Citrus Sinensis ID: 040769

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------
Protein Sequence
MDWSSTTGNLRTFVPVFPRPETSFDLLYNYNYDQFPGMDQMNKHMHAAAAAAAMAEKSSSSIGLIPAAELMEKNIHHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQGTSTRNMMNKQVSTGITEVSGEETVESTSVATINGSFSNKHHQISECNYLFNVDEEFNAAAAPLPSPFWGLLPTSFQ
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccccccHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcccHHHHHHHHHHHHHcccccHHHHHHHHHHHcEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHcccccccccccccccccccccccccccccccccccccccccccEEcccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mdwssttgnlrtfvpvfprpetsfdllynynydqfpgmdqMNKHMHAAAAAAAMAEKssssiglipAAELMEKnihhygssstssqeRKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQGTSTRNMMNKQVSTGitevsgeetvestsvatingsfsnkhhqisecnylfnvdeefnaaaaplpspfwgllptsfq
Flexible Loop (DISEMBL)
mdwssttgnlrtfvpvfprpeTSFDLLYNYNYDQFPGMDQMNKHMHAAAAAAAMAEKSSSSIGLIPAAELMEKNIHHygssstssqerkKRLTSDQLESLERSfqeeikldpdrKMKLARelglqprqiaVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMlkeqgtstrnmmnkQVSTGITEVSGEETVESTSVATINGSFSNKHHQISECNYLFNVDEEFNAAAAPLPSPFWGLLPTSFQ
Low Complexity Region (SEG)
MDWSSTTGNLRTFVPVFPRPETSFDLLYNYNYDQFPGMDQMNKhmhaaaaaaamaEKSSSSIGLIPAAELMEKNIHHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQGTSTRNMMNKQVstgitevsgeetvestsvATINGSFSNKHHQISECNYLFNVDEEFNAAAAPLPSPFWGLLPTSFQ
Disordered region (IsUnstruct)
*********LRTFVPVFPRPETSFDLLYNYNYDQFPG************************************************************************************LGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYD***********************************************************FSNKHHQISECNYLFNVDEEFNAAAAPLPSPFWGLL*****
Disordered Region (DISOPRED)
*********************************************************************************************SDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR***********SLKQEYDAVS*******************************************************************************AAAPLPSPFW*LL*****
Disordered Region (DISEMBL)
********NLRTFVPVFPRPETSFDLLYNYNYDQFPGMDQMNKH****************SIGLIPAAELMEKNIHH******************QLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQGTSTRNMMNKQVSTGITEVSGEETVESTSVATINGSFSNKHHQISECNYLFNVDEEFNAAAAPLPSPFWGLLPTSFQ
Disordered Region (DISPRO)
******TGNLRTFVPVFPRPETSFDLLYNYNYDQFPG*************************************************ERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQGT*******************************************ECNYLFNVDEEFNAAAAPLPSPFWGLLPTSF*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDWSSTTGNLRTFVPVFPRPETSFDLLYNYNYDQFPGMDQMNKHMHAAAAAAAMAEKSSSSIGLIPAAELMEKNIHHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxLKEQGTSTRNMMNKQVSTGITEVSGEETVESTSVATINGSFSNKHHQISECNYLFNVDEEFNAAAAPLPSPFWGLLPTSFQ
Positional Conservation
no confident homologs detected

---

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	257	2.2.26 [Sep-21-2011]
Q9LZR0	235	Putative homeobox-leucine	yes	no	0.821	0.897	0.472	7e-46
Q4PSR7	185	Homeobox-leucine zipper p	no	no	0.571	0.794	0.493	2e-34
Q651Z5	249	Homeobox-leucine zipper p	yes	no	0.505	0.522	0.456	7e-26
Q9XH35	249	Homeobox-leucine zipper p	N/A	no	0.505	0.522	0.456	7e-26
Q6ZA74	349	Homeobox-leucine zipper p	yes	no	0.501	0.369	0.433	1e-25
Q9XH36	350	Homeobox-leucine zipper p	N/A	no	0.501	0.368	0.433	1e-25
Q940J1	294	Homeobox-leucine zipper p	no	no	0.498	0.435	0.452	2e-25
Q6YWR4	343	Homeobox-leucine zipper p	no	no	0.420	0.314	0.495	4e-25
A2X980	345	Homeobox-leucine zipper p	N/A	no	0.420	0.313	0.495	4e-25
P46667	312	Homeobox-leucine zipper p	no	no	0.536	0.442	0.415	1e-24

>sp|Q9LZR0|ATB51_ARATH Putative homeobox-leucine zipper protein ATHB-51 OS=Arabidopsis thaliana GN=ATHB-51 PE=2 SV=2

 Score =  184 bits (466), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 112/237 (47%), Positives = 157/237 (66%), Gaps = 26/237 (10%)

Query: 1   MDWSSTTG--NLRT-FVPVFPRPETS-FDLLYNYNYDQFPGMDQMNKHMHAAAAAAAMAE 56
           M+WS+T+   N+R  F+P  P PE+S F+ L+++N+D +            A  +    +
Sbjct: 1   MEWSTTSNVENVRVAFMPP-PWPESSSFNSLHSFNFDPY------------AGNSYTPGD 47

Query: 57  KSSSSIGLIPAAELMEKNIHHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKM 116
             +  +  +P +E +  N + +  ++ +   +KKRLTS QL SLERSFQEEIKLD DRK+
Sbjct: 48  TQTGPVISVPESEKI-MNAYRF-PNNNNEMIKKKRLTSGQLASLERSFQEEIKLDSDRKV 105

Query: 117 KLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRM 176
           KL+RELGLQPRQIAVWFQNRRARWK+KQLE LYDSL+QEYD VSREK  L +EV KL+ +
Sbjct: 106 KLSRELGLQPRQIAVWFQNRRARWKAKQLEQLYDSLRQEYDVVSREKQMLHDEVKKLRAL 165

Query: 177 LKEQGTSTRNMMNKQVSTGITEVSGEE-TVESTSVATINGSFSNKH-HQISECNYLF 231
           L++QG     ++ KQ+S G  +VSGEE TVE +SV   +    N + +QI+  N ++
Sbjct: 166 LRDQG-----LIKKQISAGTIKVSGEEDTVEISSVVVAHPRTENMNANQITGGNQVY 217

Putative transcription factor.
Arabidopsis thaliana (taxid: 3702)

>sp|Q4PSR7|ATB22_ARATH Homeobox-leucine zipper protein ATHB-22 OS=Arabidopsis thaliana GN=ATHB-22 PE=2 SV=1

 Score =  145 bits (367), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 81/164 (49%), Positives = 111/164 (67%), Gaps = 17/164 (10%)

Query: 30  YNYDQFPGMDQMNKHMHAAAAAAAMAEKSSSSIGLIPAAELMEKNIHHYGSSSTSSQERK 89
           YN+D F G +Q N+ +     A          I  +P A ++E       +S    +++K
Sbjct: 22  YNFDHFSG-NQDNRCLGTMMGA-------QQDILHVPLA-MVESGYGEESNSFNGQEKKK 72

Query: 90  KRLTSDQLESLERSFQEEIKLDPDRKMKL--------ARELGLQPRQIAVWFQNRRARWK 141
           K++TS+QL+ LERSFQEEIKL+PDRKMKL        ++ELGLQPRQIAVWFQNR+ARWK
Sbjct: 73  KKMTSEQLKFLERSFQEEIKLNPDRKMKLNPDRKMKLSKELGLQPRQIAVWFQNRKARWK 132

Query: 142 SKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQGTSTR 185
           +KQLE LY+SL+QE+D VSREK  LQEE+++LK M++E  +  +
Sbjct: 133 NKQLEHLYESLRQEFDIVSREKELLQEELIQLKSMIREDSSCKK 176

Probable transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q651Z5|HOX6_ORYSJ Homeobox-leucine zipper protein HOX6 OS=Oryza sativa subsp. japonica GN=HOX6 PE=2 SV=1

 Score =  117 bits (293), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 63/138 (45%), Positives = 91/138 (65%), Gaps = 8/138 (5%)

Query: 87  ERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE 146
           +RKKR + +Q++SLE  F  + KL+P +K++LARELGLQPRQ+A+WFQN+RARWKSKQLE
Sbjct: 29  DRKKRFSEEQIKSLESMFATQTKLEPRQKLQLARELGLQPRQVAIWFQNKRARWKSKQLE 88

Query: 147 LLYDSLKQEYDA-------VSREKLKLQEEVMKLKRMLKE-QGTSTRNMMNKQVSTGITE 198
             Y +L+ +YDA       + +EKL L +++ KL  ML+E +G    N  +   S G+  
Sbjct: 89  REYSALRDDYDALLCSYESLKKEKLALIKQLEKLAEMLQEPRGKYGDNAGDDARSGGVAG 148

Query: 199 VSGEETVESTSVATINGS 216
           +  EE V +   AT+  S
Sbjct: 149 MKKEEFVGAGGAATLYSS 166

Probable transcription factor that binds to the DNA sequence 5'-CAAT[AT]ATTG-3'.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9XH35|HOX6_ORYSI Homeobox-leucine zipper protein HOX6 OS=Oryza sativa subsp. indica GN=HOX6 PE=2 SV=2

 Score =  117 bits (293), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 63/138 (45%), Positives = 91/138 (65%), Gaps = 8/138 (5%)

Query: 87  ERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE 146
           +RKKR + +Q++SLE  F  + KL+P +K++LARELGLQPRQ+A+WFQN+RARWKSKQLE
Sbjct: 29  DRKKRFSEEQIKSLESMFATQTKLEPRQKLQLARELGLQPRQVAIWFQNKRARWKSKQLE 88

Query: 147 LLYDSLKQEYDA-------VSREKLKLQEEVMKLKRMLKE-QGTSTRNMMNKQVSTGITE 198
             Y +L+ +YDA       + +EKL L +++ KL  ML+E +G    N  +   S G+  
Sbjct: 89  REYSALRDDYDALLCSYESLKKEKLALIKQLEKLAEMLQEPRGKYGDNAGDDARSGGVAG 148

Query: 199 VSGEETVESTSVATINGS 216
           +  EE V +   AT+  S
Sbjct: 149 MKKEEFVGAGGAATLYSS 166

Probable transcription factor that binds to the DNA sequence 5'-CAAT[AT]ATTG-3'.

Oryza sativa subsp. indica (taxid: 39946)

>sp|Q6ZA74|HOX5_ORYSJ Homeobox-leucine zipper protein HOX5 OS=Oryza sativa subsp. japonica GN=HOX5 PE=1 SV=1

 Score =  116 bits (291), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 62/143 (43%), Positives = 94/143 (65%), Gaps = 14/143 (9%)

Query: 87  ERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE 146
           E+K+RLT++Q++ LERSF+EE KL+P+RK +LAR LG+ PRQ+AVWFQNRRARWK+KQLE
Sbjct: 85  EKKRRLTAEQVQMLERSFEEENKLEPERKTELARRLGMAPRQVAVWFQNRRARWKTKQLE 144

Query: 147 LLYDSLKQEYDAVS-------REKLKLQEEVMKLKRMLKEQGTSTRNMMNKQVSTGITEV 199
             +D LK  YDA++        +  +L+ +V+ L   L+++ TS  +     ++T   EV
Sbjct: 145 HDFDRLKAAYDALAADHHALLSDNDRLRAQVISLTEKLQDKETSPSSAT---ITTAAQEV 201

Query: 200 S----GEETVESTSVATINGSFS 218
                  E   +T  AT++G+ +
Sbjct: 202 DQPDEHTEAASTTGFATVDGALA 224

Probable transcription activator that binds to the DNA sequence 5'-CAAT[AT]ATTG-3'.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9XH36|HOX5_ORYSI Homeobox-leucine zipper protein HOX5 OS=Oryza sativa subsp. indica GN=HOX5 PE=1 SV=1

 Score =  116 bits (291), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 62/143 (43%), Positives = 94/143 (65%), Gaps = 14/143 (9%)

Query: 87  ERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE 146
           E+K+RLT++Q++ LERSF+EE KL+P+RK +LAR LG+ PRQ+AVWFQNRRARWK+KQLE
Sbjct: 85  EKKRRLTAEQVQMLERSFEEENKLEPERKTELARRLGMAPRQVAVWFQNRRARWKTKQLE 144

Query: 147 LLYDSLKQEYDAVS-------REKLKLQEEVMKLKRMLKEQGTSTRNMMNKQVSTGITEV 199
             +D LK  YDA++        +  +L+ +V+ L   L+++ TS  +     ++T   EV
Sbjct: 145 HDFDRLKAAYDALAADHHALLSDNDRLRAQVISLTEKLQDKETSPSSAT---ITTAAQEV 201

Query: 200 S----GEETVESTSVATINGSFS 218
                  E   +T  AT++G+ +
Sbjct: 202 DQPDEHTEAASTTGFATVDGALA 224

Probable transcription activator that binds to the DNA sequence 5'-CAAT[AT]ATTG-3'.

Oryza sativa subsp. indica (taxid: 39946)

>sp|Q940J1|ATB16_ARATH Homeobox-leucine zipper protein ATHB-16 OS=Arabidopsis thaliana GN=ATHB-16 PE=2 SV=2

 Score =  115 bits (289), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 66/146 (45%), Positives = 94/146 (64%), Gaps = 18/146 (12%)

Query: 63  GLIPAAELMEK---NIHHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLA 119
           G    A L+E+   N HH G S     E+K+RL  DQ+++LE++F+ E KL+P+RK KLA
Sbjct: 36  GYDEDATLIEEYSGNHHHMGLS-----EKKRRLKVDQVKALEKNFELENKLEPERKTKLA 90

Query: 120 RELGLQPRQIAVWFQNRRARWKSKQLEL-------LYDSLKQEYDAVSREKLKLQEEVMK 172
           +ELGLQPRQ+AVWFQNRRARWK+KQLE         YDSL+  +D++ R+   L +E+ K
Sbjct: 91  QELGLQPRQVAVWFQNRRARWKTKQLEKDYGVLKGQYDSLRHNFDSLRRDNDSLLQEISK 150

Query: 173 LKRMLKEQGTSTRNMMNKQVSTGITE 198
           +K  +  +     N  NK ++ G+ E
Sbjct: 151 IKAKVNGE---EDNNNNKAITEGVKE 173

Probable transcription factor that may function as a negative regulator of the flowering time response to photoperiod. May act to repress cell expansion during plant development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6YWR4|HOX16_ORYSJ Homeobox-leucine zipper protein HOX16 OS=Oryza sativa subsp. japonica GN=HOX16 PE=2 SV=1

 Score =  115 bits (287), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 57/115 (49%), Positives = 81/115 (70%), Gaps = 7/115 (6%)

Query: 87  ERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE 146
           E+K+RLT +Q+  LERSF+EE KL+P+RK +LAR+LGLQPRQ+AVWFQNRRARWK+KQLE
Sbjct: 76  EKKRRLTPEQVHLLERSFEEENKLEPERKTELARKLGLQPRQVAVWFQNRRARWKTKQLE 135

Query: 147 -------LLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQGTSTRNMMNKQVST 194
                    +D+L+ ++DA+ ++  +L  +VM L   L+E+ T+T       V  
Sbjct: 136 RDFDRLKASFDALRADHDALLQDNHRLHSQVMSLTEKLQEKETTTEGSAGAAVDV 190

Probable transcription factor.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|A2X980|HOX16_ORYSI Homeobox-leucine zipper protein HOX16 OS=Oryza sativa subsp. indica GN=HOX16 PE=2 SV=1

 Score =  115 bits (287), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 57/115 (49%), Positives = 81/115 (70%), Gaps = 7/115 (6%)

Query: 87  ERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE 146
           E+K+RLT +Q+  LERSF+EE KL+P+RK +LAR+LGLQPRQ+AVWFQNRRARWK+KQLE
Sbjct: 78  EKKRRLTPEQVHLLERSFEEENKLEPERKTELARKLGLQPRQVAVWFQNRRARWKTKQLE 137

Query: 147 -------LLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQGTSTRNMMNKQVST 194
                    +D+L+ ++DA+ ++  +L  +VM L   L+E+ T+T       V  
Sbjct: 138 RDFDRLKASFDALRADHDALLQDNHRLHSQVMSLTEKLQEKETTTEGSAGAAVDV 192

Probable transcription factor.

Oryza sativa subsp. indica (taxid: 39946)

>sp|P46667|ATHB5_ARATH Homeobox-leucine zipper protein ATHB-5 OS=Arabidopsis thaliana GN=ATHB-5 PE=1 SV=1

 Score =  113 bits (283), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 59/142 (41%), Positives = 93/142 (65%), Gaps = 4/142 (2%)

Query: 73  KNIHHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVW 132
           +++   G +S+++ E+K+RL  +Q+++LE++F+ + KL+P+RK+KLA+ELGLQPRQ+A+W
Sbjct: 57  EDLGGVGHASSTAAEKKRRLGVEQVKALEKNFEIDNKLEPERKVKLAQELGLQPRQVAIW 116

Query: 133 FQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQGTSTRNMMNKQV 192
           FQNRRARWK+KQLE  Y  LK  +DA+ R +  LQ +   L   +KE     +  +N + 
Sbjct: 117 FQNRRARWKTKQLERDYGVLKSNFDALKRNRDSLQRDNDSLLGQIKE----LKAKLNVEG 172

Query: 193 STGITEVSGEETVESTSVATIN 214
             GI E    + VE+      N
Sbjct: 173 VKGIEENGALKAVEANQSVMAN 194

Probable transcription factor that acts as a positive regulator of ABA-responsiveness, mediating the inhibitory effect of ABA on growth during seedling establishment. Binds to the DNA sequence 5'-CAATNATTG-3'.

Arabidopsis thaliana (taxid: 3702)

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	257
255575467	223	homeobox protein, putative [Ricinus comm	0.840	0.968	0.625	2e-73
225441050	220	PREDICTED: putative homeobox-leucine zip	0.828	0.968	0.588	4e-67
449440459	240	PREDICTED: putative homeobox-leucine zip	0.871	0.933	0.527	4e-60
449521341	230	PREDICTED: putative homeobox-leucine zip	0.844	0.943	0.530	2e-57
356548373	221	PREDICTED: putative homeobox-leucine zip	0.824	0.959	0.523	5e-57
255645502	221	unknown [Glycine max]	0.824	0.959	0.519	4e-56
356533426	225	PREDICTED: putative homeobox-leucine zip	0.813	0.928	0.509	3e-54
356505302	218	PREDICTED: putative homeobox-leucine zip	0.836	0.986	0.494	1e-49
357440243	232	Homeobox-leucine zipper protein ATHB-22	0.840	0.931	0.490	1e-48
356570812	214	PREDICTED: putative homeobox-leucine zip	0.821	0.985	0.482	5e-47

>gi|255575467|ref|XP_002528635.1| homeobox protein, putative [Ricinus communis] gi|223531924|gb|EEF33738.1| homeobox protein, putative [Ricinus communis]

 Score =  281 bits (719), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 162/259 (62%), Positives = 187/259 (72%), Gaps = 43/259 (16%)

Query: 1   MDWSSTTGNLRTFVPVFPRPETSFDLLYNYNYDQF-PGMDQMNKHMHAAAAAAAMAEKSS 59
           MDW    GNLRTFV    RPETSF+ LYNYNYDQ+ PGMD   KH       AA+AE   
Sbjct: 1   MDWH---GNLRTFVS---RPETSFNFLYNYNYDQYNPGMDV--KH-------AAIAE--- 42

Query: 60  SSIGLIPAAELMEKNIHHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLA 119
           +  GLIP  + +          S  SQE+KKRLTSDQLESLERSFQEEIKLDPDRKMKL+
Sbjct: 43  TPHGLIPTMDKI----------SFGSQEKKKRLTSDQLESLERSFQEEIKLDPDRKMKLS 92

Query: 120 RELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKE 179
           RELGLQPRQIAVWFQNRRARWK+KQLE LYDSLK+E+D VS+EK  LQEEVMKLK +L+ 
Sbjct: 93  RELGLQPRQIAVWFQNRRARWKAKQLERLYDSLKEEFDVVSKEKQNLQEEVMKLKAILR- 151

Query: 180 QGTSTRNMMNKQVSTGITEVSGEETVESTSVATINGS----FSNKHHQISECNYLFNVDE 235
           Q  +TRN    QVSTG TE+SGEETVESTSVA  +        + HHQI+ECNYL NVD 
Sbjct: 152 QEKATRN----QVSTGYTEISGEETVESTSVAIRSSGGKPRGGSSHHQIAECNYLLNVD- 206

Query: 236 EFNAAAAPLPSPFWGLLPT 254
           E+N    P+ SP+W ++P+
Sbjct: 207 EYN----PVSSPYWAVIPS 221

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225441050|ref|XP_002283931.1| PREDICTED: putative homeobox-leucine zipper protein ATHB-51 [Vitis vinifera] gi|297740036|emb|CBI30218.3| unnamed protein product [Vitis vinifera]

 Score =  260 bits (664), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 150/255 (58%), Positives = 177/255 (69%), Gaps = 42/255 (16%)

Query: 1   MDWSSTTGNLRTFVPVFPRPETSFDLLYNYNYDQFPGMDQMNKHMHAAAAAAAMAEKSSS 60
           MDW+   GNLR FV    RPE+SF  LYNYNYD +PGM+   KH  +A  A AM      
Sbjct: 1   MDWN---GNLRPFVS---RPESSFTFLYNYNYDPYPGMEV--KHPVSAETAHAMVRP--- 49

Query: 61  SIGLIPAAELMEKNIHHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLAR 120
                     M+K       SS  +QE+KKRLT++QLESLERSFQEEIKL+PDRKMKLAR
Sbjct: 50  ----------MDK-------SSYGNQEKKKRLTNEQLESLERSFQEEIKLEPDRKMKLAR 92

Query: 121 ELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQ 180
           ELGLQPRQIAVWFQNRRARWK+K+LE LYD LKQEYD +S+EK KLQEEV KLK +L+EQ
Sbjct: 93  ELGLQPRQIAVWFQNRRARWKTKELERLYDVLKQEYDLMSKEKQKLQEEVSKLKGILREQ 152

Query: 181 GTSTRNMMNKQVSTGITEVSGEETVESTSVATINGSFSNK--HHQISECNYLFNVDEEFN 238
            T       KQVS G TEVSGEETVESTS+ TI  S   +   HQI++CNY++   EE+N
Sbjct: 153 AT------RKQVSMGYTEVSGEETVESTSI-TIRSSNKPRGLSHQIADCNYVYTA-EEYN 204

Query: 239 AAAAPLPSPFWGLLP 253
               P+  P+WG+LP
Sbjct: 205 ----PVSPPYWGVLP 215

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449440459|ref|XP_004138002.1| PREDICTED: putative homeobox-leucine zipper protein ATHB-51-like [Cucumis sativus]

 Score =  237 bits (604), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 142/269 (52%), Positives = 177/269 (65%), Gaps = 45/269 (16%)

Query: 1   MDWSSTTGNLRTFVPVFPRPETSFDLLYNYNYDQFPGMDQMNKHMHAAAAAAAMAEKSSS 60
           M+W+  TG+ R FV     PE+SF  LYNYN +QF G+D   KH   A A+  + +    
Sbjct: 1   MEWA--TGSFRPFVSR--APESSFGFLYNYNLEQFQGVDV--KHSAMAGASETVLQ---- 50

Query: 61  SIGLIPAAELMEKNIHHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLAR 120
             GL+P  ++          +S  + E+KKRL+S+QLESLERSFQEEIKLDPDRK KL++
Sbjct: 51  --GLVPGMDM----------NSYGNLEKKKRLSSEQLESLERSFQEEIKLDPDRKQKLSK 98

Query: 121 ELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQ 180
           ELGLQPRQIAVWFQNRRARWK+KQLE LYD+LKQE+DA+SREK KLQEEVMKLK ML+E 
Sbjct: 99  ELGLQPRQIAVWFQNRRARWKAKQLEHLYDTLKQEFDAISREKHKLQEEVMKLKSMLREL 158

Query: 181 GTSTRNMMNKQVSTGITEVSGEETVESTSVATINGS-----------FSNKHHQI--SEC 227
             + RN    QVST  T++SGEETVESTSV     S            +  H+     +C
Sbjct: 159 -QAARN----QVSTVYTDLSGEETVESTSVGAGCSSKPRPVAAAAAVAAANHYTTPPEQC 213

Query: 228 NYLFNVDEEFNAAAAPLPSPFWGLLPTSF 256
           NY+FN  EE+N    P+   FWG LP+S+
Sbjct: 214 NYVFNT-EEYN----PMSPAFWGSLPSSY 237

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449521341|ref|XP_004167688.1| PREDICTED: putative homeobox-leucine zipper protein ATHB-51-like, partial [Cucumis sativus]

 Score =  228 bits (580), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 139/262 (53%), Positives = 172/262 (65%), Gaps = 45/262 (17%)

Query: 1   MDWSSTTGNLRTFVPVFPRPETSFDLLYNYNYDQFPGMDQMNKHMHAAAAAAAMAEKSSS 60
           M+W+  TG+ R FV     PE+SF  LYNYN +QF G+D   KH   A A+  + +    
Sbjct: 1   MEWA--TGSFRPFVSR--APESSFGFLYNYNLEQFQGVDV--KHSAMAGASETVLQ---- 50

Query: 61  SIGLIPAAELMEKNIHHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLAR 120
             GL+P  ++     + YG+      E+KKRL+S+QLESLERSFQEEIKLDPDRK KL++
Sbjct: 51  --GLVPGMDM-----NSYGNL-----EKKKRLSSEQLESLERSFQEEIKLDPDRKQKLSK 98

Query: 121 ELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQ 180
           ELGLQPRQIAVWFQNRRARWK+KQLE LYD+LKQE+DA+SREK KLQEEVMKLK ML+E 
Sbjct: 99  ELGLQPRQIAVWFQNRRARWKAKQLEHLYDTLKQEFDAISREKHKLQEEVMKLKSMLREL 158

Query: 181 GTSTRNMMNKQVSTGITEVSGEETVESTSVATINGS-----------FSNKHHQI--SEC 227
             + RN    QVST  T++SGEETVESTSV     S            +  H+     +C
Sbjct: 159 -QAARN----QVSTVYTDLSGEETVESTSVGAGCSSKPRPVAAAAAVAAANHYTTPPEQC 213

Query: 228 NYLFNVDEEFNAAAAPLPSPFW 249
           NY+FN  EE+N    P+   FW
Sbjct: 214 NYVFNT-EEYN----PMSPAFW 230

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356548373|ref|XP_003542577.1| PREDICTED: putative homeobox-leucine zipper protein ATHB-51-like [Glycine max]

 Score =  226 bits (577), Expect = 5e-57,   Method: Compositional matrix adjust.
 Identities = 135/258 (52%), Positives = 165/258 (63%), Gaps = 46/258 (17%)

Query: 1   MDWSSTTGNLRTFVPVFPRPETSFDLLYNYNYDQFPGMDQMNKHMHAAAAAAAMAEKSSS 60
           M+W+   G+ R +VP   R ++S   LYNYNY  +PGM+             A+AE SS 
Sbjct: 1   MEWN---GSTRRYVP---RADSSLSFLYNYNYTPYPGME---------VKQQALAETSSP 45

Query: 61  SIGLIPAAELMEKNIHHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLAR 120
                     MEK        +  +QE+KKRLTSDQL+SLE SFQ+EIKLDPDRKMKL++
Sbjct: 46  ----------MEK-------MNCGNQEKKKRLTSDQLDSLENSFQKEIKLDPDRKMKLSK 88

Query: 121 ELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQ 180
           ELGLQPRQIAVWFQNRRARWK+KQLE LYDSLKQE+D +S+EK KL+EEVMKLK ML+EQ
Sbjct: 89  ELGLQPRQIAVWFQNRRARWKNKQLEHLYDSLKQEFDVISKEKQKLEEEVMKLKTMLREQ 148

Query: 181 GTSTRNMMNKQVSTGITEVSGEETVESTSVATINGSFSNKHHQ-----ISECNYLFNVDE 235
            + T     +QVSTG TE+SGEETVESTS A         HHQ     I E N  F + E
Sbjct: 149 ASRT-----QQVSTGYTEISGEETVESTSEALRCSKRGTLHHQQQQNNIGEGNCSFTL-E 202

Query: 236 EFNAAAAPLPSPFWGLLP 253
           ++N        P+W  +P
Sbjct: 203 DYNTVPV---LPYWPGVP 217

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255645502|gb|ACU23246.1| unknown [Glycine max]

 Score =  224 bits (570), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 134/258 (51%), Positives = 164/258 (63%), Gaps = 46/258 (17%)

Query: 1   MDWSSTTGNLRTFVPVFPRPETSFDLLYNYNYDQFPGMDQMNKHMHAAAAAAAMAEKSSS 60
           M+W+   G+ R +VP   R ++S   LYNYNY  +PGM+             A+AE SS 
Sbjct: 1   MEWN---GSTRRYVP---RADSSLSFLYNYNYTPYPGME---------VKQQALAETSSP 45

Query: 61  SIGLIPAAELMEKNIHHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLAR 120
                     MEK        +  +QE+KKRLTSDQL+SLE SFQ+EIKLDPDRKMKL++
Sbjct: 46  ----------MEK-------MNCGNQEKKKRLTSDQLDSLENSFQKEIKLDPDRKMKLSK 88

Query: 121 ELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQ 180
           ELGLQPRQIAVWFQNRRARWK+KQLE LYDSLKQE+D +S+EK K +EEVMKLK ML+EQ
Sbjct: 89  ELGLQPRQIAVWFQNRRARWKNKQLEHLYDSLKQEFDVISKEKQKPEEEVMKLKTMLREQ 148

Query: 181 GTSTRNMMNKQVSTGITEVSGEETVESTSVATINGSFSNKHHQ-----ISECNYLFNVDE 235
            + T     +QVSTG TE+SGEETVESTS A         HHQ     I E N  F + E
Sbjct: 149 ASRT-----QQVSTGYTEISGEETVESTSEALRCSKRGTLHHQQQQNNIGEGNCSFTL-E 202

Query: 236 EFNAAAAPLPSPFWGLLP 253
           ++N        P+W  +P
Sbjct: 203 DYNTVPV---LPYWPGVP 217

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356533426|ref|XP_003535265.1| PREDICTED: putative homeobox-leucine zipper protein ATHB-51-like [Glycine max]

 Score =  217 bits (553), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 129/253 (50%), Positives = 161/253 (63%), Gaps = 44/253 (17%)

Query: 8   GNLRTFVPVFPRPETSFDLLYNYNYDQFPGMDQMNKHMHAAAAAAAMAEKSSSSIGLIPA 67
           G+ R +VP   R ++S   LYNYNY  +PGM+              +A  SSS       
Sbjct: 6   GSTRRYVP---RADSSLSFLYNYNYTPYPGME---------VKQQTLAGTSSS------- 46

Query: 68  AELMEKNIHHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPR 127
              MEK        +  +QE+KKRLTSDQL+SLE SFQ+EIKLDPDRKMKL++ELGLQPR
Sbjct: 47  ---MEK-------MNCGNQEKKKRLTSDQLDSLENSFQKEIKLDPDRKMKLSKELGLQPR 96

Query: 128 QIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQGTSTRNM 187
           QIAVWFQNRRARWK+KQLE LYDSLKQE+D +S+EK KL EEVMKLK ML+EQ + T+  
Sbjct: 97  QIAVWFQNRRARWKNKQLEHLYDSLKQEFDVISKEKQKLGEEVMKLKTMLREQASRTQ-- 154

Query: 188 MNKQVSTGITEVSGE-ETVESTSVATINGSFSNKH------HQISECNYLFNVDEEFNAA 240
             +QVSTG TE+SG+ ETVESTS A         H      + I E N  F +++ +N  
Sbjct: 155 --QQVSTGYTEISGDQETVESTSEALRCSKRGTLHQQQQNNNNIGEGNCSFTLEDHYNT- 211

Query: 241 AAPLPSPFWGLLP 253
              +P P+W  +P
Sbjct: 212 ---VPVPYWPGVP 221

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356505302|ref|XP_003521430.1| PREDICTED: putative homeobox-leucine zipper protein ATHB-51-like [Glycine max]

 Score =  202 bits (514), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 126/255 (49%), Positives = 152/255 (59%), Gaps = 40/255 (15%)

Query: 1   MDWSSTTGNLRTFVPVFPRPETSFDLLYNYNYDQ-FPGMDQMNKHMHAAAAAAAMAEKSS 59
           MDW   T       P+ PRPET     YNYNY+  +PG++            AA+ E   
Sbjct: 1   MDWHHGTK------PLVPRPET-LSFFYNYNYNSPYPGVE---------VKQAALMETGE 44

Query: 60  SSIGLIPAAELMEKNIHHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLA 119
            S+   PA  LM+          + ++E+KKRLT++Q+E LERSFQEEIKLDP+RKMKL+
Sbjct: 45  GSV---PA--LMD----------SRNKEKKKRLTNNQIELLERSFQEEIKLDPERKMKLS 89

Query: 120 RELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRML-K 178
           RELGLQPRQIAVWFQNRR RWK+KQLE LYD LK +YD VS EK KLQEEVMKLK ML K
Sbjct: 90  RELGLQPRQIAVWFQNRRTRWKTKQLEHLYDVLKHQYDVVSNEKQKLQEEVMKLKAMLSK 149

Query: 179 EQGTSTRNMMNKQVSTGITEVSGEETVESTSVATINGSFSNKHHQISECNYLFNVDEEFN 238
           EQG        KQ     TE+SGEETVESTS        SN  H +++  Y     E++N
Sbjct: 150 EQG------FGKQTFGCYTEISGEETVESTSEGLTLRGKSNIEH-VADQGYCSFTVEDYN 202

Query: 239 AAAAPLPSPFWGLLP 253
                 P   W  +P
Sbjct: 203 TTVLLPPHCHWPAVP 217

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357440243|ref|XP_003590399.1| Homeobox-leucine zipper protein ATHB-22 [Medicago truncatula] gi|355479447|gb|AES60650.1| Homeobox-leucine zipper protein ATHB-22 [Medicago truncatula]

 Score =  199 bits (506), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 125/255 (49%), Positives = 155/255 (60%), Gaps = 39/255 (15%)

Query: 1   MDWSSTTGNLRTFVPVFPRPETSFDLLYNYNYDQFPGMDQMNKHMHAAAAAAAMAEKSSS 60
           M+W+   GN R+FVP   +PE+S   LYNYN   + GM ++ KH                
Sbjct: 1   MEWN---GNTRSFVP---QPESSLSFLYNYNQCSYQGMMEV-KHQDWTDT---------- 43

Query: 61  SIGLIPAAELMEKNIHHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLAR 120
              + P  E M K    YG+     QE+KKRLTS+Q+ESLE SFQEEIKLDP RKMKL++
Sbjct: 44  ---MFPEMEKMMK----YGN-----QEKKKRLTSEQMESLESSFQEEIKLDPQRKMKLSK 91

Query: 121 ELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQ 180
           ELGLQPRQIA+WFQNRRARWK+KQLE LYDSL+ +++ VS+EK +LQ+EVMKLK MLKEQ
Sbjct: 92  ELGLQPRQIAIWFQNRRARWKTKQLEHLYDSLRHQFEVVSKEKQQLQDEVMKLKAMLKEQ 151

Query: 181 GTSTRNMMNKQVSTGITEVSGEETVESTSVATI---NGSFSNKHHQ---ISECNYLFNVD 234
           G S   M        + E    ETVESTS A +   N     K HQ   I E N  FN++
Sbjct: 152 GNSCGRMQGYYTEMSVEET---ETVESTSEAALRCSNREVKGKIHQQLNIDEGNCSFNLE 208

Query: 235 EEFNAAAAPLPSPFW 249
           +       PL  P+W
Sbjct: 209 DYNINNNVPL-LPYW 222

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356570812|ref|XP_003553578.1| PREDICTED: putative homeobox-leucine zipper protein ATHB-51-like [Glycine max]

 Score =  193 bits (491), Expect = 5e-47,   Method: Compositional matrix adjust.
 Identities = 123/255 (48%), Positives = 153/255 (60%), Gaps = 44/255 (17%)

Query: 1   MDWSSTTGNLRTFVPVFPRPETSFDLLYNY-NYDQFPGMDQMNKHMHAAAAAAAMAEKSS 59
           MDW   T       P  PRPET     YNY N + +PG++            AA+ E   
Sbjct: 1   MDWHHGTK------PFVPRPET-LSFFYNYDNNNSYPGVE---------VKQAALMETGE 44

Query: 60  SSIGLIPAAELMEKNIHHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLA 119
            S+   PA +               ++E+KKRLT++Q+E LERSFQEEIKLDP+RKMKL+
Sbjct: 45  RSV---PAMD-------------RGNKEKKKRLTNNQIELLERSFQEEIKLDPERKMKLS 88

Query: 120 RELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRML-K 178
           RELGLQPRQIAVWFQNRR RWK+KQLE LYD LK +YD VS EK KLQEEV+KLK ML K
Sbjct: 89  RELGLQPRQIAVWFQNRRTRWKAKQLEHLYDMLKHQYDVVSNEKQKLQEEVIKLKAMLSK 148

Query: 179 EQGTSTRNMMNKQVSTGITEVSGEETVESTSVATINGSFSNKHHQISECNYLFNVDEEFN 238
           +QG  T+         G TE+SGEETVESTS   + G  SN  H +++  Y     E++N
Sbjct: 149 QQGYWTQKF------GGYTEISGEETVESTSEG-LRGK-SNIEH-VADQGYCSFAVEDYN 199

Query: 239 AAAAPLPSPFWGLLP 253
              + LP   W ++P
Sbjct: 200 TTVS-LPHCHWPVVP 213

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

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	257
TAIR|locus:2144578	235	HB51 "homeobox 51" [Arabidopsi	0.645	0.706	0.508	3.7e-39
TAIR|locus:2040520	185	HB22 "homeobox protein 22" [Ar	0.560	0.778	0.496	1.1e-32
TAIR|locus:2140055	294	HB16 "homeobox protein 16" [Ar	0.443	0.387	0.480	1.6e-24
TAIR|locus:2205075	294	ATHB13 [Arabidopsis thaliana (	0.428	0.374	0.495	2.6e-24
TAIR|locus:2168225	312	HB5 "homeobox protein 5" [Arab	0.392	0.323	0.514	3.3e-24
TAIR|locus:2041283	311	HB6 "homeobox protein 6" [Arab	0.369	0.305	0.539	8.7e-24
TAIR|locus:2084228	272	HB-1 "homeobox 1" [Arabidopsis	0.377	0.356	0.533	1e-22
TAIR|locus:2150901	314	HB-3 "homeobox 3" [Arabidopsis	0.392	0.321	0.529	1.3e-22
TAIR|locus:2102107	286	HB20 "homeobox protein 20" [Ar	0.431	0.388	0.470	2.6e-22
TAIR|locus:2115215	216	HB40 "homeobox protein 40" [Ar	0.350	0.416	0.555	3.4e-22

TAIR|locus:2144578 HB51 "homeobox 51" [Arabidopsis thaliana (taxid:3702)]

 Score = 418 (152.2 bits), Expect = 3.7e-39, P = 3.7e-39
 Identities = 94/185 (50%), Positives = 128/185 (69%)

Query:     1 MDWSSTTG--NLRT-FVPVFPRPETS-FDLLYNYNYDQFPGMDQMNKXXXXXXXXXXXXE 56
             M+WS+T+   N+R  F+P  P PE+S F+ L+++N+D + G                  +
Sbjct:     1 MEWSTTSNVENVRVAFMPP-PWPESSSFNSLHSFNFDPYAG------------NSYTPGD 47

Query:    57 KSSSSIGLIPAAELMEKNIHHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKM 116
               +  +  +P +E +  N + + +++ +   +KKRLTS QL SLERSFQEEIKLD DRK+
Sbjct:    48 TQTGPVISVPESEKI-MNAYRFPNNN-NEMIKKKRLTSGQLASLERSFQEEIKLDSDRKV 105

Query:   117 KLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRM 176
             KL+RELGLQPRQIAVWFQNRRARWK+KQLE LYDSL+QEYD VSREK  L +EV KL+ +
Sbjct:   106 KLSRELGLQPRQIAVWFQNRRARWKAKQLEQLYDSLRQEYDVVSREKQMLHDEVKKLRAL 165

Query:   177 LKEQG 181
             L++QG
Sbjct:   166 LRDQG 170

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

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

GO:0009965 "leaf morphogenesis" evidence=IMP

GO:0010434 "bract formation" evidence=IGI

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

GO:0048510 "regulation of timing of transition from vegetative to reproductive phase" evidence=IGI

GO:0010582 "floral meristem determinacy" evidence=IGI

GO:0048443 "stamen development" evidence=RCA

TAIR|locus:2040520 HB22 "homeobox protein 22" [Arabidopsis thaliana (taxid:3702)]

 Score = 357 (130.7 bits), Expect = 1.1e-32, P = 1.1e-32
 Identities = 80/161 (49%), Positives = 109/161 (67%)

Query:    30 YNYDQFPGMDQMNKXXXXXXXXXXXXEKSSSSIGLIPAAELMEKNIHHYGSSSTSSQERK 89
             YN+D F G +Q N+              +   I  +P A ++E       +S    +++K
Sbjct:    22 YNFDHFSG-NQDNRCLGTMMG-------AQQDILHVPLA-MVESGYGEESNSFNGQEKKK 72

Query:    90 KRLTSDQLESLERSFQEEIKLDPDRKMKL--------ARELGLQPRQIAVWFQNRRARWK 141
             K++TS+QL+ LERSFQEEIKL+PDRKMKL        ++ELGLQPRQIAVWFQNR+ARWK
Sbjct:    73 KKMTSEQLKFLERSFQEEIKLNPDRKMKLNPDRKMKLSKELGLQPRQIAVWFQNRKARWK 132

Query:   142 SKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQGT 182
             +KQLE LY+SL+QE+D VSREK  LQEE+++LK M++E  +
Sbjct:   133 NKQLEHLYESLRQEFDIVSREKELLQEELIQLKSMIREDSS 173

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

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

TAIR|locus:2140055 HB16 "homeobox protein 16" [Arabidopsis thaliana (taxid:3702)]

 Score = 280 (103.6 bits), Expect = 1.6e-24, P = 1.6e-24
 Identities = 62/129 (48%), Positives = 89/129 (68%)

Query:    68 AELMEK---NIHHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGL 124
             A L+E+   N HH G S     E+K+RL  DQ+++LE++F+ E KL+P+RK KLA+ELGL
Sbjct:    41 ATLIEEYSGNHHHMGLS-----EKKRRLKVDQVKALEKNFELENKLEPERKTKLAQELGL 95

Query:   125 QPRQIAVWFQNRRARWKSKQLE----LL---YDSLKQEYDAVSREKLKLQEEVMKLKRML 177
             QPRQ+AVWFQNRRARWK+KQLE    +L   YDSL+  +D++ R+   L +E+ K+K  +
Sbjct:    96 QPRQVAVWFQNRRARWKTKQLEKDYGVLKGQYDSLRHNFDSLRRDNDSLLQEISKIKAKV 155

Query:   178 KEQGTSTRN 186
               +  +  N
Sbjct:   156 NGEEDNNNN 164

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

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

GO:0009637 "response to blue light" evidence=IMP

GO:0030308 "negative regulation of cell growth" evidence=IMP

GO:0048510 "regulation of timing of transition from vegetative to reproductive phase" evidence=IMP

GO:0048573 "photoperiodism, flowering" evidence=RCA;IMP

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

TAIR|locus:2205075 ATHB13 [Arabidopsis thaliana (taxid:3702)]

 Score = 278 (102.9 bits), Expect = 2.6e-24, P = 2.6e-24
 Identities = 60/121 (49%), Positives = 85/121 (70%)

Query:    78 YGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRR 137
             Y    +   E+K+RL  +Q+++LE++F+   KL+P+RKM+LAR LGLQPRQIA+WFQNRR
Sbjct:    75 YSDDGSQMGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQIAIWFQNRR 134

Query:   138 ARWKSKQLELLYDSLKQEYDAVSREK-------LKLQEEVMKLKRMLKEQGTSTRNMMNK 190
             ARWK+KQLE  YD+LK+++D +  E         KLQ E+M LK   +EQ T + N+ NK
Sbjct:   135 ARWKTKQLEKDYDTLKRQFDTLKAENDLLQTHNQKLQAEIMGLKN--REQ-TESINL-NK 190

Query:   191 Q 191
             +
Sbjct:   191 E 191

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

GO:0003677 "DNA binding" evidence=IEA;ISS

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

GO:0009744 "response to sucrose stimulus" evidence=IMP

GO:0009965 "leaf morphogenesis" evidence=IMP

GO:0048826 "cotyledon morphogenesis" evidence=IMP

TAIR|locus:2168225 HB5 "homeobox protein 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 277 (102.6 bits), Expect = 3.3e-24, P = 3.3e-24
 Identities = 52/101 (51%), Positives = 78/101 (77%)

Query:    79 GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138
             G +S+++ E+K+RL  +Q+++LE++F+ + KL+P+RK+KLA+ELGLQPRQ+A+WFQNRRA
Sbjct:    63 GHASSTAAEKKRRLGVEQVKALEKNFEIDNKLEPERKVKLAQELGLQPRQVAIWFQNRRA 122

Query:   139 RWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKE 179
             RWK+KQLE  Y  LK  +DA+ R +  LQ +   L   +KE
Sbjct:   123 RWKTKQLERDYGVLKSNFDALKRNRDSLQRDNDSLLGQIKE 163

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

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

GO:0009787 "regulation of abscisic acid mediated signaling pathway" evidence=NAS

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

GO:0042803 "protein homodimerization activity" evidence=IDA

GO:0009737 "response to abscisic acid stimulus" evidence=IMP;IDA

GO:0009738 "abscisic acid mediated signaling pathway" evidence=TAS

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

TAIR|locus:2041283 HB6 "homeobox protein 6" [Arabidopsis thaliana (taxid:3702)]

 Score = 273 (101.2 bits), Expect = 8.7e-24, P = 8.7e-24
 Identities = 55/102 (53%), Positives = 79/102 (77%)

Query:    87 ERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE 146
             E+K+RL+ +Q+++LE++F+ E KL+P+RK+KLA+ELGLQPRQ+AVWFQNRRARWK+KQLE
Sbjct:    61 EKKRRLSINQVKALEKNFELENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLE 120

Query:   147 ----LL---YDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQG 181
                 +L   YDSL+  +D++ R+   L +E+ KLK  L   G
Sbjct:   121 KDYGVLKTQYDSLRHNFDSLRRDNESLLQEISKLKTKLNGGG 162

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

GO:0003677 "DNA binding" evidence=IEA;IDA

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS;IDA

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

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

GO:0009414 "response to water deprivation" evidence=IEP

GO:0005515 "protein binding" evidence=IPI

GO:0009738 "abscisic acid mediated signaling pathway" evidence=TAS

GO:0009788 "negative regulation of abscisic acid mediated signaling pathway" evidence=IMP

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

GO:0009269 "response to desiccation" evidence=RCA

GO:0009409 "response to cold" evidence=RCA

GO:0009651 "response to salt stress" evidence=RCA

GO:0009737 "response to abscisic acid stimulus" evidence=RCA

GO:0042744 "hydrogen peroxide catabolic process" evidence=RCA

TAIR|locus:2084228 HB-1 "homeobox 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 263 (97.6 bits), Expect = 1.0e-22, P = 1.0e-22
 Identities = 56/105 (53%), Positives = 77/105 (73%)

Query:    87 ERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE 146
             E+K+RLT++Q+  LE+SF+ E KL+P+RK +LA++LGLQPRQ+AVWFQNRRARWK+KQLE
Sbjct:    67 EKKRRLTTEQVHLLEKSFETENKLEPERKTQLAKKLGLQPRQVAVWFQNRRARWKTKQLE 126

Query:   147 ----LL---YDSLKQEYDAVSREKLKLQEEVMKLKRMLK-EQGTS 183
                 LL   YD L   YD++  +  KL+ EV  L   L+ +Q T+
Sbjct:   127 RDYDLLKSTYDQLLSNYDSIVMDNDKLRSEVTSLTEKLQGKQETA 171

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

GO:0003677 "DNA binding" evidence=IEA;IDA

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

GO:0009637 "response to blue light" evidence=IEP

GO:0009651 "response to salt stress" evidence=IEP

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

GO:0010167 "response to nitrate" evidence=RCA

GO:0015706 "nitrate transport" evidence=RCA

GO:0015996 "chlorophyll catabolic process" evidence=RCA

GO:0042803 "protein homodimerization activity" evidence=IDA

GO:0009965 "leaf morphogenesis" evidence=IMP

TAIR|locus:2150901 HB-3 "homeobox 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 262 (97.3 bits), Expect = 1.3e-22, P = 1.3e-22
 Identities = 54/102 (52%), Positives = 72/102 (70%)

Query:    72 EKNIHHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAV 131
             E N+   GS      E+KKRL  +Q+ +LE+SF+   KL+P+RKM+LA+ LGLQPRQIA+
Sbjct:   100 EDNLSDDGSHMMLG-EKKKRLNLEQVRALEKSFELGNKLEPERKMQLAKALGLQPRQIAI 158

Query:   132 WFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKL 173
             WFQNRRARWK+KQLE  YDSLK+++D +  +   L     KL
Sbjct:   159 WFQNRRARWKTKQLERDYDSLKKQFDVLKSDNDSLLAHNKKL 200

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

GO:0003677 "DNA binding" evidence=IEA;ISS

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

TAIR|locus:2102107 HB20 "homeobox protein 20" [Arabidopsis thaliana (taxid:3702)]

 Score = 259 (96.2 bits), Expect = 2.6e-22, P = 2.6e-22
 Identities = 56/119 (47%), Positives = 83/119 (69%)

Query:    70 LMEKNIHHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQI 129
             L E+N+   G+  T   E+KKRL  +Q+++LE+SF+   KL+P+RK++LA+ LG+QPRQI
Sbjct:    70 LDEENLSDDGAH-TMLGEKKKRLQLEQVKALEKSFELGNKLEPERKIQLAKALGMQPRQI 128

Query:   130 AVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKL-------KLQEEVMKLKRMLKEQG 181
             A+WFQNRRARWK++QLE  YDSLK++++++  +         KL  EVM LK     +G
Sbjct:   129 AIWFQNRRARWKTRQLERDYDSLKKQFESLKSDNASLLAYNKKLLAEVMALKNKECNEG 187

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

GO:0003677 "DNA binding" evidence=IEA;ISS

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

GO:0009733 "response to auxin stimulus" evidence=IEP

GO:0000041 "transition metal ion transport" evidence=RCA

TAIR|locus:2115215 HB40 "homeobox protein 40" [Arabidopsis thaliana (taxid:3702)]

 Score = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 50/90 (55%), Positives = 68/90 (75%)

Query:    88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLEL 147
             RK++LT +Q+  LE SF +E KL+ +RK +LA ELGL PRQ+AVWFQNRRARWK+K+LE 
Sbjct:    55 RKRKLTDEQVNMLEMSFGDEHKLESERKDRLAAELGLDPRQVAVWFQNRRARWKNKRLEE 114

Query:   148 LYDSLKQEYDAVSREKLKLQEEVMKLKRML 177
              Y+ LK  +D V  +K +L+ EV++LK  L
Sbjct:   115 EYNKLKNSHDNVVVDKCRLESEVIQLKEQL 144

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

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

GO:0009733 "response to auxin stimulus" evidence=IEP

---

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)
Q9LZR0	ATB51_ARATH	No assigned EC number	0.4725	0.8210	0.8978	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00021713001 SubName- Full=Chromosome chr8 scaffold_23, whole genome shotgun sequence; (218 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	257
pfam00046	57	pfam00046, Homeobox, Homeobox domain	1e-18
smart00389	57	smart00389, HOX, Homeodomain	6e-17
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	3e-16
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	6e-09
pfam02183	45	pfam02183, HALZ, Homeobox associated leucine zippe	5e-04

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

 Score = 76.7 bits (190), Expect = 1e-18
 Identities = 27/56 (48%), Positives = 39/56 (69%), Gaps = 2/56 (3%)

Query: 88  RKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
           R+KR   T +QLE LE+ F++      + + +LA++LGL  RQ+ VWFQNRRA+WK
Sbjct: 1   RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWK 56

Length = 57

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 72.3 bits (178), Expect = 6e-17
 Identities = 28/56 (50%), Positives = 39/56 (69%), Gaps = 2/56 (3%)

Query: 88  RKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
           R+KR   T +QLE LE+ FQ+      + + +LA++LGL  RQ+ VWFQNRRA+WK
Sbjct: 2   RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

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

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

 Score = 70.4 bits (173), Expect = 3e-16
 Identities = 24/57 (42%), Positives = 38/57 (66%)

Query: 88  RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144
           ++ R T +QLE LE+ F++      + + +LA+ELGL  RQ+ +WFQNRRA+ K  +
Sbjct: 3   KRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59

Length = 59

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

 Score = 53.2 bits (128), Expect = 6e-09
 Identities = 21/66 (31%), Positives = 38/66 (57%)

Query: 79  GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138
              S+  + +++R T +QL  LER F+         ++KL+  L + P+ + +WFQN+RA
Sbjct: 45  QDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRA 104

Query: 139 RWKSKQ 144
           + K K+
Sbjct: 105 KEKKKR 110

Length = 156

>gnl|CDD|202143 pfam02183, HALZ, Homeobox associated leucine zipper

 Score = 36.7 bits (86), Expect = 5e-04
 Identities = 20/45 (44%), Positives = 29/45 (64%), Gaps = 7/45 (15%)

Query: 143 KQLE----LL---YDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQ 180
           KQLE    +L   YD+LK E D++ +E  KL+ EV+ LK  L+E+
Sbjct: 1   KQLERDYEVLKRCYDALKAENDSLQKENEKLRAEVLSLKEKLQEK 45

Length = 45

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	257
KOG0483	198	consensus Transcription factor HEX, contains HOX a	99.86
KOG0489	261	consensus Transcription factor zerknullt and relat	99.8
KOG0487	308	consensus Transcription factor Abd-B, contains HOX	99.77
KOG0488	309	consensus Transcription factor BarH and related HO	99.76
KOG0848	317	consensus Transcription factor Caudal, contains HO	99.75
KOG0843	197	consensus Transcription factor EMX1 and related HO	99.73
KOG4577	383	consensus Transcription factor LIM3, contains LIM	99.72
KOG0842	307	consensus Transcription factor tinman/NKX2-3, cont	99.72
KOG0850	245	consensus Transcription factor DLX and related pro	99.68
KOG0485	268	consensus Transcription factor NKX-5.1/HMX1, conta	99.67
KOG0484	125	consensus Transcription factor PHOX2/ARIX, contain	99.67
KOG2251	228	consensus Homeobox transcription factor [Transcrip	99.66
KOG0492	246	consensus Transcription factor MSH, contains HOX d	99.66
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.65
KOG0494	332	consensus Transcription factor CHX10 and related H	99.63
KOG0844	408	consensus Transcription factor EVX1, contains HOX	99.6
KOG0493	342	consensus Transcription factor Engrailed, contains	99.58
COG5576	156	Homeodomain-containing transcription factor [Trans	99.52
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.52
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.52
KOG3802	398	consensus Transcription factor OCT-1, contains POU	99.51
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.51
KOG0491	194	consensus Transcription factor BSH, contains HOX d	99.48
KOG0486	351	consensus Transcription factor PTX1, contains HOX	99.43
KOG0847	288	consensus Transcription factor, contains HOX domai	99.35
KOG0490	235	consensus Transcription factor, contains HOX domai	99.18
KOG1168	385	consensus Transcription factor ACJ6/BRN-3, contain	99.06
KOG0849	354	consensus Transcription factor PRD and related pro	98.98
KOG0775	304	consensus Transcription factor SIX and related HOX	98.79
KOG0774	334	consensus Transcription factor PBX and related HOX	98.46
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.25
KOG2252	558	consensus CCAAT displacement protein and related h	98.03
KOG0490	235	consensus Transcription factor, contains HOX domai	98.02
KOG1146	1406	consensus Homeobox protein [General function predi	97.58
KOG0773	342	consensus Transcription factor MEIS1 and related H	96.6
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	96.28
PF02183	45	HALZ: Homeobox associated leucine zipper; InterPro	94.95
KOG3623	1007	consensus Homeobox transcription factor SIP1 [Tran	94.47
smart00340	44	HALZ homeobox associated leucin zipper.	93.75
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	93.26
PF02183	45	HALZ: Homeobox associated leucine zipper; InterPro	90.76
PRK09413	121	IS2 repressor TnpA; Reviewed	84.33

>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]

Probab=99.86  E-value=1.7e-21  Score=167.90  Aligned_cols=99  Identities=55%  Similarity=0.856  Sum_probs=93.4

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHHHHHHHHHHhHHHHHH
Q 040769           83 TSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSRE  162 (257)
Q Consensus        83 ~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~~~~l~~~~~~~~~e  162 (257)
                      .+..+++.||+.+|+..||+.|+.+.++.+.+|..||++|||.+|||+|||||||||||.++.+..++.|+.+++.+..+
T Consensus        48 ~~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~  127 (198)
T KOG0483|consen   48 SKGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSE  127 (198)
T ss_pred             cccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhh
Confidence            33557788999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhcC
Q 040769          163 KLKLQEEVMKLKRMLKEQG  181 (257)
Q Consensus       163 ~~~l~~e~~~~~~~l~~~~  181 (257)
                      +++|+.++.+|...+....
T Consensus       128 ~~~Lq~e~~eL~~~~~~~~  146 (198)
T KOG0483|consen  128 NDRLQSEVQELVAELSSLK  146 (198)
T ss_pred             hhHHHHHHHHHHHHHhhhh
Confidence            9999999999998887653

>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]

Probab=99.80  E-value=1.4e-20  Score=169.43  Aligned_cols=65  Identities=37%  Similarity=0.649  Sum_probs=60.3

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769           82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE  146 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~  146 (257)
                      .++.||.||.||..|+.+||++|..|+|+++.+|.|||..|.|+++||||||||||+||||..+.
T Consensus       156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~  220 (261)
T KOG0489|consen  156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKA  220 (261)
T ss_pred             cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcc
Confidence            34578889999999999999999999999999999999999999999999999999999985543

>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]

Probab=99.77  E-value=1.3e-19  Score=164.90  Aligned_cols=65  Identities=29%  Similarity=0.535  Sum_probs=60.9

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769           82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE  146 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~  146 (257)
                      .++.||||..+|+.|+.+||++|..|.|+++++|.+|++.|+|++|||||||||||+|+||..++
T Consensus       232 ~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re  296 (308)
T KOG0487|consen  232 ARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRE  296 (308)
T ss_pred             ccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhh
Confidence            36677888899999999999999999999999999999999999999999999999999997754

>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]

Probab=99.76  E-value=5.6e-19  Score=162.29  Aligned_cols=65  Identities=32%  Similarity=0.640  Sum_probs=59.8

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769           82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE  146 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~  146 (257)
                      .+++||.||.||..||..||+.|++.+|++..+|++||+.|||+..|||+||||||+||||...+
T Consensus       169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~  233 (309)
T KOG0488|consen  169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE  233 (309)
T ss_pred             CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence            35666778889999999999999999999999999999999999999999999999999996543

>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]

Probab=99.75  E-value=6.3e-19  Score=155.71  Aligned_cols=92  Identities=26%  Similarity=0.347  Sum_probs=74.1

Q ss_pred             hccCCCCCCCCCchHhhhhhccCCCCCCCCC---CCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCccccc
Q 040769           55 AEKSSSSIGLIPAAELMEKNIHHYGSSSTSS---QERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAV  131 (257)
Q Consensus        55 ~~~~s~s~~~~~~~~~~~~~~~~~~~~~~~~---~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkv  131 (257)
                      +..-+.+....+..+||.+..........+-   -|-|-++|+.|+.+||++|..++|.++.+|.|||.-|||+||||||
T Consensus       166 ~~~nspg~~R~s~~dwmrkpa~~~~g~~~KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKI  245 (317)
T KOG0848|consen  166 PLGNSPGKSRRSPYDWMRKPAQPGTGQNVKTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKI  245 (317)
T ss_pred             cccCCCCcCCCChhhhhhcccccCCCCCceeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhH
Confidence            3333555666677889998877664422222   2335669999999999999999999999999999999999999999


Q ss_pred             ccccchhhhhHHHHH
Q 040769          132 WFQNRRARWKSKQLE  146 (257)
Q Consensus       132 WFQNRRak~Kr~~~~  146 (257)
                      ||||||+|+||..++
T Consensus       246 WFQNRRAKERK~nKK  260 (317)
T KOG0848|consen  246 WFQNRRAKERKDNKK  260 (317)
T ss_pred             hhhhhhHHHHHHHHH
Confidence            999999999996644

>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]

Probab=99.73  E-value=2.8e-18  Score=143.99  Aligned_cols=66  Identities=33%  Similarity=0.486  Sum_probs=62.2

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHH
Q 040769           82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLEL  147 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~  147 (257)
                      ..+.||.||.||.+||..||..|+.+.|....+|.+||+.|+|++.||||||||||.|.||++.+.
T Consensus        99 ~~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~  164 (197)
T KOG0843|consen   99 SMRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED  164 (197)
T ss_pred             ccCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence            347788999999999999999999999999999999999999999999999999999999988764

>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]

Probab=99.72  E-value=2.3e-18  Score=153.57  Aligned_cols=127  Identities=25%  Similarity=0.348  Sum_probs=101.7

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH-------HHHHHHHHHHH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS-------KQLELLYDSLK  153 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr-------~~~~~~~~~l~  153 (257)
                      .....||.||.+|..||+.|+..|+..++|.+..|++|+.++||..|+|+|||||||||+||       .+|.+++.++|
T Consensus       163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfrsmK  242 (383)
T KOG4577|consen  163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFRSMK  242 (383)
T ss_pred             cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHHHhh
Confidence            45566788999999999999999999999999999999999999999999999999999998       36777788887


Q ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccccccCCCCCcccCCCccccccccccccCCCCCCCC
Q 040769          154 QEYDAVSREKLKLQEEVMKLKRMLKEQGTSTRNMMNKQVSTGITEVSGEETVESTSVATINGSFSNKH  221 (257)
Q Consensus       154 ~~~~~~~~e~~~l~~e~~~~~~~l~~~~~~~~~~~~~~~s~~~~~~~~e~t~as~~~~~~~~s~~~~~  221 (257)
                      .. +..+.|+++-       +..++...   .++.+.++++.+|...++.+.+ +.+  ++|+|+++|
T Consensus       243 ~s-gs~r~ekdsd-------~sel~~~~---dslse~~~~N~lYg~l~~~~d~-g~~--~~gsy~~~~  296 (383)
T KOG4577|consen  243 RS-GSSRAEKDSD-------DSELSFIN---DSLSEHGSPNYLYGTLGHPTDD-GNP--SNGSYSFHS  296 (383)
T ss_pred             cc-CCcccccccc-------cCcccccc---chhhhcCCccccccccCCcccC-CCc--CCCceeccC
Confidence            76 5556666652       33444332   2577789999999999998776 333  336776665

>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]

Probab=99.72  E-value=4.1e-18  Score=155.03  Aligned_cols=64  Identities=33%  Similarity=0.549  Sum_probs=58.6

Q ss_pred             CCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHHHHHHH
Q 040769           89 KKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSL  152 (257)
Q Consensus        89 R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~~~~l  152 (257)
                      |--||..|+-+||+.|+.++|++..+|++||..|.|+++||||||||||-|.||+++++..+.+
T Consensus       157 RVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~  220 (307)
T KOG0842|consen  157 RVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEAL  220 (307)
T ss_pred             ccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcc
Confidence            3339999999999999999999999999999999999999999999999999999888665443

>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]

Probab=99.68  E-value=3e-17  Score=142.54  Aligned_cols=69  Identities=30%  Similarity=0.517  Sum_probs=62.0

Q ss_pred             cCCCCCCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           76 HHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        76 ~~~~~~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      .......++.||.||.|+..||..|.+.|++++|+...+|.+||..|||+.+||||||||||.|.||..
T Consensus       113 ~~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~  181 (245)
T KOG0850|consen  113 RRPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLK  181 (245)
T ss_pred             eccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHH
Confidence            344555666677799999999999999999999999999999999999999999999999999999843

>KOG0485 consensus Transcription factor NKX-5

Probab=99.67  E-value=2.4e-17  Score=142.05  Aligned_cols=64  Identities=28%  Similarity=0.527  Sum_probs=58.7

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHH
Q 040769           82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL  145 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~  145 (257)
                      ..++||.||.|+..|+..||..|+..+|++..+|..||++|.|+++||||||||||.||||+-.
T Consensus       101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a  164 (268)
T KOG0485|consen  101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA  164 (268)
T ss_pred             ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence            3456667888999999999999999999999999999999999999999999999999998543

1/HMX1, contains HOX domain [Transcription]

>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]

Probab=99.67  E-value=9.1e-18  Score=129.34  Aligned_cols=65  Identities=31%  Similarity=0.515  Sum_probs=60.0

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769           82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE  146 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~  146 (257)
                      .+++||-|+.||..||.+||+.|...+||+.-.|++||.++.|++..|+|||||||+|.||+...
T Consensus        14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~   78 (125)
T KOG0484|consen   14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERA   78 (125)
T ss_pred             HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence            45677789999999999999999999999999999999999999999999999999999986543

>KOG2251 consensus Homeobox transcription factor [Transcription]

Probab=99.66  E-value=7.2e-17  Score=139.53  Aligned_cols=68  Identities=31%  Similarity=0.457  Sum_probs=63.8

Q ss_pred             CCCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHH
Q 040769           80 SSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLEL  147 (257)
Q Consensus        80 ~~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~  147 (257)
                      ...++.||.||+|+..|+++||..|.+..||+...|++||.+|+|.+.+|+|||+|||+|+|++++.+
T Consensus        32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            35677889999999999999999999999999999999999999999999999999999999987664

>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]

Probab=99.66  E-value=1.1e-16  Score=137.10  Aligned_cols=63  Identities=33%  Similarity=0.551  Sum_probs=58.4

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      .+..|+.|+.||..||..||+.|+..+|+++.+|.+++..|.|+++||||||||||+|.||.+
T Consensus       141 hk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ  203 (246)
T KOG0492|consen  141 HKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ  203 (246)
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence            344567788999999999999999999999999999999999999999999999999999855

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.65  E-value=7.8e-17  Score=112.12  Aligned_cols=57  Identities=42%  Similarity=0.687  Sum_probs=55.2

Q ss_pred             CCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769           86 QERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS  142 (257)
Q Consensus        86 ~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr  142 (257)
                      ||+|++||.+|+.+||.+|..++||+..++..||.+|||+..+|++||+|||+++||
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence            578999999999999999999999999999999999999999999999999999986

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

>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]

Probab=99.63  E-value=1.3e-16  Score=140.63  Aligned_cols=69  Identities=36%  Similarity=0.543  Sum_probs=61.8

Q ss_pred             CCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHHHHHHHHHHhH
Q 040769           89 KKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYD  157 (257)
Q Consensus        89 R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~~~~l~~~~~  157 (257)
                      ||.||..|++.||+.|+...||+...|+-||.++.|.+.+|+|||||||+||||+++.......-++++
T Consensus       145 RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~sT~maeyg  213 (332)
T KOG0494|consen  145 RTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGSTIMAEYG  213 (332)
T ss_pred             cchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcchhhhhhc
Confidence            777999999999999999999999999999999999999999999999999999877765555545543

>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]

Probab=99.60  E-value=2.2e-16  Score=141.85  Aligned_cols=66  Identities=32%  Similarity=0.527  Sum_probs=61.1

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHH
Q 040769           82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLEL  147 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~  147 (257)
                      ...-||-||.||.+||..||++|.+..|.++.+|.|||..|+|.+..|||||||||+|+||+++..
T Consensus       178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlam  243 (408)
T KOG0844|consen  178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAM  243 (408)
T ss_pred             cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhc
Confidence            344567799999999999999999999999999999999999999999999999999999988764

>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]

Probab=99.58  E-value=8e-16  Score=135.76  Aligned_cols=60  Identities=40%  Similarity=0.687  Sum_probs=56.3

Q ss_pred             CCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           85 SQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        85 ~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      .||.||.||.+||..|+..|+.|.|++..+|.+||.+|||.+.||||||||+|+|.||..
T Consensus       246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT  305 (342)
T KOG0493|consen  246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST  305 (342)
T ss_pred             hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence            356678899999999999999999999999999999999999999999999999999854

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.52  E-value=9.2e-15  Score=122.13  Aligned_cols=68  Identities=31%  Similarity=0.537  Sum_probs=62.1

Q ss_pred             CCCCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769           79 GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE  146 (257)
Q Consensus        79 ~~~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~  146 (257)
                      .......+++|+|.|..|+.+|++.|+.++||+...|.+|+..|+|+++.|+|||||||++.|+....
T Consensus        45 ~~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~  112 (156)
T COG5576          45 QDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG  112 (156)
T ss_pred             ccCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence            33456677889999999999999999999999999999999999999999999999999999986644

>smart00389 HOX Homeodomain

Probab=99.52  E-value=8.4e-15  Score=101.08  Aligned_cols=55  Identities=45%  Similarity=0.837  Sum_probs=52.3

Q ss_pred             CCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769           87 ERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK  141 (257)
Q Consensus        87 r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K  141 (257)
                      +.|++|+.+|+.+||..|..++||+..++..||.+|||+..+|++||+|||++.|
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            5678899999999999999999999999999999999999999999999999864

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

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.52  E-value=1.7e-14  Score=101.20  Aligned_cols=52  Identities=17%  Similarity=0.373  Sum_probs=50.3

Q ss_pred             CCCCCcCCHHHHHHHHHHhhhcCC----CCHHHHHHHHHHhCCCCcccccccccch
Q 040769           86 QERKKRLTSDQLESLERSFQEEIK----LDPDRKMKLARELGLQPRQIAVWFQNRR  137 (257)
Q Consensus        86 ~r~R~r~t~~Ql~~Le~~F~~~~~----p~~~~r~~LA~~LgL~~~qVkvWFQNRR  137 (257)
                      ||.||.||.+|+..||..|+.+.|    |+...+.+||.+|||++++|+|||||-+
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    9999999999999999999999999965

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

>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]

Probab=99.51  E-value=9.7e-15  Score=135.90  Aligned_cols=62  Identities=23%  Similarity=0.406  Sum_probs=58.7

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           83 TSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        83 ~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      .++|||||.|+...+..||++|.+|++|+..++..||.+|+|...+|+|||||||.|+||..
T Consensus       292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~  353 (398)
T KOG3802|consen  292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT  353 (398)
T ss_pred             ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence            36788899999999999999999999999999999999999999999999999999999844

>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=99.51  E-value=1.2e-14  Score=101.03  Aligned_cols=57  Identities=42%  Similarity=0.773  Sum_probs=54.2

Q ss_pred             CCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHH
Q 040769           87 ERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK  143 (257)
Q Consensus        87 r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~  143 (257)
                      ++|..|+..|+.+||.+|..++||+..++..||.++||+.++|++||+|||.+.++.
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            567889999999999999999999999999999999999999999999999998863

>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]

Probab=99.48  E-value=5.3e-15  Score=122.68  Aligned_cols=62  Identities=31%  Similarity=0.549  Sum_probs=57.8

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           83 TSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        83 ~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      .+++|-|+.|+..|+..||+.|+..+|++..+|.|||..|+|+++|||.||||||+|.||.+
T Consensus        98 ~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~  159 (194)
T KOG0491|consen   98 CRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQ  159 (194)
T ss_pred             HHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence            44566789999999999999999999999999999999999999999999999999999855

>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]

Probab=99.43  E-value=5.7e-14  Score=126.96  Aligned_cols=71  Identities=28%  Similarity=0.499  Sum_probs=63.0

Q ss_pred             CCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHHHHHHHHH
Q 040769           84 SSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQ  154 (257)
Q Consensus        84 ~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~~~~l~~  154 (257)
                      ++||.|+.||..|+.+||..|.+|.||+...|++||.-.+|++..|+|||.|||+||||++.-+..+..+.
T Consensus       111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ae~~k~  181 (351)
T KOG0486|consen  111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAELAKG  181 (351)
T ss_pred             hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHHHHhhhc
Confidence            45667888999999999999999999999999999999999999999999999999999877666443333

>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]

Probab=99.35  E-value=2.8e-13  Score=117.20  Aligned_cols=64  Identities=33%  Similarity=0.641  Sum_probs=58.6

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769           83 TSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE  146 (257)
Q Consensus        83 ~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~  146 (257)
                      ++++..|..|+..||..||+.|+..+|+-..+|.+||..||+++.||+|||||||.||||+...
T Consensus       165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa  228 (288)
T KOG0847|consen  165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA  228 (288)
T ss_pred             ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence            4555567789999999999999999999999999999999999999999999999999997644

>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]

Probab=99.18  E-value=1e-11  Score=108.55  Aligned_cols=64  Identities=30%  Similarity=0.325  Sum_probs=59.7

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHH
Q 040769           82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL  145 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~  145 (257)
                      ..++|+.|+.|+..|+++||+.|+..+||+...|+.||..+++++..|+|||||||+||++...
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            4566788999999999999999999999999999999999999999999999999999998653

>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]

Probab=99.06  E-value=8e-11  Score=105.69  Aligned_cols=64  Identities=20%  Similarity=0.397  Sum_probs=59.6

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      ..+.+|||||.+-.-+.+.||.+|...+.|+.+.+..||.+|+|.+.+|+|||+|.|+|.||..
T Consensus       305 ~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~  368 (385)
T KOG1168|consen  305 PGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK  368 (385)
T ss_pred             CccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence            3567788999999999999999999999999999999999999999999999999999999844

>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]

Probab=98.98  E-value=2.7e-10  Score=106.96  Aligned_cols=67  Identities=33%  Similarity=0.568  Sum_probs=61.0

Q ss_pred             CCCCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHH
Q 040769           79 GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL  145 (257)
Q Consensus        79 ~~~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~  145 (257)
                      ....++.+|+|+.|+..|+..||+.|+.++||+...|++||.+++|++..|+|||+|||+|++|...
T Consensus       170 ~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~  236 (354)
T KOG0849|consen  170 YALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR  236 (354)
T ss_pred             ccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence            3445666777899999999999999999999999999999999999999999999999999998653

>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]

Probab=98.79  E-value=3.8e-09  Score=94.39  Aligned_cols=51  Identities=27%  Similarity=0.442  Sum_probs=47.8

Q ss_pred             CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769           92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS  142 (257)
Q Consensus        92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr  142 (257)
                      |...-...|..+|..++||+..++.+||+.+||+..||-.||+|||+|+|-
T Consensus       183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa  233 (304)
T KOG0775|consen  183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA  233 (304)
T ss_pred             hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence            566677899999999999999999999999999999999999999999983

>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]

Probab=98.46  E-value=1.1e-07  Score=84.53  Aligned_cols=59  Identities=22%  Similarity=0.465  Sum_probs=55.1

Q ss_pred             CCCCCCcCCHHHHHHHHHHhh---hcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHH
Q 040769           85 SQERKKRLTSDQLESLERSFQ---EEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK  143 (257)
Q Consensus        85 ~~r~R~r~t~~Ql~~Le~~F~---~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~  143 (257)
                      .+|||+.|+..-.++|..+|.   .++||+.+.+++||+++|++..||-.||.|+|-+.||.
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~  249 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN  249 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence            468888999999999999997   58899999999999999999999999999999999873

>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=98.25  E-value=2.3e-07  Score=60.46  Aligned_cols=34  Identities=35%  Similarity=0.576  Sum_probs=28.9

Q ss_pred             hcCCCCHHHHHHHHHHhCCCCcccccccccchhh
Q 040769          106 EEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR  139 (257)
Q Consensus       106 ~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak  139 (257)
                      .++||+..++.+||.++||+..||..||-|.|.|
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            4789999999999999999999999999999865

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

>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]

Probab=98.03  E-value=3.6e-06  Score=81.79  Aligned_cols=59  Identities=19%  Similarity=0.290  Sum_probs=54.0

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhh
Q 040769           82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARW  140 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~  140 (257)
                      .-..||.|.+||..|.+.|..+|+.+++|+.+..+.|+.+|+|..+.|..||-|-|.|.
T Consensus       417 ~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  417 MLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             cccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            34456778889999999999999999999999999999999999999999999988774

>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]

Probab=98.02  E-value=4.5e-06  Score=72.80  Aligned_cols=65  Identities=40%  Similarity=0.627  Sum_probs=59.1

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL  145 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~  145 (257)
                      ...+.++.|+.+...|+..|+..|....+|+...+..|+..+|+.++.|++||||+|++.++...
T Consensus       149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            44556677888999999999999999999999999999999999999999999999999998553

>KOG1146 consensus Homeobox protein [General function prediction only]

Probab=97.58  E-value=5.2e-05  Score=80.06  Aligned_cols=64  Identities=25%  Similarity=0.387  Sum_probs=58.8

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHH
Q 040769           82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL  145 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~  145 (257)
                      ..++++.|++++..||.+|..+|....++...+.+.|...+++..+.|+|||||-|+|.|+...
T Consensus       900 ~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~  963 (1406)
T KOG1146|consen  900 GMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL  963 (1406)
T ss_pred             hhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence            3456778999999999999999999999999999999999999999999999999999998543

>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]

Probab=96.60  E-value=0.0026  Score=59.30  Aligned_cols=63  Identities=25%  Similarity=0.367  Sum_probs=51.6

Q ss_pred             CCCCCcCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHHH
Q 040769           86 QERKKRLTSDQLESLERSFQE---EIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELL  148 (257)
Q Consensus        86 ~r~R~r~t~~Ql~~Le~~F~~---~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~  148 (257)
                      .|++..+......+|+.+...   .+||+..++..||.++||+..||.+||-|.|-|..+--.+..
T Consensus       240 ~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~~  305 (342)
T KOG0773|consen  240 WRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIEEM  305 (342)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchHHHH
Confidence            344456999999999988443   579999999999999999999999999999988776554433

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

Probab=96.28  E-value=0.0012  Score=46.03  Aligned_cols=43  Identities=19%  Similarity=0.383  Sum_probs=31.5

Q ss_pred             HHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchh
Q 040769           96 QLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA  138 (257)
Q Consensus        96 Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRa  138 (257)
                      .+..|+++|...+.+.......|..+.+|+..||+.||-.|+.
T Consensus         9 d~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~   51 (56)
T PF11569_consen    9 DIQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ   51 (56)
T ss_dssp             --HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred             chHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence            3466999999999999999999999999999999999976654

>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []

Probab=94.95  E-value=0.073  Score=35.45  Aligned_cols=37  Identities=43%  Similarity=0.549  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHh
Q 040769          143 KQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKE  179 (257)
Q Consensus       143 ~~~~~~~~~l~~~~~~~~~e~~~l~~e~~~~~~~l~~  179 (257)
                      ++.+..|+.|+.+++.+..+.++|..|+..|+..+..
T Consensus         1 KQlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~   37 (45)
T PF02183_consen    1 KQLERDYDALKASYDSLKAEYDSLKKENEKLRAEVQE   37 (45)
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3677888888888888888888888887777776653

; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus

>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]

Probab=94.47  E-value=0.027  Score=57.14  Aligned_cols=48  Identities=19%  Similarity=0.273  Sum_probs=44.8

Q ss_pred             HHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           97 LESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        97 l~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      +..|+.+|..|..|+..+...||.+.||..+.|+.||++++++....+
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~  615 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE  615 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence            778999999999999999999999999999999999999999887643

>smart00340 HALZ homeobox associated leucin zipper

Probab=93.75  E-value=0.14  Score=33.46  Aligned_cols=33  Identities=30%  Similarity=0.451  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Q 040769          144 QLELLYDSLKQEYDAVSREKLKLQEEVMKLKRM  176 (257)
Q Consensus       144 ~~~~~~~~l~~~~~~~~~e~~~l~~e~~~~~~~  176 (257)
                      +.+.+++.||+..+.+..||.+|+.|+++|+..
T Consensus         2 QTEvdCe~LKrcce~LteeNrRL~ke~~eLral   34 (44)
T smart00340        2 QTEVDCELLKRCCESLTEENRRLQKEVQELRAL   34 (44)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            567889999999999999999999999998864

>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=93.26  E-value=0.12  Score=35.44  Aligned_cols=46  Identities=22%  Similarity=0.421  Sum_probs=34.8

Q ss_pred             CCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccc
Q 040769           86 QERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNR  136 (257)
Q Consensus        86 ~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNR  136 (257)
                      +|+|..+|-++...+-..++...     ....||+++|+...+|..|..|+
T Consensus         1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k   46 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK   46 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred             CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence            47788899988887777787765     57899999999999999999884

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.

>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []

Probab=90.76  E-value=0.76  Score=30.56  Aligned_cols=35  Identities=49%  Similarity=0.709  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Q 040769          144 QLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLK  178 (257)
Q Consensus       144 ~~~~~~~~l~~~~~~~~~e~~~l~~e~~~~~~~l~  178 (257)
                      .....++.|+.+++.+..|++.|++++..++..+.
T Consensus         9 ~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~kl~   43 (45)
T PF02183_consen    9 ALKASYDSLKAEYDSLKKENEKLRAEVQELKEKLQ   43 (45)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            34567899999999999999999999999998774

; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=84.33  E-value=3.4  Score=32.73  Aligned_cols=87  Identities=16%  Similarity=0.158  Sum_probs=50.1

Q ss_pred             CCCcCCHHHHH-HHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhh-------hHHHHHHHHHHHHHHhHHH
Q 040769           88 RKKRLTSDQLE-SLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARW-------KSKQLELLYDSLKQEYDAV  159 (257)
Q Consensus        88 ~R~r~t~~Ql~-~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~-------Kr~~~~~~~~~l~~~~~~~  159 (257)
                      +|++||.++.. ++...+...     ....+||.++|++..+|..|.+-=+...       +..........+..+...|
T Consensus         9 ~rr~ys~EfK~~aV~~~~~~g-----~sv~evA~e~gIs~~tl~~W~r~y~~~~~~~~~~~~~~~~~~~~~~~~~ei~~L   83 (121)
T PRK09413          9 KRRRRTTQEKIAIVQQSFEPG-----MTVSLVARQHGVAASQLFLWRKQYQEGSLTAVAAGEQVVPASELAAAMKQIKEL   83 (121)
T ss_pred             CCCCCCHHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHhhcccccccccccCCchhHHHHHHHHHHHH
Confidence            45668877644 444444432     2467889999999999999965422110       0000001122344555566


Q ss_pred             HHHHHHHHHHHHHHHHHHHh
Q 040769          160 SREKLKLQEEVMKLKRMLKE  179 (257)
Q Consensus       160 ~~e~~~l~~e~~~~~~~l~~  179 (257)
                      ..+...|+.|+.-|+..+..
T Consensus        84 ~~el~~L~~E~diLKKa~~~  103 (121)
T PRK09413         84 QRLLGKKTMENELLKEAVEY  103 (121)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            66666777777666666653

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	257
2dmu_A	70	Solution Structure Of The Homeobox Domain Of Homeob		2e-07
2e1o_A	70	Solution Structure Of Rsgi Ruh-028, A Homeobox Doma		3e-06
2cue_A	80	Solution Structure Of The Homeobox Domain Of The Hu		1e-05
3a02_A	60	Crystal Structure Of Aristaless Homeodomain Length		1e-05
2r5y_A	88	Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO		2e-05
2m34_A	71	Nmr Structure Of The Homeodomain Transcription Fact		2e-05
3hdd_A	60	Engrailed Homeodomain Dna Complex Length = 60		2e-05
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		2e-05
1hdd_C	61	Crystal Structure Of An Engrailed Homeodomain-Dna C		2e-05
1enh_A	54	Structural Studies Of The Engrailed Homeodomain Len		4e-05
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		4e-05
1p7j_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		4e-05
2djn_A	70	The Solution Structure Of The Homeobox Domain Of Hu		4e-05
1p7i_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		5e-05
2hdd_A	61	Engrailed Homeodomain Q50k Variant Dna Complex Leng		6e-05
2cra_A	70	Solution Structure Of The Homeobox Domain Of Human		8e-05
1du0_A	57	Engrailed Homeodomain Q50a Variant Dna Complex Leng		1e-04
2lp0_A	60	The Solution Structure Of Homeodomain-Protein Compl		1e-04
1puf_A	77	Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo		2e-04
1ztr_A	61	Solution Structure Of Engrailed Homeodomain L16a Mu		2e-04
2m0c_A	75	Solution Nmr Structure Of Homeobox Domain Of Human		2e-04
1san_A	62	The Des(1-6)antennapedia Homeodomain: Comparison Of		2e-04
2dmt_A	80	Solution Structure Of The Homeobox Domain Of Homeob		3e-04
3cmy_A	61	Structure Of A Homeodomain In Complex With Dna Leng		3e-04
9ant_A	62	Antennapedia Homeodomain-Dna Complex Length = 62		3e-04
1hom_A	68	Determination Of The Three-Dimensional Structure Of		4e-04
1ahd_P	68	Determination Of The Nmr Solution Structure Of An A		4e-04
3a01_A	93	Crystal Structure Of Aristaless And Clawless Homeod		5e-04
2l7z_A	73	Nmr Structure Of A13 Homedomain Length = 73		7e-04
2h1k_A	63	Crystal Structure Of The Pdx1 Homeodomain In Comple		8e-04

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/63 (41%), Positives = 41/63 (65%)
Query: 79  GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138
           GSS +S +  +   T +QLE+LE  FQE    D   + +LAR++ L+  ++ VWF+NRRA
Sbjct: 1   GSSGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRA 60
Query: 139 RWK 141
           +W+
Sbjct: 61  KWR 63

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/51 (43%), Positives = 33/51 (64%)
Query: 91  RLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
           R ++DQ   LE+ F+ +  L P  + +LA+ L L  RQ+  WFQNRRA+W+
Sbjct: 13  RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 63

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/63 (38%), Positives = 38/63 (60%)
Query: 79  GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138
           GSS +S Q  +   T +Q+E+LE+ F+     D   + +LA ++ L   +I VWF NRRA
Sbjct: 1   GSSGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRA 60
Query: 139 RWK 141
           +W+
Sbjct: 61  KWR 63

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/53 (43%), Positives = 34/53 (64%)
Query: 92  LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144
            TS QLE LE++F      D   + +LA ++GL   +I VWFQNRRA+W+ ++
Sbjct: 6   FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 37/69 (53%), Gaps = 4/69 (5%)
Query: 77  HYGSSSTSSQERKKR----LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVW 132
           H G+S+ ++    KR     T  Q   LE+ F     L   R++++A  L L  RQI +W
Sbjct: 16  HLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIW 75
Query: 133 FQNRRARWK 141
           FQNRR +WK
Sbjct: 76  FQNRRMKWK 84

>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 = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/57 (40%), Positives = 34/57 (59%)
Query: 85  SQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
           S+ R+   TS+QL  LE+ F  +  L    + ++A  L L   Q+ +WFQNRRA+WK
Sbjct: 7   SRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 63

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 32/50 (64%)
Query: 92  LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
            +S+QL  L+R F E   L   R+ +L+ ELGL   QI +WFQN+RA+ K
Sbjct: 8   FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 57

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/53 (43%), Positives = 34/53 (64%)
Query: 92  LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144
            TS QLE LE++F      D   + +LA ++GL   +I VWFQNRRA+W+ ++
Sbjct: 6   FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58

>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 = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 32/50 (64%)
Query: 92  LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
            +S+QL  L+R F E   L   R+ +L+ ELGL   QI +WFQN+RA+ K
Sbjct: 10  FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 59

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 31/48 (64%)
Query: 92  LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR 139
            +S+QL  L+R F E   L   R+ +L+ ELGL   QI +WFQN+RA+
Sbjct: 6   FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 23/53 (43%), Positives = 34/53 (64%)
Query: 92  LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144
            TS QLE LE++F      D   + +LA ++GL   +I VWFQNRRA+W+ ++
Sbjct: 13  FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 65

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 31/50 (62%)
Query: 92  LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
            +S+QL  L+R F E   L   R+ +L+ ELGL   QI +WFQN RA+ K
Sbjct: 8   FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIK 57

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/63 (38%), Positives = 39/63 (61%)
Query: 79  GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138
           GSS +S ++ +   +S QL +L+R FQ+   L    + +LA  LGL   Q+ +WFQN+R+
Sbjct: 1   GSSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRS 60
Query: 139 RWK 141
           + K
Sbjct: 61  KIK 63

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 31/50 (62%)
Query: 92  LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
            +S+QL  L+R F E   L   R+ +L+ ELGL   QI +WFQN RA+ K
Sbjct: 8   FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIK 57

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 22/50 (44%), Positives = 32/50 (64%)
Query: 92  LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
            +S+QL  L+R F E   L   R+ +L+ ELGL   QI +WF+N+RA+ K
Sbjct: 10  FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 59

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 24/62 (38%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 82  STSSQERKKRL--TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR 139
           S+ S  RKKR+  +  QL  LER +     +  D++ K++    L  RQI +WFQNRR +
Sbjct: 2   SSGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVK 61
Query: 140 WK 141
            K
Sbjct: 62  EK 63

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/50 (44%), Positives = 31/50 (62%)
Query: 92  LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
            +S+QL  L+R F E   L   R+ +L+ ELGL   QI +WF N+RA+ K
Sbjct: 6   FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIK 55

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 33/57 (57%), Gaps = 2/57 (3%)
Query: 88  RKKRL--TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142
           RKKR   T  Q   LE+ F   + L  DR+ ++AR L L  RQ+ +WFQNRR + K 
Sbjct: 2   RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/56 (44%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 88  RKKRL--TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
           RKKR   T  Q   LE+ F   + L  DR+ ++AR L L  RQ+ +WFQNRR + K
Sbjct: 14  RKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMK 69

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 30/48 (62%)
Query: 92  LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR 139
            +S+QL   +R F E   L   R+ +L+ ELGL   QI +WFQN+RA+
Sbjct: 10  FSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 57

>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 = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/68 (38%), Positives = 40/68 (58%), Gaps = 4/68 (5%)
Query: 81  SSTSSQERKKR----LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNR 136
           S  S++ +K+R     TS QLE LE+ FQ+    D   + +LA    L   ++ VWFQNR
Sbjct: 1   SHMSNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNR 60
Query: 137 RARWKSKQ 144
           RA+W+ ++
Sbjct: 61  RAKWRKRE 68

>pdb|1SAN|A Chain A, The Des(1-6)antennapedia Homeodomain: Comparison Of The Nmr Solution Structure And The Dna Binding Affinity With The Intact Antennapedia Homeodomain Length = 62

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 28/49 (57%)
Query: 93  TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
           T  Q   LE+ F     L   R++++A  L L  RQI +WFQNRR +WK
Sbjct: 4   TRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 52

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 34/63 (53%)
Query: 79  GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138
           G+ +   +  +   T  QL  LE+ F+++  L    ++ LA  LGL   Q+  W+QNRR 
Sbjct: 11  GTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRM 70
Query: 139 RWK 141
           +WK
Sbjct: 71  KWK 73

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 32/52 (61%)
Query: 92  LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK 143
            T++QLE LER+F+     D   + +LA+   L   ++ VWF NRRARW+ +
Sbjct: 9   FTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 28/49 (57%)
Query: 93  TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
           T  Q   LE+ F     L   R++++A  L L  RQI +WFQNRR +WK
Sbjct: 11  TRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 59

>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 = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 28/50 (56%)
Query: 93  TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142
           T  Q   LE+ F     L   R++++A  L L  RQI +WFQNRR +WK 
Sbjct: 10  TRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 59

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 28/49 (57%)
Query: 93  TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
           T  Q   LE+ F     L   R++++A  L L  RQI +WFQNRR +WK
Sbjct: 10  TRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 58

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 2/78 (2%)
Query: 71  MEKNIHHYGSSSTSSQERKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQ 128
           M + I H   + T  + +K R   T  Q+  LE+ F ++  L    +  LAR L +   Q
Sbjct: 1   MARRIGHPYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQ 60
Query: 129 IAVWFQNRRARWKSKQLE 146
           +  WFQNRR +W+ +  E
Sbjct: 61  VKTWFQNRRTKWRRQTAE 78

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 88  RKKRL--TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
           RKKR+  T  QL+ LER +     +  D++ +++    L  RQ+ +WFQNRR + K
Sbjct: 8   RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 63

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 30/52 (57%)
Query: 93  TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144
           T  QL  LE+ F     +   R+++LA  L L  R I +WFQNRR +WK ++
Sbjct: 11  TRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE 62

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	257
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	6e-26
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	1e-17
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	2e-17
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	1e-16
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	2e-15
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	1e-14
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	1e-14
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	5e-14
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	8e-14
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	1e-13
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	2e-13
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	3e-13
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	4e-13
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	4e-13
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	5e-13
1e3o_C	160	Octamer-binding transcription factor 1; transcript	8e-13
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	1e-12
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	1e-12
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	1e-12
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	2e-12
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	2e-12
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	3e-12
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	5e-12
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	6e-12
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	7e-12
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	8e-12
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	1e-11
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	1e-11
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	1e-11
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	2e-11
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	2e-11
1uhs_A	72	HOP, homeodomain only protein; structural genomics	3e-11
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	4e-11
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	5e-11
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	5e-11
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	2e-10
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	2e-10
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	5e-10
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	5e-10
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	6e-10
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	7e-10
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	8e-10
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	1e-09
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	1e-09
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	2e-09
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	2e-09
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	2e-09
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	2e-09
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	2e-09
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	3e-09
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	4e-09
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	5e-09
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	5e-09
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	2e-07
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	2e-07
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	1e-05
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	8e-05
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	8e-05
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	1e-04
2e19_A	64	Transcription factor 8; homeobox domain, structura	2e-04

>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 = 95.7 bits (239), Expect = 6e-26
 Identities = 18/57 (31%), Positives = 31/57 (54%)

Query: 85  SQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
           S + K  ++      LE  F+ +  L+   K ++A++ G+ P Q+ VWF N+R R K
Sbjct: 5   SPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61

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

 Score = 74.0 bits (182), Expect = 1e-17
 Identities = 16/65 (24%), Positives = 30/65 (46%)

Query: 80  SSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR 139
           S S+ +   K + + +QL +L+ SF             L +  GL  R++  WF +RR  
Sbjct: 3   SGSSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYH 62

Query: 140 WKSKQ 144
            ++ +
Sbjct: 63  CRNLK 67

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

 Score = 73.6 bits (181), Expect = 2e-17
 Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 85  SQERKKRLTSDQLESLERSFQEEIK-LDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK 143
           S +     T DQ+E LE +F +  K  DP     +A E GL   Q   WF+ R A W+  
Sbjct: 2   SAQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 61

Query: 144 Q 144
           +
Sbjct: 62  E 62

>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 = 71.5 bits (175), Expect = 1e-16
 Identities = 19/66 (28%), Positives = 32/66 (48%)

Query: 79  GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138
           GSS +S   + K    +QL +LE SF +      +   +L  E  +  R+I  WF  RR 
Sbjct: 1   GSSGSSGPTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRK 60

Query: 139 RWKSKQ 144
           +  +++
Sbjct: 61  KVNAEE 66

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

 Score = 68.3 bits (167), Expect = 2e-15
 Identities = 26/69 (37%), Positives = 38/69 (55%), Gaps = 8/69 (11%)

Query: 79  GSSSTSSQERKKR----LTSDQLESLERSFQEEIKLDPDRKMK--LARELGLQPRQIAVW 132
           G +     +R KR    +T +QLE L + +  +    P RKM   +A E+GL+ R + VW
Sbjct: 7   GGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSN--PTRKMLDHIAHEVGLKKRVVQVW 64

Query: 133 FQNRRARWK 141
           FQN RAR +
Sbjct: 65  FQNTRARER 73

>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 = 65.8 bits (161), Expect = 1e-14
 Identities = 18/63 (28%), Positives = 32/63 (50%)

Query: 79  GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138
           GSS +S +  + R+T DQL  L + F        ++  ++A + GL  + I  WF+N   
Sbjct: 1   GSSGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLF 60

Query: 139 RWK 141
           + +
Sbjct: 61  KER 63

>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 = 66.5 bits (162), Expect = 1e-14
 Identities = 18/67 (26%), Positives = 28/67 (41%)

Query: 78  YGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRR 137
            G+    + ++ K  T  Q++ LE SF +          +L  E  L  R+I  WF  RR
Sbjct: 6   SGAYPDFAPQKFKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERR 65

Query: 138 ARWKSKQ 144
               S +
Sbjct: 66  KLRDSME 72

>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 = 65.0 bits (158), Expect = 5e-14
 Identities = 15/60 (25%), Positives = 28/60 (46%)

Query: 85  SQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144
           + ++ K  T++QL  L+ SF     L  +   +L  +  L  R+I  WF  ++     K+
Sbjct: 11  TPQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE 70

>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 = 63.7 bits (155), Expect = 8e-14
 Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 3/65 (4%)

Query: 79  GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKM--KLARELGLQPRQIAVWFQNR 136
           GSS +S    + +++ + L  L+    + + L PD++    L+ +L L    I  +FQN+
Sbjct: 1   GSSGSSGPRSRTKISLEALGILQSFIHD-VGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQ 59

Query: 137 RARWK 141
           R   K
Sbjct: 60  RYHVK 64

>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 = 63.1 bits (154), Expect = 1e-13
 Identities = 22/66 (33%), Positives = 30/66 (45%)

Query: 79  GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138
           GSS +S +  + R T  QL  L+  F        D   +L+  L L  R I VWFQN R 
Sbjct: 1   GSSGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQ 60

Query: 139 RWKSKQ 144
           + +   
Sbjct: 61  KARKSG 66

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

 Score = 65.7 bits (159), Expect = 2e-13
 Identities = 17/76 (22%), Positives = 35/76 (46%)

Query: 71  MEKNIHHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIA 130
             K   H      + ++ +   T  Q  +L   F+E  +   + ++ ++++LGL+   ++
Sbjct: 83  KRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVS 142

Query: 131 VWFQNRRARWKSKQLE 146
            +F N R R   K LE
Sbjct: 143 NFFMNARRRSLDKWLE 158

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

 Score = 65.0 bits (158), Expect = 3e-13
 Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 2/76 (2%)

Query: 68  AELMEKNIHHYGSSSTSSQERKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQ 125
            +    +  +    +   ++RKKR  +      +LE  F +  K        LA  L L+
Sbjct: 80  TDSSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLE 139

Query: 126 PRQIAVWFQNRRARWK 141
              + VWF NRR + K
Sbjct: 140 KEVVRVWFCNRRQKEK 155

>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 = 64.2 bits (156), Expect = 4e-13
 Identities = 24/119 (20%), Positives = 48/119 (40%), Gaps = 4/119 (3%)

Query: 23  SFDLLYNYNYDQFPGMDQMNKHMHAAAAAAAMAEKSSSSIGLIPAAELMEKNIHHYGSSS 82
           +   ++   + Q       N  +    +     +  +     +  AE +    +    ++
Sbjct: 29  ALAAVHGSEFSQTTICRFENLQL----SFKNACKLKAILSKWLEEAEQVGALYNEKVGAN 84

Query: 83  TSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
              ++R+  ++    ++LER F E  K      M++A EL L+   + VWF NRR R K
Sbjct: 85  ERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREK 143

>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 = 61.7 bits (150), Expect = 4e-13
 Identities = 14/65 (21%), Positives = 25/65 (38%), Gaps = 2/65 (3%)

Query: 85  SQERKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142
           +         T +Q+  L+ SF +    D     +L    GL   +I  WF + R R + 
Sbjct: 2   AHHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR 61

Query: 143 KQLEL 147
             + +
Sbjct: 62  GIVHI 66

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

 Score = 61.6 bits (150), Expect = 5e-13
 Identities = 25/65 (38%), Positives = 37/65 (56%), Gaps = 2/65 (3%)

Query: 82  STSSQERKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR 139
           S+ S  RK R   +S QL +L+R FQ+   L    + +LA  LGL   Q+ +WFQN+R++
Sbjct: 2   SSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSK 61

Query: 140 WKSKQ 144
            K   
Sbjct: 62  IKKSG 66

>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 = 63.4 bits (154), Expect = 8e-13
 Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 2/68 (2%)

Query: 76  HHYGSSSTSSQERKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWF 133
            +       S+ RKKR  + ++   +LE+SF E  K   +    +A +L ++   I VWF
Sbjct: 90  LNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWF 149

Query: 134 QNRRARWK 141
            NRR + K
Sbjct: 150 SNRRQKEK 157

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

 Score = 61.4 bits (149), Expect = 1e-12
 Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 3/86 (3%)

Query: 71  MEKNIHHYGSSSTSSQERKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQ 128
           M + I H   + T  + +K R   T  Q+  LE+ F ++  L    +  LAR L +   Q
Sbjct: 1   MARRIGHPYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQ 60

Query: 129 IAVWFQNRRARWKSKQLELLYDSLKQ 154
           +  WFQNRR +W+ +Q     ++ +Q
Sbjct: 61  VKTWFQNRRTKWR-RQTAEEREAERQ 85

>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 = 60.9 bits (148), Expect = 1e-12
 Identities = 24/70 (34%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 79  GSSSTSSQERKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNR 136
            S    +++RK+R   T  Q   LER F+++  L    +  LA  + L P Q+ +WFQN 
Sbjct: 1   ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNH 60

Query: 137 RARWKSKQLE 146
           R + K  Q E
Sbjct: 61  RYKTKRAQNE 70

>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 = 60.4 bits (147), Expect = 1e-12
 Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 8/66 (12%)

Query: 88  RKKR----LTSDQLESLERSFQEEIKLDPDRKMK--LARELGLQPRQIAVWFQNRRARWK 141
           +  R    L   QL +L   +    +  PD  MK  L    GL PR I VWFQN+R + K
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPR--PDALMKEQLVEMTGLSPRVIRVWFQNKRCKDK 59

Query: 142 SKQLEL 147
            + + +
Sbjct: 60  KRSIMM 65

>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 60.2 bits (146), Expect = 2e-12
 Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 9/67 (13%)

Query: 85  SQERKKR-----LTSDQLESLERSFQEEIKLDPDRKM--KLARELGLQPRQIAVWFQNRR 137
           S     +         QL +++  F       PD K   +LA++ GL  R + VWFQN R
Sbjct: 2   SSGSSGKRMRTSFKHHQLRTMKSYFAINHN--PDAKDLKQLAQKTGLTKRVLQVWFQNAR 59

Query: 138 ARWKSKQ 144
           A+++   
Sbjct: 60  AKFRRNL 66

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

 Score = 60.2 bits (146), Expect = 2e-12
 Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 2/68 (2%)

Query: 79  GSSSTSSQERKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNR 136
                  +++K R   +S QL  L   FQ +  L   +  +L+  L L  +Q+  WFQN+
Sbjct: 14  KEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQ 73

Query: 137 RARWKSKQ 144
           R + K  Q
Sbjct: 74  RMKSKRWQ 81

>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 = 59.7 bits (145), Expect = 3e-12
 Identities = 26/68 (38%), Positives = 40/68 (58%)

Query: 79  GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138
           GSS +S +  + R ++DQ   LE+ F+ +  L P  + +LA+ L L  RQ+  WFQNRRA
Sbjct: 1   GSSGSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRA 60

Query: 139 RWKSKQLE 146
           +W+     
Sbjct: 61  KWRRSGPS 68

>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 = 59.4 bits (144), Expect = 5e-12
 Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 2/67 (2%)

Query: 80  SSSTSSQERKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRR 137
             + + + R+ R   T  QL  LE+ F+++  L    ++ LA  LGL   Q+  W+QNRR
Sbjct: 10  PGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRR 69

Query: 138 ARWKSKQ 144
            +WK   
Sbjct: 70  MKWKKSG 76

>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 = 61.3 bits (148), Expect = 6e-12
 Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 2/75 (2%)

Query: 69  ELMEKNIHHYGSSSTSSQERKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQP 126
           +  E       S +     ++KR  + +    SLE  F +  K    +   +A +LGL+ 
Sbjct: 78  DNNENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEK 137

Query: 127 RQIAVWFQNRRARWK 141
             + VWF NRR + K
Sbjct: 138 DVVRVWFSNRRQKGK 152

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

 Score = 58.4 bits (142), Expect = 7e-12
 Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 2/59 (3%)

Query: 88  RKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144
           +K R   +  QL +L+  FQ++  L   +  +L+  L L  +Q+  WFQN+R + K  Q
Sbjct: 4   QKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRWQ 62

>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 = 58.1 bits (141), Expect = 8e-12
 Identities = 22/49 (44%), Positives = 32/49 (65%)

Query: 93  TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
           +S+QL  L+R F E   L   R+ +L+ ELGL   QI +WF+N+RA+ K
Sbjct: 11  SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 59

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

 Score = 57.6 bits (140), Expect = 1e-11
 Identities = 22/56 (39%), Positives = 33/56 (58%), Gaps = 2/56 (3%)

Query: 88  RKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
           RK R   T+ QL +LER F+++  L    + + +  L L   Q+ +WFQNRRA+ K
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56

>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 = 60.0 bits (145), Expect = 1e-11
 Identities = 19/120 (15%), Positives = 39/120 (32%), Gaps = 1/120 (0%)

Query: 23  SFDLLYNYNYDQFPGMDQMNKHMHAAAAAAAMAEKSSSSIGLIPAAELMEKNIHHYGSSS 82
           +        Y Q          +   +A                  +  ++N+  +    
Sbjct: 30  AMTATEGPAYSQSAISRFEKLDITPKSAQKLKPVLEKWLNEAELRNQEGQQNLMEFVGGE 89

Query: 83  TSSQERKK-RLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
            S + +++   T   +E+L   F++          ++A+EL      + VWF NRR   K
Sbjct: 90  PSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLK 149

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

 Score = 57.2 bits (139), Expect = 1e-11
 Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 2/56 (3%)

Query: 88  RKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
           RK R   +  Q+  LER F+++  L    + +LA  L L   Q+ +WFQNRR + K
Sbjct: 3   RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

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

 Score = 57.4 bits (139), Expect = 2e-11
 Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 2/64 (3%)

Query: 85  SQERKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142
                    ++  Q+  LER F  +  L    +  LA+ L L   Q+ +WFQNRR + K 
Sbjct: 2   GHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61

Query: 143 KQLE 146
           KQL 
Sbjct: 62  KQLS 65

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

 Score = 57.1 bits (138), Expect = 2e-11
 Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 88  RKKRLTSDQLESLERSFQEEIK-LDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
                  +  ++LE+ F    K  D  R   L+++L    R+I  WF++RR + K
Sbjct: 11  DSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 65

>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 = 57.0 bits (138), Expect = 3e-11
 Identities = 20/54 (37%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 92  LTSDQLESLERSFQEEIK-LDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144
           +T DQ+E LE +F +  K  DP     +A E GL   Q   WF+ R A W+  +
Sbjct: 8   MTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 61

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

 Score = 56.2 bits (136), Expect = 4e-11
 Identities = 17/49 (34%), Positives = 26/49 (53%)

Query: 93  TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
           +  Q+  LER F  +  L    +  LA+ L +   Q+  WFQNRR +W+
Sbjct: 5   SRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWR 53

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

 Score = 56.4 bits (136), Expect = 5e-11
 Identities = 22/63 (34%), Positives = 36/63 (57%)

Query: 79  GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138
           GSS +S ++++   +  QL  LER +     +  D++ K++    L  RQI +WFQNRR 
Sbjct: 1   GSSGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRV 60

Query: 139 RWK 141
           + K
Sbjct: 61  KEK 63

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

 Score = 56.2 bits (136), Expect = 5e-11
 Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 88  RKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL 145
           RK+R   +  Q+  LER F+++  L    +  LA  + L P Q+ +WFQN R + K +  
Sbjct: 3   RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62

Query: 146 E 146
           +
Sbjct: 63  D 63

>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 = 54.7 bits (132), Expect = 2e-10
 Identities = 22/52 (42%), Positives = 31/52 (59%)

Query: 93  TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144
           T DQL  LE+ F +E  +   R+ +LA +L L    I VWFQNRR + K ++
Sbjct: 9   TRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQR 60

>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 = 55.6 bits (133), Expect = 2e-10
 Identities = 21/74 (28%), Positives = 33/74 (44%)

Query: 77  HYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNR 136
              +  + S  +  + T +QL  L+ +F       P+   KLA+E GL    I  WF + 
Sbjct: 17  QGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDT 76

Query: 137 RARWKSKQLELLYD 150
           R  WK+  L+  Y 
Sbjct: 77  RYAWKNGNLKWYYY 90

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

 Score = 53.7 bits (129), Expect = 5e-10
 Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 2/62 (3%)

Query: 82  STSSQERKKRL--TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR 139
           S   + RKKR+  T  QL+ LER +     +  D++ +++    L  RQ+ +WFQNRR +
Sbjct: 2   SHMLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVK 61

Query: 140 WK 141
            K
Sbjct: 62  EK 63

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

 Score = 54.1 bits (130), Expect = 5e-10
 Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 2/76 (2%)

Query: 71  MEKNIHHYGSSSTSSQERKKRL--TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQ 128
           M++      + + + + +++R   T  Q   LE+ F     L   R++++A  L L  RQ
Sbjct: 12  MKRVHLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQ 71

Query: 129 IAVWFQNRRARWKSKQ 144
           I +WFQNRR +WK + 
Sbjct: 72  IKIWFQNRRMKWKKEH 87

>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 = 53.2 bits (128), Expect = 6e-10
 Identities = 19/52 (36%), Positives = 28/52 (53%)

Query: 93  TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144
           TS Q+  LE+ F +   L   R   L+ +L L   Q+ +WF+NRR R K + 
Sbjct: 10  TSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQS 61

>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 = 53.6 bits (129), Expect = 7e-10
 Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 9/67 (13%)

Query: 85  SQERKKR-----LTSDQLESLERSFQEEIKLDPDRKM--KLARELGLQPRQIAVWFQNRR 137
           S     R      T  QL+ LE  F +     PD  M  ++A ++ L   ++ VWF+NRR
Sbjct: 2   SSGSSGRRERTTFTRAQLDVLEALFAK--TRYPDIFMREEVALKINLPESRVQVWFKNRR 59

Query: 138 ARWKSKQ 144
           A+ + +Q
Sbjct: 60  AKCRQQQ 66

>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 = 53.1 bits (128), Expect = 8e-10
 Identities = 24/65 (36%), Positives = 36/65 (55%), Gaps = 5/65 (7%)

Query: 85  SQERKKR-----LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR 139
           S     R      T +QLE+LE  FQE    D   + +LAR++ L+  ++ VWF+NRRA+
Sbjct: 2   SSGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAK 61

Query: 140 WKSKQ 144
           W+   
Sbjct: 62  WRRSG 66

>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 = 52.3 bits (126), Expect = 1e-09
 Identities = 20/52 (38%), Positives = 29/52 (55%)

Query: 93  TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144
           T +Q+E LE  F+       D    LA++L L+  +I +WFQNRRA+ K   
Sbjct: 9   TQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSH 60

>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 = 52.6 bits (126), Expect = 1e-09
 Identities = 25/62 (40%), Positives = 34/62 (54%), Gaps = 2/62 (3%)

Query: 82  STSSQERKKRL--TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR 139
             +   RKKR   T  Q   LE+ F   + L  DR+ ++AR L L  RQ+ +WFQNRR +
Sbjct: 8   LHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMK 67

Query: 140 WK 141
            K
Sbjct: 68  MK 69

>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 = 52.5 bits (126), Expect = 2e-09
 Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 2/64 (3%)

Query: 80  SSSTSSQERKKRL--TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRR 137
            + T+   R+ R   T  Q   LE+ F     L   R++++A  L L  RQI +WFQNRR
Sbjct: 13  IAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRR 72

Query: 138 ARWK 141
            + K
Sbjct: 73  MKLK 76

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

 Score = 52.4 bits (126), Expect = 2e-09
 Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 9/67 (13%)

Query: 85  SQERKKR-----LTSDQLESLERSFQEEIKLDPDRKM--KLARELGLQPRQIAVWFQNRR 137
           S     +      T +Q+E+LE+ F+      PD     +LA ++ L   +I VWF NRR
Sbjct: 2   SSGSSGQRNRTSFTQEQIEALEKEFER--THYPDVFARERLAAKIDLPEARIQVWFSNRR 59

Query: 138 ARWKSKQ 144
           A+W+ ++
Sbjct: 60  AKWRREE 66

>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 = 51.5 bits (124), Expect = 2e-09
 Identities = 24/54 (44%), Positives = 34/54 (62%), Gaps = 4/54 (7%)

Query: 93  TSDQLESLERSFQEEIKLDPDRKM--KLARELGLQPRQIAVWFQNRRARWKSKQ 144
           TS QLE LE++F       PD     +LA ++GL   +I VWFQNRRA+W+ ++
Sbjct: 7   TSFQLEELEKAFSR--THYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58

>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 = 52.3 bits (125), Expect = 2e-09
 Identities = 21/71 (29%), Positives = 30/71 (42%)

Query: 84  SSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK 143
           SS    KR T +QL  L+  F +      +   KL +  GL   +I  WF + R   K  
Sbjct: 2   SSGSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG 61

Query: 144 QLELLYDSLKQ 154
           QL+   D+   
Sbjct: 62  QLKWFRDNASG 72

>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 = 52.0 bits (125), Expect = 2e-09
 Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 9/72 (12%)

Query: 80  SSSTSSQERKKR-----LTSDQLESLERSFQEEIKLDPDRKM--KLARELGLQPRQIAVW 132
           S    + +RK+R      ++ QL+ LER+F+      PD     +LA+   L   +I VW
Sbjct: 8   SEPGIALKRKQRRSRTTFSASQLDELERAFERTQY--PDIYTREELAQRTNLTEARIQVW 65

Query: 133 FQNRRARWKSKQ 144
           FQNRRAR + + 
Sbjct: 66  FQNRRARLRKQH 77

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

 Score = 51.2 bits (123), Expect = 3e-09
 Identities = 21/52 (40%), Positives = 30/52 (57%)

Query: 93  TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144
           T  QL  LE+ F     +   R+++LA  L L  R I +WFQNRR +WK ++
Sbjct: 11  TRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE 62

>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 = 50.9 bits (122), Expect = 4e-09
 Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 2/57 (3%)

Query: 87  ERKKRL--TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
            ++ R   T  Q   LE+ F     L   R++++A  L L  RQI +WFQNRR +WK
Sbjct: 2   RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 58

>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 = 50.8 bits (122), Expect = 5e-09
 Identities = 20/58 (34%), Positives = 34/58 (58%)

Query: 93  TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYD 150
           TS QL+ LE +FQ     D   + ++A    L   ++ VWF+NRRA+W+ ++  ++ D
Sbjct: 11  TSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEFIVTD 68

>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 = 51.4 bits (123), Expect = 5e-09
 Identities = 22/73 (30%), Positives = 32/73 (43%), Gaps = 4/73 (5%)

Query: 73  KNIHHYGSSSTSSQERKKRL----TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQ 128
           +N       S         L    T+ QL  LE+ F     L   R++++A  L L   Q
Sbjct: 18  RNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQ 77

Query: 129 IAVWFQNRRARWK 141
           + +WFQNRR + K
Sbjct: 78  VKIWFQNRRMKQK 90

>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 = 47.3 bits (112), Expect = 2e-07
 Identities = 19/80 (23%), Positives = 28/80 (35%), Gaps = 17/80 (21%)

Query: 82  STSSQERKKRLT--SDQLESLERSFQ----------EEI-----KLDPDRKMKLARELGL 124
           S+ S  R  R T   + L  +E  F           EEI      +      KL+    +
Sbjct: 2   SSGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERV 61

Query: 125 QPRQIAVWFQNRRARWKSKQ 144
              ++  WF NRR   K + 
Sbjct: 62  TSLKVYNWFANRRKEIKRRA 81

>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 = 46.0 bits (109), Expect = 2e-07
 Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 1/55 (1%)

Query: 88  RKKRLTSDQLESLERSFQEEIK-LDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
                T+     LE+ F    K  D  R   L+++L    R I  WF+ RR + K
Sbjct: 3   SGSSGTAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 57

>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain, hoogsteen base PAIR, transcription/DNA complex; HET: 5IU; 2.10A {Synthetic} SCOP: a.4.1.1 Length = 60

 Score = 41.1 bits (97), Expect = 1e-05
 Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 3/58 (5%)

Query: 88  RKKRLTSDQLESLERSFQEEIK---LDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142
           R  R T + +  LE  F + I+   LD      L +   L   QI  W  NRR + K+
Sbjct: 1   RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration calorimetry, protein-DNA complex, transcription/DNA complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1akh_B* 1apl_C* 1yrn_B* Length = 83

 Score = 39.4 bits (92), Expect = 8e-05
 Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 3/62 (4%)

Query: 84  SSQERKKRLTSDQLESLERSFQEEIK---LDPDRKMKLARELGLQPRQIAVWFQNRRARW 140
           +   R  R T + +  LE  F + I+   LD      L +   L   QI  W   RRA+ 
Sbjct: 1   TKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKE 60

Query: 141 KS 142
           K+
Sbjct: 61  KT 62

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

 Score = 39.5 bits (92), Expect = 8e-05
 Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 3/66 (4%)

Query: 80  SSSTSSQERKKRLTSDQLESLERSFQEEIK---LDPDRKMKLARELGLQPRQIAVWFQNR 136
            + ++   R  R T + +  LE  F + I+   LD      L +   L   QI  W  NR
Sbjct: 22  INKSTKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNR 81

Query: 137 RARWKS 142
           R + K+
Sbjct: 82  RRKEKT 87

>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 = 39.2 bits (90), Expect = 1e-04
 Identities = 14/73 (19%), Positives = 34/73 (46%), Gaps = 5/73 (6%)

Query: 79  GSSSTSSQERKK-RLTSDQLESLERSFQEEI----KLDPDRKMKLARELGLQPRQIAVWF 133
           GSS +S   + + + +   L +L++ +   +     +  ++   +A EL +    +  W 
Sbjct: 1   GSSGSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWI 60

Query: 134 QNRRARWKSKQLE 146
            NRR +++   +E
Sbjct: 61  GNRRRKYRLMGIE 73

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

 Score = 38.1 bits (88), Expect = 2e-04
 Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 4/66 (6%)

Query: 79  GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138
           GSS +S Q   K    + L  L+  +    +   +   K+A  + L    +  WF+  +A
Sbjct: 1   GSSGSSGQPPLK----NLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQA 56

Query: 139 RWKSKQ 144
              S Q
Sbjct: 57  GQISVQ 62

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	257
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.81
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.81
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.81
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.8
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.8
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.8
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.8
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.8
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.8
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.8
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.8
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.79
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.79
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.79
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.78
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.78
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.78
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.78
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.78
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.78
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.78
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.77
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.77
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.77
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.77
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.77
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.77
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.77
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.77
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.77
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.76
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.76
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.76
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.76
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.76
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.76
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.75
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.75
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.75
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.75
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.75
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.75
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.75
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.75
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.75
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.74
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.74
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.74
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.73
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.72
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.72
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.72
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.72
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.71
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.71
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.7
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.7
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.69
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.69
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.69
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.69
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.68
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.68
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.68
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.67
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.67
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.67
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.67
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.66
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.64
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.62
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.6
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.46
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.43
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.42
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.35
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.31
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.87
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	93.44

>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=99.81  E-value=1e-20  Score=136.65  Aligned_cols=65  Identities=32%  Similarity=0.559  Sum_probs=60.6

Q ss_pred             CCCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           80 SSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        80 ~~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      +...+.+|+|++||..|+.+||..|..++||+..++.+||.+|||+++||+|||||||+|+|+..
T Consensus         2 s~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~   66 (70)
T 2cra_A            2 SSGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSG   66 (70)
T ss_dssp             CSSCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccC
Confidence            35566788899999999999999999999999999999999999999999999999999999854

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

Probab=99.81  E-value=2e-20  Score=138.48  Aligned_cols=66  Identities=33%  Similarity=0.607  Sum_probs=61.1

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE  146 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~  146 (257)
                      .....+|+|++||..|+.+||..|..++||+..++.+||..|||++++|+|||||||+|+|+....
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~   68 (80)
T 2cue_A            3 SGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL   68 (80)
T ss_dssp             SCCSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhh
Confidence            445677889999999999999999999999999999999999999999999999999999986544

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

Probab=99.81  E-value=1.7e-20  Score=135.40  Aligned_cols=65  Identities=38%  Similarity=0.674  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           80 SSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        80 ~~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      +.....+|+|++||.+|+.+||..|..++||+..++.+||.+|||+++||+|||||||+|+|+..
T Consensus         2 s~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~   66 (70)
T 2dmu_A            2 SSGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSG   66 (70)
T ss_dssp             CSTTSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTS
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccC
Confidence            34556788899999999999999999999999999999999999999999999999999999854

>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=99.80  E-value=3.4e-20  Score=137.08  Aligned_cols=64  Identities=28%  Similarity=0.501  Sum_probs=60.0

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      ...+.+|+|++||.+|+.+||.+|..++||+..++.+||.+|||++++|+|||||||+|+|++.
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   66 (80)
T 2dmq_A            3 SGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNL   66 (80)
T ss_dssp             CCCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHH
Confidence            4456788899999999999999999999999999999999999999999999999999999854

>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=99.80  E-value=3.4e-20  Score=133.85  Aligned_cols=64  Identities=38%  Similarity=0.693  Sum_probs=59.5

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      ...+.+++|++||.+|+.+||..|..++||+..++.+||.+|||+++||+|||||||+|+|+..
T Consensus         3 ~~~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~   66 (70)
T 2e1o_A            3 SGSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSG   66 (70)
T ss_dssp             CCCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCC
Confidence            4455677899999999999999999999999999999999999999999999999999999854

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

Probab=99.80  E-value=2.8e-20  Score=137.67  Aligned_cols=65  Identities=31%  Similarity=0.485  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           80 SSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        80 ~~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      +...+.+|+|++||.+|+.+||..|..++||+..+|.+||.+|||++++|+|||||||+|+|+.+
T Consensus         2 s~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~   66 (80)
T 2dms_A            2 SSGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQ   66 (80)
T ss_dssp             CCCCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTT
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHH
Confidence            34566788899999999999999999999999999999999999999999999999999999854

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

Probab=99.80  E-value=1.4e-20  Score=132.78  Aligned_cols=61  Identities=30%  Similarity=0.450  Sum_probs=53.5

Q ss_pred             CCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           84 SSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        84 ~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      +.+|+|+.||..|+.+||..|..++||+..++.+||..|||++++|+|||||||+|+|+.+
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~q   62 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRWQ   62 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGGC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhcC
Confidence            4578899999999999999999999999999999999999999999999999999999853

>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=99.80  E-value=4.5e-20  Score=135.66  Aligned_cols=67  Identities=31%  Similarity=0.462  Sum_probs=61.5

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLEL  147 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~  147 (257)
                      ...+.+|+|++||..|+.+||..|..++||+..++.+||..|||+++||+|||||||+|+|+.+.+.
T Consensus         5 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~~   71 (77)
T 1nk2_P            5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEK   71 (77)
T ss_dssp             CSCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhccc
Confidence            3456677899999999999999999999999999999999999999999999999999999976553

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

Probab=99.80  E-value=2.2e-20  Score=132.16  Aligned_cols=61  Identities=36%  Similarity=0.635  Sum_probs=56.1

Q ss_pred             CCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           84 SSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        84 ~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      +.+|+|++||..|+.+||..|..++||+..++.+||..|||+++||+|||||||+|+|+.+
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   62 (63)
T 2h1k_A            2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE   62 (63)
T ss_dssp             ---CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhhc
Confidence            4678899999999999999999999999999999999999999999999999999999853

>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=99.80  E-value=2.4e-20  Score=134.54  Aligned_cols=65  Identities=32%  Similarity=0.451  Sum_probs=60.7

Q ss_pred             CCCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           80 SSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        80 ~~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      +...+.+++|++||.+|+.+||..|..++||+..++.+||.+|||+++||+|||||||+|+|+..
T Consensus         2 ~~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2da2_A            2 SSGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSG   66 (70)
T ss_dssp             CCSCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCS
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhcc
Confidence            35567788899999999999999999999999999999999999999999999999999999854

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

Probab=99.80  E-value=2.2e-20  Score=134.84  Aligned_cols=65  Identities=35%  Similarity=0.552  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           80 SSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        80 ~~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      +...+.+|+|++||..|+.+||..|..++||+..++.+||.+|||+++||+|||||||+|+|+..
T Consensus         2 s~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2djn_A            2 SSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSG   66 (70)
T ss_dssp             CSCCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSS
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccC
Confidence            35566788899999999999999999999999999999999999999999999999999999853

>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=99.79  E-value=3.1e-20  Score=133.93  Aligned_cols=65  Identities=26%  Similarity=0.412  Sum_probs=60.4

Q ss_pred             CCCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           80 SSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        80 ~~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      +...+.+|+|++||.+|+.+||..|..++||+..++.+||..|||+++||+|||||||+|+|+..
T Consensus         2 ~~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2da1_A            2 SSGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSG   66 (70)
T ss_dssp             CSSCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhc
Confidence            34566788899999999999999999999999999999999999999999999999999999854

>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=99.79  E-value=4.8e-20  Score=136.46  Aligned_cols=64  Identities=31%  Similarity=0.602  Sum_probs=59.7

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      ...+.+|+|++||..|+.+||..|..++||+..+|.+||..|||+++||+|||||||+|+|+..
T Consensus        13 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   76 (80)
T 2dmt_A           13 KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSG   76 (80)
T ss_dssp             CCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhccc
Confidence            4556778899999999999999999999999999999999999999999999999999999853

>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=99.79  E-value=1e-19  Score=133.80  Aligned_cols=66  Identities=33%  Similarity=0.546  Sum_probs=60.9

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE  146 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~  146 (257)
                      ..+..+++|++||..|+.+||..|..++||+..++.+||..|||+++||+|||||||+|+|+...+
T Consensus         9 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k~   74 (77)
T 1puf_A            9 HARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             CCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhhh
Confidence            345567889999999999999999999999999999999999999999999999999999997654

>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=99.78  E-value=4.8e-20  Score=129.53  Aligned_cols=58  Identities=38%  Similarity=0.689  Sum_probs=53.3

Q ss_pred             CCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769           85 SQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS  142 (257)
Q Consensus        85 ~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr  142 (257)
                      .+|.|+.||..|+.+||..|..++||+..++.+||..|||+++||+|||||||+|+|+
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            5788999999999999999999999999999999999999999999999999999997

>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=99.78  E-value=4e-20  Score=136.46  Aligned_cols=64  Identities=28%  Similarity=0.447  Sum_probs=59.7

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      ...+.+|+|++||.+|+.+||..|..++||+..++.+||.+|||+++||+|||||||+|+|+.+
T Consensus        13 ~~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   76 (80)
T 2da3_A           13 EPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSG   76 (80)
T ss_dssp             CCCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhc
Confidence            3456778899999999999999999999999999999999999999999999999999999854

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

Probab=99.78  E-value=8.8e-20  Score=131.02  Aligned_cols=62  Identities=31%  Similarity=0.507  Sum_probs=58.6

Q ss_pred             CCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHH
Q 040769           84 SSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL  145 (257)
Q Consensus        84 ~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~  145 (257)
                      +++|+|++||..|+.+||..|..++||+..++.+||..|||++++|+|||||||+|+|+...
T Consensus         1 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~   62 (68)
T 1zq3_P            1 GPRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD   62 (68)
T ss_dssp             CCSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhc
Confidence            35788999999999999999999999999999999999999999999999999999998654

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

Probab=99.78  E-value=8.3e-20  Score=126.89  Aligned_cols=57  Identities=33%  Similarity=0.587  Sum_probs=55.3

Q ss_pred             CCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769           86 QERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS  142 (257)
Q Consensus        86 ~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr  142 (257)
                      +|+|++||..|+.+||..|..++||+..++.+||..|||+++||++||||||+|+|+
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            478999999999999999999999999999999999999999999999999999997

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

Probab=99.78  E-value=5.3e-20  Score=137.23  Aligned_cols=64  Identities=30%  Similarity=0.413  Sum_probs=59.9

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      ...+.+|+|++||..|+.+||..|..++||+..+|.+||..|||+++||+|||||||+|+|+.+
T Consensus        18 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   81 (84)
T 2kt0_A           18 VPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQ   81 (84)
T ss_dssp             CCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHh
Confidence            4566778899999999999999999999999999999999999999999999999999999854

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

Probab=99.78  E-value=1.4e-19  Score=131.69  Aligned_cols=63  Identities=27%  Similarity=0.492  Sum_probs=58.9

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      ..+.+|+|++||..|+.+||..|..++||+..++.+||..|||+++||+|||||||+|+|+..
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   66 (73)
T 2l7z_A            4 MLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVI   66 (73)
T ss_dssp             SSCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHh
Confidence            345678899999999999999999999999999999999999999999999999999999853

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

Probab=99.78  E-value=7.5e-20  Score=139.34  Aligned_cols=66  Identities=29%  Similarity=0.583  Sum_probs=60.7

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE  146 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~  146 (257)
                      ...+.+|+|++||..|+.+||..|..++||+..+|.+||..|||+++||+|||||||+|+|+...+
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            345567889999999999999999999999999999999999999999999999999999996644

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

Probab=99.77  E-value=6.7e-20  Score=135.62  Aligned_cols=64  Identities=16%  Similarity=0.361  Sum_probs=59.5

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhhc----CCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQEE----IKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~~----~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      ...+.+|+|+.||.+|+.+||.+|..+    +||+..+|.+||.+|||+++||+|||||||+|+|+..
T Consensus         4 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~~   71 (80)
T 2da4_A            4 GSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMG   71 (80)
T ss_dssp             CCCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhcc
Confidence            445677889999999999999999999    9999999999999999999999999999999999843

>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=99.77  E-value=1.1e-19  Score=134.87  Aligned_cols=61  Identities=16%  Similarity=0.306  Sum_probs=57.5

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhh----cCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769           82 STSSQERKKRLTSDQLESLERSFQE----EIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS  142 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~----~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr  142 (257)
                      ..+++|+|+.||.+|+.+||..|+.    ++||+..+|.+||.+|||+++||+|||||||+|+|+
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            3567788999999999999999999    999999999999999999999999999999999985

>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=1.5e-19  Score=132.35  Aligned_cols=60  Identities=25%  Similarity=0.410  Sum_probs=56.3

Q ss_pred             CCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           85 SQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        85 ~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      ..++|++||.+|+.+||..|..++||+..+|.+||.+|||+++||+|||||||+|+|++.
T Consensus         7 ~~~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~   66 (75)
T 2da5_A            7 GPTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEE   66 (75)
T ss_dssp             SSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSS
T ss_pred             CCCCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhh
Confidence            346788899999999999999999999999999999999999999999999999999854

>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=99.77  E-value=7.6e-20  Score=135.81  Aligned_cols=62  Identities=32%  Similarity=0.526  Sum_probs=54.6

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           83 TSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        83 ~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      +..+|+|++||..|+.+||..|..++||+..+|.+||.+|||++++|+|||||||+|+||..
T Consensus        18 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   79 (81)
T 1b8i_A           18 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEI   79 (81)
T ss_dssp             ------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhc
Confidence            45678899999999999999999999999999999999999999999999999999999864

>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=99.77  E-value=2.5e-19  Score=132.85  Aligned_cols=64  Identities=31%  Similarity=0.537  Sum_probs=58.9

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHH
Q 040769           82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL  145 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~  145 (257)
                      ..+.+|+|++||..|+.+||..|..++||+..++.+||.+|||+++||+|||||||+|+|++..
T Consensus        15 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~   78 (81)
T 1fjl_A           15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   78 (81)
T ss_dssp             --CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhcc
Confidence            4566788999999999999999999999999999999999999999999999999999998654

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

Probab=99.77  E-value=1.4e-19  Score=126.73  Aligned_cols=58  Identities=38%  Similarity=0.584  Sum_probs=55.4

Q ss_pred             CCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHH
Q 040769           86 QERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK  143 (257)
Q Consensus        86 ~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~  143 (257)
                      +|.|++||..|+.+||..|..++||+..++.+||.+|||++++|++||||||+|+|++
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            5789999999999999999999999999999999999999999999999999999984

>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=99.77  E-value=5.6e-20  Score=132.00  Aligned_cols=62  Identities=32%  Similarity=0.595  Sum_probs=58.7

Q ss_pred             CCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHH
Q 040769           84 SSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL  145 (257)
Q Consensus        84 ~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~  145 (257)
                      +++|+|++||..|+.+||..|..++||+..++.+||..|||++++|+|||||||+|+|+...
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~   63 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREE   63 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhh
Confidence            56788999999999999999999999999999999999999999999999999999998653

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

Probab=99.77  E-value=1e-19  Score=130.68  Aligned_cols=60  Identities=35%  Similarity=0.636  Sum_probs=57.2

Q ss_pred             CCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           85 SQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        85 ~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      ++|+|++||..|+.+||..|..++||+..++.+||..|||+++||+|||||||+|+|+..
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   61 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN   61 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhc
Confidence            467899999999999999999999999999999999999999999999999999999864

>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=99.77  E-value=9.2e-20  Score=130.05  Aligned_cols=61  Identities=31%  Similarity=0.511  Sum_probs=57.9

Q ss_pred             CCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           84 SSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        84 ~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      +++|+|++||.+|+.+||..|..++||+..++.+||..|||+++||++||||||+|+|++.
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            4578899999999999999999999999999999999999999999999999999999854

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

Probab=99.76  E-value=1.9e-19  Score=124.69  Aligned_cols=57  Identities=32%  Similarity=0.518  Sum_probs=54.8

Q ss_pred             CCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769           85 SQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK  141 (257)
Q Consensus        85 ~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K  141 (257)
                      +++.|++|+..|+.+||..|..++||+..++.+||.+|||+++||+|||||||+|+|
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            567899999999999999999999999999999999999999999999999999986

>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=99.76  E-value=1.7e-19  Score=133.82  Aligned_cols=61  Identities=21%  Similarity=0.370  Sum_probs=56.9

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhh-----cCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQE-----EIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS  142 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~-----~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr  142 (257)
                      ...+++|+|+.||.+|+.+|| .|..     ++||+..+|.+||.+|||+++||+|||||||+|+|+
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            445677889999999999999 7999     999999999999999999999999999999999985

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

Probab=99.76  E-value=2.5e-19  Score=128.68  Aligned_cols=60  Identities=30%  Similarity=0.552  Sum_probs=57.2

Q ss_pred             CCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           85 SQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        85 ~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      .+|+|++||..|+.+||..|..++||+..++.+||..|||++++|+|||||||+|+|+..
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~   61 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA   61 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhh
Confidence            467899999999999999999999999999999999999999999999999999999864

>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=99.76  E-value=3.2e-19  Score=130.91  Aligned_cols=58  Identities=29%  Similarity=0.331  Sum_probs=55.2

Q ss_pred             CCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           87 ERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        87 r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      .+|++||.+|+.+||+.|..++||+..+|.+||..+||+++||+|||||||+|+|+.+
T Consensus         5 ~~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~   62 (76)
T 2ecc_A            5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ   62 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHH
Confidence            4577899999999999999999999999999999999999999999999999999854

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

Probab=99.76  E-value=1.8e-19  Score=135.74  Aligned_cols=63  Identities=33%  Similarity=0.623  Sum_probs=55.3

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      .++.+|+|++||..|+.+||..|..++||+..+|.+||..|||++++|+|||||||+|+|+..
T Consensus        25 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   87 (88)
T 2r5y_A           25 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH   87 (88)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhhc
Confidence            345678899999999999999999999999999999999999999999999999999999853

>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=99.76  E-value=3.8e-19  Score=129.01  Aligned_cols=59  Identities=34%  Similarity=0.582  Sum_probs=55.9

Q ss_pred             CCCCCcCCHHHHHHHHHHhhh-cCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           86 QERKKRLTSDQLESLERSFQE-EIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        86 ~r~R~r~t~~Ql~~Le~~F~~-~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      .++|++||..|+.+||..|.. ++||+..++.+||.+|||+++||+|||||||+|+|+..
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~   61 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhc
Confidence            467899999999999999996 99999999999999999999999999999999999854

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

Probab=99.75  E-value=4.6e-19  Score=129.13  Aligned_cols=64  Identities=34%  Similarity=0.588  Sum_probs=59.5

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      ..+++++.|++|+..|+.+||..|..++||+..++.+||..|||++++|+|||||||+|+|++.
T Consensus         5 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   68 (75)
T 2m0c_A            5 NKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRE   68 (75)
T ss_dssp             CCSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHH
Confidence            3456678899999999999999999999999999999999999999999999999999999854

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

Probab=99.75  E-value=4.8e-19  Score=128.84  Aligned_cols=59  Identities=32%  Similarity=0.536  Sum_probs=56.0

Q ss_pred             CCCCCcCCHHHHHHHHHHhhh-cCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           86 QERKKRLTSDQLESLERSFQE-EIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        86 ~r~R~r~t~~Ql~~Le~~F~~-~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      +++|++||..|+.+||..|.. ++||+..++.+||.+|||+++||+|||||||+|+|+..
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~   62 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   62 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhc
Confidence            577999999999999999995 99999999999999999999999999999999999854

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

Probab=99.75  E-value=3.1e-19  Score=124.99  Aligned_cols=57  Identities=40%  Similarity=0.662  Sum_probs=50.7

Q ss_pred             CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      .|++||.+|+.+||..|..++||+..++.+||.+|||+++||++||||||+|+|+.+
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~   58 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE   58 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC---
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhc
Confidence            478999999999999999999999999999999999999999999999999999864

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

Probab=99.75  E-value=6.6e-19  Score=134.45  Aligned_cols=66  Identities=23%  Similarity=0.351  Sum_probs=60.9

Q ss_pred             CCCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhC---------------CCCcccccccccchhhhhHHH
Q 040769           80 SSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELG---------------LQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        80 ~~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~Lg---------------L~~~qVkvWFQNRRak~Kr~~  144 (257)
                      +...+.+|.|+.|+..|+.+||.+|+.++||+..+|.+||..||               |++.+|++||||||+|+|++.
T Consensus         2 ~~~~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~   81 (95)
T 2cuf_A            2 SSGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRA   81 (95)
T ss_dssp             CSSSCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHh
Confidence            34566778899999999999999999999999999999999999               999999999999999999865


Q ss_pred             H
Q 040769          145 L  145 (257)
Q Consensus       145 ~  145 (257)
                      .
T Consensus        82 ~   82 (95)
T 2cuf_A           82 N   82 (95)
T ss_dssp             H
T ss_pred             h
Confidence            3

>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=99.75  E-value=3.2e-19  Score=125.12  Aligned_cols=59  Identities=31%  Similarity=0.539  Sum_probs=48.6

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769           83 TSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK  141 (257)
Q Consensus        83 ~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K  141 (257)
                      .+.+++|++|+..|+.+||..|..++||+..++.+||..|||+++||++||||||+|+|
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            35667899999999999999999999999999999999999999999999999999986

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

Probab=99.75  E-value=3.3e-19  Score=136.61  Aligned_cols=63  Identities=32%  Similarity=0.537  Sum_probs=56.2

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHH
Q 040769           83 TSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL  145 (257)
Q Consensus        83 ~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~  145 (257)
                      +..+++|++||..|+.+||..|..++||+..+|.+||..|||+++||+|||||||+|+|+...
T Consensus        32 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   94 (97)
T 1b72_A           32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   94 (97)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhc
Confidence            456788999999999999999999999999999999999999999999999999999998764

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

Probab=99.75  E-value=4.5e-19  Score=126.79  Aligned_cols=60  Identities=33%  Similarity=0.511  Sum_probs=57.2

Q ss_pred             CCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHH
Q 040769           86 QERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL  145 (257)
Q Consensus        86 ~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~  145 (257)
                      +|+|++||..|+.+||..|..++||+..++.+||.+|||++++|++||||||+|+|+...
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~   61 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR   61 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCC
T ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhch
Confidence            678999999999999999999999999999999999999999999999999999998653

>1x2n_A Homeobox protein pknox1; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.75  E-value=8.8e-19  Score=127.31  Aligned_cols=64  Identities=20%  Similarity=0.269  Sum_probs=59.4

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQE---EIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~---~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      ...+.+++|++|+..|+.+||.+|..   ++||+..++.+||.++||+++||++||||||+|+|+..
T Consensus         3 ~~~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~   69 (73)
T 1x2n_A            3 SGSSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSG   69 (73)
T ss_dssp             CCSSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhccccc
Confidence            45567788999999999999999987   99999999999999999999999999999999999864

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

Probab=99.75  E-value=5.1e-19  Score=122.34  Aligned_cols=54  Identities=31%  Similarity=0.645  Sum_probs=51.0

Q ss_pred             CcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHH
Q 040769           90 KRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK  143 (257)
Q Consensus        90 ~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~  143 (257)
                      +.||..|+.+||..|..++||+..+|.+||..|||+++||+|||||||+|+||+
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

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

Probab=99.74  E-value=4.7e-19  Score=129.86  Aligned_cols=62  Identities=23%  Similarity=0.396  Sum_probs=57.6

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           83 TSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        83 ~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      ..+.+.|++||.+|+.+||..|..++||+..+|.+||.+|||+++||+|||||||+|+|+..
T Consensus         6 ~~~~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~   67 (76)
T 2dn0_A            6 SGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLK   67 (76)
T ss_dssp             SCCCCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCC
T ss_pred             CCCCCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhc
Confidence            34556799999999999999999999999999999999999999999999999999999854

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

Probab=99.74  E-value=5.5e-19  Score=135.19  Aligned_cols=65  Identities=31%  Similarity=0.502  Sum_probs=57.4

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769           82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE  146 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~  146 (257)
                      ....+|+|++||..|+.+||..|..++||+..+|.+||.+|||+++||+|||||||+|+|+.+.+
T Consensus        22 ~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~lk   86 (96)
T 3nar_A           22 KSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNLK   86 (96)
T ss_dssp             -----CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTCCH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhccc
Confidence            34456789999999999999999999999999999999999999999999999999999996644

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

Probab=99.74  E-value=1e-18  Score=127.21  Aligned_cols=61  Identities=21%  Similarity=0.343  Sum_probs=57.5

Q ss_pred             CCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           84 SSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        84 ~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      +.++.|++||.+|+.+||..|..++||+..++.+||.+|||+++||+|||||||+|+|+.+
T Consensus         5 ~~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   65 (74)
T 2ly9_A            5 DSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSK   65 (74)
T ss_dssp             CCCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTT
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhC
Confidence            3467799999999999999999999999999999999999999999999999999999854

>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=99.73  E-value=2e-18  Score=128.72  Aligned_cols=64  Identities=25%  Similarity=0.345  Sum_probs=58.5

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQE---EIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~---~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      ...+++++|++|+.+|+.+||.+|..   ++||+..+|.+||.++||+++||+|||||||+|+|+..
T Consensus         3 ~~~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~   69 (83)
T 2dmn_A            3 SGSSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDM   69 (83)
T ss_dssp             CCCCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHH
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHH
Confidence            44567788999999999999999987   69999999999999999999999999999999998743

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

Probab=99.72  E-value=1.2e-18  Score=123.32  Aligned_cols=58  Identities=24%  Similarity=0.444  Sum_probs=55.7

Q ss_pred             CCCCCCcCCHHHHHHHHHHh---hhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769           85 SQERKKRLTSDQLESLERSF---QEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS  142 (257)
Q Consensus        85 ~~r~R~r~t~~Ql~~Le~~F---~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr  142 (257)
                      .+++|++|+..|+.+||.+|   ..++||+..++.+||.+|||+++||++||||||+|+||
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            46789999999999999999   89999999999999999999999999999999999986

>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=99.72  E-value=1e-18  Score=126.95  Aligned_cols=61  Identities=23%  Similarity=0.443  Sum_probs=57.5

Q ss_pred             CCCCCcCCHHHHHHHHHHh---hhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769           86 QERKKRLTSDQLESLERSF---QEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE  146 (257)
Q Consensus        86 ~r~R~r~t~~Ql~~Le~~F---~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~  146 (257)
                      +|+|++|+..|+.+||.+|   ..++||+..++.+||..+||+++||++||||||+|+|+....
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            6789999999999999999   899999999999999999999999999999999999986543

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

Probab=99.72  E-value=1.3e-18  Score=131.48  Aligned_cols=56  Identities=27%  Similarity=0.400  Sum_probs=52.9

Q ss_pred             CCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           89 KKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        89 R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      .++||.+|+.+||+.|..++||+..+|.+||..|||+++||+|||||||+|||++.
T Consensus        15 ~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~   70 (89)
T 2ecb_A           15 FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE   70 (89)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCC
T ss_pred             hccCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHH
Confidence            34899999999999999999999999999999999999999999999999999743

>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=99.72  E-value=2.3e-18  Score=120.41  Aligned_cols=56  Identities=30%  Similarity=0.416  Sum_probs=53.7

Q ss_pred             CCCcCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHH
Q 040769           88 RKKRLTSDQLESLERSFQE---EIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK  143 (257)
Q Consensus        88 ~R~r~t~~Ql~~Le~~F~~---~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~  143 (257)
                      +|++|+.+|+.+||.+|..   ++||+..++.+||.++||+++||++||||||+|+|+.
T Consensus         1 rr~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A            1 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CCCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             CcCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            4789999999999999999   9999999999999999999999999999999999973

>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=99.71  E-value=2.4e-18  Score=129.04  Aligned_cols=61  Identities=23%  Similarity=0.443  Sum_probs=56.8

Q ss_pred             CCCCCcCCHHHHHHHHHHh---hhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769           86 QERKKRLTSDQLESLERSF---QEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE  146 (257)
Q Consensus        86 ~r~R~r~t~~Ql~~Le~~F---~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~  146 (257)
                      ||+|++|+..|+.+||.+|   ..++||+..+|.+||.+|||+++||++||||||+|+|+....
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~   65 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGK   65 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGG
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhcccc
Confidence            6789999999999999999   899999999999999999999999999999999999986533

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

Probab=99.71  E-value=1.1e-18  Score=126.94  Aligned_cols=59  Identities=24%  Similarity=0.362  Sum_probs=55.2

Q ss_pred             CCCCCCcCCHHHHHHHHHHh-hhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHH
Q 040769           85 SQERKKRLTSDQLESLERSF-QEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK  143 (257)
Q Consensus        85 ~~r~R~r~t~~Ql~~Le~~F-~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~  143 (257)
                      ..++|++++.+|+.+||+.| ..++||+..+|.+||.+|||+++||+|||||||+|+|+.
T Consensus         8 g~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~   67 (72)
T 2cqx_A            8 GIKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPS   67 (72)
T ss_dssp             CCCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCC
Confidence            34668889999999999999 999999999999999999999999999999999999974

>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=99.70  E-value=1.1e-17  Score=129.15  Aligned_cols=65  Identities=18%  Similarity=0.231  Sum_probs=59.8

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHh---------------------CCCCcccccccccchhhh
Q 040769           82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLAREL---------------------GLQPRQIAVWFQNRRARW  140 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~L---------------------gL~~~qVkvWFQNRRak~  140 (257)
                      ..++||.|+.|+..|+.+||+.|..++||+..+|++||.+|                     +|++.+|+|||||||+|+
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            45677889999999999999999999999999999999999                     799999999999999999


Q ss_pred             hHHHHH
Q 040769          141 KSKQLE  146 (257)
Q Consensus       141 Kr~~~~  146 (257)
                      |+++..
T Consensus        83 kr~~~~   88 (102)
T 2da6_A           83 AFRQKL   88 (102)
T ss_dssp             HHHHHH
T ss_pred             HHhhHh
Confidence            986543

>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=99.70  E-value=6.4e-18  Score=120.51  Aligned_cols=60  Identities=22%  Similarity=0.343  Sum_probs=55.8

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhh-cCCCCHHHHHHHHHHhCCCCcccccccccchhhh
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQE-EIKLDPDRKMKLARELGLQPRQIAVWFQNRRARW  140 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~-~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~  140 (257)
                      +...++|.||.|+.+|+.+|+..|+. +.||+.+.|..||.+|||++++|+|||||||--.
T Consensus         3 ~~~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~~   63 (71)
T 1wi3_A            3 SGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHV   63 (71)
T ss_dssp             CCCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceeee
Confidence            45567888999999999999999999 9999999999999999999999999999999644

>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=99.69  E-value=8.3e-18  Score=126.27  Aligned_cols=60  Identities=28%  Similarity=0.401  Sum_probs=56.3

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769           83 TSSQERKKRLTSDQLESLERSFQE---EIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS  142 (257)
Q Consensus        83 ~~~~r~R~r~t~~Ql~~Le~~F~~---~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr  142 (257)
                      ..++++|++|+.+|+.+||.+|..   ++||+..+|.+||.++||+++||++||||||+|+|.
T Consensus        25 ~~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k~   87 (87)
T 1mnm_C           25 STKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   87 (87)
T ss_dssp             ESSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccC
Confidence            456677899999999999999999   999999999999999999999999999999999983

>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=99.69  E-value=6.4e-18  Score=127.63  Aligned_cols=58  Identities=29%  Similarity=0.353  Sum_probs=53.6

Q ss_pred             CCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           87 ERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        87 r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      +++++||.+|+.+||..|..++||+..+|.+||.+|||++++|+|||||||+|+|++.
T Consensus        15 ~k~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~   72 (89)
T 2dmp_A           15 QKFKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSME   72 (89)
T ss_dssp             SCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSC
T ss_pred             cccccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHh
Confidence            3455699999999999999999999999999999999999999999999999998743

>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=99.69  E-value=8.1e-18  Score=125.37  Aligned_cols=59  Identities=29%  Similarity=0.370  Sum_probs=54.7

Q ss_pred             CCCCCcCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           86 QERKKRLTSDQLESLERSFQE---EIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        86 ~r~R~r~t~~Ql~~Le~~F~~---~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      +++|++|+..|+.+||.+|..   ++||+..++.+||..+||+++||++||||||+|+|+..
T Consensus         3 ~krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~   64 (83)
T 1le8_B            3 PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTIT   64 (83)
T ss_dssp             --CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHccccccc
Confidence            456778999999999999999   99999999999999999999999999999999999854

>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=99.69  E-value=5.8e-18  Score=138.93  Aligned_cols=62  Identities=32%  Similarity=0.537  Sum_probs=55.5

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHH
Q 040769           82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK  143 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~  143 (257)
                      ..+++|+|++||..|+.+||..|..++||+..+|.+||..|||+++||+|||||||+|+||+
T Consensus        84 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           84 NERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            44567789999999999999999999999999999999999999999999999999999985

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

Probab=99.68  E-value=1.3e-17  Score=137.43  Aligned_cols=62  Identities=24%  Similarity=0.475  Sum_probs=58.5

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS  142 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr  142 (257)
                      ...++||+|++|+..|+.+||..|..++||+..+|.+||.+|||+++||+|||||||+|+||
T Consensus        89 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           89 EPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             SCCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            34567788999999999999999999999999999999999999999999999999999996

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

Probab=99.68  E-value=1.4e-17  Score=118.55  Aligned_cols=53  Identities=26%  Similarity=0.391  Sum_probs=50.5

Q ss_pred             CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      -|.+|+.+||..|..++||+..+|.+||..|||+++||++||||||+|+|+-+
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            47899999999999999999999999999999999999999999999999744

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

Probab=99.68  E-value=1.4e-17  Score=118.38  Aligned_cols=54  Identities=17%  Similarity=0.228  Sum_probs=51.0

Q ss_pred             CCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769           89 KKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS  142 (257)
Q Consensus        89 R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr  142 (257)
                      +..++.+|+.+||+.|..++||+..+|.+||.+|||++++|+|||||||+|.++
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            455679999999999999999999999999999999999999999999999886

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

Probab=99.67  E-value=7.4e-18  Score=121.61  Aligned_cols=54  Identities=37%  Similarity=0.612  Sum_probs=51.9

Q ss_pred             cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           91 RLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        91 r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      .+|..|+.+||+.|..++||+..+|.+||.+|||+++||+|||||||+|+|+++
T Consensus        10 ~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~   63 (69)
T 2l9r_A           10 HMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ   63 (69)
T ss_dssp             CCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSS
T ss_pred             cCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhh
Confidence            479999999999999999999999999999999999999999999999999865

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

Probab=99.67  E-value=1.4e-17  Score=138.52  Aligned_cols=61  Identities=26%  Similarity=0.469  Sum_probs=54.7

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHH
Q 040769           83 TSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK  143 (257)
Q Consensus        83 ~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~  143 (257)
                      .++||+|++||..|+.+||..|..++||+..+|.+||.+|||+++||+|||||||+|+||+
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            4667889999999999999999999999999999999999999999999999999999984

>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=99.67  E-value=7.7e-18  Score=119.65  Aligned_cols=49  Identities=29%  Similarity=0.428  Sum_probs=46.4

Q ss_pred             HHHHHHHHHHh-hhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769           94 SDQLESLERSF-QEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS  142 (257)
Q Consensus        94 ~~Ql~~Le~~F-~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr  142 (257)
                      ..|+.+||+.| ..++||+..+|.+||.+|||+++||+|||||||+|+|+
T Consensus         9 ~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~   58 (64)
T 1x2m_A            9 AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   58 (64)
T ss_dssp             SCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             chHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCC
Confidence            45899999999 57999999999999999999999999999999999986

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

Probab=99.67  E-value=1.3e-17  Score=139.30  Aligned_cols=64  Identities=23%  Similarity=0.320  Sum_probs=52.3

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHH
Q 040769           82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL  145 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~  145 (257)
                      ..++||+|++|+..|+.+||..|..++||+..+|.+||..|||+++||+|||||||+|+||...
T Consensus        96 ~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~  159 (164)
T 2xsd_C           96 QGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTP  159 (164)
T ss_dssp             ----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC
T ss_pred             cccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhccC
Confidence            4566788999999999999999999999999999999999999999999999999999998653

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

Probab=99.66  E-value=1.5e-17  Score=128.14  Aligned_cols=65  Identities=15%  Similarity=0.304  Sum_probs=54.3

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHH------------------hC---CCCcccccccccchhhh
Q 040769           82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARE------------------LG---LQPRQIAVWFQNRRARW  140 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~------------------Lg---L~~~qVkvWFQNRRak~  140 (257)
                      ..+.+|.|+.|+..|+.+||..|..++||+..+|.+||..                  ||   |++.+|+|||||||+++
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            3456778999999999999999999999999999999999                  88   99999999999999999


Q ss_pred             hHHHHH
Q 040769          141 KSKQLE  146 (257)
Q Consensus       141 Kr~~~~  146 (257)
                      |+++..
T Consensus        86 k~k~~~   91 (99)
T 1lfb_A           86 AFRHKL   91 (99)
T ss_dssp             SCCC--
T ss_pred             HHhchh
Confidence            987643

>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=99.64  E-value=4.6e-17  Score=134.79  Aligned_cols=61  Identities=26%  Similarity=0.430  Sum_probs=57.6

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHH
Q 040769           83 TSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK  143 (257)
Q Consensus        83 ~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~  143 (257)
                      .+++|+|++|+..|+.+||..|..++||+..+|.+||.+|||+++||+|||||||+|+||.
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             cCCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            4677889999999999999999999999999999999999999999999999999999973

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

Probab=99.62  E-value=1.1e-16  Score=133.35  Aligned_cols=64  Identities=22%  Similarity=0.364  Sum_probs=54.9

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHH
Q 040769           82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL  145 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~  145 (257)
                      ..+.||+|++||..|+.+||..|..++||+..+|.+||.+|||+++||+|||||||+|+|+...
T Consensus        94 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~  157 (164)
T 2d5v_A           94 GNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWL  157 (164)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC--
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccCC
Confidence            4456788999999999999999999999999999999999999999999999999999998553

>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=99.60  E-value=1.8e-16  Score=113.50  Aligned_cols=59  Identities=19%  Similarity=0.225  Sum_probs=50.9

Q ss_pred             CcCCHHHHHHHHHHhh---hcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHHH
Q 040769           90 KRLTSDQLESLERSFQ---EEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELL  148 (257)
Q Consensus        90 ~r~t~~Ql~~Le~~F~---~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~  148 (257)
                      .+|+.+|+.+|+.+|.   .++||+..+|.+||.++||+++||++||||||+|+|+...++.
T Consensus         3 g~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~~   64 (67)
T 3k2a_A            3 GIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQS   64 (67)
T ss_dssp             ---CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC----
T ss_pred             CcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHHHHh
Confidence            3799999999999999   9999999999999999999999999999999999998766543

>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=99.46  E-value=6.6e-15  Score=126.03  Aligned_cols=61  Identities=13%  Similarity=0.265  Sum_probs=53.7

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhC---------------------CCCcccccccccchhhh
Q 040769           82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELG---------------------LQPRQIAVWFQNRRARW  140 (257)
Q Consensus        82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~Lg---------------------L~~~qVkvWFQNRRak~  140 (257)
                      ..+.||.|+.|+..|+.+||+.|..++||+..+|.+||..|+                     |++.+|++||||||+|+
T Consensus       112 ~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~~  191 (194)
T 1ic8_A          112 TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEE  191 (194)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHHC
T ss_pred             cccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhhh
Confidence            355678889999999999999999999999999999999999                     99999999999999998


Q ss_pred             hH
Q 040769          141 KS  142 (257)
Q Consensus       141 Kr  142 (257)
                      |.
T Consensus       192 k~  193 (194)
T 1ic8_A          192 AF  193 (194)
T ss_dssp             C-
T ss_pred             hc
Confidence            75

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

Probab=99.43  E-value=3.7e-14  Score=101.62  Aligned_cols=46  Identities=20%  Similarity=0.500  Sum_probs=44.2

Q ss_pred             HHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhh
Q 040769           94 SDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR  139 (257)
Q Consensus        94 ~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak  139 (257)
                      .+|+.+||.+|..|++|+.+++..||..+||+.++|+|||||||++
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

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

Probab=99.42  E-value=7.5e-14  Score=105.09  Aligned_cols=54  Identities=22%  Similarity=0.306  Sum_probs=50.9

Q ss_pred             cCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           91 RLTSDQLESLERSFQE---EIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        91 r~t~~Ql~~Le~~F~~---~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      .|+.+++.+|+.+|..   ++||+..+|.+||.++||+++||++||||||.|+|+..
T Consensus        11 ~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~   67 (89)
T 2lk2_A           11 MLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDM   67 (89)
T ss_dssp             CCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHH
Confidence            4899999999999987   99999999999999999999999999999999998754

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

Probab=99.35  E-value=2.7e-13  Score=117.64  Aligned_cols=61  Identities=13%  Similarity=0.275  Sum_probs=53.4

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhC---------------------CCCcccccccccchhh
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELG---------------------LQPRQIAVWFQNRRAR  139 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~Lg---------------------L~~~qVkvWFQNRRak  139 (257)
                      ..++.||.|+.|++.|+.+||+.|..++||+..+|++||..||                     |++.+|++||||||++
T Consensus       138 ~~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~~  217 (221)
T 2h8r_A          138 TNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKE  217 (221)
T ss_dssp             ----CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHTT
T ss_pred             ccCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhhh
Confidence            3455677788899999999999999999999999999999998                     8999999999999997


Q ss_pred             hh
Q 040769          140 WK  141 (257)
Q Consensus       140 ~K  141 (257)
                      ..
T Consensus       218 ~~  219 (221)
T 2h8r_A          218 EA  219 (221)
T ss_dssp             CC
T ss_pred             hh
Confidence            53

>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=99.31  E-value=2.3e-13  Score=125.98  Aligned_cols=56  Identities=29%  Similarity=0.531  Sum_probs=52.8

Q ss_pred             CCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769           86 QERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK  141 (257)
Q Consensus        86 ~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K  141 (257)
                      ++.|+.++..|+..||+.|+.++||+..+|.+||.+|||+++||+|||||||+|+|
T Consensus       366 ~~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          366 TAAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            34567799999999999999999999999999999999999999999999999986

>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=98.87  E-value=3e-10  Score=71.65  Aligned_cols=22  Identities=50%  Similarity=1.054  Sum_probs=19.1

Q ss_pred             cccccccccchhhhhHHHHHHH
Q 040769          127 RQIAVWFQNRRARWKSKQLELL  148 (257)
Q Consensus       127 ~qVkvWFQNRRak~Kr~~~~~~  148 (257)
                      +||+|||||||+|||+++.+..
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~~   22 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFNDA   22 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHHT
T ss_pred             CCceeccHHHHHHHHHHhHHHH
Confidence            6999999999999999876643

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

Probab=93.44  E-value=0.029  Score=39.78  Aligned_cols=39  Identities=23%  Similarity=0.451  Sum_probs=36.7

Q ss_pred             HHHHHHHhhhcCCCCHHHHHHHHHHhCCCCccccccccc
Q 040769           97 LESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQN  135 (257)
Q Consensus        97 l~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQN  135 (257)
                      .+.|+.+|...+.+.......|+.+..|+-.||+-||-.
T Consensus        18 ~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~   56 (70)
T 2ys9_A           18 IQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDS   56 (70)
T ss_dssp             CHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             chHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHh
Confidence            478999999999999999999999999999999999953

---

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	257
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	2e-17
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	4e-17
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	7e-17
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	1e-16
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	1e-16
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	2e-16
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	5e-16
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	4e-15
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	6e-15
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	1e-14
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	1e-14
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	2e-14
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	2e-14
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	2e-14
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	2e-14
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	3e-14
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	3e-14
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	4e-14
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	4e-14
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	6e-14
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	1e-13
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	1e-13
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	3e-13
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	4e-13
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	6e-13
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	9e-13
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	1e-12
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	4e-12
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	1e-11
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	3e-11
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	7e-11
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	6e-09

>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 = 72.2 bits (177), Expect = 2e-17
 Identities = 25/69 (36%), Positives = 36/69 (52%), Gaps = 2/69 (2%)

Query: 80  SSSTSSQERKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRR 137
           +   +   RKKR   T  Q   LE+ F   + L  DR+ ++AR L L  RQ+ +WFQNRR
Sbjct: 6   NWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRR 65

Query: 138 ARWKSKQLE 146
            + K    +
Sbjct: 66  MKMKKINKD 74

>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 = 71.0 bits (174), Expect = 4e-17
 Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 3/58 (5%)

Query: 88  RKKRLTSDQLESLERSFQEEIK---LDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142
           R  R T + +  LE  F + I+   LD      L +   L   QI  W  NRR + K+
Sbjct: 1   RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

>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 = 70.6 bits (173), Expect = 7e-17
 Identities = 22/51 (43%), Positives = 33/51 (64%)

Query: 91  RLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
           R ++DQ   LE+ F+ +  L P  + +LA+ L L  RQ+  WFQNRRA+W+
Sbjct: 6   RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 56

>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 = 70.2 bits (172), Expect = 1e-16
 Identities = 20/59 (33%), Positives = 36/59 (61%), Gaps = 2/59 (3%)

Query: 88  RKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144
           ++ R   T +Q+E+LE+ F+     D   + +LA ++ L   +I VWF NRRA+W+ ++
Sbjct: 2   QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREE 60

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.9 bits (171), Expect = 1e-16
 Identities = 22/56 (39%), Positives = 31/56 (55%), Gaps = 2/56 (3%)

Query: 88  RKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
           RKKR   +  QL  LER +     +  D++ K++    L  RQI +WFQNRR + K
Sbjct: 2   RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK 57

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 66

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 69.5 bits (170), Expect = 2e-16
 Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 2/62 (3%)

Query: 88  RKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL 145
            + R  L   QL +L   +    + D   K +L    GL PR I VWFQN+R + K + +
Sbjct: 4   TRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI 63

Query: 146 EL 147
            +
Sbjct: 64  MM 65

>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 = 68.3 bits (167), Expect = 5e-16
 Identities = 21/51 (41%), Positives = 29/51 (56%)

Query: 93  TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK 143
           T  Q   LE+ F     L   R++++A  L L  RQI +WFQNRR +WK +
Sbjct: 5   TRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 55

>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 = 66.2 bits (161), Expect = 4e-15
 Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 87  ERKKRLTSDQLESLERSFQEEIKL-DPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144
           E    +T DQ+E LE +F +  K  DP     +A E GL   Q   WF+ R A W+  +
Sbjct: 3   EGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 61

>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 = 66.2 bits (161), Expect = 6e-15
 Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 2/69 (2%)

Query: 80  SSSTSSQERKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRR 137
           S          R   T+ QL  LE+ F     L   R++++A  L L   Q+ +WFQNRR
Sbjct: 20  SEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRR 79

Query: 138 ARWKSKQLE 146
            + K ++ E
Sbjct: 80  MKQKKRERE 88

>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 = 64.6 bits (157), Expect = 1e-14
 Identities = 21/59 (35%), Positives = 35/59 (59%), Gaps = 2/59 (3%)

Query: 88  RKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144
           R++R   TS QL+ LE +FQ     D   + ++A    L   ++ VWF+NRRA+W+ ++
Sbjct: 2   RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 60

>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 = 64.2 bits (156), Expect = 1e-14
 Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 2/58 (3%)

Query: 89  KKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144
           K+R  ++    ++LER F E  K      M++A EL L+   + VWF NRR R K  +
Sbjct: 1   KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRVK 58

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 65

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 64.5 bits (157), Expect = 2e-14
 Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 2/59 (3%)

Query: 88  RKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144
           R+ R   ++ QL+ LER+F+     D   + +LA+   L   +I VWFQNRRAR + + 
Sbjct: 3   RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH 61

>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 = 64.2 bits (156), Expect = 2e-14
 Identities = 22/56 (39%), Positives = 33/56 (58%), Gaps = 2/56 (3%)

Query: 88  RKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
           RK R   T+ QL +LER F+++  L    + + +  L L   Q+ +WFQNRRA+ K
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 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 = 64.2 bits (156), Expect = 2e-14
 Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 88  RKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL 145
           RK+R   +  Q+  LER F+++  L    +  LA  + L P Q+ +WFQN R + K +  
Sbjct: 3   RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62

Query: 146 E 146
           +
Sbjct: 63  D 63

>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 = 63.6 bits (155), Expect = 2e-14
 Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 93  TSDQLESLERSFQEEIK-LDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
           T+     LE+ F    K  D  R   L+++L    R I  WF+ RR + K
Sbjct: 1   TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 50

>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 = 63.3 bits (154), Expect = 3e-14
 Identities = 23/53 (43%), Positives = 32/53 (60%), Gaps = 2/53 (3%)

Query: 89  KKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR 139
           + R   +S+QL  L+R F E   L   R+ +L+ ELGL   QI +WFQN RA+
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 67

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 63.8 bits (155), Expect = 3e-14
 Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 2/61 (3%)

Query: 88  RKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL 145
           R+ R   TS Q+  LE+ F +   L   R   L+ +L L   Q+ +WF+NRR R K +  
Sbjct: 2   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 61

Query: 146 E 146
           +
Sbjct: 62  Q 62

>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 = 63.4 bits (154), Expect = 4e-14
 Identities = 22/49 (44%), Positives = 29/49 (59%)

Query: 93  TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
           T DQL  LE+ F +E  +   R+ +LA +L L    I VWFQNRR + K
Sbjct: 7   TRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDK 55

>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 = 63.0 bits (153), Expect = 4e-14
 Identities = 17/53 (32%), Positives = 30/53 (56%)

Query: 89  KKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
           K  ++      LE+ F+ +  L+   K ++A++ G+ P Q+ VWF N+R R K
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 = 63.1 bits (153), Expect = 6e-14
 Identities = 25/75 (33%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 79  GSSSTSSQERKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNR 136
            S    +++RK+R   T  Q   LER F+++  L    +  LA  + L P Q+ +WFQN 
Sbjct: 1   ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNH 60

Query: 137 RARWKSKQLELLYDS 151
           R + K  Q E  Y+ 
Sbjct: 61  RYKTKRAQNEKGYEG 75

>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 = 62.1 bits (150), Expect = 1e-13
 Identities = 16/69 (23%), Positives = 31/69 (44%)

Query: 84  SSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK 143
            + ++ K  T++QL  L+ SF     L  +   +L  +  L  R+I  WF  ++     K
Sbjct: 3   FTPQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALK 62

Query: 144 QLELLYDSL 152
           + ++  D  
Sbjct: 63  EEKMEIDES 71

>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 = 61.7 bits (150), Expect = 1e-13
 Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 3/59 (5%)

Query: 84  SSQERKKRLTSDQLESLERSFQEEIK---LDPDRKMKLARELGLQPRQIAVWFQNRRAR 139
           S + ++  L       +     + I       D K ++A +  L   Q+  WF N R R
Sbjct: 1   SGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRR 59

>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 = 61.2 bits (148), Expect = 3e-13
 Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 8/72 (11%)

Query: 79  GSSSTSSQERKKR----LTSDQLESLERSFQEEI----KLDPDRKMKLARELGLQPRQIA 130
           GS+ +SS    KR     T++Q E +    +       K D     +   E G++ + + 
Sbjct: 7   GSNPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLK 66

Query: 131 VWFQNRRARWKS 142
           +W  N +    S
Sbjct: 67  IWMHNNKNSGPS 78

>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 = 60.8 bits (147), Expect = 4e-13
 Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 5/64 (7%)

Query: 88  RKKR--LTSDQLESLERSFQEEIK---LDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142
           R+KR        E L   F   +       + K +LA++ G+   Q++ WF N+R R+K 
Sbjct: 2   RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61

Query: 143 KQLE 146
              +
Sbjct: 62  NIGK 65

>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 = 60.2 bits (146), Expect = 6e-13
 Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 88  RKKRLTSDQLESLERSFQEEIK-LDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
                  +  ++LE+ F    K  D  R   L+++L    R+I  WF++RR + K
Sbjct: 4   DSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

>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 = 59.7 bits (144), Expect = 9e-13
 Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 1/64 (1%)

Query: 79  GSSSTSSQERKKRLTSDQLESLERSFQEE-IKLDPDRKMKLARELGLQPRQIAVWFQNRR 137
           GSS +S    + +++ + L  L+    +  +  D +    L+ +L L    I  +FQN+R
Sbjct: 1   GSSGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQR 60

Query: 138 ARWK 141
              K
Sbjct: 61  YHVK 64

>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 = 59.1 bits (143), Expect = 1e-12
 Identities = 11/47 (23%), Positives = 25/47 (53%)

Query: 91  RLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRR 137
             T  Q  +L   F+E  +   + ++ ++++LGL+   ++ +F N R
Sbjct: 4   VFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-leucine zipper protein Homez
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.2 bits (140), Expect = 4e-12
 Identities = 21/68 (30%), Positives = 30/68 (44%)

Query: 84  SSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK 143
           SS    KR T +QL  L+  F +      +   KL +  GL   +I  WF + R   K  
Sbjct: 2   SSGSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG 61

Query: 144 QLELLYDS 151
           QL+   D+
Sbjct: 62  QLKWFRDN 69

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 67

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-3 POU Homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 56.9 bits (137), Expect = 1e-11
 Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 2/62 (3%)

Query: 82  STSSQERKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR 139
           +     ++KR  + +    SLE  F +  K    +   +A +LGL+   + VWF NRR +
Sbjct: 3   TLVQARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQK 62

Query: 140 WK 141
            K
Sbjct: 63  GK 64

>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 = 56.2 bits (135), Expect = 3e-11
 Identities = 14/74 (18%), Positives = 24/74 (32%), Gaps = 17/74 (22%)

Query: 88  RKKR--LTSDQLESLERSFQEEIKLDPDRKMKLAREL---------------GLQPRQIA 130
           R  R     + L  +E  F E    D  ++ ++A                   +   ++ 
Sbjct: 1   RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVY 60

Query: 131 VWFQNRRARWKSKQ 144
            WF NRR   K + 
Sbjct: 61  NWFANRRKEIKRRA 74

>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 = 54.2 bits (130), Expect = 7e-11
 Identities = 16/54 (29%), Positives = 29/54 (53%)

Query: 88  RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
           ++  + ++   +LE+SF E  K   +    +A +L ++   I VWF NRR + K
Sbjct: 1   KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEK 54

>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 = 49.8 bits (118), Expect = 6e-09
 Identities = 8/77 (10%), Positives = 22/77 (28%), Gaps = 21/77 (27%)

Query: 89  KKRLTSDQLESLERSFQEEIKLDPDRKMKLAREL---------------------GLQPR 127
           + +      + L ++++ +     + +  L  E                       +   
Sbjct: 1   RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 128 QIAVWFQNRRARWKSKQ 144
           ++  WF NRR     + 
Sbjct: 61  RVYNWFANRRKEEAFRH 77

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	257
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.84
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.83
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.83
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.82
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.82
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.82
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.82
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.81
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.81
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.81
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.8
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.8
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.79
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.79
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.79
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.77
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.77
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.76
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.76
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.76
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.75
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.74
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.7
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.69
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.69
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.68
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.67
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.65
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.63
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.62
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.61
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.57
d1hlva1	66	DNA-binding domain of centromere binding protein B	89.47
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	83.86

>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=99.84  E-value=2.8e-22  Score=138.45  Aligned_cols=57  Identities=32%  Similarity=0.591  Sum_probs=55.2

Q ss_pred             CCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769           86 QERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS  142 (257)
Q Consensus        86 ~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr  142 (257)
                      ||+|++||.+|+.+||..|..++||+..+|.+||..|||+++||+|||||||+|+||
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            577999999999999999999999999999999999999999999999999999985

>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=99.83  E-value=1.7e-21  Score=141.84  Aligned_cols=66  Identities=33%  Similarity=0.546  Sum_probs=60.7

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE  146 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~  146 (257)
                      .....+|+|++||.+|+.+||.+|..++||+..+|.+||..|||+++||+|||||||+|+|+...+
T Consensus         9 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~   74 (77)
T d1pufa_           9 HARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             CCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHH
Confidence            344567789999999999999999999999999999999999999999999999999999986654

>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=99.83  E-value=1e-21  Score=135.15  Aligned_cols=57  Identities=39%  Similarity=0.744  Sum_probs=55.1

Q ss_pred             CCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769           86 QERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS  142 (257)
Q Consensus        86 ~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr  142 (257)
                      |+.|++||+.|+.+||..|..++||+..++.+||..|||+++||+|||||||+|+||
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            467999999999999999999999999999999999999999999999999999986

>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=99.82  E-value=9.7e-22  Score=134.66  Aligned_cols=55  Identities=38%  Similarity=0.685  Sum_probs=53.6

Q ss_pred             CCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHH
Q 040769           89 KKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK  143 (257)
Q Consensus        89 R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~  143 (257)
                      |++||.+|+.+||..|..++||+..+|.+||..|||++++|+|||||||+|+||+
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

>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=99.82  E-value=1.6e-21  Score=138.45  Aligned_cols=61  Identities=31%  Similarity=0.513  Sum_probs=57.6

Q ss_pred             CCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHH
Q 040769           85 SQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL  145 (257)
Q Consensus        85 ~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~  145 (257)
                      +||+|++||.+|+.+||..|..++||+..+|.+||..|||++++|+|||||||+|+|+...
T Consensus         1 Prr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~   61 (67)
T d1zq3p1           1 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD   61 (67)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhh
Confidence            3678999999999999999999999999999999999999999999999999999998553

>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=99.82  E-value=1.7e-21  Score=134.51  Aligned_cols=57  Identities=33%  Similarity=0.587  Sum_probs=55.3

Q ss_pred             CCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769           86 QERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS  142 (257)
Q Consensus        86 ~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr  142 (257)
                      ||+|++||.+|+.+||..|..++||+..++.+||..|||++++|+|||||||+|+||
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

>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=99.82  E-value=1.8e-21  Score=133.97  Aligned_cols=56  Identities=39%  Similarity=0.587  Sum_probs=54.6

Q ss_pred             CCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769           87 ERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS  142 (257)
Q Consensus        87 r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr  142 (257)
                      |+|+.||.+|+.+||..|..++||+..++.+||.+|||++++|+|||||||+|+||
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            57999999999999999999999999999999999999999999999999999997

>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=99.81  E-value=5.7e-21  Score=134.74  Aligned_cols=62  Identities=32%  Similarity=0.555  Sum_probs=58.4

Q ss_pred             CCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHH
Q 040769           84 SSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL  145 (257)
Q Consensus        84 ~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~  145 (257)
                      ++||.|++||.+|+.+||..|..++||+..++.+||..|||+++||+|||||||+|+|+++.
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~   62 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   62 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhccc
Confidence            35678999999999999999999999999999999999999999999999999999998654

>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=99.81  E-value=3.6e-21  Score=140.14  Aligned_cols=64  Identities=31%  Similarity=0.491  Sum_probs=59.0

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      ...+++|.|++||.+|+.+||.+|..++||+..++.+||..|||+++||+|||||||+|+|+.+
T Consensus         5 ~p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   68 (77)
T d1vnda_           5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ   68 (77)
T ss_dssp             CSSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHh
Confidence            3455677889999999999999999999999999999999999999999999999999999754

>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=99.81  E-value=4.8e-21  Score=129.86  Aligned_cols=53  Identities=42%  Similarity=0.720  Sum_probs=51.5

Q ss_pred             CCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhh
Q 040769           87 ERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR  139 (257)
Q Consensus        87 r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak  139 (257)
                      |.|+.||.+|+.+||..|..++||+..+|.+||..|||+++||+|||||||+|
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            56899999999999999999999999999999999999999999999999987

>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=99.80  E-value=4e-21  Score=143.22  Aligned_cols=62  Identities=32%  Similarity=0.558  Sum_probs=55.6

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           83 TSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        83 ~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      +.++|+|++||.+|+.+||..|..++||+..+|.+||.+|||++++|+|||||||+|+||++
T Consensus        25 ~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~   86 (88)
T d1b72a_          25 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRE   86 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhc
Confidence            45578899999999999999999999999999999999999999999999999999999865

>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=99.80  E-value=1.3e-20  Score=135.42  Aligned_cols=59  Identities=34%  Similarity=0.582  Sum_probs=55.4

Q ss_pred             CCCCCcCCHHHHHHHHHHhhh-cCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           86 QERKKRLTSDQLESLERSFQE-EIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        86 ~r~R~r~t~~Ql~~Le~~F~~-~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      +++|++||.+|+.+||..|.. ++||+...|.+||.+|||++++|+|||||||+|+|+.+
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~   61 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhcc
Confidence            578999999999999999986 78999999999999999999999999999999999743

>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=99.79  E-value=2.3e-20  Score=132.75  Aligned_cols=61  Identities=33%  Similarity=0.620  Sum_probs=57.4

Q ss_pred             CCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769           86 QERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE  146 (257)
Q Consensus        86 ~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~  146 (257)
                      +|+|++||.+|+.+||..|..++||+...|.+||..|||++++|+|||||||+|+|+....
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~   62 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL   62 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhhh
Confidence            5789999999999999999999999999999999999999999999999999999985433

>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=99.79  E-value=6.1e-21  Score=132.53  Aligned_cols=59  Identities=32%  Similarity=0.619  Sum_probs=56.7

Q ss_pred             CCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHH
Q 040769           85 SQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK  143 (257)
Q Consensus        85 ~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~  143 (257)
                      +||+|++||.+|+.+||..|..++||+..++.+||.+|||++++|++||||||+|+|+.
T Consensus         1 Qrr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1           1 QRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             SSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            36789999999999999999999999999999999999999999999999999999985

>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=99.79  E-value=2.2e-20  Score=132.83  Aligned_cols=60  Identities=30%  Similarity=0.552  Sum_probs=57.0

Q ss_pred             CCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           85 SQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        85 ~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      +||.|++||..|+.+||..|..++||+..+|.+||..|||++++|+|||||||+|+|+..
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~   61 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA   61 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhcc
Confidence            467899999999999999999999999999999999999999999999999999999853

>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=99.77  E-value=3.9e-20  Score=132.55  Aligned_cols=62  Identities=23%  Similarity=0.323  Sum_probs=57.1

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhh-hcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQ-EEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS  142 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~-~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr  142 (257)
                      .....+|+|++||.+|+.+||++|. .++||+..++++||.+|||+++||++||||||+|+|+
T Consensus         3 s~~~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk   65 (71)
T d1wi3a_           3 SGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             CCCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhcc
Confidence            3455678899999999999999997 5899999999999999999999999999999999986

>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=99.77  E-value=4.3e-20  Score=130.92  Aligned_cols=61  Identities=26%  Similarity=0.398  Sum_probs=57.5

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHH
Q 040769           83 TSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK  143 (257)
Q Consensus        83 ~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~  143 (257)
                      ..++|+|++|+.+|+.+||.+|..++||+..++.+||.+|||++++|+|||||||+|+||.
T Consensus         6 ~~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_           6 QARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             CCSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             hccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            3457889999999999999999999999999999999999999999999999999999873

>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=99.76  E-value=7.4e-20  Score=129.32  Aligned_cols=61  Identities=31%  Similarity=0.511  Sum_probs=57.7

Q ss_pred             CCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           84 SSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        84 ~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      +.+|.|++||.+|+.+||..|..|+||+..++.+||.+|||++++|++||||||+|.|+..
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~~   62 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHHH
Confidence            4578899999999999999999999999999999999999999999999999999998753

>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=99.76  E-value=9.1e-20  Score=125.69  Aligned_cols=57  Identities=35%  Similarity=0.571  Sum_probs=55.0

Q ss_pred             CCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHH
Q 040769           87 ERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK  143 (257)
Q Consensus        87 r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~  143 (257)
                      |+|+.|+.+|+.+||..|..++||+..++.+||.+|||++++|+|||||||+|+|+.
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            579999999999999999999999999999999999999999999999999999974

>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=99.76  E-value=9.1e-20  Score=123.47  Aligned_cols=53  Identities=32%  Similarity=0.593  Sum_probs=51.7

Q ss_pred             CCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769           89 KKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK  141 (257)
Q Consensus        89 R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K  141 (257)
                      |++||++|+.+||..|..++||+..++.+||.+|||+++||++||||||+|.|
T Consensus         1 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~K   53 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   53 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTTC
T ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhccC
Confidence            78999999999999999999999999999999999999999999999999976

>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=99.75  E-value=2.5e-19  Score=131.79  Aligned_cols=59  Identities=20%  Similarity=0.360  Sum_probs=55.8

Q ss_pred             CCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhC---------------CCCcccccccccchhhhhHHH
Q 040769           86 QERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELG---------------LQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        86 ~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~Lg---------------L~~~qVkvWFQNRRak~Kr~~  144 (257)
                      ||+|++||++|+.+||.+|..++||+..+|.+||..+|               |++.+|+|||||||+|+|++.
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~   74 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRA   74 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhh
Confidence            57899999999999999999999999999999999886               999999999999999999854

>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=99.74  E-value=3e-19  Score=122.63  Aligned_cols=56  Identities=29%  Similarity=0.488  Sum_probs=54.2

Q ss_pred             CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHH
Q 040769           88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK  143 (257)
Q Consensus        88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~  143 (257)
                      +||+|+.+|+.+||..|..++||+..++.+||.+|||+++||++||||||+|+|+.
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            58999999999999999999999999999999999999999999999999999973

>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=99.70  E-value=2.1e-18  Score=126.20  Aligned_cols=62  Identities=18%  Similarity=0.283  Sum_probs=56.1

Q ss_pred             CCCCCCCCCCcCCHHHHHHHHHHhhh----cCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769           81 SSTSSQERKKRLTSDQLESLERSFQE----EIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS  142 (257)
Q Consensus        81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~----~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr  142 (257)
                      ...++||.|++||.+|+++|+.+|+.    ++||+..++.+||.+|||++++|+|||||+|++.|+
T Consensus        13 ~~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          13 SGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            34456678999999999999999886    789999999999999999999999999999998875

>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=99.69  E-value=5e-18  Score=122.95  Aligned_cols=58  Identities=29%  Similarity=0.331  Sum_probs=54.2

Q ss_pred             CCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           87 ERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        87 r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      ..++++|.+|+.+||.+|..++||+..++.+||..|||+++||++||||||+|+|+.+
T Consensus         5 s~~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~~   62 (76)
T d2ecca1           5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ   62 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhch
Confidence            4466789999999999999999999999999999999999999999999999999743

>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=99.69  E-value=4.6e-18  Score=123.19  Aligned_cols=57  Identities=26%  Similarity=0.408  Sum_probs=52.3

Q ss_pred             CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      +|+++|.+|+.+||.+|..++||+..++.+||..|||++++|++||||||+|.|+.+
T Consensus         7 k~k~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~   63 (76)
T d2ecba1           7 KFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE   63 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHh
Confidence            344569999999999999999999999999999999999999999999999887643

>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=99.68  E-value=3.7e-18  Score=114.05  Aligned_cols=50  Identities=22%  Similarity=0.404  Sum_probs=48.7

Q ss_pred             CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccch
Q 040769           88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRR  137 (257)
Q Consensus        88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRR  137 (257)
                      .|++||.+|+.+||..|..++||+..++.+||.+|||++++|++||||||
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            38999999999999999999999999999999999999999999999998

>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=99.67  E-value=1.1e-17  Score=120.13  Aligned_cols=59  Identities=24%  Similarity=0.475  Sum_probs=55.0

Q ss_pred             CCCCCcCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769           86 QERKKRLTSDQLESLERSFQE---EIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        86 ~r~R~r~t~~Ql~~Le~~F~~---~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~  144 (257)
                      ||+|++|+.+|+.+||.+|..   ++||+..++.+||.++||+++||++||||+|+|+|+..
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~   63 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccc
Confidence            578999999999999999974   88999999999999999999999999999999998743

>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=99.65  E-value=8.2e-18  Score=113.25  Aligned_cols=50  Identities=30%  Similarity=0.455  Sum_probs=47.1

Q ss_pred             CHHHHHHHHHHhhh-cCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769           93 TSDQLESLERSFQE-EIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS  142 (257)
Q Consensus        93 t~~Ql~~Le~~F~~-~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr  142 (257)
                      |.+|+.+||.+|.. ++||+..++.+||.+|||++++|+|||||||+|+|+
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            56899999999987 689999999999999999999999999999999985

>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=99.63  E-value=5.8e-17  Score=112.15  Aligned_cols=54  Identities=30%  Similarity=0.415  Sum_probs=50.1

Q ss_pred             CCcCCHHHHHHHHHHhhhc---CCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769           89 KKRLTSDQLESLERSFQEE---IKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS  142 (257)
Q Consensus        89 R~r~t~~Ql~~Le~~F~~~---~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr  142 (257)
                      +.||+.+|+.+||.+|..+   +||+..++.+||.++||+++||++||||+|+|.|+
T Consensus         2 ~~Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           2 GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            4569999999999999764   69999999999999999999999999999999875

>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=99.62  E-value=2.6e-17  Score=119.59  Aligned_cols=56  Identities=14%  Similarity=0.286  Sum_probs=52.7

Q ss_pred             CCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhC---------------------CCCcccccccccchhhhhHHH
Q 040769           89 KKRLTSDQLESLERSFQEEIKLDPDRKMKLARELG---------------------LQPRQIAVWFQNRRARWKSKQ  144 (257)
Q Consensus        89 R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~Lg---------------------L~~~qVkvWFQNRRak~Kr~~  144 (257)
                      |++||+.|+.+||.+|+.++||+..+|..||.+|+                     |++.+|++||||||+|+|++.
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            67899999999999999999999999999999995                     889999999999999999753

>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=99.61  E-value=4.1e-17  Score=112.54  Aligned_cols=55  Identities=25%  Similarity=0.396  Sum_probs=51.6

Q ss_pred             CCCCcCCHHHHHHHHHHhhh-cCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769           87 ERKKRLTSDQLESLERSFQE-EIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK  141 (257)
Q Consensus        87 r~R~r~t~~Ql~~Le~~F~~-~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K  141 (257)
                      |.+++++.++..+||++|.. ++||+..++.+||.+|||+++||++||||||+++|
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            56788999999999999986 68999999999999999999999999999999987

>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=99.57  E-value=7.3e-16  Score=107.20  Aligned_cols=57  Identities=19%  Similarity=0.269  Sum_probs=52.3

Q ss_pred             CCCCCCcCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769           85 SQERKKRLTSDQLESLERSFQE---EIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK  141 (257)
Q Consensus        85 ~~r~R~r~t~~Ql~~Le~~F~~---~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K  141 (257)
                      .+++|++|+.+++.+|+.+|..   ++||+..++.+||.++||+.+||++||+|+|+|..
T Consensus         2 ~krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R~l   61 (62)
T d1x2na1           2 GKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRIL   61 (62)
T ss_dssp             SCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhc
Confidence            3567889999999999999985   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=89.47  E-value=0.14  Score=34.15  Aligned_cols=46  Identities=20%  Similarity=0.421  Sum_probs=38.4

Q ss_pred             CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccc
Q 040769           88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNR  136 (257)
Q Consensus        88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNR  136 (257)
                      +|+.+|-.+...+-..|+.++...   +.+||+.+|+...+|..|..||
T Consensus         4 kRk~LT~~eK~~ii~~~e~g~k~s---q~eIA~~fGv~~STvs~IlKnK   49 (66)
T d1hlva1           4 KRRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNK   49 (66)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTH
T ss_pred             ccccCCHHHHHHHHHHHHcCCcch---HHHHHHHhCCChhHHHHHHHHH
Confidence            466799998888888888886554   6689999999999999999884

>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=83.86  E-value=0.37  Score=29.75  Aligned_cols=42  Identities=17%  Similarity=0.342  Sum_probs=35.2

Q ss_pred             CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccc
Q 040769           88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQ  134 (257)
Q Consensus        88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQ  134 (257)
                      ++..+|++|++.+...+....     -+.+||+.+|++...|--||-
T Consensus         2 R~~~lt~~q~~~a~~l~~~G~-----s~~~iA~~~gVSr~TiYry~p   43 (47)
T d1ijwc_           2 RPRAINKHEQEQISRLLEKGH-----PRQQLAIIFGIGVSTLYRYFP   43 (47)
T ss_dssp             CCCSSCHHHHHHHHHHHHTTC-----CHHHHHHHHTCCHHHHHHHSC
T ss_pred             CCCcCCHHHHHHHHHHHHCCC-----CHHHHHHHHCcCHHHHHhhCC
Confidence            355799999999999997653     378899999999998888874