSHQLNALEKVFERTH-YPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
               T    Q+  LE  F + + +PD      +A +  L+E + Q WF+ R A++RR+E
Sbjct: 2  SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 61

Query: 87 RNFISHRNLD 96
                R++ 
Sbjct: 62 GLPSECRSVT 71

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

 Score = 96.4 bits (240), Expect = 2e-27
 Identities = 18/69 (26%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 28 RRNRTTFNSHQLNALEKVFERTH-YPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
           +  +     Q+  LE  F + + +PD      +A +  L+E + Q WF+ R A++RR+E
Sbjct: 3  AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 62

Query: 87 RNFISHRNL 95
                R++
Sbjct: 63 GLPSECRSV 71

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

 Score = 92.5 bits (230), Expect = 6e-26
 Identities = 18/68 (26%), Positives = 27/68 (39%)

Query: 21 ERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRA 80
                    +   +  QL+AL+  F R  +P     E L K   LS   V+ WF +RR 
Sbjct: 2  SSGSSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRY 61

Query: 81 KFRRNERN 88
            R  + +
Sbjct: 62 HCRNLKGS 69

>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 = 89.7 bits (222), Expect = 1e-24
 Identities = 20/79 (25%), Positives = 29/79 (36%), Gaps = 15/79 (18%)

Query: 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVC---------------LSE 68
              R +R T+    L  +E  F    YPD   REE+A                   ++ 
Sbjct: 4  GSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTS 63

Query: 69 ARVQVWFQNRRAKFRRNER 87
           +V  WF NRR + +R   
Sbjct: 64 LKVYNWFANRRKEIKRRAN 82

>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 = 89.4 bits (221), Expect = 7e-24
 Identities = 19/75 (25%), Positives = 35/75 (46%)

Query: 11  CDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEAR 70
            +   +    E      +R RT+  +    +LE +F ++  P       +A ++ L +  
Sbjct: 80  NENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDV 139

Query: 71  VQVWFQNRRAKFRRN 85
           V+VWF NRR K +R+
Sbjct: 140 VRVWFSNRRQKGKRS 154

>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 = 89.3 bits (221), Expect = 7e-24
 Identities = 19/73 (26%), Positives = 34/73 (46%)

Query: 12  DGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARV 71
                  +      + R+ RTT +    +ALE+ F     P +     +A+++ L +  V
Sbjct: 72  QVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVV 131

Query: 72  QVWFQNRRAKFRR 84
           +VWF NRR + +R
Sbjct: 132 RVWFCNRRQREKR 144

>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 = 89.3 bits (221), Expect = 9e-24
 Identities = 20/75 (26%), Positives = 32/75 (42%)

Query: 10  RCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEA 69
           +   ++          K R+ RT+F    + AL   FE+   P      E+AK++     
Sbjct: 76  QEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDRE 135

Query: 70  RVQVWFQNRRAKFRR 84
            V+VWF NRR   + 
Sbjct: 136 VVRVWFSNRRQTLKN 150

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

 Score = 87.0 bits (215), Expect = 1e-22
 Identities = 21/64 (32%), Positives = 30/64 (46%)

Query: 24  KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
           + + R+ RT+       ALE  F +   P A     LA  + L +  V+VWF NRR K +
Sbjct: 96  QGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEK 155

Query: 84  RNER 87
           R   
Sbjct: 156 RMTP 159

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

 Score = 83.1 bits (205), Expect = 2e-21
 Identities = 18/84 (21%), Positives = 35/84 (41%)

Query: 1   MEYDWMLTLRCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREEL 60
                  +        +        + R+ RT+  ++   ALEK F     P +     +
Sbjct: 75  EANLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLI 134

Query: 61  AKKVCLSEARVQVWFQNRRAKFRR 84
           A+++ + +  ++VWF NRR K +R
Sbjct: 135 AEQLNMEKEVIRVWFSNRRQKEKR 158

>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 = 79.5 bits (197), Expect = 5e-21
 Identities = 18/59 (30%), Positives = 35/59 (59%)

Query: 23 RKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81
          +K K  + +++ +      LE+VF R    ++  +EE+AKK  ++  +V+VWF N+R +
Sbjct: 1  KKEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 59

>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens} Length = 66

 Score = 79.1 bits (195), Expect = 8e-21
 Identities = 11/63 (17%), Positives = 26/63 (41%)

Query: 26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
              +       Q+  L+  F ++ +PD      L +   L+ + ++ WF + R + +R 
Sbjct: 3  HHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRG 62

Query: 86 ERN 88
            +
Sbjct: 63 IVH 65

>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 = 77.2 bits (190), Expect = 4e-20
 Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 1/61 (1%)

Query: 26 KPRRNRTTFNSHQLNALEKVFERT-HYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
             R+RT  +   L  L+        YPD      L+ ++ L +  +  +FQN+R   + 
Sbjct: 6  SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH 65

Query: 85 N 85
          +
Sbjct: 66 S 66

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

 Score = 75.6 bits (186), Expect = 3e-19
 Identities = 26/75 (34%), Positives = 41/75 (54%)

Query: 13 GEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQ 72
                +   +  K RR+RT F   QL  LEK FE+  Y     R +LA+ + LS+ +V+
Sbjct: 3  SGSSGGEPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVK 62

Query: 73 VWFQNRRAKFRRNER 87
           W+QNRR K++++  
Sbjct: 63 TWYQNRRMKWKKSGP 77

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

 Score = 72.8 bits (179), Expect = 2e-18
 Identities = 23/64 (35%), Positives = 42/64 (65%)

Query: 25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
             R+ RT ++S QL AL++ F++T Y     R ELA  + L++ +V++WFQN+R+K ++
Sbjct: 5  SSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64

Query: 85 NERN 88
          +  +
Sbjct: 65 SGPS 68

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

 Score = 73.7 bits (181), Expect = 2e-18
 Identities = 26/63 (41%), Positives = 40/63 (63%)

Query: 22 RRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81
          R  PK ++ RT+F   Q+  LEK F +  Y  +  R  LA+ + +++A+V+ WFQNRR K
Sbjct: 12 RTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTK 71

Query: 82 FRR 84
          +RR
Sbjct: 72 WRR 74

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

 Score = 72.4 bits (178), Expect = 3e-18
 Identities = 21/63 (33%), Positives = 34/63 (53%)

Query: 26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
              + +  +  Q+  LE+ F    Y  A  R  LAK + L+E +V++WFQNRR K +R 
Sbjct: 3  HHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRK 62

Query: 86 ERN 88
          + +
Sbjct: 63 QLS 65

>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 = 72.1 bits (177), Expect = 5e-18
 Identities = 26/64 (40%), Positives = 37/64 (57%)

Query: 25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
             +  +  F++ Q   LEK FE   Y     R+ LAK + LSE +V+ WFQNRRAK+RR
Sbjct: 5  SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64

Query: 85 NERN 88
          +  +
Sbjct: 65 SGPS 68

>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 = 75.3 bits (184), Expect = 5e-18
 Identities = 21/95 (22%), Positives = 31/95 (32%), Gaps = 21/95 (22%)

Query: 11  CDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVC----- 65
               ++    E    K RRNR  +       L + +ER   P    RE L ++       
Sbjct: 99  GGLIEEPTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECI 158

Query: 66  ----------------LSEARVQVWFQNRRAKFRR 84
                           ++E RV  WF NRR +   
Sbjct: 159 QRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAF 193

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

 Score = 72.1 bits (177), Expect = 6e-18
 Identities = 23/66 (34%), Positives = 33/66 (50%)

Query: 22 RRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81
              K R+ R  F   Q   LE+ F +  Y  A  RE LA  + L+  +V++WFQN R K
Sbjct: 4  GLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYK 63

Query: 82 FRRNER 87
           +R + 
Sbjct: 64 TKRAQN 69

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

 Score = 71.1 bits (175), Expect = 9e-18
 Identities = 25/57 (43%), Positives = 36/57 (63%)

Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
          R+ RT F + QL ALE+ F +  Y     R E +  + L+E +V++WFQNRRAK +R
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

 Score = 71.4 bits (175), Expect = 1e-17
 Identities = 24/75 (32%), Positives = 39/75 (52%)

Query: 14 EDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQV 73
                 ++   K ++ RT F+S QL  L   F+R  Y      +EL+  + LS  +V+ 
Sbjct: 9  NSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKT 68

Query: 74 WFQNRRAKFRRNERN 88
          WFQN+R K +R ++N
Sbjct: 69 WFQNQRMKSKRWQKN 83

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

 Score = 75.1 bits (183), Expect = 1e-17
 Identities = 25/95 (26%), Positives = 34/95 (35%), Gaps = 23/95 (24%)

Query: 12  DGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVC------ 65
            G+ DD   E    K RRNR  +       L + ++R   P    RE L ++        
Sbjct: 127 PGQSDDACSEPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQ 186

Query: 66  ---------------LSEARVQVWFQNRR--AKFR 83
                          ++E RV  WF NRR    FR
Sbjct: 187 RGVSPSKAHGLGSNLVTEVRVYNWFANRRKEEAFR 221

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

 Score = 70.4 bits (173), Expect = 2e-17
 Identities = 21/61 (34%), Positives = 35/61 (57%)

Query: 26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
            ++ RT F+  QL AL+  F++  Y      +EL+  + LS  +V+ WFQN+R K +R 
Sbjct: 2  TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW 61

Query: 86 E 86
          +
Sbjct: 62 Q 62

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

 Score = 70.5 bits (173), Expect = 2e-17
 Identities = 22/61 (36%), Positives = 36/61 (59%)

Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
          R+ R  F+  Q+  LE+ F++  Y  A  RE LA  + L+  +V++WFQN R K +R  +
Sbjct: 3  RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62

Query: 88 N 88
          +
Sbjct: 63 D 63

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

 Score = 68.8 bits (169), Expect = 6e-17
 Identities = 21/56 (37%), Positives = 35/56 (62%)

Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
          R+ R  F+  Q+  LE+ F++  Y  A  R++LA  + L+  +V++WFQNRR K +
Sbjct: 3  RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

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

 Score = 69.9 bits (170), Expect = 9e-17
 Identities = 20/85 (23%), Positives = 29/85 (34%), Gaps = 21/85 (24%)

Query: 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVC------------------ 65
            K RRNR  +       L + +ER   P    RE L ++                    
Sbjct: 6  TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLG 65

Query: 66 ---LSEARVQVWFQNRRAKFRRNER 87
             ++E RV  WF NRR +     +
Sbjct: 66 SNLVTEVRVYNWFANRRKEEAFRHK 90

>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 = 68.1 bits (166), Expect = 3e-16
 Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 3/68 (4%)

Query: 20 YERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRR 79
          Y    P+  + +T     Q+  LE  F ++ +P     + L  +  LS   +  WF  RR
Sbjct: 9  YPDFAPQKFKEKT---QGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERR 65

Query: 80 AKFRRNER 87
                E+
Sbjct: 66 KLRDSMEQ 73

>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 = 67.1 bits (164), Expect = 4e-16
 Identities = 24/62 (38%), Positives = 36/62 (58%)

Query: 27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
          PRR RTTF S Q+  LE+ F +  Y  A    +L+ K+ L  A+V++WF+NRR + +   
Sbjct: 2  PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQS 61

Query: 87 RN 88
            
Sbjct: 62 DQ 63

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

 Score = 66.6 bits (163), Expect = 5e-16
 Identities = 23/53 (43%), Positives = 35/53 (66%)

Query: 32 TTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
          T+F+  Q+  LE+ F R  Y  +  R  LAK + +++A+V+ WFQNRR K+RR
Sbjct: 2  TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRR 54

>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 = 67.2 bits (164), Expect = 7e-16
 Identities = 31/87 (35%), Positives = 42/87 (48%), Gaps = 1/87 (1%)

Query: 1  MEYDWMLTLRCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREEL 60
            +DWM   R   +      E     P   RT F + QL  LEK F    Y     R E+
Sbjct: 9  RTFDWMKVKRNPPKTAKVS-EPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEI 67

Query: 61 AKKVCLSEARVQVWFQNRRAKFRRNER 87
          A  + L+E +V++WFQNRR K ++ ER
Sbjct: 68 AATLELNETQVKIWFQNRRMKQKKRER 94

>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 = 64.7 bits (158), Expect = 3e-15
 Identities = 21/58 (36%), Positives = 40/58 (68%)

Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          +R RT F+S QL  L++ F    Y     R++L+ ++ L+EA++++WF+N+RAK +++
Sbjct: 4  KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKKS 61

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

 Score = 63.9 bits (156), Expect = 6e-15
 Identities = 27/57 (47%), Positives = 35/57 (61%)

Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
          RR RT F   QL  LEK F + +Y     R ELA ++ L E+ ++VWFQNRR K +R
Sbjct: 2  RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 58

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

 Score = 66.1 bits (160), Expect = 1e-14
 Identities = 14/85 (16%), Positives = 31/85 (36%)

Query: 10  RCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEA 69
                 +    + R   P++ R  F   Q   L  +F+    P   ++  +++++ L  +
Sbjct: 80  AACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELS 139

Query: 70  RVQVWFQNRRAKFRRNERNFISHRN 94
            V  +F N R +          H +
Sbjct: 140 TVSNFFMNARRRSLDKWLEHHHHHH 164

>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 = 63.8 bits (155), Expect = 1e-14
 Identities = 16/64 (25%), Positives = 23/64 (35%), Gaps = 3/64 (4%)

Query: 23 RKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKF 82
            P   + R      QL ALE  F +   P     + L  +  ++   +  WF  RR K 
Sbjct: 6  SGPTKYKERA---PEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKV 62

Query: 83 RRNE 86
             E
Sbjct: 63 NAEE 66

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

 Score = 64.1 bits (156), Expect = 1e-14
 Identities = 24/85 (28%), Positives = 43/85 (50%), Gaps = 5/85 (5%)

Query: 3  YDWMLTLRCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAK 62
          Y WM  +       + +      + +R RT++  +Q   LEK F    Y     R E+A 
Sbjct: 9  YPWMKRVHLGTSTVNAN-----GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAH 63

Query: 63 KVCLSEARVQVWFQNRRAKFRRNER 87
           + L+E ++++WFQNRR K+++  +
Sbjct: 64 ALSLTERQIKIWFQNRRMKWKKEHK 88

>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 = 63.9 bits (155), Expect = 1e-14
 Identities = 12/80 (15%), Positives = 25/80 (31%), Gaps = 3/80 (3%)

Query: 24  KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
            P+  + +T   + QL  L+  F  +          L  +  L+   +  WF  ++    
Sbjct: 11  TPQKFKEKT---AEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKA 67

Query: 84  RNERNFISHRNLDAPTSEQP 103
             E       +    +S   
Sbjct: 68  LKEEKMEIDESNAGSSSGPS 87

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

 Score = 61.6 bits (150), Expect = 5e-14
 Identities = 24/61 (39%), Positives = 34/61 (55%)

Query: 26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
            +R RT +   QL  LEK F    Y     R ELA  + L+E  +++WFQNRR K+++ 
Sbjct: 2  SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61

Query: 86 E 86
          E
Sbjct: 62 E 62

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

 Score = 61.4 bits (149), Expect = 1e-13
 Identities = 27/85 (31%), Positives = 40/85 (47%), Gaps = 12/85 (14%)

Query: 3  YDWMLTLRCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAK 62
          Y WM     +G              RR R T+  +Q   LEK F   HY     R E+A 
Sbjct: 8  YPWMAIAGTNGL------------RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAH 55

Query: 63 KVCLSEARVQVWFQNRRAKFRRNER 87
           + L+E ++++WFQNRR K ++  +
Sbjct: 56 ALSLTERQIKIWFQNRRMKLKKEIQ 80

>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 = 60.1 bits (146), Expect = 2e-13
 Identities = 21/62 (33%), Positives = 35/62 (56%)

Query: 27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
           +R R T+  +Q   LEK F    Y     R E+A  + L+E ++++WFQNRR K+++  
Sbjct: 2  RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61

Query: 87 RN 88
          + 
Sbjct: 62 KT 63

>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 = 59.5 bits (144), Expect = 4e-13
 Identities = 17/64 (26%), Positives = 33/64 (51%)

Query: 25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
             R+ R  ++  QL  LE+ +    +     R +++    LSE ++ +WFQNRR K ++
Sbjct: 5  SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64

Query: 85 NERN 88
          +  +
Sbjct: 65 SGPS 68

>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 = 58.7 bits (141), Expect = 2e-12
 Identities = 15/69 (21%), Positives = 27/69 (39%)

Query: 18 YDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQN 77
          +     K             QL+ L+  F RT +P     ++LAK+  L+   +  WF +
Sbjct: 16 FQGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGD 75

Query: 78 RRAKFRRNE 86
           R  ++   
Sbjct: 76 TRYAWKNGN 84

>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 = 57.9 bits (140), Expect = 2e-12
 Identities = 22/66 (33%), Positives = 35/66 (53%)

Query: 23 RKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKF 82
               R+ R  +  HQ   LEK F    Y     R E+A+ + L+E +V++WFQNRR K 
Sbjct: 9  HARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKM 68

Query: 83 RRNERN 88
          ++  ++
Sbjct: 69 KKINKD 74

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

 Score = 56.8 bits (137), Expect = 5e-12
 Identities = 18/63 (28%), Positives = 30/63 (47%)

Query: 25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
           + R+ R  +   QL  LE+ +    +     R  ++    LSE +V +WFQNRR K ++
Sbjct: 5  LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64

Query: 85 NER 87
             
Sbjct: 65 VIN 67

>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 = 51.2 bits (122), Expect = 7e-10
 Identities = 10/62 (16%), Positives = 22/62 (35%), Gaps = 3/62 (4%)

Query: 25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
              + +T     QL  L+  F +  +      ++L +   L    +  WF + R   + 
Sbjct: 4  GSSGKRKT---KEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH 60

Query: 85 NE 86
           +
Sbjct: 61 GQ 62

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

 Score = 50.6 bits (121), Expect = 1e-09
 Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 29 RNRTTFNSHQLNALEKVFER-THYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          ++         + LEKVF   T YPD    + L+K++  S  ++Q WF++RR + + +
Sbjct: 10 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPS 67

>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.4.1.1 Length = 64

 Score = 44.4 bits (105), Expect = 2e-07
 Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 5/59 (8%)

Query: 26 KPRRNRTTFNSHQLNALEKVF-ERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
                   N+     LEKVF   T +PD    E L+K++      +Q WF+ RR + +
Sbjct: 3  SGSSGTAQPNA----ILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 57

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

 Score = 43.9 bits (103), Expect = 4e-07
 Identities = 11/51 (21%), Positives = 21/51 (41%)

Query: 37 HQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
          + L+ L+  +     P A    ++A  V L    V+ WF+  +A     + 
Sbjct: 13 NLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISVQS 63

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

 Score = 42.6 bits (99), Expect = 2e-06
 Identities = 15/65 (23%), Positives = 27/65 (41%), Gaps = 4/65 (6%)

Query: 24 KPKPRRNRTTFNSHQLNALEKVFER----THYPDAFVREELAKKVCLSEARVQVWFQNRR 79
               ++RT F+   L  L+K ++              E +A ++ +    V+ W  NRR
Sbjct: 5  SSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRR 64

Query: 80 AKFRR 84
           K+R 
Sbjct: 65 RKYRL 69

>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 71

 Score = 38.2 bits (88), Expect = 7e-05
 Identities = 10/52 (19%), Positives = 24/52 (46%)

Query: 37 HQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88
            ++ L+  +     P++    +++  V L +  V+ WF+ R+     N R+
Sbjct: 15 DHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVYQYSNSRS 66

>2da6_A Hepatocyte nuclear factor 1-beta; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 102

 Score = 37.2 bits (85), Expect = 3e-04
 Identities = 18/100 (18%), Positives = 31/100 (31%), Gaps = 23/100 (23%)

Query: 25  PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVC------------------- 65
               RNR  +       L + ++R   P    RE L ++                     
Sbjct: 4   GSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGS 63

Query: 66  --LSEARVQVWFQNRRAKFRRNERNFISHRNLDAPTSEQP 103
             ++E RV  WF NRR +     R  ++     + +    
Sbjct: 64  NLVTEVRVYNWFANRRKEEAF--RQKLAMDAYSSNSGPSS 101

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	143
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.88
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.87
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.87
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.87
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.86
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.86
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.86
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.86
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.86
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.86
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.86
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.85
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.85
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.85
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.85
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.85
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.85
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.85
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.84
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.84
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.84
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.84
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.84
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.84
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.84
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.84
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.84
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.84
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.84
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.84
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.84
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.83
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.83
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.83
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.83
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.83
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.83
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.83
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.83
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.83
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.82
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.82
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.82
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.82
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.82
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.82
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.81
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.81
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.81
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.81
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.81
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.81
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.8
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.8
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.8
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.8
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.8
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.8
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.79
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.79
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.78
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.77
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.77
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.77
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.77
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.76
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.76
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.76
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.74
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.74
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.74
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.72
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.68
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.6
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.6
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.58
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.4
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.78
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	96.84
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	88.99
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	88.46
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	88.09
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	87.66
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	83.29
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	81.72
3c57_A	95	Two component transcriptional regulatory protein;	80.95

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

Probab=99.88  E-value=1.2e-22  Score=131.09  Aligned_cols=80  Identities=30%  Similarity=0.546  Sum_probs=61.9

Q ss_pred             CcccccccccCCCCCCcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123           2 EYDWMLTLRCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK   81 (143)
Q Consensus         2 ~~~w~~~~~~~~~~~~~~~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k   81 (143)
                      -|+||.....+.+..     ....+.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         8 ~~pwm~~~~~~~~~~-----~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k   82 (88)
T 2r5y_A            8 IYPWMKRVHLGTSTV-----NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMK   82 (88)
T ss_dssp             CCGGGSCC--------------------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCchhhccCCCCCCC-----CCCCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHH
Confidence            489998765433222     123346788999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhh
Q psy2123          82 FRRNE   86 (143)
Q Consensus        82 ~rk~~   86 (143)
                      +|+..
T Consensus        83 ~kk~~   87 (88)
T 2r5y_A           83 WKKEH   87 (88)
T ss_dssp             HHTTC
T ss_pred             hHhhc
Confidence            99864

>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=99.87  E-value=4.6e-22  Score=126.26  Aligned_cols=65  Identities=40%  Similarity=0.643  Sum_probs=60.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          23 RKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        23 ~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      ..++.++.|+.|+..|+.+|+..|..++||+..+++.||..|||++.+|++||||||+|+||..+
T Consensus        13 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~~   77 (80)
T 2dmt_A           13 KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGP   77 (80)
T ss_dssp             CCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCCS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcccC
Confidence            45567889999999999999999999999999999999999999999999999999999998654

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

Probab=99.87  E-value=8.8e-22  Score=124.92  Aligned_cols=65  Identities=54%  Similarity=0.904  Sum_probs=60.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        24 ~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      ..+.++.|+.|+..|+.+|+..|..++||+..+++.||..+||++.+|++||||||+|+|+..+.
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~   68 (80)
T 2dms_A            4 GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQ   68 (80)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHc
Confidence            34578899999999999999999999999999999999999999999999999999999997654

>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=99.87  E-value=4e-22  Score=130.89  Aligned_cols=86  Identities=36%  Similarity=0.562  Sum_probs=62.9

Q ss_pred             CcccccccccCCCCCCcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123           2 EYDWMLTLRCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK   81 (143)
Q Consensus         2 ~~~w~~~~~~~~~~~~~~~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k   81 (143)
                      .|+||...+........ ......+.++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||||||+|
T Consensus        10 ~~~W~~~~r~~~~~~~~-~~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k   88 (97)
T 1b72_A           10 TFDWMKVKRNPPKTAKV-SEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMK   88 (97)
T ss_dssp             CCGGGGC---------------------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             cccccccccCCCCCCCC-CCCCCCCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHH
Confidence            58999976632221111 11222456788999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhh
Q psy2123          82 FRRNERN   88 (143)
Q Consensus        82 ~rk~~~~   88 (143)
                      +|+..+.
T Consensus        89 ~kk~~~~   95 (97)
T 1b72_A           89 QKKRERE   95 (97)
T ss_dssp             HHHHHTC
T ss_pred             HhHHhcc
Confidence            9997654

>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=99.86  E-value=1.7e-21  Score=122.76  Aligned_cols=68  Identities=34%  Similarity=0.510  Sum_probs=62.3

Q ss_pred             cCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123          22 RRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF   89 (143)
Q Consensus        22 ~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~   89 (143)
                      +...+.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+.....
T Consensus         4 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~~   71 (77)
T 1nk2_P            4 GLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEK   71 (77)
T ss_dssp             CCSCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhccc
Confidence            34556788899999999999999999999999999999999999999999999999999999876543

>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=99.86  E-value=2e-21  Score=123.23  Aligned_cols=64  Identities=45%  Similarity=0.677  Sum_probs=60.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        25 ~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      .+.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+....
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (80)
T 2dmq_A            5 SSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLR   68 (80)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHH
Confidence            4567889999999999999999999999999999999999999999999999999999997654

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

Probab=99.86  E-value=1.3e-21  Score=124.21  Aligned_cols=67  Identities=60%  Similarity=0.936  Sum_probs=62.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhhcc
Q psy2123          25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFIS   91 (143)
Q Consensus        25 ~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~~~   91 (143)
                      .+.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+..+....
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~~~   71 (80)
T 2cue_A            5 SSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQ   71 (80)
T ss_dssp             CSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhhhc
Confidence            4567889999999999999999999999999999999999999999999999999999998876543

>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=99.86  E-value=5.7e-22  Score=125.69  Aligned_cols=66  Identities=32%  Similarity=0.464  Sum_probs=61.0

Q ss_pred             cCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          22 RRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        22 ~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      ....+.+|.|+.|+.+|+.+|+..|..++||+..++++||..|||++.+|++||||||+|+||...
T Consensus        12 ~~~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   77 (80)
T 2da3_A           12 EEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSGP   77 (80)
T ss_dssp             CCCCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhcc
Confidence            345567889999999999999999999999999999999999999999999999999999998643

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

Probab=99.86  E-value=9e-22  Score=125.92  Aligned_cols=67  Identities=34%  Similarity=0.534  Sum_probs=61.7

Q ss_pred             ccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          21 ERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        21 ~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      .....+.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+..+
T Consensus        16 ~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k   82 (84)
T 2kt0_A           16 DKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK   82 (84)
T ss_dssp             CCCCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCC
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhh
Confidence            3445667889999999999999999999999999999999999999999999999999999998654

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

Probab=99.86  E-value=1.9e-21  Score=120.41  Aligned_cols=63  Identities=54%  Similarity=0.892  Sum_probs=59.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        25 ~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      .+.++.|+.|+..|+.+|+..|..++||+..+++.||..+||++.+|++||||||+|+|+...
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2dmu_A            5 SSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP   67 (70)
T ss_dssp             TSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTST
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccCC
Confidence            346788999999999999999999999999999999999999999999999999999998654

>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=99.86  E-value=1.3e-21  Score=121.10  Aligned_cols=64  Identities=33%  Similarity=0.517  Sum_probs=59.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        24 ~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      ..+.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+..+
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2da2_A            4 GSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGP   67 (70)
T ss_dssp             SCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhccc
Confidence            3456788999999999999999999999999999999999999999999999999999998654

>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=99.85  E-value=1.1e-21  Score=121.52  Aligned_cols=63  Identities=27%  Similarity=0.532  Sum_probs=59.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        25 ~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      .+.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+...
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (70)
T 2cra_A            5 SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGP   67 (70)
T ss_dssp             CCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSCT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccCC
Confidence            456788999999999999999999999999999999999999999999999999999998653

>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=99.85  E-value=4.2e-21  Score=120.96  Aligned_cols=65  Identities=34%  Similarity=0.549  Sum_probs=61.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        24 ~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      .++.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+..+.
T Consensus        10 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k~   74 (77)
T 1puf_A           10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhhh
Confidence            34567889999999999999999999999999999999999999999999999999999998765

>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=99.85  E-value=1.3e-21  Score=121.15  Aligned_cols=64  Identities=27%  Similarity=0.400  Sum_probs=60.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        24 ~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      ..+.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+..+
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2da1_A            4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGP   67 (70)
T ss_dssp             SCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhcc
Confidence            3457789999999999999999999999999999999999999999999999999999998654

>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=99.85  E-value=4.2e-21  Score=118.83  Aligned_cols=63  Identities=41%  Similarity=0.610  Sum_probs=59.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        25 ~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      .+.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+...
T Consensus         5 ~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2e1o_A            5 SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGP   67 (70)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCCC
Confidence            346678999999999999999999999999999999999999999999999999999998654

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

Probab=99.85  E-value=3.6e-21  Score=116.82  Aligned_cols=60  Identities=40%  Similarity=0.628  Sum_probs=56.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123          27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE   86 (143)
Q Consensus        27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~   86 (143)
                      .++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+.+
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   62 (63)
T 2h1k_A            3 NKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE   62 (63)
T ss_dssp             --CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhhc
Confidence            567899999999999999999999999999999999999999999999999999999863

>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=99.85  E-value=3.1e-21  Score=116.33  Aligned_cols=58  Identities=36%  Similarity=0.725  Sum_probs=53.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123          27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR   84 (143)
Q Consensus        27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk   84 (143)
                      .++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+||
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            4678999999999999999999999999999999999999999999999999999987

>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=99.85  E-value=2.8e-21  Score=122.92  Aligned_cols=61  Identities=38%  Similarity=0.622  Sum_probs=54.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123          26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE   86 (143)
Q Consensus        26 ~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~   86 (143)
                      +.++.|+.|+..|+.+|+..|..++||+..+++.||..+||++.+|++||||||+|+||..
T Consensus        19 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   79 (81)
T 1b8i_A           19 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEI   79 (81)
T ss_dssp             -----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhc
Confidence            4578899999999999999999999999999999999999999999999999999999864

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

Probab=99.84  E-value=6e-21  Score=113.92  Aligned_cols=57  Identities=44%  Similarity=0.751  Sum_probs=55.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123          28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR   84 (143)
Q Consensus        28 rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk   84 (143)
                      ++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            478999999999999999999999999999999999999999999999999999987

>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=99.84  E-value=2.3e-21  Score=122.98  Aligned_cols=61  Identities=20%  Similarity=0.314  Sum_probs=57.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHh----cCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123          24 KPKPRRNRTTFNSHQLNALEKVFER----THYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR   84 (143)
Q Consensus        24 ~~~~rr~R~~~~~~q~~~L~~~f~~----~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk   84 (143)
                      ..+.+|.|+.|+.+|+.+|+..|+.    ++||+..++++||..|||++.+|+|||||||+|+|+
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           14 GGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            4567889999999999999999999    999999999999999999999999999999999775

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

Probab=99.84  E-value=1.9e-21  Score=120.41  Aligned_cols=63  Identities=37%  Similarity=0.662  Sum_probs=59.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123          24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE   86 (143)
Q Consensus        24 ~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~   86 (143)
                      ..+.++.|+.|+..|+.+|+..|..++||+..+++.||..+||++.+|++||||||+|+|+..
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2djn_A            4 GSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSG   66 (70)
T ss_dssp             CCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccC
Confidence            345678899999999999999999999999999999999999999999999999999998854

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

Probab=99.84  E-value=6e-21  Score=117.53  Aligned_cols=63  Identities=35%  Similarity=0.624  Sum_probs=59.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123          27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF   89 (143)
Q Consensus        27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~   89 (143)
                      .++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+|+|+..+..
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~~~   64 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDK   64 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhhHh
Confidence            467899999999999999999999999999999999999999999999999999999976543

>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=99.84  E-value=6.9e-21  Score=121.04  Aligned_cols=65  Identities=58%  Similarity=1.006  Sum_probs=59.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        24 ~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      .++.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+....
T Consensus        15 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~~   79 (81)
T 1fjl_A           15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHTS   79 (81)
T ss_dssp             --CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhccc
Confidence            45678899999999999999999999999999999999999999999999999999999997653

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

Probab=99.84  E-value=2.5e-21  Score=117.17  Aligned_cols=60  Identities=35%  Similarity=0.530  Sum_probs=52.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123          26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN   85 (143)
Q Consensus        26 ~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~   85 (143)
                      +.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+.
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            357889999999999999999999999999999999999999999999999999999885

>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=99.84  E-value=4.2e-21  Score=118.23  Aligned_cols=62  Identities=34%  Similarity=0.612  Sum_probs=58.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      .++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+..+.
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~~   63 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKT   63 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSCC
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhccc
Confidence            46789999999999999999999999999999999999999999999999999999997653

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

Probab=99.84  E-value=6.2e-21  Score=119.40  Aligned_cols=66  Identities=67%  Similarity=0.989  Sum_probs=61.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123          24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF   89 (143)
Q Consensus        24 ~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~   89 (143)
                      ..++++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+..+.+
T Consensus         6 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r~~   71 (75)
T 2m0c_A            6 KGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRERFG   71 (75)
T ss_dssp             CSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHhhh
Confidence            345678899999999999999999999999999999999999999999999999999999976653

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

Probab=99.84  E-value=8.9e-21  Score=116.75  Aligned_cols=62  Identities=39%  Similarity=0.660  Sum_probs=58.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      .++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+....
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~   63 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ   63 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhcc
Confidence            46789999999999999999999999999999999999999999999999999999997654

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

Probab=99.84  E-value=1e-20  Score=123.23  Aligned_cols=66  Identities=38%  Similarity=0.685  Sum_probs=61.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          23 RKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        23 ~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      ..++.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+....
T Consensus        13 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~   78 (93)
T 3a01_A           13 TPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAE   78 (93)
T ss_dssp             CCCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHH
Confidence            345677899999999999999999999999999999999999999999999999999999997654

>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=99.84  E-value=4.3e-21  Score=117.48  Aligned_cols=61  Identities=36%  Similarity=0.623  Sum_probs=57.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123          26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE   86 (143)
Q Consensus        26 ~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~   86 (143)
                      +.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+..
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   62 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHHh
Confidence            3578899999999999999999999999999999999999999999999999999998864

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

Probab=99.84  E-value=8.2e-21  Score=118.47  Aligned_cols=63  Identities=29%  Similarity=0.496  Sum_probs=59.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        25 ~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      .+.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+...
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   67 (73)
T 2l7z_A            5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVIN   67 (73)
T ss_dssp             SCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHhc
Confidence            346788999999999999999999999999999999999999999999999999999998654

>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=99.84  E-value=3.2e-21  Score=122.30  Aligned_cols=61  Identities=16%  Similarity=0.311  Sum_probs=56.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh-----cCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123          23 RKPKPRRNRTTFNSHQLNALEKVFER-----THYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR   84 (143)
Q Consensus        23 ~~~~~rr~R~~~~~~q~~~L~~~f~~-----~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk   84 (143)
                      ...+++|.||.|+.+|+.+|+ .|..     ++||+..++++||..|||++.+|+|||||||+|+++
T Consensus        13 ~~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           13 SGGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            345678899999999999999 7999     999999999999999999999999999999999775

>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=99.83  E-value=3.6e-21  Score=118.50  Aligned_cols=64  Identities=53%  Similarity=0.847  Sum_probs=60.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123          26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF   89 (143)
Q Consensus        26 ~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~   89 (143)
                      +.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+..+..
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~~~   65 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEFI   65 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhhcc
Confidence            3578899999999999999999999999999999999999999999999999999999987643

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

Probab=99.83  E-value=1.2e-20  Score=113.35  Aligned_cols=58  Identities=47%  Similarity=0.690  Sum_probs=55.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123          28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN   85 (143)
Q Consensus        28 rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~   85 (143)
                      ++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+.
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   59 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHhHhhcc
Confidence            5789999999999999999999999999999999999999999999999999999874

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

Probab=99.83  E-value=2.5e-20  Score=116.27  Aligned_cols=61  Identities=28%  Similarity=0.414  Sum_probs=57.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh-cCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          28 RRNRTTFNSHQLNALEKVFER-THYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        28 rr~R~~~~~~q~~~L~~~f~~-~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      ++.|+.|+..|+.+|+..|.. ++||+..++..||..+||++.+|++||||||+|+|+..+.
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~~~   64 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGL   64 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhccC
Confidence            467899999999999999995 9999999999999999999999999999999999997653

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

Probab=99.83  E-value=3.1e-21  Score=137.69  Aligned_cols=86  Identities=28%  Similarity=0.404  Sum_probs=58.9

Q ss_pred             cccccccccC-CCCCCcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123           3 YDWMLTLRCD-GEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK   81 (143)
Q Consensus         3 ~~w~~~~~~~-~~~~~~~~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k   81 (143)
                      +.||++.+.. +.....+......+++|.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|
T Consensus        74 ~~wl~eae~~~~~~~~~~~~~~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k  153 (164)
T 2xsd_C           74 NKWLEETDSSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQK  153 (164)
T ss_dssp             HHHHHHHCC-----------------------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHhhhccccCCCcccccccccccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHH
Confidence            4588887732 222333333445667889999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhh
Q psy2123          82 FRRNERN   88 (143)
Q Consensus        82 ~rk~~~~   88 (143)
                      +||..+.
T Consensus       154 ~kr~~~~  160 (164)
T 2xsd_C          154 EKRMTPA  160 (164)
T ss_dssp             HTBSCC-
T ss_pred             HhhccCC
Confidence            9997643

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

Probab=99.83  E-value=2.6e-20  Score=121.75  Aligned_cols=65  Identities=31%  Similarity=0.545  Sum_probs=61.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcC---------------CChhHHHHHHhhHHHHHHHhhhh
Q psy2123          24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVC---------------LSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        24 ~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lg---------------l~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      ..+.+|.|+.|+..|+.+|+.+|..++||+..+++.||..||               |++.+|++||||||+|+|+..+.
T Consensus         4 ~~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~~   83 (95)
T 2cuf_A            4 GSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANI   83 (95)
T ss_dssp             SSCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhhc
Confidence            356788999999999999999999999999999999999999               99999999999999999998764

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

Probab=99.83  E-value=8.4e-21  Score=120.36  Aligned_cols=63  Identities=24%  Similarity=0.340  Sum_probs=59.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhc----CCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123          24 KPKPRRNRTTFNSHQLNALEKVFERT----HYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE   86 (143)
Q Consensus        24 ~~~~rr~R~~~~~~q~~~L~~~f~~~----~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~   86 (143)
                      ..+.++.|+.|+.+|+.+|+.+|..+    +||+..++++||..+||++.+|++||||||+|+|+..
T Consensus         5 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~~   71 (80)
T 2da4_A            5 SSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMG   71 (80)
T ss_dssp             CCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhcc
Confidence            34577889999999999999999999    9999999999999999999999999999999999853

>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=99.83  E-value=2.5e-20  Score=115.93  Aligned_cols=61  Identities=30%  Similarity=0.462  Sum_probs=57.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh-cCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          28 RRNRTTFNSHQLNALEKVFER-THYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        28 rr~R~~~~~~q~~~L~~~f~~-~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      .+.|+.|+..|+.+|+..|.. ++||+..++..||..+||++.+|++||||||+|+|+..+.
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~~~   63 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGL   63 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhccC
Confidence            367899999999999999996 9999999999999999999999999999999999997643

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

Probab=99.83  E-value=1.3e-20  Score=115.66  Aligned_cols=61  Identities=48%  Similarity=0.821  Sum_probs=57.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        28 rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      ++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+..+.
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~~   62 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRE   62 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCCT
T ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhchh
Confidence            6789999999999999999999999999999999999999999999999999999986543

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

Probab=99.83  E-value=1.5e-20  Score=112.97  Aligned_cols=58  Identities=66%  Similarity=1.070  Sum_probs=50.7

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          30 NRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        30 ~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      .|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+..+
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~k   59 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK   59 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC----
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhcc
Confidence            4789999999999999999999999999999999999999999999999999998654

>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=99.82  E-value=7.3e-20  Score=120.25  Aligned_cols=68  Identities=25%  Similarity=0.403  Sum_probs=62.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHc---------------------CCChhHHHHHHhhHHHHH
Q psy2123          24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKV---------------------CLSEARVQVWFQNRRAKF   82 (143)
Q Consensus        24 ~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~l---------------------gl~~~~V~~WFqNrR~k~   82 (143)
                      .++.||.|+.|++.|+.+|+..|..++||+..++++||..|                     +|++.+|++||||||+++
T Consensus         3 ~~~~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k~   82 (102)
T 2da6_A            3 SGSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEE   82 (102)
T ss_dssp             TCCSCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHHH
Confidence            45678899999999999999999999999999999999999                     799999999999999999


Q ss_pred             HHhhhhhcc
Q psy2123          83 RRNERNFIS   91 (143)
Q Consensus        83 rk~~~~~~~   91 (143)
                      ++..+....
T Consensus        83 kr~~~~~~~   91 (102)
T 2da6_A           83 AFRQKLAMD   91 (102)
T ss_dssp             HHHHHHHHS
T ss_pred             HHhhHhhhc
Confidence            998776543

>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=99.82  E-value=1.2e-20  Score=113.65  Aligned_cols=59  Identities=29%  Similarity=0.522  Sum_probs=48.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHH
Q psy2123          25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR   83 (143)
Q Consensus        25 ~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~r   83 (143)
                      .+.++.|+.|+..|+.+|+.+|..++||+..++..||..+||++.+|++||+|||+++|
T Consensus         3 ~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            3 EKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             ---------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            45678899999999999999999999999999999999999999999999999999865

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

Probab=99.82  E-value=2.5e-20  Score=111.04  Aligned_cols=57  Identities=37%  Similarity=0.628  Sum_probs=54.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHH
Q psy2123          27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR   83 (143)
Q Consensus        27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~r   83 (143)
                      .++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|
T Consensus         2 ~rr~Rt~~t~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~k   58 (58)
T 3rkq_A            2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK   58 (58)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHC
T ss_pred             cCCCCCCcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhhccCC
Confidence            467899999999999999999999999999999999999999999999999999975

>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=99.82  E-value=5.9e-20  Score=114.86  Aligned_cols=60  Identities=15%  Similarity=0.276  Sum_probs=55.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          29 RNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        29 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      ..|..|+.+|+.+|+..|..++||+..++++||..+||++.+|++||||||+|+|+....
T Consensus         5 ~~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~l~   64 (76)
T 2ecc_A            5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLK   64 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCCS
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHHHH
Confidence            346679999999999999999999999999999999999999999999999999986543

>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=99.82  E-value=4.9e-20  Score=115.49  Aligned_cols=60  Identities=23%  Similarity=0.375  Sum_probs=56.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          29 RNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        29 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      ++|..|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+..+.
T Consensus         9 ~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~~   68 (75)
T 2da5_A            9 TKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETK   68 (75)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSCS
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhhc
Confidence            456679999999999999999999999999999999999999999999999999997654

>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=99.82  E-value=1.4e-20  Score=131.99  Aligned_cols=81  Identities=26%  Similarity=0.386  Sum_probs=61.6

Q ss_pred             ccccccccCCCCCCcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHH
Q psy2123           4 DWMLTLRCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR   83 (143)
Q Consensus         4 ~w~~~~~~~~~~~~~~~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~r   83 (143)
                      .|+++.+..+... .+..+...+++|.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|
T Consensus        65 ~wl~e~e~~~~~~-~~~~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~k  143 (146)
T 1au7_A           65 KWLEEAEQVGALY-NEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREK  143 (146)
T ss_dssp             HHHHHCCC-----------------CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             HHHHHhhcccCcc-CcccCCCCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhh
Confidence            5888877443222 122334456778899999999999999999999999999999999999999999999999999998


Q ss_pred             Hh
Q psy2123          84 RN   85 (143)
Q Consensus        84 k~   85 (143)
                      |.
T Consensus       144 r~  145 (146)
T 1au7_A          144 RV  145 (146)
T ss_dssp             SC
T ss_pred             cc
Confidence            74

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

Probab=99.81  E-value=5e-20  Score=109.24  Aligned_cols=54  Identities=43%  Similarity=0.721  Sum_probs=50.9

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123          32 TTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN   85 (143)
Q Consensus        32 ~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~   85 (143)
                      |.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+||.
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~   55 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ   55 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhhccc
Confidence            579999999999999999999999999999999999999999999999999985

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

Probab=99.81  E-value=1.1e-19  Score=117.15  Aligned_cols=56  Identities=16%  Similarity=0.261  Sum_probs=53.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      .|+.+|+.+|+..|..++||+..++.+||..+||++++|+|||||||+|+++.++.
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~~   72 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEK   72 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSC
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHHH
Confidence            78999999999999999999999999999999999999999999999999987654

>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=99.81  E-value=9.7e-20  Score=113.51  Aligned_cols=63  Identities=19%  Similarity=0.359  Sum_probs=58.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          25 PKPRRNRTTFNSHQLNALEKVFER---THYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        25 ~~~rr~R~~~~~~q~~~L~~~f~~---~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      .+.++.|+.|+..|+.+|+.+|..   ++||+..+++.||..+||++.+|++||+|||+|+++...
T Consensus         5 ~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~   70 (73)
T 1x2n_A            5 SSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSGP   70 (73)
T ss_dssp             SSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhcccccc
Confidence            456788999999999999999987   999999999999999999999999999999999998654

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

Probab=99.81  E-value=7.7e-20  Score=114.22  Aligned_cols=61  Identities=20%  Similarity=0.326  Sum_probs=57.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      .++.|+.|+..|+.+|+..|..++||+..++++||..+||++.+|++||||||+|+|+...
T Consensus         6 ~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   66 (74)
T 2ly9_A            6 SFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKS   66 (74)
T ss_dssp             CCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTTC
T ss_pred             CCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhCc
Confidence            4678999999999999999999999999999999999999999999999999999998654

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

Probab=99.81  E-value=6e-20  Score=115.36  Aligned_cols=61  Identities=30%  Similarity=0.421  Sum_probs=56.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      ..+.|+.|+..|+.+|+..|..++||+..+++.||..+||++.+|++||||||+|+|+..+
T Consensus         8 ~~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~   68 (76)
T 2dn0_A            8 ASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKG   68 (76)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCS
T ss_pred             CCCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhcc
Confidence            3456899999999999999999999999999999999999999999999999999998654

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

Probab=99.81  E-value=6.4e-20  Score=120.10  Aligned_cols=63  Identities=24%  Similarity=0.419  Sum_probs=56.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123          24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE   86 (143)
Q Consensus        24 ~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~   86 (143)
                      ....++.|+.|+..|+.+|+..|..++||+..++++||..+||++.+|++||||||+|+|+..
T Consensus        22 ~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   84 (96)
T 3nar_A           22 KSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGN   84 (96)
T ss_dssp             -----CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhc
Confidence            445667899999999999999999999999999999999999999999999999999999864

>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=99.80  E-value=2.8e-19  Score=114.12  Aligned_cols=65  Identities=17%  Similarity=0.331  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          24 KPKPRRNRTTFNSHQLNALEKVFER---THYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        24 ~~~~rr~R~~~~~~q~~~L~~~f~~---~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      ..+.++.|+.|+..|+.+|+.+|..   ++||+..+++.||..+||++.+|++||+|+|+|+++....
T Consensus         4 ~~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~~   71 (83)
T 2dmn_A            4 GSSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQ   71 (83)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHTC
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHHH
Confidence            3456788999999999999999987   5999999999999999999999999999999999886543

>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=99.80  E-value=5.5e-20  Score=118.29  Aligned_cols=62  Identities=35%  Similarity=0.673  Sum_probs=57.8

Q ss_pred             CCCCCCCCHHHHHHHHHHH---HhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123          28 RRNRTTFNSHQLNALEKVF---ERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF   89 (143)
Q Consensus        28 rr~R~~~~~~q~~~L~~~f---~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~   89 (143)
                      ||.|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.+|++||+|||+|+|+.....
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~   66 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKF   66 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGGG
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhccccc
Confidence            5789999999999999999   8999999999999999999999999999999999999876554

>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=99.80  E-value=3.9e-20  Score=130.36  Aligned_cols=82  Identities=27%  Similarity=0.479  Sum_probs=66.9

Q ss_pred             cccccccccC---CCCCC-cccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhH
Q psy2123           3 YDWMLTLRCD---GEDDD-YDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNR   78 (143)
Q Consensus         3 ~~w~~~~~~~---~~~~~-~~~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNr   78 (143)
                      +.||++.+..   +.... ....+...+++|.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++|||||
T Consensus        65 ~~Wl~e~e~~~~~~~~~~~~~~~~~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNr  144 (151)
T 3d1n_I           65 EKWLNEAELRNQEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNR  144 (151)
T ss_dssp             HHHHHHHHHHHHHCSTTHHHHHCSSCCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHhccccCcccccccCCCCCCCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHH
Confidence            4588876632   11111 1122344567889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHH
Q psy2123          79 RAKFRR   84 (143)
Q Consensus        79 R~k~rk   84 (143)
                      |+|+||
T Consensus       145 R~k~Kk  150 (151)
T 3d1n_I          145 RQTLKN  150 (151)
T ss_dssp             HHHHTC
T ss_pred             HhccCC
Confidence            999986

>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=99.80  E-value=1.9e-19  Score=112.12  Aligned_cols=61  Identities=34%  Similarity=0.646  Sum_probs=57.5

Q ss_pred             CCCCCCCCHHHHHHHHHHH---HhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          28 RRNRTTFNSHQLNALEKVF---ERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        28 rr~R~~~~~~q~~~L~~~f---~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      ++.|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.+|++||+|||+|+|+....
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~   65 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGK   65 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccccccc
Confidence            5789999999999999999   899999999999999999999999999999999999986554

>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=2e-19  Score=108.96  Aligned_cols=59  Identities=24%  Similarity=0.352  Sum_probs=55.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHh-cCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHH
Q psy2123          24 KPKPRRNRTTFNSHQLNALEKVFER-THYPDAFVREELAKKVCLSEARVQVWFQNRRAKF   82 (143)
Q Consensus        24 ~~~~rr~R~~~~~~q~~~L~~~f~~-~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~   82 (143)
                      .++++|.||.|+.+|+.+|+..|+. +.||+...++.||.++||++++|++||||+|--.
T Consensus         4 ~~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~~   63 (71)
T 1wi3_A            4 GSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHV   63 (71)
T ss_dssp             CCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceeee
Confidence            4567899999999999999999999 9999999999999999999999999999999753

>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=99.80  E-value=5.1e-19  Score=114.30  Aligned_cols=58  Identities=22%  Similarity=0.362  Sum_probs=54.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123          32 TTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF   89 (143)
Q Consensus        32 ~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~   89 (143)
                      ..|+..|+.+|+..|..++||+..+++.||..+||++.+|++||||||+|+|+.++..
T Consensus        18 k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~~~   75 (89)
T 2dmp_A           18 KEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAV   75 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCSCC
T ss_pred             ccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhHhh
Confidence            3489999999999999999999999999999999999999999999999999876543

>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=99.79  E-value=8.3e-20  Score=129.82  Aligned_cols=61  Identities=30%  Similarity=0.480  Sum_probs=54.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123          25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN   85 (143)
Q Consensus        25 ~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~   85 (143)
                      .+.||.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+||.
T Consensus        99 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C           99 SRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            4678899999999999999999999999999999999999999999999999999999984

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

Probab=99.79  E-value=9.8e-20  Score=110.71  Aligned_cols=58  Identities=28%  Similarity=0.533  Sum_probs=55.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHH---HhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123          27 PRRNRTTFNSHQLNALEKVF---ERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR   84 (143)
Q Consensus        27 ~rr~R~~~~~~q~~~L~~~f---~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk   84 (143)
                      .++.|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.+|++||+|+|+++||
T Consensus         3 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A            3 GHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             CCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            56789999999999999999   89999999999999999999999999999999999876

>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=99.78  E-value=4.9e-19  Score=106.28  Aligned_cols=55  Identities=29%  Similarity=0.440  Sum_probs=52.9

Q ss_pred             CCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123          31 RTTFNSHQLNALEKVFER---THYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN   85 (143)
Q Consensus        31 R~~~~~~q~~~L~~~f~~---~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~   85 (143)
                      |+.|+..|+.+|+.+|..   ++||+..++..||..+||++.+|++||+|||+++|+.
T Consensus         2 r~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A            2 GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             cCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            678999999999999999   9999999999999999999999999999999999873

>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=99.77  E-value=8.9e-20  Score=129.03  Aligned_cols=82  Identities=24%  Similarity=0.370  Sum_probs=64.6

Q ss_pred             ccccccccCCCC-CCcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHH
Q psy2123           4 DWMLTLRCDGED-DDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKF   82 (143)
Q Consensus         4 ~w~~~~~~~~~~-~~~~~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~   82 (143)
                      .|+.+.+..... +..+.+....+.+|.|+.|+..|+.+|+..|..++||+..++.+||..+||++.+|++||||||+|+
T Consensus        72 ~Wl~eae~~~~~~~~~~~~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~  151 (155)
T 3l1p_A           72 KWVEEADNNENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKG  151 (155)
T ss_dssp             HHHHHHTTCHHHHHSSCC---CCCSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHH
T ss_pred             HHhhhhhcccCccccccccccccCCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccc
Confidence            488776632211 1111122224567889999999999999999999999999999999999999999999999999999


Q ss_pred             HHh
Q psy2123          83 RRN   85 (143)
Q Consensus        83 rk~   85 (143)
                      ||.
T Consensus       152 Kr~  154 (155)
T 3l1p_A          152 KRS  154 (155)
T ss_dssp             HC-
T ss_pred             cCC
Confidence            974

>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=99.77  E-value=8.6e-19  Score=111.82  Aligned_cols=59  Identities=27%  Similarity=0.379  Sum_probs=54.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          29 RNRTTFNSHQLNALEKVFER---THYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        29 r~R~~~~~~q~~~L~~~f~~---~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      +.|+.|+..|+.+|+.+|..   ++||+..++..||..+||++.+|++||||||+|+|+...
T Consensus         4 krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~~   65 (83)
T 1le8_B            4 YRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITI   65 (83)
T ss_dssp             -CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHcccccccc
Confidence            45667999999999999999   999999999999999999999999999999999998643

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

Probab=99.77  E-value=1.3e-18  Score=111.92  Aligned_cols=58  Identities=28%  Similarity=0.418  Sum_probs=54.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHH
Q psy2123          26 KPRRNRTTFNSHQLNALEKVFER---THYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR   83 (143)
Q Consensus        26 ~~rr~R~~~~~~q~~~L~~~f~~---~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~r   83 (143)
                      ++++.|+.|+..|+.+|+.+|..   ++||+..++..||..+||++.+|++||+|||+|+|
T Consensus        26 ~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k   86 (87)
T 1mnm_C           26 TKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK   86 (87)
T ss_dssp             SSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcc
Confidence            35566899999999999999999   99999999999999999999999999999999987

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

Probab=99.77  E-value=2.5e-19  Score=111.42  Aligned_cols=58  Identities=29%  Similarity=0.479  Sum_probs=53.8

Q ss_pred             CCCCCCCCHHHHHHHHHHH-HhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123          28 RRNRTTFNSHQLNALEKVF-ERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN   85 (143)
Q Consensus        28 rr~R~~~~~~q~~~L~~~f-~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~   85 (143)
                      .+.|..++.+|+.+||..| ..++||+..++.+||..+||++++|++||||||+|+|+.
T Consensus         9 ~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~   67 (72)
T 2cqx_A            9 IKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPS   67 (72)
T ss_dssp             CCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCC
Confidence            4556678889999999999 999999999999999999999999999999999999974

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

Probab=99.76  E-value=3.8e-19  Score=116.90  Aligned_cols=65  Identities=31%  Similarity=0.455  Sum_probs=53.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHH------------------cC---CChhHHHHHHhhHHHHH
Q psy2123          24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKK------------------VC---LSEARVQVWFQNRRAKF   82 (143)
Q Consensus        24 ~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~------------------lg---l~~~~V~~WFqNrR~k~   82 (143)
                      .++.+|.|+.|+..|+.+|+..|..++||+..++++||..                  ||   |++.+|++||||||+++
T Consensus         6 ~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k~   85 (99)
T 1lfb_A            6 TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEE   85 (99)
T ss_dssp             -------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHHH
Confidence            4567889999999999999999999999999999999999                  88   99999999999999988


Q ss_pred             HHhhhh
Q psy2123          83 RRNERN   88 (143)
Q Consensus        83 rk~~~~   88 (143)
                      +++.+.
T Consensus        86 k~k~~~   91 (99)
T 1lfb_A           86 AFRHKL   91 (99)
T ss_dssp             SCCC--
T ss_pred             HHhchh
Confidence            776543

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

Probab=99.76  E-value=1.4e-18  Score=105.29  Aligned_cols=53  Identities=21%  Similarity=0.416  Sum_probs=50.3

Q ss_pred             CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123          34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE   86 (143)
Q Consensus        34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~   86 (143)
                      -+.+|+.+|+..|..++||+..++.+||..+||++.+|++||||||+|+|+..
T Consensus        11 ~~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg~   63 (66)
T 3nau_A           11 KTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGI   63 (66)
T ss_dssp             CCHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhccC
Confidence            46899999999999999999999999999999999999999999999999753

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

Probab=99.76  E-value=9.7e-19  Score=107.76  Aligned_cols=57  Identities=37%  Similarity=0.600  Sum_probs=53.3

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          31 RTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        31 R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      -..++..|+..|+..|..++||+..++.+||..+||++++|++||||||+|+|+...
T Consensus         8 ~~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~~   64 (69)
T 2l9r_A            8 HSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQL   64 (69)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSSS
T ss_pred             CCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhhh
Confidence            346899999999999999999999999999999999999999999999999998654

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

Probab=99.74  E-value=1.1e-18  Score=124.31  Aligned_cols=65  Identities=20%  Similarity=0.330  Sum_probs=54.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          23 RKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        23 ~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      ...+.+|.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|+|+...
T Consensus        93 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~  157 (164)
T 2d5v_A           93 RGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWL  157 (164)
T ss_dssp             -------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC--
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccCC
Confidence            34567889999999999999999999999999999999999999999999999999999887543

>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=2.3e-18  Score=104.69  Aligned_cols=54  Identities=20%  Similarity=0.210  Sum_probs=50.2

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123          31 RTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR   84 (143)
Q Consensus        31 R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk   84 (143)
                      +..+...|+.+|+..|..++||+..++.+||..+||++++|++||||||+|.++
T Consensus         7 ~~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~   60 (64)
T 2e19_A            7 GQPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS   60 (64)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSC
T ss_pred             CCCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCC
Confidence            345678999999999999999999999999999999999999999999998765

>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=99.74  E-value=1.3e-18  Score=105.36  Aligned_cols=50  Identities=32%  Similarity=0.450  Sum_probs=46.4

Q ss_pred             HHHHHHHHHHH-HhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123          36 SHQLNALEKVF-ERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN   85 (143)
Q Consensus        36 ~~q~~~L~~~f-~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~   85 (143)
                      +.|+.+||..| ..++||+..++.+||.+|||+++||++||||||+|+|+.
T Consensus         9 ~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~~   59 (64)
T 1x2m_A            9 AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPS   59 (64)
T ss_dssp             SCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCCS
T ss_pred             chHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCCC
Confidence            45899999999 578999999999999999999999999999999998863

>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=99.72  E-value=1.4e-18  Score=126.63  Aligned_cols=62  Identities=32%  Similarity=0.462  Sum_probs=53.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcC---------------------CChhHHHHHHhhHHHH
Q psy2123          23 RKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVC---------------------LSEARVQVWFQNRRAK   81 (143)
Q Consensus        23 ~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lg---------------------l~~~~V~~WFqNrR~k   81 (143)
                      ..++.||.|+.|+..|+.+|+..|..++||+..++++||..|+                     |++.+|++||||||++
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            3456788999999999999999999999999999999999999                     9999999999999998


Q ss_pred             HHH
Q psy2123          82 FRR   84 (143)
Q Consensus        82 ~rk   84 (143)
                      ++.
T Consensus       191 ~k~  193 (194)
T 1ic8_A          191 EAF  193 (194)
T ss_dssp             CC-
T ss_pred             hhc
Confidence            764

>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=99.68  E-value=8.8e-17  Score=98.49  Aligned_cols=55  Identities=22%  Similarity=0.327  Sum_probs=50.2

Q ss_pred             CCCHHHHHHHHHHHH---hcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          33 TFNSHQLNALEKVFE---RTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        33 ~~~~~q~~~L~~~f~---~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      .|+.+|+.+|+.+|.   .++||+..++..||..+||++.+|++||+|+|+|.++...
T Consensus         4 ~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~   61 (67)
T 3k2a_A            4 IFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMI   61 (67)
T ss_dssp             --CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC-
T ss_pred             cCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHH
Confidence            689999999999999   9999999999999999999999999999999999997543

>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=99.60  E-value=1.4e-15  Score=92.61  Aligned_cols=46  Identities=17%  Similarity=0.346  Sum_probs=44.2

Q ss_pred             HHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123          36 SHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK   81 (143)
Q Consensus        36 ~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k   81 (143)
                      .+|+.+|+.+|..+++|+..++..||..+||++++|++||||||+.
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~   59 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVY   59 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhcccc
Confidence            5789999999999999999999999999999999999999999974

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

Probab=99.60  E-value=8.8e-16  Score=113.31  Aligned_cols=62  Identities=32%  Similarity=0.502  Sum_probs=53.4

Q ss_pred             ccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcC---------------------CChhHHHHHHhhHH
Q psy2123          21 ERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVC---------------------LSEARVQVWFQNRR   79 (143)
Q Consensus        21 ~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lg---------------------l~~~~V~~WFqNrR   79 (143)
                      ....++.||.|+.|++.|+.+|+.+|..++||+..++++||..||                     |++.+|++||+|||
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            344567889999999999999999999999999999999999988                     89999999999999


Q ss_pred             HHH
Q psy2123          80 AKF   82 (143)
Q Consensus        80 ~k~   82 (143)
                      ++.
T Consensus       216 ~~~  218 (221)
T 2h8r_A          216 KEE  218 (221)
T ss_dssp             TTC
T ss_pred             hhh
Confidence            864

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

Probab=99.58  E-value=1.2e-14  Score=93.08  Aligned_cols=58  Identities=19%  Similarity=0.311  Sum_probs=53.1

Q ss_pred             CCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          31 RTTFNSHQLNALEKVFER---THYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        31 R~~~~~~q~~~L~~~f~~---~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      -..|..+++.+|+.+|..   ++||+..++.+||.++||++.||++||+|+|.|.++....
T Consensus         9 ~~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~~   69 (89)
T 2lk2_A            9 SHMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLR   69 (89)
T ss_dssp             CCCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHHH
Confidence            346899999999999987   9999999999999999999999999999999999886544

>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=99.40  E-value=1.4e-13  Score=109.12  Aligned_cols=55  Identities=29%  Similarity=0.494  Sum_probs=51.6

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHH
Q psy2123          29 RNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR   83 (143)
Q Consensus        29 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~r   83 (143)
                      +-++.++..|+..|+..|..++||+..+|++||.++||+++||++||||||+|+|
T Consensus       367 ~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          367 AAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            4567899999999999999999999999999999999999999999999998864

>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=98.78  E-value=3.3e-10  Score=60.76  Aligned_cols=21  Identities=38%  Similarity=0.820  Sum_probs=18.4

Q ss_pred             hHHHHHHhhHHHHHHHhhhhh
Q psy2123          69 ARVQVWFQNRRAKFRRNERNF   89 (143)
Q Consensus        69 ~~V~~WFqNrR~k~rk~~~~~   89 (143)
                      +||+|||||||+|+||.....
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~   21 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFND   21 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHH
T ss_pred             CCceeccHHHHHHHHHHhHHH
Confidence            479999999999999987763

>2ys9_A Homeobox and leucine zipper protein homez; homeodomain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.84  E-value=0.002  Score=38.82  Aligned_cols=40  Identities=20%  Similarity=0.331  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhh
Q psy2123          38 QLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQN   77 (143)
Q Consensus        38 q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqN   77 (143)
                      -..+|+++|...+.+.......|+.+..|+..+|+-||-.
T Consensus        17 ~~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~   56 (70)
T 2ys9_A           17 DIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDS   56 (70)
T ss_dssp             CCHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             cchHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHh
Confidence            3579999999999999999999999999999999999964

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=88.99  E-value=1.4  Score=24.78  Aligned_cols=47  Identities=17%  Similarity=0.238  Sum_probs=31.7

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhH
Q psy2123          31 RTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNR   78 (143)
Q Consensus        31 R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNr   78 (143)
                      |..|+.+....+...+... ........++|..+|++...|..|....
T Consensus         3 r~~ys~efK~~~~~~~~~g-~s~~~~~~~vA~~~gIs~~tl~~W~~~~   49 (59)
T 2glo_A            3 RRIFTPHFKLQVLESYRND-NDCKGNQRATARKYNIHRRQIQKWLQCE   49 (59)
T ss_dssp             CCCCCHHHHHHHHHHHHHC-TTTTTCHHHHHHHTTSCHHHHHHHHTTH
T ss_pred             CCcCCHHHHHHHHHHHHcC-CCcchHHHHHHHHHCcCHHHHHHHHHHH
Confidence            3468888766664444432 2212225689999999999999997643

>1hlv_A CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} SCOP: a.4.1.7 a.4.1.7 PDB: 1bw6_A

Probab=88.46  E-value=2.1  Score=27.70  Aligned_cols=49  Identities=14%  Similarity=0.229  Sum_probs=37.8

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123          30 NRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK   81 (143)
Q Consensus        30 ~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k   81 (143)
                      .|..++.++...+-..+..+.....   .+||..+|++...|..|..++...
T Consensus         4 ~r~~~t~e~K~~iv~~~~~~g~~~~---~~~A~~~gvs~stl~~~~~~~~~~   52 (131)
T 1hlv_A            4 KRRQLTFREKSRIIQEVEENPDLRK---GEIARRFNIPPSTLSTILKNKRAI   52 (131)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSCH---HHHHHHHTCCHHHHHHHHHTHHHH
T ss_pred             cceeCCHHHHHHHHHHHHHCCCCcH---HHHHHHhCCCHHHHHHHHhchhhh
Confidence            5678999998777777755555543   367899999999999999887654

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=88.09  E-value=1.9  Score=26.33  Aligned_cols=49  Identities=10%  Similarity=0.254  Sum_probs=36.3

Q ss_pred             CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      ++..+..+|...|-..     ....+||..+|++...|+.+...-+.+.++...
T Consensus        38 L~~~~r~vl~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~   86 (92)
T 3hug_A           38 LSAEHRAVIQRSYYRG-----WSTAQIATDLGIAEGTVKSRLHYAVRALRLTLQ   86 (92)
T ss_dssp             SCHHHHHHHHHHHTSC-----CCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            5666777776655322     135788999999999999999888888776544

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=87.66  E-value=3.2  Score=25.14  Aligned_cols=46  Identities=11%  Similarity=0.229  Sum_probs=32.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhh
Q psy2123          27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQN   77 (143)
Q Consensus        27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqN   77 (143)
                      .++.+..|+.++.......+. ...    -..++|..+|++...|..|...
T Consensus        16 ~~~~~~~ys~e~k~~~v~~~~-~g~----s~~~iA~~~gIs~sTl~rW~k~   61 (87)
T 2elh_A           16 GKRPLRSLTPRDKIHAIQRIH-DGE----SKASVARDIGVPESTLRGWCKN   61 (87)
T ss_dssp             CSSCCSSCCHHHHHHHHHHHH-HTC----CHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHH-CCC----CHHHHHHHHCcCHHHHHHHHHH
Confidence            344566788888655555554 222    2567899999999999999853

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=83.29  E-value=3.1  Score=23.51  Aligned_cols=48  Identities=10%  Similarity=0.016  Sum_probs=36.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123          33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN   85 (143)
Q Consensus        33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~   85 (143)
                      .+++.+..+|...|-..     ....++|..+|++...|+.+...-+.+.++.
T Consensus        15 ~L~~~~r~il~l~~~~g-----~s~~eIA~~lgis~~tv~~~~~ra~~~l~~~   62 (70)
T 2o8x_A           15 DLTTDQREALLLTQLLG-----LSYADAAAVCGCPVGTIRSRVARARDALLAD   62 (70)
T ss_dssp             SSCHHHHHHHHHHHTSC-----CCHHHHHHHHTSCHHHHHHHHHHHHHHHHC-
T ss_pred             hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            36788888888876433     2356889999999999999988777666653

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=81.72  E-value=5.7  Score=24.89  Aligned_cols=47  Identities=17%  Similarity=0.116  Sum_probs=36.1

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHH
Q psy2123          31 RTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR   83 (143)
Q Consensus        31 R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~r   83 (143)
                      ...+++.+..+|...++--      ...+||..+|++...|+.+..+-+.|..
T Consensus        32 ~~~Lt~re~~Vl~l~~~G~------s~~EIA~~L~iS~~TV~~~l~ri~~KLg   78 (99)
T 1p4w_A           32 DKRLSPKESEVLRLFAEGF------LVTEIAKKLNRSIKTISSQKKSAMMKLG   78 (99)
T ss_dssp             SSSCCHHHHHHHHHHHHTC------CHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             cCCCCHHHHHHHHHHHcCC------CHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence            4568999999998765322      2478999999999999999886665543

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=80.95  E-value=3.9  Score=25.21  Aligned_cols=47  Identities=17%  Similarity=0.242  Sum_probs=36.3

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123          33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN   85 (143)
Q Consensus        33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~   85 (143)
                      .+++.+..+|...+..  +    ...+||..+|++...|+.+..+-+.|.+..
T Consensus        27 ~Lt~~e~~vl~l~~~g--~----s~~eIA~~l~is~~tV~~~l~r~~~kL~~~   73 (95)
T 3c57_A           27 GLTDQERTLLGLLSEG--L----TNKQIADRMFLAEKTVKNYVSRLLAKLGME   73 (95)
T ss_dssp             CCCHHHHHHHHHHHTT--C----CHHHHHHHHTCCHHHHHHHHHHHHHHHTCC
T ss_pred             cCCHHHHHHHHHHHcC--C----CHHHHHHHHCcCHHHHHHHHHHHHHHHcCC
Confidence            5889999999886432  2    246899999999999999888777666543

---

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	143
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	1e-24
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	1e-23
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	7e-23
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	3e-22
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	3e-22
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	7e-22
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	1e-21
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	1e-21
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	2e-20
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	5e-20
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	8e-20
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	8e-20
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	8e-20
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	9e-20
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	1e-19
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	5e-19
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	6e-19
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	9e-19
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	4e-18
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	6e-18
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	9e-18
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	2e-17
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	2e-17
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	2e-17
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	5e-17
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	4e-16
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	7e-16
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	1e-15
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	1e-15
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	2e-15
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	9e-12
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	2e-10

>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 = 87.9 bits (218), Expect = 1e-24
 Identities = 40/60 (66%), Positives = 47/60 (78%)

Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
          +RNRT+F   Q+ ALEK FERTHYPD F RE LA K+ L EAR+QVWF NRRAK+RR E+
Sbjct: 2  QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 61

>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 = 85.3 bits (211), Expect = 1e-23
 Identities = 22/74 (29%), Positives = 37/74 (50%)

Query: 15 DDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVW 74
          ++           R+ R  +  HQ   LEK F    Y     R E+A+ + L+E +V++W
Sbjct: 1  NNPAANWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIW 60

Query: 75 FQNRRAKFRRNERN 88
          FQNRR K ++  ++
Sbjct: 61 FQNRRMKMKKINKD 74

>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 = 83.0 bits (205), Expect = 7e-23
 Identities = 22/62 (35%), Positives = 33/62 (53%)

Query: 26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          K  R RT  N  QL+ L   +     PDA ++E+L +   LS   ++VWFQN+R K ++ 
Sbjct: 2  KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

Query: 86 ER 87
            
Sbjct: 62 SI 63

>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 = 81.4 bits (201), Expect = 3e-22
 Identities = 20/54 (37%), Positives = 32/54 (59%)

Query: 31 RTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
          R T+  +Q   LEK F    Y     R E+A  + L+E ++++WFQNRR K+++
Sbjct: 1  RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 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 = 81.4 bits (201), Expect = 3e-22
 Identities = 26/57 (45%), Positives = 35/57 (61%)

Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
          +  +  F++ Q   LEK FE   Y     R+ LAK + LSE +V+ WFQNRRAK+RR
Sbjct: 1  KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 57

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 80.3 bits (198), Expect = 7e-22
 Identities = 17/57 (29%), Positives = 31/57 (54%)

Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
          R+ R  ++  QL  LE+ +    +     R +++    LSE ++ +WFQNRR K ++
Sbjct: 2  RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 58

>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 = 80.8 bits (199), Expect = 1e-21
 Identities = 31/85 (36%), Positives = 42/85 (49%), Gaps = 1/85 (1%)

Query: 3  YDWMLTLRCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAK 62
          +DWM   R   +      E     P   RT F + QL  LEK F    Y     R E+A 
Sbjct: 4  FDWMKVKRNPPKTAKVS-EPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAA 62

Query: 63 KVCLSEARVQVWFQNRRAKFRRNER 87
           + L+E +V++WFQNRR K ++ ER
Sbjct: 63 TLELNETQVKIWFQNRRMKQKKRER 87

>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 = 80.0 bits (197), Expect = 1e-21
 Identities = 37/62 (59%), Positives = 49/62 (79%)

Query: 26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          K RR+RTTF++ QL+ LE+ FERT YPD + REELA++  L+EAR+QVWFQNRRA+ R+ 
Sbjct: 1  KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 60

Query: 86 ER 87
            
Sbjct: 61 HT 62

>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 = 77.8 bits (191), Expect = 2e-20
 Identities = 20/75 (26%), Positives = 29/75 (38%), Gaps = 15/75 (20%)

Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVC---------------LSEARVQ 72
          R +R T+    L  +E  F    YPD   REE+A                   ++  +V 
Sbjct: 1  RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVY 60

Query: 73 VWFQNRRAKFRRNER 87
           WF NRR + +R   
Sbjct: 61 NWFANRRKEIKRRAN 75

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 75.8 bits (186), Expect = 5e-20
 Identities = 34/59 (57%), Positives = 41/59 (69%)

Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
          RR RT F S QL  LE  F+R  YPD   REE+A    L+EARV+VWF+NRRAK+R+ E
Sbjct: 2  RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 60

>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 = 75.3 bits (185), Expect = 8e-20
 Identities = 22/53 (41%), Positives = 35/53 (66%)

Query: 29 RNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81
          R RT F+S QL  L++ F    Y     R++L+ ++ L+EA++++WFQN RAK
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>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 = 75.3 bits (185), Expect = 8e-20
 Identities = 25/57 (43%), Positives = 36/57 (63%)

Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
          R+ RT F + QL ALE+ F +  Y     R E +  + L+E +V++WFQNRRAK +R
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>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 = 75.3 bits (185), Expect = 8e-20
 Identities = 26/56 (46%), Positives = 34/56 (60%)

Query: 29 RNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
          R RT F   QL  LEK F + +Y     R ELA ++ L E+ ++VWFQNRR K +R
Sbjct: 1  RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 56

>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 = 75.4 bits (185), Expect = 9e-20
 Identities = 24/62 (38%), Positives = 36/62 (58%)

Query: 27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
          PRR RTTF S Q+  LE+ F +  Y  A    +L+ K+ L  A+V++WF+NRR + +   
Sbjct: 1  PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQS 60

Query: 87 RN 88
            
Sbjct: 61 DQ 62

>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 = 74.9 bits (184), Expect = 1e-19
 Identities = 18/56 (32%), Positives = 31/56 (55%)

Query: 29 RNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
          + RTT +    +ALE+ F     P +     +A+++ L +  V+VWF NRR + +R
Sbjct: 1  KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 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 = 73.4 bits (180), Expect = 5e-19
 Identities = 22/61 (36%), Positives = 36/61 (59%)

Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
          R+ R  F+  Q+  LE+ F++  Y  A  RE LA  + L+  +V++WFQN R K +R  +
Sbjct: 3  RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62

Query: 88 N 88
          +
Sbjct: 63 D 63

>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 = 73.1 bits (179), Expect = 6e-19
 Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 1/62 (1%)

Query: 28 RRNRTTFNSHQLNALEKVFERT-HYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
               T    Q+  LE  F +   +PD      +A +  L+E + Q WF+ R A++RR+E
Sbjct: 2  SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 61

Query: 87 RN 88
            
Sbjct: 62 GL 63

>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 = 72.7 bits (178), Expect = 9e-19
 Identities = 19/64 (29%), Positives = 31/64 (48%)

Query: 21 ERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRA 80
          E      +R RT+  +    +LE +F +   P       +A ++ L +  V+VWF NRR 
Sbjct: 2  ETLVQARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQ 61

Query: 81 KFRR 84
          K +R
Sbjct: 62 KGKR 65

>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 = 70.7 bits (173), Expect = 4e-18
 Identities = 16/53 (30%), Positives = 32/53 (60%)

Query: 31 RTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
          +++ +      LE+VF R    ++  +EE+AKK  ++  +V+VWF N+R + +
Sbjct: 1  KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53

>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 = 70.8 bits (173), Expect = 6e-18
 Identities = 23/63 (36%), Positives = 33/63 (52%)

Query: 25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
           K R+ R  F   Q   LE+ F +  Y  A  RE LA  + L+  +V++WFQN R K +R
Sbjct: 7  NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66

Query: 85 NER 87
           + 
Sbjct: 67 AQN 69

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Length = 73

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.4 bits (172), Expect = 9e-18
 Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 3/71 (4%)

Query: 28 RRNRTTFNSHQLNALEKVFE---RTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
          RR R  FN      L + F       YP    +EELAKK  ++ ++V  WF N+R ++++
Sbjct: 2  RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61

Query: 85 NERNFISHRNL 95
          N   F    N+
Sbjct: 62 NIGKFQEEANI 72

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Length = 62

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.4 bits (170), Expect = 2e-17
 Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 3/60 (5%)

Query: 28 RRNRTTFNSHQLNALEKVFERTH---YPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
          +  R     H  N +     +     YP    ++++A +  L+  +V  WF N R +  +
Sbjct: 3  KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQ 62

>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 = 68.7 bits (168), Expect = 2e-17
 Identities = 11/49 (22%), Positives = 22/49 (44%)

Query: 31 RTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRR 79
          R  F   Q   L  +F+    P   ++  +++++ L  + V  +F N R
Sbjct: 2  RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 52

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.6 bits (168), Expect = 2e-17
 Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 36 SHQLNALEKVF-ERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
          +     LEKVF   T +PD    E L+K++      +Q WF+ RR + + +
Sbjct: 2  AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPS 52

>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 = 67.9 bits (166), Expect = 5e-17
 Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 29 RNRTTFNSHQLNALEKVFER-THYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
          ++         + LEKVF   T YPD    + L+K++  S  ++Q WF++RR + +
Sbjct: 3  KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 80

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 66.6 bits (162), Expect = 4e-16
 Identities = 11/65 (16%), Positives = 21/65 (32%), Gaps = 4/65 (6%)

Query: 24 KPKPRRNRTTFNSHQLNALEKVFER----THYPDAFVREELAKKVCLSEARVQVWFQNRR 79
              +R RT F + Q   +    ER        D    E+   +  +    +++W  N +
Sbjct: 14 GGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNK 73

Query: 80 AKFRR 84
               
Sbjct: 74 NSGPS 78

>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 = 65.5 bits (159), Expect = 7e-16
 Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 1/61 (1%)

Query: 26 KPRRNRTTFNSHQLNALEKVFERT-HYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
             R+RT  +   L  L+        YPD      L+ ++ L +  +  +FQN+R   + 
Sbjct: 6  SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH 65

Query: 85 N 85
          +
Sbjct: 66 S 66

>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 = 64.6 bits (157), Expect = 1e-15
 Identities = 17/54 (31%), Positives = 30/54 (55%)

Query: 31 RTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
          RT+  ++   ALEK F     P +     +A+++ + +  ++VWF NRR K +R
Sbjct: 2  RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 55

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Length = 78

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Rat (Rattus rattus) [TaxId: 10117]

 Score = 65.2 bits (158), Expect = 1e-15
 Identities = 16/78 (20%), Positives = 25/78 (32%), Gaps = 21/78 (26%)

Query: 31 RTTFNSHQLNALEKVFERTHYPDAFVREELAKKV---------------------CLSEA 69
          R  +       L + +ER   P    RE L ++                       ++E 
Sbjct: 1  RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 70 RVQVWFQNRRAKFRRNER 87
          RV  WF NRR +     +
Sbjct: 61 RVYNWFANRRKEEAFRHK 78

>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 = 64.0 bits (156), Expect = 2e-15
 Identities = 18/60 (30%), Positives = 24/60 (40%), Gaps = 5/60 (8%)

Query: 28 RRNRTTFNSHQLNALEKVFE---RTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
          R +R  F    +  LE  F       Y D    E L K   LS  +++ W  NRR K + 
Sbjct: 1  RGHR--FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

>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 = 55.1 bits (132), Expect = 9e-12
 Identities = 11/64 (17%), Positives = 22/64 (34%), Gaps = 3/64 (4%)

Query: 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
           P+  + +T   + QL  L+  F  +          L  +  L+   +  WF  ++    
Sbjct: 4  TPQKFKEKT---AEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKA 60

Query: 84 RNER 87
            E 
Sbjct: 61 LKEE 64

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-leucine zipper protein Homez
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.7 bits (123), Expect = 2e-10
 Identities = 9/66 (13%), Positives = 21/66 (31%)

Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
            +       QL  L+  F +  +      ++L +   L    +  WF + R   +  + 
Sbjct: 4  GSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQL 63

Query: 88 NFISHR 93
           +    
Sbjct: 64 KWFRDN 69

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	143
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.91
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.89
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.88
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.88
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.88
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.88
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.88
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.88
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.88
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.87
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.87
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.86
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.86
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.85
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.85
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.84
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.84
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.84
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.84
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.83
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.82
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.82
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.79
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.79
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.78
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.78
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.77
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.75
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.74
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.72
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.7
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.7
d1hlva1	66	DNA-binding domain of centromere binding protein B	93.95
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	88.37
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	87.45
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	85.97

>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=99.91  E-value=1e-24  Score=138.92  Aligned_cols=85  Identities=36%  Similarity=0.558  Sum_probs=61.7

Q ss_pred             CcccccccccCCCCCCcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123           2 EYDWMLTLRCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK   81 (143)
Q Consensus         2 ~~~w~~~~~~~~~~~~~~~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k   81 (143)
                      -|+||...+....... .......++++.|+.|++.|+.+|+..|..++||+..++++||..|||++++|+|||||||+|
T Consensus         3 ~y~wm~~~r~~p~~~~-~~~~~~~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k   81 (88)
T d1b72a_           3 TFDWMKVKRNPPKTAK-VSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMK   81 (88)
T ss_dssp             CCGGGGC---------------------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCCCCCCCCC-CCCCCCCCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHH
Confidence            4999976553222111 112222345678999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhh
Q psy2123          82 FRRNER   87 (143)
Q Consensus        82 ~rk~~~   87 (143)
                      +||..+
T Consensus        82 ~Kk~~~   87 (88)
T d1b72a_          82 QKKRER   87 (88)
T ss_dssp             HHHHHT
T ss_pred             HHHhcc
Confidence            998754

>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=99.89  E-value=1.4e-23  Score=123.81  Aligned_cols=57  Identities=30%  Similarity=0.599  Sum_probs=54.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123          28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR   84 (143)
Q Consensus        28 rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk   84 (143)
                      +|.|+.|+..|+.+|+..|..++||+..++++||..+||++.+|++||||||+|+||
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            567899999999999999999999999999999999999999999999999999875

>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=99.88  E-value=4e-23  Score=122.04  Aligned_cols=57  Identities=44%  Similarity=0.751  Sum_probs=55.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123          28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR   84 (143)
Q Consensus        28 rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk   84 (143)
                      ||.|+.|++.|+.+|+..|+.++||+..++++||..+||++.+|++||||||+|+||
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            467999999999999999999999999999999999999999999999999999997

>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=99.88  E-value=5.3e-23  Score=124.78  Aligned_cols=62  Identities=39%  Similarity=0.660  Sum_probs=58.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      ++|.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|+|||||||+++|+....
T Consensus         1 Prr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~~   62 (67)
T d1zq3p1           1 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ   62 (67)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhhh
Confidence            35779999999999999999999999999999999999999999999999999999986543

>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=99.88  E-value=1.1e-22  Score=126.43  Aligned_cols=65  Identities=34%  Similarity=0.549  Sum_probs=60.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        24 ~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      .+..++.|+.|+..|+.+|+..|..++||+..+++.||..|||++.+|+|||||||+|+|+..+.
T Consensus        10 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~   74 (77)
T d1pufa_          10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHH
Confidence            33456789999999999999999999999999999999999999999999999999999987664

>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=99.88  E-value=7.1e-23  Score=120.49  Aligned_cols=57  Identities=46%  Similarity=0.685  Sum_probs=54.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123          28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR   84 (143)
Q Consensus        28 rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk   84 (143)
                      ++.|+.|++.|+.+|+..|..++||+..++++||..|||++.+|++||||||+++||
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k~kk   57 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR   57 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhhccC
Confidence            467899999999999999999999999999999999999999999999999999986

>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=99.88  E-value=1.1e-22  Score=122.63  Aligned_cols=63  Identities=59%  Similarity=1.026  Sum_probs=59.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        26 ~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      +.||.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||+|+|+|+....
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~~   63 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHTS   63 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhcccc
Confidence            357889999999999999999999999999999999999999999999999999999987653

>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=99.88  E-value=8.7e-23  Score=120.10  Aligned_cols=56  Identities=46%  Similarity=0.682  Sum_probs=54.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123          29 RNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR   84 (143)
Q Consensus        29 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk   84 (143)
                      |.|+.|++.|+.+|+..|..++||+..++++||..+||++.+|++||||||+|+||
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk   56 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR   56 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhc
Confidence            56899999999999999999999999999999999999999999999999999997

>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=99.88  E-value=6.8e-23  Score=119.82  Aligned_cols=55  Identities=36%  Similarity=0.623  Sum_probs=53.6

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123          31 RTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN   85 (143)
Q Consensus        31 R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~   85 (143)
                      |+.|+..|+.+|+..|..++||+..++.+||..|||++++|+|||||||+|+||.
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk~   55 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   55 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhhc
Confidence            7899999999999999999999999999999999999999999999999999984

>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=99.87  E-value=2.3e-23  Score=129.62  Aligned_cols=66  Identities=35%  Similarity=0.538  Sum_probs=60.7

Q ss_pred             cCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          22 RRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        22 ~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      +.+.+++|.|++|+.+|+.+|+..|..++||+..+++.||..+||++.+|++||||||+|.|+...
T Consensus         4 g~p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   69 (77)
T d1vnda_           4 GLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQN   69 (77)
T ss_dssp             CCSSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHhh
Confidence            445667888999999999999999999999999999999999999999999999999999887543

>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=99.87  E-value=1.7e-22  Score=117.25  Aligned_cols=53  Identities=42%  Similarity=0.726  Sum_probs=51.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123          29 RNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK   81 (143)
Q Consensus        29 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k   81 (143)
                      |.|+.|++.|+.+|+..|..++||+..++.+||..+||++.+|++||||||+|
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            56899999999999999999999999999999999999999999999999986

>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=99.86  E-value=3.4e-22  Score=121.47  Aligned_cols=62  Identities=35%  Similarity=0.652  Sum_probs=58.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123          27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      +||.|+.|++.|+.+|+..|..++||+..++..||..+||++.+|++||||+|+++|+..+.
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~~~   63 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKD   63 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhcccc
Confidence            36789999999999999999999999999999999999999999999999999999986543

>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=99.86  E-value=5.7e-22  Score=120.50  Aligned_cols=62  Identities=65%  Similarity=1.031  Sum_probs=58.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123          28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF   89 (143)
Q Consensus        28 rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~   89 (143)
                      +|.|+.|++.|+.+|+..|..++||+..+++.||..+||++.+|++||||+|+++|+..+..
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~~   63 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLR   63 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhhhh
Confidence            56799999999999999999999999999999999999999999999999999999876543

>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=99.85  E-value=1.1e-21  Score=120.27  Aligned_cols=60  Identities=30%  Similarity=0.486  Sum_probs=55.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh-cCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          28 RRNRTTFNSHQLNALEKVFER-THYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        28 rr~R~~~~~~q~~~L~~~f~~-~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      ++.|+.|+.+|+.+|+..|.. ++||+..++++||..+||++++|++||||||+|+||...
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~~   62 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   62 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhccC
Confidence            467899999999999999986 789999999999999999999999999999999998653

>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=99.85  E-value=2.9e-22  Score=119.07  Aligned_cols=58  Identities=57%  Similarity=0.924  Sum_probs=56.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123          28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN   85 (143)
Q Consensus        28 rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~   85 (143)
                      ||.|+.|+++|+.+|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            5789999999999999999999999999999999999999999999999999999985

>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=99.84  E-value=1.1e-21  Score=118.56  Aligned_cols=62  Identities=35%  Similarity=0.600  Sum_probs=58.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        26 ~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      +.+|.|+.|+++|+.+|+..|..|+||+..+++.||..+||++.+|++||||+|++.|+...
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~~~   63 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI   63 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCCC
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHHHH
Confidence            46788999999999999999999999999999999999999999999999999999887543

>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=99.84  E-value=2e-21  Score=114.53  Aligned_cols=57  Identities=32%  Similarity=0.483  Sum_probs=54.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123          29 RNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN   85 (143)
Q Consensus        29 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~   85 (143)
                      |.|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||||+|+++|+.
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr~   57 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV   57 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHhc
Confidence            568999999999999999999999999999999999999999999999999998874

>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=99.84  E-value=1.4e-21  Score=118.30  Aligned_cols=60  Identities=30%  Similarity=0.461  Sum_probs=56.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123          26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN   85 (143)
Q Consensus        26 ~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~   85 (143)
                      .++|.|+.|++.|+.+|+.+|..++||+..++++||..+||++.+|++||||+|+++||.
T Consensus         7 ~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_           7 ARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             CSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             ccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            356789999999999999999999999999999999999999999999999999998763

>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=99.84  E-value=4.4e-21  Score=120.61  Aligned_cols=61  Identities=33%  Similarity=0.592  Sum_probs=57.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcC---------------CChhHHHHHHhhHHHHHHHhhhh
Q psy2123          28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVC---------------LSEARVQVWFQNRRAKFRRNERN   88 (143)
Q Consensus        28 rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lg---------------l~~~~V~~WFqNrR~k~rk~~~~   88 (143)
                      |+.|+.|++.|+.+|+.+|..++||+..++++||..+|               |++.+|++||||||+|+|+....
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~~   76 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANI   76 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhhH
Confidence            57899999999999999999999999999999999875               99999999999999999997654

>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=99.83  E-value=3.2e-21  Score=111.72  Aligned_cols=53  Identities=30%  Similarity=0.550  Sum_probs=51.1

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHH
Q psy2123          31 RTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR   83 (143)
Q Consensus        31 R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~r   83 (143)
                      |+.|+++|+.+|+..|..++||+..++..||..+||++.+|++||||||+|.|
T Consensus         1 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~K   53 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   53 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTTC
T ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhccC
Confidence            68899999999999999999999999999999999999999999999999864

>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=99.82  E-value=7.6e-21  Score=116.49  Aligned_cols=59  Identities=24%  Similarity=0.365  Sum_probs=55.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHH-hcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123          26 KPRRNRTTFNSHQLNALEKVFE-RTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR   84 (143)
Q Consensus        26 ~~rr~R~~~~~~q~~~L~~~f~-~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk   84 (143)
                      ..++.|+.|+++|+.+|+.+|. .++||+..++++||.++||+..+|++||||+|++.|+
T Consensus         6 ~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk   65 (71)
T d1wi3a_           6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             CCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             CCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhcc
Confidence            3567899999999999999997 4899999999999999999999999999999999876

>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=99.82  E-value=9.1e-21  Score=111.30  Aligned_cols=56  Identities=30%  Similarity=0.465  Sum_probs=54.0

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123          30 NRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN   85 (143)
Q Consensus        30 ~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~   85 (143)
                      +||.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||||+|+++||.
T Consensus         1 kRT~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk~   56 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI   56 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHcc
Confidence            48999999999999999999999999999999999999999999999999999874

>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=99.79  E-value=4.8e-20  Score=115.27  Aligned_cols=61  Identities=18%  Similarity=0.302  Sum_probs=55.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHh----cCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123          24 KPKPRRNRTTFNSHQLNALEKVFER----THYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR   84 (143)
Q Consensus        24 ~~~~rr~R~~~~~~q~~~L~~~f~~----~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk   84 (143)
                      ..+.+|.|+.|+.+|+.+|+.+|++    ++||+..++++||..|||++.+|+|||||+|++.++
T Consensus        14 ~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          14 GGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             ccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            3456788999999999999999986    789999999999999999999999999999987653

>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=99.79  E-value=2.1e-19  Score=111.36  Aligned_cols=55  Identities=16%  Similarity=0.261  Sum_probs=51.1

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      .++++|+.+|+..|..++||+..+++.||..+||++.+|++||||||++.++...
T Consensus        10 ~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~   64 (76)
T d2ecba1          10 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEE   64 (76)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCS
T ss_pred             CCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhH
Confidence            3589999999999999999999999999999999999999999999998776544

>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=99.78  E-value=4.8e-19  Score=109.68  Aligned_cols=57  Identities=16%  Similarity=0.300  Sum_probs=53.2

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123          30 NRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE   86 (143)
Q Consensus        30 ~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~   86 (143)
                      .+..++.+|+.+|+..|..++||+..++..||..+||+..+|++||+|+|+++|+..
T Consensus         6 ~~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~~   62 (76)
T d2ecca1           6 SGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ   62 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhch
Confidence            345689999999999999999999999999999999999999999999999999753

>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=99.78  E-value=5.4e-20  Score=105.29  Aligned_cols=50  Identities=22%  Similarity=0.382  Sum_probs=48.8

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHH
Q psy2123          30 NRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRR   79 (143)
Q Consensus        30 ~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR   79 (143)
                      +|+.|+++|+.+|+..|..++||+..++.+||..+||++++|++||||||
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            58999999999999999999999999999999999999999999999987

>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=99.77  E-value=8.4e-19  Score=107.78  Aligned_cols=60  Identities=35%  Similarity=0.653  Sum_probs=55.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHH---hcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123          28 RRNRTTFNSHQLNALEKVFE---RTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER   87 (143)
Q Consensus        28 rr~R~~~~~~q~~~L~~~f~---~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~   87 (143)
                      ||.|+.|+.+|+.+|+.+|.   .++||+..+++.||..+||+..+|++||+|+|++.++...
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~~   64 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG   64 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccch
Confidence            56789999999999999997   4889999999999999999999999999999999987543

>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=99.75  E-value=4.4e-19  Score=110.07  Aligned_cols=56  Identities=29%  Similarity=0.436  Sum_probs=52.4

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcC---------------------CChhHHHHHHhhHHHHHHHhh
Q psy2123          31 RTTFNSHQLNALEKVFERTHYPDAFVREELAKKVC---------------------LSEARVQVWFQNRRAKFRRNE   86 (143)
Q Consensus        31 R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lg---------------------l~~~~V~~WFqNrR~k~rk~~   86 (143)
                      |++|++.|+.+|+.+|+.++||+..+++.||.+|+                     |++.+|++||+|||++.|+..
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr~~   77 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFRH   77 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCCC
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHHhc
Confidence            67899999999999999999999999999999994                     899999999999999988753

>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=99.74  E-value=5e-19  Score=101.82  Aligned_cols=50  Identities=32%  Similarity=0.459  Sum_probs=46.5

Q ss_pred             CHHHHHHHHHHHHh-cCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123          35 NSHQLNALEKVFER-THYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR   84 (143)
Q Consensus        35 ~~~q~~~L~~~f~~-~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk   84 (143)
                      |++|..+||.+|.. ++||+..+++.||..+||++++|++||||||+++|+
T Consensus         1 T~~q~~iLE~~F~~~~~~P~~~~~~~LA~~~~ls~~qV~~WFqNrR~k~k~   51 (52)
T d1x2ma1           1 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   51 (52)
T ss_dssp             SSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             ChhHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccCc
Confidence            45789999999986 789999999999999999999999999999999875

>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=99.72  E-value=2e-18  Score=101.76  Aligned_cols=55  Identities=31%  Similarity=0.518  Sum_probs=50.6

Q ss_pred             CCCCCCCHHHHHHHHHHHHh-cCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHH
Q psy2123          29 RNRTTFNSHQLNALEKVFER-THYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR   83 (143)
Q Consensus        29 r~R~~~~~~q~~~L~~~f~~-~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~r   83 (143)
                      +.+..++.++..+||.+|.. ++||+..+++.||.++||++++|++||||||+++|
T Consensus         3 k~~~~~k~~~~~iLE~~F~~~~~yPs~~~~~~LA~~lgls~~qV~~WFqNrR~k~r   58 (59)
T d2cqxa1           3 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK   58 (59)
T ss_dssp             CCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCccccHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccC
Confidence            45677888899999999986 68999999999999999999999999999999976

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.70  E-value=2.2e-17  Score=97.57  Aligned_cols=52  Identities=31%  Similarity=0.491  Sum_probs=48.5

Q ss_pred             CCCHHHHHHHHHHHHhc---CCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123          33 TFNSHQLNALEKVFERT---HYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR   84 (143)
Q Consensus        33 ~~~~~q~~~L~~~f~~~---~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk   84 (143)
                      +|+.+|+.+|+.+|..+   +||+..+++.||..+||+..+|++||+|+|++.|+
T Consensus         4 Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           4 RFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             SCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            49999999999999764   79999999999999999999999999999998875

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=4.4e-17  Score=96.84  Aligned_cols=56  Identities=21%  Similarity=0.406  Sum_probs=51.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHH
Q psy2123          28 RRNRTTFNSHQLNALEKVFER---THYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR   83 (143)
Q Consensus        28 rr~R~~~~~~q~~~L~~~f~~---~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~r   83 (143)
                      ++.|+.|+++++.+|+.+|..   ++||+..++..||..+||+..+|++||+|+|+|..
T Consensus         3 krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R~l   61 (62)
T d1x2na1           3 KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRIL   61 (62)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhc
Confidence            456788999999999999985   78999999999999999999999999999998754

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.95  E-value=0.16  Score=28.70  Aligned_cols=49  Identities=14%  Similarity=0.258  Sum_probs=38.7

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHH
Q psy2123          31 RTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKF   82 (143)
Q Consensus        31 R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~   82 (143)
                      |..++-.+...+-..|+..+...   ...||..+|+....|..|..|+..=.
T Consensus         5 Rk~LT~~eK~~ii~~~e~g~k~s---q~eIA~~fGv~~STvs~IlKnK~kil   53 (66)
T d1hlva1           5 RRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNKRAIL   53 (66)
T ss_dssp             SCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTHHHHH
T ss_pred             cccCCHHHHHHHHHHHHcCCcch---HHHHHHHhCCChhHHHHHHHHHHHHH
Confidence            44588888777778888776554   45689999999999999999965443

>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=88.37  E-value=0.86  Score=23.67  Aligned_cols=40  Identities=20%  Similarity=0.433  Sum_probs=33.4

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHh
Q psy2123          32 TTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQ   76 (143)
Q Consensus        32 ~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFq   76 (143)
                      ..++++|+......+... .+    ..+||..+|++...|..||-
T Consensus         4 ~~lt~~q~~~a~~l~~~G-~s----~~~iA~~~gVSr~TiYry~p   43 (47)
T d1ijwc_           4 RAINKHEQEQISRLLEKG-HP----RQQLAIIFGIGVSTLYRYFP   43 (47)
T ss_dssp             CSSCHHHHHHHHHHHHTT-CC----HHHHHHHHTCCHHHHHHHSC
T ss_pred             CcCCHHHHHHHHHHHHCC-CC----HHHHHHHHCcCHHHHHhhCC
Confidence            468999999999998743 33    67899999999999999983

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=87.45  E-value=0.93  Score=24.89  Aligned_cols=47  Identities=13%  Similarity=-0.026  Sum_probs=34.4

Q ss_pred             CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123          34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN   85 (143)
Q Consensus        34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~   85 (143)
                      +.+.+..++...|-...     ...++|..+|++...|+...+.-|.+.++.
T Consensus        19 Lp~~~r~v~~l~~~~~~-----s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~   65 (68)
T d1or7a1          19 LPEDLRMAITLRELDGL-----SYEEIAAIMDCPVGTVRSRIFRAREAIDNK   65 (68)
T ss_dssp             SCHHHHHHHHHHHTTCC-----CHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            44566666666654332     357899999999999999998877776654

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=85.97  E-value=1.3  Score=24.22  Aligned_cols=47  Identities=17%  Similarity=0.155  Sum_probs=35.5

Q ss_pred             CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123          34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN   85 (143)
Q Consensus        34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~   85 (143)
                      +++.+..++...|-...     ...++|..+|++...|+.....-+.+.|+.
T Consensus        22 L~~~~r~v~~l~~~~~~-----s~~eIA~~lgis~~tv~~~~~ra~~~Lr~~   68 (71)
T d1rp3a2          22 LPEREKLVIQLIFYEEL-----PAKEVAKILETSVSRVSQLKAKALERLREM   68 (71)
T ss_dssp             SCHHHHHHHHHHHTSCC-----CHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhHhC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            56777778877774432     467899999999999999887777666654