Psyllid ID: psy5541

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-
Protein Sequence
MESVTSLIYFFTLRILLHAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMGASTPMMSPAPDSVGYSKEANLYAAKKAAGASPYSMGASTPMMSPAPDSVGYSSMEDRMHNTNMLPNYIEGANDINTDPQGPRKQDISDILQQILNITDQSLDEAQAR
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHcccccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHcHHcHHHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccHHHHHHc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHccccccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHcccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHccHHHHHHHHHHHHHccHHHHHcc
Coil and Loop (DISEMBL)
MESVTSLIYFFTLRILLHAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREqsrtrpitpkEIERMVQIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYshlsnpypseeaKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKkaagaspysmgastpmmspapdsvgyskEANLYAAKkaagaspysmgastpmmspapdsvgyssmedrmhntnmlpnyiegandintdpqgprkqDISDILQQILNITDQSLDEAQAR
Flexible Loop (DISEMBL)
MESVTSLIYFFTLRILLHAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLreqsrtrpitpkeIERMVQIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITlsqvsnwfgnkRIRYKKNIGKAQEEANLYAAKKAAGASPYSMGASTPMMSPAPDSVGYSKEANLYAAKKAAGASPYSMGASTPMMSPAPDSVGYSSMEDRMHNTNMLPNYIEGANDINTDPQGPRKQDISDILQQILNITDQSLDEAQAR
Low Complexity Region (SEG)
MESVTSLIYFFTLRILLHAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYaakkaagaSPYSMGASTPMMSPAPDSVGYSkeanlyaakkaagaSPYSMGASTPMMSPAPDSVGYSSMEDRMHNTNMLPNYIEGANDINTDPQGPRKQDISDILQQILNITDQSLDEAQAR
Disordered region (IsUnstruct)
****TSLIYFFTLRILLHAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLRE******ITPKEIERMVQIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARR********ASEILNEYFYSHL************LARKCNITLSQVSNWFGNKRIRYKKNIG*******************************************************************************************************************I**************
Disordered Region (DISOPRED)
******LIYFFTLRILLH*****DYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLR*************************************************************EILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRY***************************************************************************************************************************************
Disordered Region (DISEMBL)
MESVTSLIYFFTLRILLHAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPY*********ARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMGASTPMMSPAPDSVGYSKEANLYAAKKAAGASPYSMGASTPMMSPAPDSVGYSSMEDRMHNTNMLPNYIEGANDINTDPQGPRKQDISDILQQILNITDQSLDEAQAR
Disordered Region (DISPRO)
***VTSLIYFFTLRILLHAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKK*****************************NLYAAKKAAGASPYSMGASTPMMSPAPDSVGYSSMEDRMHNTNMLPNYIEGANDINTDPQGPRKQDISDILQQILNITDQSLD*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MESVTSLIYFFTLRILLHAIEHSDYxxxxxxxxxxxxxxxxxxxxxCSEFTTHVMNLLREQSRTRPITPKEIERMVQIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMGASTPMMSPAPDSVGYSKEANLYAAKKAAGASPYSMGASTPMMSPAPDSVGYSSMEDRMHNTNMLPNYIEGANDINTDPQGPRKQDISDILQQILNITDQSLDEAQAR
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	301	2.2.26 [Sep-21-2011]
Q7PMT1	362	Homeobox protein extraden	yes	N/A	0.661	0.549	0.907	1e-104
Q29CT2	376	Homeobox protein extraden	yes	N/A	0.704	0.563	0.836	1e-104
P40427	376	Homeobox protein extraden	yes	N/A	0.704	0.563	0.836	1e-103
P41778	430	Pre-B-cell leukemia trans	yes	N/A	0.631	0.441	0.821	1e-89
P40424	430	Pre-B-cell leukemia trans	yes	N/A	0.631	0.441	0.821	1e-89
Q8QGC4	347	Pre-B-cell leukemia trans	N/A	N/A	0.594	0.515	0.821	2e-88
B4F6V6	347	Pre-B-cell leukemia trans	no	N/A	0.588	0.510	0.829	3e-88
O35317	434	Pre-B-cell leukemia trans	no	N/A	0.528	0.366	0.915	4e-88
P40426	434	Pre-B-cell leukemia trans	no	N/A	0.528	0.366	0.915	4e-88
B3DM47	422	Pre-B-cell leukemia trans	no	N/A	0.657	0.469	0.782	1e-87

>sp|Q7PMT1|EXD_ANOGA Homeobox protein extradenticle OS=Anopheles gambiae GN=exd PE=3 SV=2

 Score =  379 bits (974), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 187/206 (90%), Positives = 192/206 (93%), Gaps = 7/206 (3%)

Query: 18  HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
           +AIEHSDYRAKLAQIR IY QELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ
Sbjct: 136 NAIEHSDYRAKLAQIRQIYHQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 195

Query: 78  IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
           IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS
Sbjct: 196 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 255

Query: 138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM---- 193
           EEAKEELARKC IT+SQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM    
Sbjct: 256 EEAKEELARKCGITVSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMGGPP 315

Query: 194 -GASTPMMSPAP--DSVGYSKEANLY 216
            GA+TPMMSPAP  DS+GYS  +  Y
Sbjct: 316 SGAATPMMSPAPAQDSMGYSLGSGGY 341

Transcription factor which acts with the selector homeodomain proteins altering the regulation of downstream target genes such as wingless (wg), teashirt (tsh) and decapentaplegic (dpp), thus affecting segmental identity.
Anopheles gambiae (taxid: 7165)

>sp|Q29CT2|EXD_DROPS Homeobox protein extradenticle OS=Drosophila pseudoobscura pseudoobscura GN=exd PE=3 SV=1

 Score =  376 bits (966), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 189/226 (83%), Positives = 199/226 (88%), Gaps = 14/226 (6%)

Query: 18  HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
           +AIEHSDYRAKLAQIR IY QELEKYEQAC+EFTTHVMNLLREQSRTRPITPKEIERMVQ
Sbjct: 148 NAIEHSDYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIERMVQ 207

Query: 78  IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
           IIH+KFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS
Sbjct: 208 IIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 267

Query: 138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM---- 193
           EEAKEELARKC IT+SQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM    
Sbjct: 268 EEAKEELARKCGITVSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMAGPP 327

Query: 194 -GASTPMMSPAP--DSVGYSKEANLYAAKKAAGASPY--SMGASTP 234
            G +TPMMSPAP  DS+GY+  +  Y  ++     PY  SMG   P
Sbjct: 328 SGTTTPMMSPAPPQDSMGYTMGSGGYDQQQ-----PYDNSMGGYDP 368

Transcription factor which acts with the selector homeodomain proteins altering the regulation of downstream target genes such as wingless (wg), teashirt (tsh) and decapentaplegic (dpp), thus affecting segmental identity. Delimits the eye field and prevent inappropriate eye development. Required for proper localization of chordotonal organs within the peripheral nervous system.

Drosophila pseudoobscura pseudoobscura (taxid: 46245)

>sp|P40427|EXD_DROME Homeobox protein extradenticle OS=Drosophila melanogaster GN=exd PE=1 SV=1

 Score =  375 bits (964), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 189/226 (83%), Positives = 198/226 (87%), Gaps = 14/226 (6%)

Query: 18  HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
           +AIEHSDYRAKLAQIR IY QELEKYEQAC+EFTTHVMNLLREQSRTRPITPKEIERMVQ
Sbjct: 148 NAIEHSDYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIERMVQ 207

Query: 78  IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
           IIH+KFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS
Sbjct: 208 IIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 267

Query: 138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM---- 193
           EEAKEELARKC IT+SQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM    
Sbjct: 268 EEAKEELARKCGITVSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMAGPP 327

Query: 194 -GASTPMMSPAP--DSVGYSKEANLYAAKKAAGASPY--SMGASTP 234
            G +TPMMSPAP  DS+GY   +  Y  ++     PY  SMG   P
Sbjct: 328 SGTTTPMMSPAPPQDSMGYPMGSGGYDQQQ-----PYDNSMGGYDP 368

Transcription factor which acts with the selector homeodomain proteins altering the regulation of downstream target genes such as wingless (wg), teashirt (tsh) and decapentaplegic (dpp), thus affecting segmental identity. Delimits the eye field and prevent inappropriate eye development. Required for proper localization of chordotonal organs within the peripheral nervous system.

Drosophila melanogaster (taxid: 7227)

>sp|P41778|PBX1_MOUSE Pre-B-cell leukemia transcription factor 1 OS=Mus musculus GN=Pbx1 PE=1 SV=2

 Score =  329 bits (844), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 156/190 (82%), Positives = 168/190 (88%)

Query: 19  AIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQI 78
           ++EHSDYRAKL+QIR IY  ELEKYEQAC+EFTTHVMNLLREQSRTRPI+PKEIERMV I
Sbjct: 144 SVEHSDYRAKLSQIRQIYHTELEKYEQACNEFTTHVMNLLREQSRTRPISPKEIERMVSI 203

Query: 79  IHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSE 138
           IHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNF+KQA+EILNEYFYSHLSNPYPSE
Sbjct: 204 IHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFNKQATEILNEYFYSHLSNPYPSE 263

Query: 139 EAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMGASTP 198
           EAKEELA+KC IT+SQVSNWFGNKRIRYKKNIGK QEEAN+YAAK A  A+  S   S  
Sbjct: 264 EAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAAKTAVTATNVSAHGSQA 323

Query: 199 MMSPAPDSVG 208
                P+S G
Sbjct: 324 NSPSTPNSAG 333

Plays a role in the cAMP-dependent regulation of CYP17 gene expression via its cAMP-regulatory sequence (CRS1) 5'-ATCAATCAA-3'. Acts as a transcriptional activator of PF4 in complex with MEIS1. May have a role in steroidogenesis and, subsequently, sexual development and differentiation.

Mus musculus (taxid: 10090)

>sp|P40424|PBX1_HUMAN Pre-B-cell leukemia transcription factor 1 OS=Homo sapiens GN=PBX1 PE=1 SV=1

 Score =  329 bits (844), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 156/190 (82%), Positives = 168/190 (88%)

Query: 19  AIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQI 78
           ++EHSDYRAKL+QIR IY  ELEKYEQAC+EFTTHVMNLLREQSRTRPI+PKEIERMV I
Sbjct: 144 SVEHSDYRAKLSQIRQIYHTELEKYEQACNEFTTHVMNLLREQSRTRPISPKEIERMVSI 203

Query: 79  IHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSE 138
           IHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNF+KQA+EILNEYFYSHLSNPYPSE
Sbjct: 204 IHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFNKQATEILNEYFYSHLSNPYPSE 263

Query: 139 EAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMGASTP 198
           EAKEELA+KC IT+SQVSNWFGNKRIRYKKNIGK QEEAN+YAAK A  A+  S   S  
Sbjct: 264 EAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAAKTAVTATNVSAHGSQA 323

Query: 199 MMSPAPDSVG 208
                P+S G
Sbjct: 324 NSPSTPNSAG 333

Binds the sequence 5'-ATCAATCAA-3'. Acts as a transcriptional activator of PF4 in complex with MEIS1. Converted into a potent transcriptional activator by the (1;19) translocation. May have a role in steroidogenesis and, subsequently, sexual development and differentiation.

Homo sapiens (taxid: 9606)

>sp|Q8QGC4|PBX1_XENLA Pre-B-cell leukemia transcription factor 1 OS=Xenopus laevis GN=pbx1 PE=1 SV=1

 Score =  325 bits (833), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 156/190 (82%), Positives = 167/190 (87%)

Query: 19  AIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQI 78
           + EHSDYRAKL+QIR IY  ELEKYEQAC+EFTTHVMNLLREQSRTRPI+PKEIERMV I
Sbjct: 144 STEHSDYRAKLSQIRQIYHTELEKYEQACNEFTTHVMNLLREQSRTRPISPKEIERMVSI 203

Query: 79  IHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSE 138
           IHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNF+KQA+EILNEYFYSHLSNPYPSE
Sbjct: 204 IHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFNKQATEILNEYFYSHLSNPYPSE 263

Query: 139 EAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMGASTP 198
           EAKEELA+KC IT+SQVSNWFGNKRIRYKKNIGK QEEAN+YAAK A  A+  S+  S  
Sbjct: 264 EAKEELAKKCAITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAAKTAVNATNVSVHGSQA 323

Query: 199 MMSPAPDSVG 208
                P S G
Sbjct: 324 NSPSTPSSAG 333

Acts as a transcriptional activator in complex with isoform 2 of meis1, to induce posterior neural and neural crest gene expression, and thereby specify hindbrain and neural crest cell fate. Binds to a highly conserved region in the promoter of the neural crest gene zic3. Required for the nuclear transport or retention of isoform 2 of meis1.

Xenopus laevis (taxid: 8355)

>sp|B4F6V6|PBX1_XENTR Pre-B-cell leukemia transcription factor 1 OS=Xenopus tropicalis GN=pbx1 PE=2 SV=1

 Score =  325 bits (832), Expect = 3e-88,   Method: Compositional matrix adjust.
 Identities = 156/188 (82%), Positives = 166/188 (88%)

Query: 21  EHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQIIH 80
           EHSDYRAKL+QIR IY  ELEKYEQAC+EFTTHVMNLLREQSRTRPI+PKEIERMV IIH
Sbjct: 146 EHSDYRAKLSQIRQIYHTELEKYEQACNEFTTHVMNLLREQSRTRPISPKEIERMVSIIH 205

Query: 81  RKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEA 140
           RKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNF+KQA+EILNEYFYSHLSNPYPSEEA
Sbjct: 206 RKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFNKQATEILNEYFYSHLSNPYPSEEA 265

Query: 141 KEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMGASTPMM 200
           KEELA+KC IT+SQVSNWFGNKRIRYKKNIGK QEEAN+YAAK A  A+  S+  S    
Sbjct: 266 KEELAKKCAITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAAKTAVNATNVSVHGSQANS 325

Query: 201 SPAPDSVG 208
              P S G
Sbjct: 326 PSTPSSAG 333

Acts as a transcriptional activator in complex with isoform 2 of meis1, to induce posterior neural and neural crest gene expression, and thereby specify hindbrain and neural crest cell fate. Binds to a highly conserved region in the promoter of the neural crest gene zic3. Required for the nuclear transport or retention of meis1.

Xenopus tropicalis (taxid: 8364)

>sp|O35317|PBX3_MOUSE Pre-B-cell leukemia transcription factor 3 OS=Mus musculus GN=Pbx3 PE=2 SV=1

 Score =  324 bits (831), Expect = 4e-88,   Method: Compositional matrix adjust.
 Identities = 152/166 (91%), Positives = 160/166 (96%)

Query: 18  HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
           ++IEHSDYRAKL QIR IY  ELEKYEQAC+EFTTHVMNLLREQSRTRPI+PKEIERMV 
Sbjct: 145 NSIEHSDYRAKLTQIRQIYHTELEKYEQACNEFTTHVMNLLREQSRTRPISPKEIERMVG 204

Query: 78  IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
           IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQA+EILNEYFYSHLSNPYPS
Sbjct: 205 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPS 264

Query: 138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAK 183
           EEAKEELA+KC+IT+SQVSNWFGNKRIRYKKNIGK QEEANLYAAK
Sbjct: 265 EEAKEELAKKCSITVSQVSNWFGNKRIRYKKNIGKFQEEANLYAAK 310

Transcriptional activator that binds the sequence 5'-ATCAATCAA-3'.

Mus musculus (taxid: 10090)

>sp|P40426|PBX3_HUMAN Pre-B-cell leukemia transcription factor 3 OS=Homo sapiens GN=PBX3 PE=1 SV=1

 Score =  324 bits (831), Expect = 4e-88,   Method: Compositional matrix adjust.
 Identities = 152/166 (91%), Positives = 160/166 (96%)

Query: 18  HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
           ++IEHSDYRAKL QIR IY  ELEKYEQAC+EFTTHVMNLLREQSRTRPI+PKEIERMV 
Sbjct: 145 NSIEHSDYRAKLTQIRQIYHTELEKYEQACNEFTTHVMNLLREQSRTRPISPKEIERMVG 204

Query: 78  IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
           IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQA+EILNEYFYSHLSNPYPS
Sbjct: 205 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPS 264

Query: 138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAK 183
           EEAKEELA+KC+IT+SQVSNWFGNKRIRYKKNIGK QEEANLYAAK
Sbjct: 265 EEAKEELAKKCSITVSQVSNWFGNKRIRYKKNIGKFQEEANLYAAK 310

Transcriptional activator that binds the sequence 5'-ATCAATCAA-3'.

Homo sapiens (taxid: 9606)

>sp|B3DM47|PBX2_XENTR Pre-B-cell leukemia transcription factor 2 OS=Xenopus tropicalis GN=pbx2 PE=2 SV=1

 Score =  323 bits (828), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 158/202 (78%), Positives = 171/202 (84%), Gaps = 4/202 (1%)

Query: 18  HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
           ++IEHSDYR KL+QIR IY  ELEKYEQAC+EFTTHVMNLLREQSRTRPI+PKEIERMV 
Sbjct: 147 NSIEHSDYRNKLSQIRQIYHAELEKYEQACNEFTTHVMNLLREQSRTRPISPKEIERMVG 206

Query: 78  IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
           IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQA+E+LNEYFYSHLSNPYPS
Sbjct: 207 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEVLNEYFYSHLSNPYPS 266

Query: 138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAG-ASPYSMGAS 196
           EEAKEELA+KC IT+SQVSNWFGNKRIRYKKNIGK QEEAN+YA K A   A     GA+
Sbjct: 267 EEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAVKTAVSVAQGGHSGAN 326

Query: 197 TPMMSPAPDSVGYSKEANLYAA 218
           +P     P S G     NL  +
Sbjct: 327 SPT---TPTSAGSGGSFNLSGS 345

Transcriptional activator that binds the sequence 5'-ATCAATCAA-3'.

Xenopus tropicalis (taxid: 8364)

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	301
170044999	288	homeobox protein extradenticle [Culex qu	0.691	0.722	0.879	1e-103
158298056	362	AGAP004696-PA [Anopheles gambiae str. PE	0.661	0.549	0.907	1e-103
126002456	376	GA21419 [Drosophila pseudoobscura pseudo	0.704	0.563	0.836	1e-102
328776690	420	PREDICTED: homeobox protein extradenticl	0.744	0.533	0.771	1e-102
17647403	376	extradenticle, isoform A [Drosophila mel	0.704	0.563	0.836	1e-101
195059587	374	GH17639 [Drosophila grimshawi] gi|195398	0.704	0.566	0.836	1e-101
195432671	376	GK20113 [Drosophila willistoni] gi|19416	0.704	0.563	0.836	1e-101
195176039	266	GL10055 [Drosophila persimilis] gi|19410	0.704	0.796	0.836	1e-101
289739669	374	transcription factor PBX [Glossina morsi	0.641	0.516	0.915	1e-101
380030551	327	PREDICTED: homeobox protein extradenticl	0.744	0.685	0.771	1e-101

>gi|170044999|ref|XP_001850112.1| homeobox protein extradenticle [Culex quinquefasciatus] gi|167868064|gb|EDS31447.1| homeobox protein extradenticle [Culex quinquefasciatus]

 Score =  381 bits (979), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 189/215 (87%), Positives = 196/215 (91%), Gaps = 7/215 (3%)

Query: 18  HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
           +AIEHSDYRAKLAQIR IY QELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ
Sbjct: 60  NAIEHSDYRAKLAQIRQIYHQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 119

Query: 78  IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
           IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS
Sbjct: 120 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 179

Query: 138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM---- 193
           EEAKEELARKC IT+SQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM    
Sbjct: 180 EEAKEELARKCGITVSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMGGPP 239

Query: 194 -GASTPMMSPAP--DSVGYSKEANLYAAKKAAGAS 225
            GA+TPMMSPAP  DS+GYS  +  Y  ++A   S
Sbjct: 240 SGAATPMMSPAPAQDSMGYSLGSGGYDQQQAYDGS 274

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158298056|ref|XP_318146.2| AGAP004696-PA [Anopheles gambiae str. PEST] gi|190359338|sp|Q7PMT1.2|EXD_ANOGA RecName: Full=Homeobox protein extradenticle gi|157014624|gb|EAA13242.3| AGAP004696-PA [Anopheles gambiae str. PEST]

 Score =  379 bits (974), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 187/206 (90%), Positives = 192/206 (93%), Gaps = 7/206 (3%)

Query: 18  HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
           +AIEHSDYRAKLAQIR IY QELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ
Sbjct: 136 NAIEHSDYRAKLAQIRQIYHQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 195

Query: 78  IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
           IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS
Sbjct: 196 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 255

Query: 138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM---- 193
           EEAKEELARKC IT+SQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM    
Sbjct: 256 EEAKEELARKCGITVSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMGGPP 315

Query: 194 -GASTPMMSPAP--DSVGYSKEANLY 216
            GA+TPMMSPAP  DS+GYS  +  Y
Sbjct: 316 SGAATPMMSPAPAQDSMGYSLGSGGY 341

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|126002456|ref|XP_001352352.1| GA21419 [Drosophila pseudoobscura pseudoobscura] gi|122072797|sp|Q29CT2.1|EXD_DROPS RecName: Full=Homeobox protein extradenticle gi|54640619|gb|EAL29404.1| GA21419 [Drosophila pseudoobscura pseudoobscura]

 Score =  376 bits (966), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 189/226 (83%), Positives = 199/226 (88%), Gaps = 14/226 (6%)

Query: 18  HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
           +AIEHSDYRAKLAQIR IY QELEKYEQAC+EFTTHVMNLLREQSRTRPITPKEIERMVQ
Sbjct: 148 NAIEHSDYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIERMVQ 207

Query: 78  IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
           IIH+KFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS
Sbjct: 208 IIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 267

Query: 138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM---- 193
           EEAKEELARKC IT+SQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM    
Sbjct: 268 EEAKEELARKCGITVSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMAGPP 327

Query: 194 -GASTPMMSPAP--DSVGYSKEANLYAAKKAAGASPY--SMGASTP 234
            G +TPMMSPAP  DS+GY+  +  Y  ++     PY  SMG   P
Sbjct: 328 SGTTTPMMSPAPPQDSMGYTMGSGGYDQQQ-----PYDNSMGGYDP 368

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328776690|ref|XP_392297.4| PREDICTED: homeobox protein extradenticle [Apis mellifera]

 Score =  376 bits (966), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 192/249 (77%), Positives = 203/249 (81%), Gaps = 25/249 (10%)

Query: 18  HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
           +AIEHSDYRAKLAQIR IY QELEKYEQAC+EFTTHVMNLLREQSRTRPITPKEIERMVQ
Sbjct: 161 NAIEHSDYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIERMVQ 220

Query: 78  IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
           IIH+KFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS
Sbjct: 221 IIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 280

Query: 138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMGAS- 196
           EEAKEELARKC IT+SQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMG + 
Sbjct: 281 EEAKEELARKCGITVSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMGGAS 340

Query: 197 ----TPMMSPAP-----DSVGYSKEANLYAAKKAAGASPYSMGASTPMMSPAPDSVGYSS 247
               TPMMSPAP     D  GY    N        G+ PY+ G           S+GY  
Sbjct: 341 QGTPTPMMSPAPPGGPQDMAGYGMGIN----GSDYGSQPYNDG-----------SMGYDP 385

Query: 248 MEDRMHNTN 256
           M   ++NT+
Sbjct: 386 MHQFVNNTD 394

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|17647403|ref|NP_523360.1| extradenticle, isoform A [Drosophila melanogaster] gi|24642377|ref|NP_727923.1| extradenticle, isoform B [Drosophila melanogaster] gi|24642379|ref|NP_727924.1| extradenticle, isoform C [Drosophila melanogaster] gi|442616520|ref|NP_001259592.1| extradenticle, isoform D [Drosophila melanogaster] gi|442616522|ref|NP_001259593.1| extradenticle, isoform E [Drosophila melanogaster] gi|194894027|ref|XP_001977992.1| GG17938 [Drosophila erecta] gi|195357052|ref|XP_002044928.1| GM11678 [Drosophila sechellia] gi|195567036|ref|XP_002107081.1| GD17261 [Drosophila simulans] gi|729455|sp|P40427.1|EXD_DROME RecName: Full=Homeobox protein extradenticle; Short=Dpbx gi|304678|gb|AAC37182.1| extradenticle [Drosophila melanogaster] gi|1002788|gb|AAC46903.1| extradenticle [Drosophila melanogaster] gi|7293171|gb|AAF48555.1| extradenticle, isoform A [Drosophila melanogaster] gi|7293172|gb|AAF48556.1| extradenticle, isoform B [Drosophila melanogaster] gi|16768788|gb|AAL28613.1| LD03509p [Drosophila melanogaster] gi|22832323|gb|AAN09379.1| extradenticle, isoform C [Drosophila melanogaster] gi|190649641|gb|EDV46919.1| GG17938 [Drosophila erecta] gi|194124270|gb|EDW46313.1| GM11678 [Drosophila sechellia] gi|194204478|gb|EDX18054.1| GD17261 [Drosophila simulans] gi|220942464|gb|ACL83775.1| exd-PA [synthetic construct] gi|220953060|gb|ACL89073.1| exd-PA [synthetic construct] gi|440216818|gb|AGB95434.1| extradenticle, isoform D [Drosophila melanogaster] gi|440216819|gb|AGB95435.1| extradenticle, isoform E [Drosophila melanogaster]

 Score =  375 bits (964), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 189/226 (83%), Positives = 198/226 (87%), Gaps = 14/226 (6%)

Query: 18  HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
           +AIEHSDYRAKLAQIR IY QELEKYEQAC+EFTTHVMNLLREQSRTRPITPKEIERMVQ
Sbjct: 148 NAIEHSDYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIERMVQ 207

Query: 78  IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
           IIH+KFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS
Sbjct: 208 IIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 267

Query: 138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM---- 193
           EEAKEELARKC IT+SQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM    
Sbjct: 268 EEAKEELARKCGITVSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMAGPP 327

Query: 194 -GASTPMMSPAP--DSVGYSKEANLYAAKKAAGASPY--SMGASTP 234
            G +TPMMSPAP  DS+GY   +  Y  ++     PY  SMG   P
Sbjct: 328 SGTTTPMMSPAPPQDSMGYPMGSGGYDQQQ-----PYDNSMGGYDP 368

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195059587|ref|XP_001995667.1| GH17639 [Drosophila grimshawi] gi|195398807|ref|XP_002058012.1| GJ15726 [Drosophila virilis] gi|193896453|gb|EDV95319.1| GH17639 [Drosophila grimshawi] gi|194150436|gb|EDW66120.1| GJ15726 [Drosophila virilis]

 Score =  375 bits (964), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 189/226 (83%), Positives = 198/226 (87%), Gaps = 14/226 (6%)

Query: 18  HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
           +AIEHSDYRAKLAQIR IY QELEKYEQAC+EFTTHVMNLLREQSRTRPITPKEIERMVQ
Sbjct: 146 NAIEHSDYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIERMVQ 205

Query: 78  IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
           IIH+KFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS
Sbjct: 206 IIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 265

Query: 138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM---- 193
           EEAKEELARKC IT+SQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM    
Sbjct: 266 EEAKEELARKCGITVSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMAGPP 325

Query: 194 -GASTPMMSPAP--DSVGYSKEANLYAAKKAAGASPY--SMGASTP 234
            G +TPMMSPAP  DS+GY   +  Y  ++     PY  SMG   P
Sbjct: 326 SGTTTPMMSPAPPQDSMGYPMGSGGYDQQQ-----PYDNSMGGYDP 366

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195432671|ref|XP_002064340.1| GK20113 [Drosophila willistoni] gi|194160425|gb|EDW75326.1| GK20113 [Drosophila willistoni]

 Score =  375 bits (963), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 189/226 (83%), Positives = 198/226 (87%), Gaps = 14/226 (6%)

Query: 18  HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
           +AIEHSDYRAKLAQIR IY QELEKYEQAC+EFTTHVMNLLREQSRTRPITPKEIERMVQ
Sbjct: 148 NAIEHSDYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIERMVQ 207

Query: 78  IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
           IIH+KFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS
Sbjct: 208 IIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 267

Query: 138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM---- 193
           EEAKEELARKC IT+SQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM    
Sbjct: 268 EEAKEELARKCGITVSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMAGPP 327

Query: 194 -GASTPMMSPAP--DSVGYSKEANLYAAKKAAGASPY--SMGASTP 234
            G +TPMMSPAP  DS+GY   +  Y  ++     PY  SMG   P
Sbjct: 328 SGTTTPMMSPAPPQDSMGYPMGSGGYDQQQ-----PYDNSMGGYDP 368

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195176039|ref|XP_002028669.1| GL10055 [Drosophila persimilis] gi|194108907|gb|EDW30950.1| GL10055 [Drosophila persimilis]

 Score =  375 bits (963), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 189/226 (83%), Positives = 199/226 (88%), Gaps = 14/226 (6%)

Query: 18  HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
           +AIEHSDYRAKLAQIR IY QELEKYEQAC+EFTTHVMNLLREQSRTRPITPKEIERMVQ
Sbjct: 38  NAIEHSDYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIERMVQ 97

Query: 78  IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
           IIH+KFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS
Sbjct: 98  IIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 157

Query: 138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM---- 193
           EEAKEELARKC IT+SQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM    
Sbjct: 158 EEAKEELARKCGITVSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMAGPP 217

Query: 194 -GASTPMMSPAP--DSVGYSKEANLYAAKKAAGASPY--SMGASTP 234
            G +TPMMSPAP  DS+GY+  +  Y  ++     PY  SMG   P
Sbjct: 218 SGTTTPMMSPAPPQDSMGYTMGSGGYDQQQ-----PYDNSMGGYDP 258

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|289739669|gb|ADD18582.1| transcription factor PBX [Glossina morsitans morsitans]

 Score =  375 bits (962), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 183/200 (91%), Positives = 189/200 (94%), Gaps = 7/200 (3%)

Query: 18  HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
           +AIEHSDYRAKLAQIR IY QELEKYEQAC+EFTTHVMNLLREQSRTRPITPKEIERMVQ
Sbjct: 148 NAIEHSDYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIERMVQ 207

Query: 78  IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
           IIH+KFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS
Sbjct: 208 IIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 267

Query: 138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM---- 193
           EEAKEELARKC IT+SQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM    
Sbjct: 268 EEAKEELARKCGITVSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMAGPP 327

Query: 194 -GASTPMMSPAP--DSVGYS 210
            G +TPMMSPAP  DS+GYS
Sbjct: 328 SGTTTPMMSPAPPQDSMGYS 347

Source: Glossina morsitans morsitans

Species: Glossina morsitans

Genus: Glossina

Family: Glossinidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380030551|ref|XP_003698909.1| PREDICTED: homeobox protein extradenticle-like [Apis florea]

 Score =  375 bits (962), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 192/249 (77%), Positives = 203/249 (81%), Gaps = 25/249 (10%)

Query: 18  HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
           +AIEHSDYRAKLAQIR IY QELEKYEQAC+EFTTHVMNLLREQSRTRPITPKEIERMVQ
Sbjct: 66  NAIEHSDYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIERMVQ 125

Query: 78  IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
           IIH+KFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS
Sbjct: 126 IIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 185

Query: 138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMGAS- 196
           EEAKEELARKC IT+SQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMG + 
Sbjct: 186 EEAKEELARKCGITVSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMGGAS 245

Query: 197 ----TPMMSPAP-----DSVGYSKEANLYAAKKAAGASPYSMGASTPMMSPAPDSVGYSS 247
               TPMMSPAP     D  GY    N        G+ PY+ G           S+GY  
Sbjct: 246 QGTPTPMMSPAPPGGPQDMAGYGMGIN----GSDYGSQPYNDG-----------SMGYDP 290

Query: 248 MEDRMHNTN 256
           M   ++NT+
Sbjct: 291 MHQFVNNTD 299

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	301
UNIPROTKB|Q7PMT1	362	exd "Homeobox protein extraden	0.641	0.533	0.89	4.6e-89
UNIPROTKB|Q29CT2	376	exd "Homeobox protein extraden	0.641	0.513	0.87	1.1e-87
FB|FBgn0000611	376	exd "extradenticle" [Drosophil	0.637	0.510	0.874	1.4e-87
ZFIN|ZDB-GENE-000201-18	343	pbx4 "pre-B-cell leukemia tran	0.634	0.556	0.811	2.3e-78
UNIPROTKB|F1MJ02	430	PBX1 "Uncharacterized protein"	0.641	0.448	0.787	1e-77
UNIPROTKB|F1PDM8	430	PBX1 "Uncharacterized protein"	0.641	0.448	0.787	1e-77
UNIPROTKB|P40424	430	PBX1 "Pre-B-cell leukemia tran	0.641	0.448	0.787	1e-77
MGI|MGI:97495	430	Pbx1 "pre B cell leukemia home	0.641	0.448	0.787	1e-77
ZFIN|ZDB-GENE-070424-11	429	zgc:158824 "zgc:158824" [Danio	0.843	0.592	0.637	1e-77
UNIPROTKB|E1BSR7	358	PBX1 "Uncharacterized protein"	0.641	0.539	0.787	1e-77

UNIPROTKB|Q7PMT1 exd "Homeobox protein extradenticle" [Anopheles gambiae (taxid:7165)]

 Score = 889 (318.0 bits), Expect = 4.6e-89, P = 4.6e-89
 Identities = 178/200 (89%), Positives = 182/200 (91%)

Query:    18 HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
             +AIEHSDYRAKLAQIR IY QELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ
Sbjct:   136 NAIEHSDYRAKLAQIRQIYHQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 195

Query:    78 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
             IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS
Sbjct:   196 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 255

Query:   138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYXXXXXXXXSPYSMG--- 194
             EEAKEELARKC IT+SQVSNWFGNKRIRYKKNIGKAQEEANLY        SPYSMG   
Sbjct:   256 EEAKEELARKCGITVSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMGGPP 315

Query:   195 --ASTPMMSPAP--DSVGYS 210
               A+TPMMSPAP  DS+GYS
Sbjct:   316 SGAATPMMSPAPAQDSMGYS 335

GO:0000060 "protein import into nucleus, translocation" evidence=ISS

GO:0001654 "eye development" evidence=ISS

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005667 "transcription factor complex" evidence=ISS

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0007422 "peripheral nervous system development" evidence=ISS

UNIPROTKB|Q29CT2 exd "Homeobox protein extradenticle" [Drosophila pseudoobscura pseudoobscura (taxid:46245)]

 Score = 876 (313.4 bits), Expect = 1.1e-87, P = 1.1e-87
 Identities = 174/200 (87%), Positives = 181/200 (90%)

Query:    18 HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
             +AIEHSDYRAKLAQIR IY QELEKYEQAC+EFTTHVMNLLREQSRTRPITPKEIERMVQ
Sbjct:   148 NAIEHSDYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIERMVQ 207

Query:    78 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
             IIH+KFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS
Sbjct:   208 IIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 267

Query:   138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYXXXXXXXXSPYSM---- 193
             EEAKEELARKC IT+SQVSNWFGNKRIRYKKNIGKAQEEANLY        SPYSM    
Sbjct:   268 EEAKEELARKCGITVSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMAGPP 327

Query:   194 -GASTPMMSPAP--DSVGYS 210
              G +TPMMSPAP  DS+GY+
Sbjct:   328 SGTTTPMMSPAPPQDSMGYT 347

GO:0000060 "protein import into nucleus, translocation" evidence=ISS

GO:0001654 "eye development" evidence=ISS

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005667 "transcription factor complex" evidence=ISS

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0007422 "peripheral nervous system development" evidence=ISS

FB|FBgn0000611 exd "extradenticle" [Drosophila melanogaster (taxid:7227)]

 Score = 875 (313.1 bits), Expect = 1.4e-87, P = 1.4e-87
 Identities = 174/199 (87%), Positives = 180/199 (90%)

Query:    18 HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
             +AIEHSDYRAKLAQIR IY QELEKYEQAC+EFTTHVMNLLREQSRTRPITPKEIERMVQ
Sbjct:   148 NAIEHSDYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIERMVQ 207

Query:    78 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
             IIH+KFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS
Sbjct:   208 IIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 267

Query:   138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYXXXXXXXXSPYSM---- 193
             EEAKEELARKC IT+SQVSNWFGNKRIRYKKNIGKAQEEANLY        SPYSM    
Sbjct:   268 EEAKEELARKCGITVSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMAGPP 327

Query:   194 -GASTPMMSPAP--DSVGY 209
              G +TPMMSPAP  DS+GY
Sbjct:   328 SGTTTPMMSPAPPQDSMGY 346

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

GO:0005667 "transcription factor complex" evidence=IDA;IPI

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IDA;TAS

GO:0005634 "nucleus" evidence=NAS;IDA;TAS

GO:0046982 "protein heterodimerization activity" evidence=IPI

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

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

GO:0000060 "protein import into nucleus, translocation" evidence=IMP

GO:0001654 "eye development" evidence=IMP

GO:0007422 "peripheral nervous system development" evidence=IMP

GO:0033613 "activating transcription factor binding" evidence=IPI

GO:0003713 "transcription coactivator activity" evidence=IDA

GO:0003677 "DNA binding" evidence=IDA

GO:0007479 "leg disc proximal/distal pattern formation" evidence=TAS

GO:0007420 "brain development" evidence=IMP

GO:0007432 "salivary gland boundary specification" evidence=NAS;TAS

GO:0007438 "oenocyte development" evidence=IMP

GO:0008134 "transcription factor binding" evidence=IPI

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

GO:0042659 "regulation of cell fate specification" evidence=IMP

GO:0007525 "somatic muscle development" evidence=IMP

ZFIN|ZDB-GENE-000201-18 pbx4 "pre-B-cell leukemia transcription factor 4" [Danio rerio (taxid:7955)]

 Score = 788 (282.4 bits), Expect = 2.3e-78, P = 2.3e-78
 Identities = 155/191 (81%), Positives = 164/191 (85%)

Query:    19 AIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQI 78
             +IEHSDYRAKLAQIR IY  ELEKYEQACSEFT HVMNLLREQSRTRPI+PKEIERMV I
Sbjct:   142 SIEHSDYRAKLAQIRQIYHSELEKYEQACSEFTNHVMNLLREQSRTRPISPKEIERMVAI 201

Query:    79 IHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSE 138
             IHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNF+KQA+E+LNEYFYSHLSNPYPSE
Sbjct:   202 IHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFNKQATEVLNEYFYSHLSNPYPSE 261

Query:   139 EAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYXXXXXXXXSPYSMGASTP 198
             EAKEELA+KC IT+SQVSNWFGNKRIRYKKNIGK QEEANLY        +  S  AS  
Sbjct:   262 EAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANLYAVKTAVDAANVSAQASQA 321

Query:   199 MMSPAPDSVGY 209
                  P+S GY
Sbjct:   322 NSPATPNSGGY 332

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

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

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

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

GO:0005634 "nucleus" evidence=IEA;IDA

GO:0001764 "neuron migration" evidence=IDA

GO:0030182 "neuron differentiation" evidence=IMP

GO:0005667 "transcription factor complex" evidence=IC

GO:0007411 "axon guidance" evidence=IDA

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

GO:0048741 "skeletal muscle fiber development" evidence=IGI

GO:0048666 "neuron development" evidence=IMP

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

GO:0005515 "protein binding" evidence=IPI

GO:0007420 "brain development" evidence=IMP

GO:0060059 "embryonic retina morphogenesis in camera-type eye" evidence=IGI

GO:0030901 "midbrain development" evidence=IGI

GO:0030902 "hindbrain development" evidence=IGI

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

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

GO:0031016 "pancreas development" evidence=IMP

UNIPROTKB|F1MJ02 PBX1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 782 (280.3 bits), Expect = 1.0e-77, P = 1.0e-77
 Identities = 152/193 (78%), Positives = 165/193 (85%)

Query:    18 HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
             +++EHSDYRAKL+QIR IY  ELEKYEQAC+EFTTHVMNLLREQSRTRPI+PKEIERMV 
Sbjct:   143 NSVEHSDYRAKLSQIRQIYHTELEKYEQACNEFTTHVMNLLREQSRTRPISPKEIERMVS 202

Query:    78 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
             IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNF+KQA+EILNEYFYSHLSNPYPS
Sbjct:   203 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFNKQATEILNEYFYSHLSNPYPS 262

Query:   138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYXXXXXXXXSPYSMGAST 197
             EEAKEELA+KC IT+SQVSNWFGNKRIRYKKNIGK QEEAN+Y        +  S   S 
Sbjct:   263 EEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAAKTAVTATNVSAHGSQ 322

Query:   198 PMMSPAPDSVGYS 210
                   P+S G S
Sbjct:   323 ANSPSTPNSAGSS 335

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

GO:0048538 "thymus development" evidence=IEA

GO:0048536 "spleen development" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

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

GO:0045665 "negative regulation of neuron differentiation" evidence=IEA

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

GO:0043433 "negative regulation of sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0035162 "embryonic hemopoiesis" evidence=IEA

GO:0030326 "embryonic limb morphogenesis" evidence=IEA

GO:0030325 "adrenal gland development" evidence=IEA

GO:0030278 "regulation of ossification" evidence=IEA

GO:0009954 "proximal/distal pattern formation" evidence=IEA

GO:0009952 "anterior/posterior pattern specification" evidence=IEA

GO:0009887 "organ morphogenesis" evidence=IEA

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

GO:0008134 "transcription factor binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

GO:0001658 "branching involved in ureteric bud morphogenesis" evidence=IEA

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

UNIPROTKB|F1PDM8 PBX1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 782 (280.3 bits), Expect = 1.0e-77, P = 1.0e-77
 Identities = 152/193 (78%), Positives = 165/193 (85%)

Query:    18 HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
             +++EHSDYRAKL+QIR IY  ELEKYEQAC+EFTTHVMNLLREQSRTRPI+PKEIERMV 
Sbjct:   143 NSVEHSDYRAKLSQIRQIYHTELEKYEQACNEFTTHVMNLLREQSRTRPISPKEIERMVS 202

Query:    78 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
             IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNF+KQA+EILNEYFYSHLSNPYPS
Sbjct:   203 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFNKQATEILNEYFYSHLSNPYPS 262

Query:   138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYXXXXXXXXSPYSMGAST 197
             EEAKEELA+KC IT+SQVSNWFGNKRIRYKKNIGK QEEAN+Y        +  S   S 
Sbjct:   263 EEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAAKTAVTATNVSAHGSQ 322

Query:   198 PMMSPAPDSVGYS 210
                   P+S G S
Sbjct:   323 ANSPSTPNSAGSS 335

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

GO:0048538 "thymus development" evidence=IEA

GO:0048536 "spleen development" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

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

GO:0045665 "negative regulation of neuron differentiation" evidence=IEA

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

GO:0043433 "negative regulation of sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0035162 "embryonic hemopoiesis" evidence=IEA

GO:0030326 "embryonic limb morphogenesis" evidence=IEA

GO:0030325 "adrenal gland development" evidence=IEA

GO:0030278 "regulation of ossification" evidence=IEA

GO:0009954 "proximal/distal pattern formation" evidence=IEA

GO:0009952 "anterior/posterior pattern specification" evidence=IEA

GO:0009887 "organ morphogenesis" evidence=IEA

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

GO:0008134 "transcription factor binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

GO:0001658 "branching involved in ureteric bud morphogenesis" evidence=IEA

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

UNIPROTKB|P40424 PBX1 "Pre-B-cell leukemia transcription factor 1" [Homo sapiens (taxid:9606)]

 Score = 782 (280.3 bits), Expect = 1.0e-77, P = 1.0e-77
 Identities = 152/193 (78%), Positives = 165/193 (85%)

Query:    18 HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
             +++EHSDYRAKL+QIR IY  ELEKYEQAC+EFTTHVMNLLREQSRTRPI+PKEIERMV 
Sbjct:   143 NSVEHSDYRAKLSQIRQIYHTELEKYEQACNEFTTHVMNLLREQSRTRPISPKEIERMVS 202

Query:    78 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
             IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNF+KQA+EILNEYFYSHLSNPYPS
Sbjct:   203 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFNKQATEILNEYFYSHLSNPYPS 262

Query:   138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYXXXXXXXXSPYSMGAST 197
             EEAKEELA+KC IT+SQVSNWFGNKRIRYKKNIGK QEEAN+Y        +  S   S 
Sbjct:   263 EEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAAKTAVTATNVSAHGSQ 322

Query:   198 PMMSPAPDSVGYS 210
                   P+S G S
Sbjct:   323 ANSPSTPNSAGSS 335

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

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

GO:0006694 "steroid biosynthetic process" evidence=IEA

GO:0007548 "sex differentiation" evidence=IEA

GO:0001658 "branching involved in ureteric bud morphogenesis" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

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

GO:0009887 "organ morphogenesis" evidence=IEA

GO:0009952 "anterior/posterior pattern specification" evidence=IEA

GO:0009954 "proximal/distal pattern formation" evidence=IEA

GO:0030278 "regulation of ossification" evidence=IEA

GO:0030325 "adrenal gland development" evidence=IEA

GO:0030326 "embryonic limb morphogenesis" evidence=IEA

GO:0035162 "embryonic hemopoiesis" evidence=IEA

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

GO:0045665 "negative regulation of neuron differentiation" evidence=IEA

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

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0048536 "spleen development" evidence=IEA

GO:0048538 "thymus development" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0003677 "DNA binding" evidence=IDA

GO:0008134 "transcription factor binding" evidence=IPI

GO:0043433 "negative regulation of sequence-specific DNA binding transcription factor activity" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

MGI|MGI:97495 Pbx1 "pre B cell leukemia homeobox 1" [Mus musculus (taxid:10090)]

 Score = 782 (280.3 bits), Expect = 1.0e-77, P = 1.0e-77
 Identities = 152/193 (78%), Positives = 165/193 (85%)

Query:    18 HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
             +++EHSDYRAKL+QIR IY  ELEKYEQAC+EFTTHVMNLLREQSRTRPI+PKEIERMV 
Sbjct:   143 NSVEHSDYRAKLSQIRQIYHTELEKYEQACNEFTTHVMNLLREQSRTRPISPKEIERMVS 202

Query:    78 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
             IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNF+KQA+EILNEYFYSHLSNPYPS
Sbjct:   203 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFNKQATEILNEYFYSHLSNPYPS 262

Query:   138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYXXXXXXXXSPYSMGAST 197
             EEAKEELA+KC IT+SQVSNWFGNKRIRYKKNIGK QEEAN+Y        +  S   S 
Sbjct:   263 EEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAAKTAVTATNVSAHGSQ 322

Query:   198 PMMSPAPDSVGYS 210
                   P+S G S
Sbjct:   323 ANSPSTPNSAGSS 335

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=IDA

GO:0001655 "urogenital system development" evidence=IMP

GO:0001658 "branching involved in ureteric bud morphogenesis" evidence=IDA

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005667 "transcription factor complex" evidence=IDA

GO:0005737 "cytoplasm" evidence=ISO;IDA

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

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

GO:0006694 "steroid biosynthetic process" evidence=IEA

GO:0007548 "sex differentiation" evidence=IEA

GO:0008134 "transcription factor binding" evidence=ISO

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

GO:0009887 "organ morphogenesis" evidence=IMP

GO:0009952 "anterior/posterior pattern specification" evidence=IMP

GO:0009954 "proximal/distal pattern formation" evidence=IGI;IMP

GO:0010971 "positive regulation of G2/M transition of mitotic cell cycle" evidence=IMP

GO:0030154 "cell differentiation" evidence=IEA

GO:0030278 "regulation of ossification" evidence=IMP

GO:0030325 "adrenal gland development" evidence=IMP

GO:0030326 "embryonic limb morphogenesis" evidence=IGI

GO:0035162 "embryonic hemopoiesis" evidence=IMP

GO:0042127 "regulation of cell proliferation" evidence=IMP

GO:0043433 "negative regulation of sequence-specific DNA binding transcription factor activity" evidence=ISO

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

GO:0045665 "negative regulation of neuron differentiation" evidence=IGI

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

GO:0046982 "protein heterodimerization activity" evidence=IPI

GO:0048536 "spleen development" evidence=IGI;IMP

GO:0048538 "thymus development" evidence=IMP

GO:0048568 "embryonic organ development" evidence=IMP

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

ZFIN|ZDB-GENE-070424-11 zgc:158824 "zgc:158824" [Danio rerio (taxid:7955)]

 Score = 782 (280.3 bits), Expect = 1.0e-77, P = 1.0e-77
 Identities = 165/259 (63%), Positives = 187/259 (72%)

Query:    18 HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
             ++ EHSDYRAKL+QIR IY  ELEKYEQAC+EFTTHVMNLLREQSRTRPI+PKEIERMV 
Sbjct:   142 NSAEHSDYRAKLSQIRQIYHTELEKYEQACNEFTTHVMNLLREQSRTRPISPKEIERMVG 201

Query:    78 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
             IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNF+KQA+EILNEYFYSHLSNPYPS
Sbjct:   202 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFNKQATEILNEYFYSHLSNPYPS 261

Query:   138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYXXXXXXXXSPYSMGAST 197
             EEAKEELA+KC+IT+SQVSNWFGNKRIRYKKNIGK QEEAN+Y        +  S   S 
Sbjct:   262 EEAKEELAKKCSITVSQVSNWFGNKRIRYKKNIGKFQEEANMYAARTAVNAASVSAHGSQ 321

Query:   198 PMMSPAPDSVGYSXXXXXXXXXXXXXXSPYSMGASTPMMSPAPDSVGYSSMEDRMHNTNM 257
                   P+S G S              S  S+   +   S    +V  S ++   H  + 
Sbjct:   322 ANSPSTPNSAG-SAGSFNMSNSGDLFMSVQSLNGDSYQGSQVGANV-QSQVDTLRHVISQ 379

Query:   258 LPNYIEG--ANDINTDPQG 274
                Y +G  AN + + PQG
Sbjct:   380 TGGYSDGLAANQMYS-PQG 397

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

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

UNIPROTKB|E1BSR7 PBX1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 782 (280.3 bits), Expect = 1.0e-77, P = 1.0e-77
 Identities = 152/193 (78%), Positives = 165/193 (85%)

Query:    18 HAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQ 77
             +++EHSDYRAKL+QIR IY  ELEKYEQAC+EFTTHVMNLLREQSRTRPI+PKEIERMV 
Sbjct:    71 NSVEHSDYRAKLSQIRQIYHTELEKYEQACNEFTTHVMNLLREQSRTRPISPKEIERMVS 130

Query:    78 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPS 137
             IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNF+KQA+EILNEYFYSHLSNPYPS
Sbjct:   131 IIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFNKQATEILNEYFYSHLSNPYPS 190

Query:   138 EEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLYXXXXXXXXSPYSMGAST 197
             EEAKEELA+KC IT+SQVSNWFGNKRIRYKKNIGK QEEAN+Y        +  S   S 
Sbjct:   191 EEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAAKTAVTATNVSAHGSQ 250

Query:   198 PMMSPAPDSVGYS 210
                   P+S G S
Sbjct:   251 ANSPSTPNSAGSS 263

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

GO:0001658 "branching involved in ureteric bud morphogenesis" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

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

GO:0009887 "organ morphogenesis" evidence=IEA

GO:0009952 "anterior/posterior pattern specification" evidence=IEA

GO:0009954 "proximal/distal pattern formation" evidence=IEA

GO:0030278 "regulation of ossification" evidence=IEA

GO:0030325 "adrenal gland development" evidence=IEA

GO:0030326 "embryonic limb morphogenesis" evidence=IEA

GO:0035162 "embryonic hemopoiesis" evidence=IEA

GO:0043433 "negative regulation of sequence-specific DNA binding transcription factor activity" evidence=IEA

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

GO:0045665 "negative regulation of neuron differentiation" evidence=IEA

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

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0048536 "spleen development" evidence=IEA

GO:0048538 "thymus development" evidence=IEA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q7PMT1	EXD_ANOGA	No assigned EC number	0.9077	0.6611	0.5497	yes	N/A
Q29CT2	EXD_DROPS	No assigned EC number	0.8362	0.7043	0.5638	yes	N/A
O35317	PBX3_MOUSE	No assigned EC number	0.9156	0.5282	0.3663	no	N/A
P41779	HM20_CAEEL	No assigned EC number	0.7252	0.6046	0.5384	yes	N/A
P41778	PBX1_MOUSE	No assigned EC number	0.8210	0.6312	0.4418	yes	N/A
P40424	PBX1_HUMAN	No assigned EC number	0.8210	0.6312	0.4418	yes	N/A
P40426	PBX3_HUMAN	No assigned EC number	0.9156	0.5282	0.3663	no	N/A
P40427	EXD_DROME	No assigned EC number	0.8362	0.7043	0.5638	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	301
pfam03792	192	pfam03792, PBC, PBC domain	5e-54
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	6e-17
pfam05920	40	pfam05920, Homeobox_KN, Homeobox KN domain	3e-15
pfam00046	57	pfam00046, Homeobox, Homeobox domain	5e-15
smart00389	57	smart00389, HOX, Homeodomain	9e-15
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	4e-07
pfam03792	192	pfam03792, PBC, PBC domain	8e-07

>gnl|CDD|217730 pfam03792, PBC, PBC domain

 Score =  174 bits (442), Expect = 5e-54
 Identities = 74/88 (84%), Positives = 78/88 (88%)

Query: 20  IEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQII 79
           IEHSDYRAKL+QIR IY  ELEKYEQAC EFT HVMNLLREQSRTRPI+ +EIERMV II
Sbjct: 105 IEHSDYRAKLSQIRQIYHSELEKYEQACKEFTQHVMNLLREQSRTRPISQREIERMVNII 164

Query: 80  HRKFSSIQMQLKQSTCEAVMILRSRFLD 107
            RKF+ IQ QLKQSTCEAVMILRSRFLD
Sbjct: 165 SRKFNKIQFQLKQSTCEAVMILRSRFLD 192

The PBC domain is a member of the TALE (three-amino-acid loop extension) superclass of homeodomain proteins. Length = 192

>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 = 73.0 bits (180), Expect = 6e-17
 Identities = 26/61 (42%), Positives = 37/61 (60%), Gaps = 3/61 (4%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           RRKR  F+ +  E L + F     NPYPS E +EELA++  +T  QV  WF N+R + K+
Sbjct: 1   RRKRTRFTPEQLEELEKEF---EKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57

Query: 169 N 169
           +
Sbjct: 58  S 58

Length = 59

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

 Score = 67.9 bits (167), Expect = 3e-15
 Identities = 21/39 (53%), Positives = 25/39 (64%)

Query: 127 FYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIR 165
              HL NPYPSEE K ELAR+  ++  Q+ NWF N R R
Sbjct: 2   LLEHLHNPYPSEEEKSELARQTGLSRKQIDNWFINARRR 40

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

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

 Score = 67.9 bits (167), Expect = 5e-15
 Identities = 26/60 (43%), Positives = 36/60 (60%), Gaps = 3/60 (5%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           RRKR  F+ +  E L + F     N YPS E +EELA+K  +T  QV  WF N+R ++K+
Sbjct: 1   RRKRTTFTPEQLEELEKEF---EKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57

Length = 57

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 67.3 bits (165), Expect = 9e-15
 Identities = 26/59 (44%), Positives = 37/59 (62%), Gaps = 3/59 (5%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
           RRKR +F+ +  E L + F     NPYPS E +EELA+K  ++  QV  WF N+R ++K
Sbjct: 2   RRKRTSFTPEQLEELEKEF---QKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

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

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

 Score = 48.6 bits (116), Expect = 4e-07
 Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 3/62 (4%)

Query: 107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRY 166
             + KRR  + +   +L   F     NPYPS   + +L+   N+    V  WF NKR + 
Sbjct: 50  PPKSKRRRTTDEQLMVLEREF---EINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKE 106

Query: 167 KK 168
           KK
Sbjct: 107 KK 108

Length = 156

>gnl|CDD|217730 pfam03792, PBC, PBC domain

 Score = 48.3 bits (115), Expect = 8e-07
 Identities = 22/28 (78%), Positives = 24/28 (85%)

Query: 274 GPRKQDISDILQQILNITDQSLDEAQAR 301
             R QDISD+LQQI+ ITDQSLDEAQAR
Sbjct: 3   AQRSQDISDLLQQIMKITDQSLDEAQAR 30

The PBC domain is a member of the TALE (three-amino-acid loop extension) superclass of homeodomain proteins. Length = 192

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	301
KOG0774|consensus	334		100.0
KOG3802|consensus	398		99.86
PF03792	191	PBC: PBC domain; InterPro: IPR005542 Pbx proteins	99.69
KOG0842|consensus	307		99.6
KOG0484|consensus	125		99.59
KOG0489|consensus	261		99.58
KOG0843|consensus	197		99.57
KOG0485|consensus	268		99.57
KOG0488|consensus	309		99.57
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.57
KOG0850|consensus	245		99.53
KOG0492|consensus	246		99.5
KOG0487|consensus	308		99.49
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.48
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.48
KOG2251|consensus	228		99.46
KOG1168|consensus	385		99.44
KOG0848|consensus	317		99.42
KOG0494|consensus	332		99.4
KOG0775|consensus	304		99.4
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	99.39
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.33
KOG0493|consensus	342		99.3
KOG0491|consensus	194		99.3
KOG0483|consensus	198		99.26
KOG0486|consensus	351		99.25
KOG4577|consensus	383		99.24
KOG0844|consensus	408		99.19
COG5576	156	Homeodomain-containing transcription factor [Trans	99.17
KOG0773|consensus	342		99.1
KOG0847|consensus	288		99.06
KOG2252|consensus	558		98.86
KOG0490|consensus	235		98.86
KOG0849|consensus	354		98.73
KOG0490|consensus	235		97.51
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	96.86
PF03791	52	KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEIN	96.76
KOG1146|consensus	1406		96.69
PF07526	140	POX: Associated with HOX; InterPro: IPR006563 This	94.94
KOG0773|consensus	342		94.51
smart00574	140	POX domain associated with HOX domains.	94.33
PF00157	75	Pou: Pou domain - N-terminal to homeobox domain; I	92.04
KOG3623|consensus	1007		91.71
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	91.7

>KOG0774|consensus

Probab=100.00  E-value=7.3e-39  Score=281.65  Aligned_cols=170  Identities=89%  Similarity=1.298  Sum_probs=164.2

Q ss_pred             CChHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhhhhhHHHHHHhhhHHHHHHH
Q psy5541          21 EHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQIIHRKFSSIQMQLKQSTCEAVMI  100 (301)
Q Consensus        21 e~~~~~~kl~qv~~~~~~el~ky~~~~~~f~~~~~~~l~~q~~~~~l~~~~~~~~~~~~~~~f~~~~~~l~~~~~~~~~~  100 (301)
                      .+.+|+.||.||+++|+.||+||++.|++||+.++++|+.|++++|++++++++|.+.|+++|+.++.+||+..|+.++.
T Consensus       101 ~hsdYR~kL~qiR~iy~~ElekyeqaCneftthV~nlL~eQsr~RPi~~ke~e~m~~~i~~kF~~iq~~lkqstce~vmi  180 (334)
T KOG0774|consen  101 DHSDYRAKLLQIRQIYHNELEKYEQACNEFTTHVMNLLREQSRTRPIMPKEIERMVQIISKKFSHIQMQLKQSTCEAVMI  180 (334)
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            48899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHHHHHHHH
Q psy5541         101 LRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLY  180 (301)
Q Consensus       101 l~~~~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~~~~~~~  180 (301)
                      |+.++.+.||||++|++..+++|..||+.|..||||++++|++||.++|++..||.+||.|.|.|+||...+..++++.+
T Consensus       181 Lr~r~ldarRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~~ee~~l~  260 (334)
T KOG0774|consen  181 LRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKNQEEANLY  260 (334)
T ss_pred             HHHHHHHHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhhhhhhhhH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999988888


Q ss_pred             HhhhcCCCCC
Q psy5541         181 AAKKAAGASP  190 (301)
Q Consensus       181 ~~~~~~~~~~  190 (301)
                      ..+.+....+
T Consensus       261 ~~kk~~~~~~  270 (334)
T KOG0774|consen  261 AAKKAVDATP  270 (334)
T ss_pred             hhcccccCCC
Confidence            8877766554

>KOG3802|consensus

Probab=99.86  E-value=8.7e-23  Score=190.91  Aligned_cols=128  Identities=23%  Similarity=0.366  Sum_probs=111.0

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhcCCCCCChHHH-HHHHHHHhhhhhHHHHHHhhhHHHHHHHhhhhhh-----------
Q psy5541          39 ELEKYEQACSEFTTHVMNLLREQSRTRPITPKEI-ERMVQIIHRKFSSIQMQLKQSTCEAVMILRSRFL-----------  106 (301)
Q Consensus        39 el~ky~~~~~~f~~~~~~~l~~q~~~~~l~~~~~-~~~~~~~~~~f~~~~~~l~~~~~~~~~~l~~~~~-----------  106 (301)
                      .+++++++++.|+.++|.++++|++++....+.+ ..++++.+|+|+.++..+| ++|+ ++.|..+|+           
T Consensus       204 ~leELEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALqLSFK-NMCK-LKPLL~KWLeEAes~~~~~~  281 (398)
T KOG3802|consen  204 DLEELEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEALQLSFK-NMCK-LKPLLEKWLEEAESRESTGS  281 (398)
T ss_pred             CHHHHHHHHHHHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHhhccCHH-HHhh-hHHHHHHHHHHHhcccccCC
Confidence            3555666699999999999999999997666665 5688999999999999998 5674 555555543           


Q ss_pred             -----------hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         107 -----------DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       107 -----------~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                                 ++|||||.|....+..||..|   .+|+.|+.+|+..||++|+|.+++|+|||||||+|.||...
T Consensus       282 ~~~~e~i~a~~RkRKKRTSie~~vr~aLE~~F---~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  282 PNSIEKIGAQSRKRKKRTSIEVNVRGALEKHF---LKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             CCCHHHhhccccccccccceeHHHHHHHHHHH---HhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence                       368899999999999999999   99999999999999999999999999999999999999653

>PF03792 PBC: PBC domain; InterPro: IPR005542 Pbx proteins are members of the TALE (three-amino-acid loop extension) family of atypical homeodomain proteins, whose members are characterised by a three-residue insertion in the first helix of the homeodomain involved in their interaction with Hox proteins

Probab=99.69  E-value=1.5e-16  Score=135.90  Aligned_cols=91  Identities=82%  Similarity=1.192  Sum_probs=88.3

Q ss_pred             cCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhhhhhHHHHHHhhhHH
Q psy5541          16 LLHAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQIIHRKFSSIQMQLKQSTC   95 (301)
Q Consensus        16 ~~~~le~~~~~~kl~qv~~~~~~el~ky~~~~~~f~~~~~~~l~~q~~~~~l~~~~~~~~~~~~~~~f~~~~~~l~~~~~   95 (301)
                      +++.+++++|..||.+|+.+|+.||++|++.|++|+.++.++|+.|+++||++++++++|...|+++|+.++.+||+++|
T Consensus       100 ~~~~~d~~dYr~kL~~ir~~y~~el~kye~ac~eF~~hV~~lLreQs~~RPIs~keiE~m~~~i~~Kf~~iq~qLKQstC  179 (191)
T PF03792_consen  100 ADNSIDHSDYRAKLSQIRQIYHSELEKYEQACNEFTEHVMNLLREQSEFRPISPKEIERMVNIIHRKFSKIQMQLKQSTC  179 (191)
T ss_pred             cccccchHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            47889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhhhh
Q psy5541          96 EAVMILRSRFL  106 (301)
Q Consensus        96 ~~~~~l~~~~~  106 (301)
                      ++++.|+.+++
T Consensus       180 EaVm~LRsRfl  190 (191)
T PF03792_consen  180 EAVMILRSRFL  190 (191)
T ss_pred             HHHHHHHHHhc
Confidence            99999988875

Examination of Pbx1 has shown that, in addition to the homeodomain, a short 16-residue C-terminal tail is essential for maximal cooperative interactions with Hox partners as well as for maximal monomeric binding of Pbx1 to DNA. The PBX domain is a bipartite acidic domain [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005634 nucleus

>KOG0842|consensus

Probab=99.60  E-value=1.4e-15  Score=140.05  Aligned_cols=66  Identities=29%  Similarity=0.411  Sum_probs=60.6

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHHH
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQE  175 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~~  175 (301)
                      ++||.|..|++.|+-+||+.|   ....|.+..||+.||..++||++||+|||||||-|.||.......
T Consensus       152 ~kRKrRVLFSqAQV~ELERRF---rqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~  217 (307)
T KOG0842|consen  152 KKRKRRVLFSQAQVYELERRF---RQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKAL  217 (307)
T ss_pred             cccccccccchhHHHHHHHHH---HhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhh
Confidence            466778899999999999999   999999999999999999999999999999999999998665444

>KOG0484|consensus

Probab=99.59  E-value=1.7e-15  Score=116.79  Aligned_cols=66  Identities=30%  Similarity=0.503  Sum_probs=61.0

Q ss_pred             hhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhH
Q psy5541         105 FLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKA  173 (301)
Q Consensus       105 ~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~  173 (301)
                      ..|+||-|++|+..|+..||+.|   ...+||++-.|++||.++.|++..|+|||||||+|.+|+.+..
T Consensus        14 krKQRRIRTTFTS~QLkELErvF---~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a   79 (125)
T KOG0484|consen   14 KRKQRRIRTTFTSAQLKELERVF---AETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAA   79 (125)
T ss_pred             HHHhhhhhhhhhHHHHHHHHHHH---HhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHH
Confidence            34668899999999999999999   9999999999999999999999999999999999999976543

>KOG0489|consensus

Probab=99.58  E-value=1.1e-15  Score=139.99  Aligned_cols=65  Identities=28%  Similarity=0.458  Sum_probs=60.7

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhH
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKA  173 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~  173 (301)
                      .+.||.|+.|+..|+.+||+.|   ..|.|.+...|.+||..|+|+++||+|||||||+||||..+..
T Consensus       157 ~~~kR~RtayT~~QllELEkEF---hfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~  221 (261)
T KOG0489|consen  157 GKSKRRRTAFTRYQLLELEKEF---HFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAK  221 (261)
T ss_pred             CCCCCCCcccchhhhhhhhhhh---ccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccc
Confidence            3468899999999999999999   9999999999999999999999999999999999999986543

>KOG0843|consensus

Probab=99.57  E-value=1.8e-15  Score=127.70  Aligned_cols=62  Identities=26%  Similarity=0.429  Sum_probs=59.5

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      +.||.||.|+.+|+..||..|   ..+.|-...||+.||+.|+|++.||+|||||||.|.||...
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F---~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~  162 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAF---EGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQ  162 (197)
T ss_pred             CCCccccccCHHHHHHHHHHH---hcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHH
Confidence            678999999999999999999   99999999999999999999999999999999999999754

>KOG0485|consensus

Probab=99.57  E-value=3.6e-15  Score=129.10  Aligned_cols=66  Identities=27%  Similarity=0.417  Sum_probs=61.2

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHHH
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQE  175 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~~  175 (301)
                      ++||.||+|+..|+..||..|   ....|.+..+|..||.++.|+++||++||||||.||||+.....+
T Consensus       103 RKKktRTvFSraQV~qLEs~F---e~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~e  168 (268)
T KOG0485|consen  103 RKKKTRTVFSRAQVFQLESTF---ELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLE  168 (268)
T ss_pred             ccccchhhhhHHHHHHHHHHH---HHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhh
Confidence            467889999999999999999   999999999999999999999999999999999999998765444

>KOG0488|consensus

Probab=99.57  E-value=1.4e-15  Score=141.85  Aligned_cols=67  Identities=28%  Similarity=0.420  Sum_probs=62.3

Q ss_pred             hhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHH
Q psy5541         105 FLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQ  174 (301)
Q Consensus       105 ~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~  174 (301)
                      ..|+||.||.|+..|+..||+.|   ++..|.+..+|.+||..+||+..||++||||||+||||+.....
T Consensus       169 pkK~RksRTaFT~~Ql~~LEkrF---~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~  235 (309)
T KOG0488|consen  169 PKKRRKSRTAFSDHQLFELEKRF---EKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGG  235 (309)
T ss_pred             CcccccchhhhhHHHHHHHHHHH---HHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhh
Confidence            35677889999999999999999   99999999999999999999999999999999999999887633

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.57  E-value=2.3e-15  Score=106.06  Aligned_cols=57  Identities=51%  Similarity=0.896  Sum_probs=54.9

Q ss_pred             CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541         109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK  168 (301)
Q Consensus       109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk  168 (301)
                      ||+|+.|+.+++.+|+.+|   ..++||+..+++.||..+||+..+|.+||+|+|.++||
T Consensus         1 kr~r~~~t~~q~~~L~~~f---~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYF---QENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHH---HHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHH---HHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence            5789999999999999999   88999999999999999999999999999999999986

; 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 ....

>KOG0850|consensus

Probab=99.53  E-value=5.3e-15  Score=129.36  Aligned_cols=66  Identities=29%  Similarity=0.416  Sum_probs=61.6

Q ss_pred             hhhhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         103 SRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       103 ~~~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      .+..|-||.||.++.-|+..|++.|   +++.|.-..||.+||..|||+.+||+|||||||.|.||.++
T Consensus       117 gk~KK~RKPRTIYSS~QLqaL~rRF---QkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k  182 (245)
T KOG0850|consen  117 GKGKKVRKPRTIYSSLQLQALNRRF---QQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK  182 (245)
T ss_pred             CCcccccCCcccccHHHHHHHHHHH---hhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence            3445668899999999999999999   99999999999999999999999999999999999999876

>KOG0492|consensus

Probab=99.50  E-value=2.9e-14  Score=122.76  Aligned_cols=67  Identities=27%  Similarity=0.377  Sum_probs=61.3

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHHH
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQE  175 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~~  175 (301)
                      ...|+.|+-|+..|+..||+-|   ....|.++.||.+++..+.|+++||++||||||+|.||..+...+
T Consensus       142 k~nRkPRtPFTtqQLlaLErkf---rekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~E  208 (246)
T KOG0492|consen  142 KPNRKPRTPFTTQQLLALERKF---REKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELE  208 (246)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHH---hHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHH
Confidence            3467889999999999999999   999999999999999999999999999999999999997654444

>KOG0487|consensus

Probab=99.49  E-value=9.8e-15  Score=134.49  Aligned_cols=62  Identities=37%  Similarity=0.533  Sum_probs=59.0

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      ..||||--+++.|+.+||+.|   ..|.|.+.+.|.+|++.|+||++||+|||||||+|.||..+
T Consensus       234 ~~RKKRcPYTK~QtlELEkEF---lfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r  295 (308)
T KOG0487|consen  234 RGRKKRCPYTKHQTLELEKEF---LFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR  295 (308)
T ss_pred             ccccccCCchHHHHHHHHHHH---HHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence            467889999999999999999   99999999999999999999999999999999999999875

>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=99.48  E-value=4.8e-14  Score=99.44  Aligned_cols=57  Identities=44%  Similarity=0.740  Sum_probs=54.1

Q ss_pred             CCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541         110 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN  169 (301)
Q Consensus       110 r~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~  169 (301)
                      ++|+.|+.+++.+|+.+|   ..++||+..++..||..+||+..+|++||+|+|.+.++.
T Consensus         2 ~~r~~~~~~~~~~Le~~f---~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~   58 (59)
T cd00086           2 RKRTRFTPEQLEELEKEF---EKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS   58 (59)
T ss_pred             CCCCcCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence            577899999999999999   889999999999999999999999999999999998864

>smart00389 HOX Homeodomain

Probab=99.48  E-value=5e-14  Score=98.54  Aligned_cols=55  Identities=45%  Similarity=0.770  Sum_probs=52.1

Q ss_pred             CCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhh
Q psy5541         110 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK  167 (301)
Q Consensus       110 r~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~k  167 (301)
                      +.|+.|+.+++.+|+.+|   ..++||+..++..||..+||+..+|++||+|+|.+.+
T Consensus         2 k~r~~~~~~~~~~L~~~f---~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~   56 (56)
T smart00389        2 RKRTSFTPEQLEELEKEF---QKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK   56 (56)
T ss_pred             CCCCcCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence            567889999999999999   9999999999999999999999999999999999864

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

>KOG2251|consensus

Probab=99.46  E-value=3.5e-14  Score=123.69  Aligned_cols=67  Identities=33%  Similarity=0.552  Sum_probs=62.4

Q ss_pred             hhhhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhh
Q psy5541         103 SRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGK  172 (301)
Q Consensus       103 ~~~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~  172 (301)
                      ...++.||.||+|+..|+++||..|   .+..||+...|++||.+++|.+.+|+|||.|||+|+|++...
T Consensus        32 ~~pRkqRRERTtFtr~QlevLe~LF---~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q   98 (228)
T KOG2251|consen   32 SGPRKQRRERTTFTRKQLEVLEALF---AKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ   98 (228)
T ss_pred             ccchhcccccceecHHHHHHHHHHH---HhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence            3456778999999999999999999   999999999999999999999999999999999999997653

>KOG1168|consensus

Probab=99.44  E-value=3.5e-14  Score=127.68  Aligned_cols=122  Identities=25%  Similarity=0.368  Sum_probs=90.9

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhcCCCCCChHH----HHHHHHHHhhhhhHH--------------HHHHhhhHHHHHHH
Q psy5541          39 ELEKYEQACSEFTTHVMNLLREQSRTRPITPKE----IERMVQIIHRKFSSI--------------QMQLKQSTCEAVMI  100 (301)
Q Consensus        39 el~ky~~~~~~f~~~~~~~l~~q~~~~~l~~~~----~~~~~~~~~~~f~~~--------------~~~l~~~~~~~~~~  100 (301)
                      +||.|   +++|++++|.++-+|.+++-.....    ...++++.+|+|+.+              +.||..    +...
T Consensus       218 eLEaF---AErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLTLSHNNMiALKPILqaWLEe----AE~a  290 (385)
T KOG1168|consen  218 ELEAF---AERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLTLSHNNMIALKPILQAWLEE----AEAA  290 (385)
T ss_pred             HHHHH---HHHHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeeeeccccCcchhhhHHHHHHHHH----HHHH
Confidence            45555   8899999999999998876322211    134556667777655              223321    1111


Q ss_pred             hhhhh-----------hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541         101 LRSRF-----------LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN  169 (301)
Q Consensus       101 l~~~~-----------~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~  169 (301)
                      .+.+.           ..+|||||.+-.-..+.||.+|   ...|.|+.+.+..||+++.|.+..|+|||||+|+|.||.
T Consensus       291 ~keK~~~pd~~~l~~~~ekKRKRTSIAAPEKRsLEayF---avQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm  367 (385)
T KOG1168|consen  291 MKEKDTKPDINELLPGGEKKRKRTSIAAPEKRSLEAYF---AVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM  367 (385)
T ss_pred             HHhhccCCchhhccCccccccccccccCcccccHHHHh---ccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence            22221           2368899999999999999999   999999999999999999999999999999999999984


Q ss_pred             h
Q psy5541         170 I  170 (301)
Q Consensus       170 ~  170 (301)
                      .
T Consensus       368 ~  368 (385)
T KOG1168|consen  368 K  368 (385)
T ss_pred             h
Confidence            3

>KOG0848|consensus

Probab=99.42  E-value=1.1e-13  Score=123.43  Aligned_cols=63  Identities=25%  Similarity=0.385  Sum_probs=59.0

Q ss_pred             CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHH
Q psy5541         109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQ  174 (301)
Q Consensus       109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~  174 (301)
                      -|-|.+++..|+-+||+.|   ..++|.++..|.+||..|||+++||++||||||+|+||.+++..
T Consensus       200 DKYRvVYTDhQRLELEKEf---h~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~  262 (317)
T KOG0848|consen  200 DKYRVVYTDHQRLELEKEF---HTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR  262 (317)
T ss_pred             cceeEEecchhhhhhhhhh---ccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence            4568899999999999999   99999999999999999999999999999999999999887764

>KOG0494|consensus

Probab=99.40  E-value=1.7e-13  Score=121.57  Aligned_cols=62  Identities=31%  Similarity=0.528  Sum_probs=57.2

Q ss_pred             cCCC-CCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhh
Q psy5541         108 ARRK-RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGK  172 (301)
Q Consensus       108 ~rr~-R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~  172 (301)
                      +||. ||.|+..|+..||+.|   ...+||+...|+.||.+|+|.+..|+|||||||+||||..+.
T Consensus       140 kRRh~RTiFT~~Qle~LEkaF---keaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~  202 (332)
T KOG0494|consen  140 KRRHFRTIFTSYQLEELEKAF---KEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR  202 (332)
T ss_pred             ccccccchhhHHHHHHHHHHH---hhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence            3444 8999999999999999   999999999999999999999999999999999999997553

>KOG0775|consensus

Probab=99.40  E-value=8.8e-13  Score=118.02  Aligned_cols=63  Identities=38%  Similarity=0.704  Sum_probs=55.0

Q ss_pred             hhhhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541         103 SRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK  168 (301)
Q Consensus       103 ~~~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk  168 (301)
                      +.+|+.--+--+|....+..|++||   ..++||++.+|.+||+.|||+..||.|||.|||+|.|-
T Consensus       171 rTIWDGEet~yCFKekSR~~LrewY---~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa  233 (304)
T KOG0775|consen  171 RTIWDGEETVYCFKEKSRSLLREWY---LQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA  233 (304)
T ss_pred             CccccCceeeeehhHhhHHHHHHHH---hcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence            3444444444578888899999999   99999999999999999999999999999999999984

>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=99.39  E-value=2.2e-13  Score=88.99  Aligned_cols=40  Identities=53%  Similarity=0.932  Sum_probs=35.5

Q ss_pred             HhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHH
Q psy5541         126 YFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIR  165 (301)
Q Consensus       126 ~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r  165 (301)
                      ||.+|..+|||+.++|..||..+||+..||.+||.|.|+|
T Consensus         1 Wl~~h~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR   40 (40)
T PF05920_consen    1 WLLEHLHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR   40 (40)
T ss_dssp             HHHHTTTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred             CHHHHCCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence            6788999999999999999999999999999999999987

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

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.33  E-value=1.2e-12  Score=92.31  Aligned_cols=52  Identities=17%  Similarity=0.402  Sum_probs=50.2

Q ss_pred             CCCCCCCCHHHHHHHHhHhhcCCCCCC----CCHHHHHHHHHHcCCCchhhhhhhhhhH
Q psy5541         109 RRKRRNFSKQASEILNEYFYSHLSNPY----PSEEAKEELARKCNITLSQVSNWFGNKR  163 (301)
Q Consensus       109 rr~R~~~~~~q~~~L~~~f~~h~~~~y----Ps~~~r~~LA~~~~L~~~qV~~WFqNrR  163 (301)
                      ||.||.|+.+|+..|+..|   ..++|    |+..++.+||..+||++.+|+|||+|-+
T Consensus         2 kR~RT~Ft~~Q~~~Le~~f---e~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         2 KRRRTKFTAEQKEKMRDFA---EKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCHHHHHHHHHHH---HHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            7899999999999999999   99999    9999999999999999999999999964

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

>KOG0493|consensus

Probab=99.30  E-value=1.3e-12  Score=116.13  Aligned_cols=59  Identities=34%  Similarity=0.575  Sum_probs=56.5

Q ss_pred             CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541         109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI  170 (301)
Q Consensus       109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~  170 (301)
                      ||.||.|+.+|+..|+..|   ..+.|.++..|.+||.+|+|.+.||++||||+|+|.||-.
T Consensus       247 KRPRTAFtaeQL~RLK~EF---~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT  305 (342)
T KOG0493|consen  247 KRPRTAFTAEQLQRLKAEF---QENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST  305 (342)
T ss_pred             cCccccccHHHHHHHHHHH---hhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence            5789999999999999999   9999999999999999999999999999999999999954

>KOG0491|consensus

Probab=99.30  E-value=5.8e-13  Score=110.92  Aligned_cols=65  Identities=29%  Similarity=0.450  Sum_probs=60.4

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhH
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKA  173 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~  173 (301)
                      .+++|.|++|+..|+..|++.|   +...|.+..++.+||..++|+++||+.||||||.|.||..++.
T Consensus        98 ~~r~K~Rtvfs~~ql~~l~~rF---e~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~  162 (194)
T KOG0491|consen   98 CRRRKARTVFSDPQLSGLEKRF---ERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNN  162 (194)
T ss_pred             HHhhhhcccccCccccccHHHH---hhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence            4557789999999999999999   9999999999999999999999999999999999999986644

>KOG0483|consensus

Probab=99.26  E-value=3.8e-12  Score=111.14  Aligned_cols=61  Identities=28%  Similarity=0.474  Sum_probs=56.3

Q ss_pred             CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhh
Q psy5541         109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGK  172 (301)
Q Consensus       109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~  172 (301)
                      .+++.+|+.+|+..||..|   ..+.|..+..|..||..+||.++||.|||||||+|||.....
T Consensus        51 ~~kk~Rlt~eQ~~~LE~~F---~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE  111 (198)
T KOG0483|consen   51 KGKKRRLTSEQVKFLEKSF---ESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLE  111 (198)
T ss_pred             ccccccccHHHHHHhHHhh---ccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhh
Confidence            4566789999999999999   999999999999999999999999999999999999986543

>KOG0486|consensus

Probab=99.25  E-value=2.9e-12  Score=116.71  Aligned_cols=69  Identities=32%  Similarity=0.554  Sum_probs=63.5

Q ss_pred             hhhhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHH
Q psy5541         103 SRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQ  174 (301)
Q Consensus       103 ~~~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~  174 (301)
                      .++.|+||.|+-|+..|+..||.||   .++.||+...|++||..++|++..|+|||.|||+||||..+...
T Consensus       107 kki~KqrrQrthFtSqqlqele~tF---~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~  175 (351)
T KOG0486|consen  107 KKISKQRRQRTHFTSQQLQELEATF---QRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ  175 (351)
T ss_pred             chhhhhhhhhhhhHHHHHHHHHHHH---hhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence            4456788899999999999999999   99999999999999999999999999999999999999866544

>KOG4577|consensus

Probab=99.24  E-value=5.5e-11  Score=107.16  Aligned_cols=65  Identities=23%  Similarity=0.471  Sum_probs=60.9

Q ss_pred             cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHHH
Q psy5541         108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQE  175 (301)
Q Consensus       108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~~  175 (301)
                      .||+||+++..|++.|+..|   ...|.|-...|++|+..|||+.+.|+|||||||+|+||-++....
T Consensus       167 nKRPRTTItAKqLETLK~AY---n~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR  231 (383)
T KOG4577|consen  167 NKRPRTTITAKQLETLKQAY---NTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGR  231 (383)
T ss_pred             cCCCcceeeHHHHHHHHHHh---cCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcch
Confidence            57899999999999999999   999999999999999999999999999999999999998776554

>KOG0844|consensus

Probab=99.19  E-value=5.1e-11  Score=108.10  Aligned_cols=65  Identities=26%  Similarity=0.404  Sum_probs=60.0

Q ss_pred             cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHHH
Q psy5541         108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQE  175 (301)
Q Consensus       108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~~  175 (301)
                      -||-||.|+.+|+..||+.|   .+.-|-+...|.+||..++|.+..|+|||||||.|.||+...+.+
T Consensus       181 mRRYRTAFTReQIaRLEKEF---yrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaW  245 (408)
T KOG0844|consen  181 MRRYRTAFTREQIARLEKEF---YRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAW  245 (408)
T ss_pred             HHHHHhhhhHHHHHHHHHHH---HHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccC
Confidence            36789999999999999999   788899999999999999999999999999999999998876543

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.17  E-value=3.5e-11  Score=101.65  Aligned_cols=64  Identities=31%  Similarity=0.459  Sum_probs=59.3

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhH
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKA  173 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~  173 (301)
                      ..+++|++.+..|+.+|++.|   ..+|||+...|..|+..++|+++-|++||||+|++.|+.....
T Consensus        50 ~~~~~r~R~t~~Q~~vL~~~F---~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~  113 (156)
T COG5576          50 PPKSKRRRTTDEQLMVLEREF---EINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGK  113 (156)
T ss_pred             cCcccceechHHHHHHHHHHh---ccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccc
Confidence            356788899999999999999   9999999999999999999999999999999999999976543

>KOG0773|consensus

Probab=99.10  E-value=7.2e-11  Score=112.14  Aligned_cols=66  Identities=38%  Similarity=0.662  Sum_probs=61.6

Q ss_pred             cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhH
Q psy5541         108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKA  173 (301)
Q Consensus       108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~  173 (301)
                      ++|+++.|++..+.+|+.|+++|..+|||+..+|..||.+|||+..||.|||+|+|.|.|+.....
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~  304 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIEE  304 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchHHH
Confidence            456778999999999999999999999999999999999999999999999999999999987643

>KOG0847|consensus

Probab=99.06  E-value=5.8e-11  Score=103.27  Aligned_cols=61  Identities=28%  Similarity=0.492  Sum_probs=56.8

Q ss_pred             cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      ++..|.+|+..|+..|+..|   ....|+-..++.+||..+|+++.||+|||||||.||||+..
T Consensus       167 rk~srPTf~g~qi~~le~~f---eqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA  227 (288)
T KOG0847|consen  167 RKQSRPTFTGHQIYQLERKF---EQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA  227 (288)
T ss_pred             ccccCCCccchhhhhhhhhh---hhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence            44568889999999999999   99999999999999999999999999999999999999754

>KOG2252|consensus

Probab=98.86  E-value=5.3e-09  Score=102.12  Aligned_cols=124  Identities=26%  Similarity=0.405  Sum_probs=93.1

Q ss_pred             HHHHHHHHHHHHhHHHHHHHHHHhhcCCCC--CChHHHHHHHHHHhhhhhHHHHHHhhhHHHH-HHHhhhh---------
Q psy5541          37 QQELEKYEQACSEFTTHVMNLLREQSRTRP--ITPKEIERMVQIIHRKFSSIQMQLKQSTCEA-VMILRSR---------  104 (301)
Q Consensus        37 ~~el~ky~~~~~~f~~~~~~~l~~q~~~~~--l~~~~~~~~~~~~~~~f~~~~~~l~~~~~~~-~~~l~~~---------  104 (301)
                      ..||++|.---+-|-+++.  +++|+-...  ..++.|..+.. -+..|..+..||.+-.... +..|+.+         
T Consensus       336 ~~eLk~~sIpQaiFAervL--cRSQGTLSDLLrnPKPW~klKs-GRetFrRM~~WL~eP~~~r~m~~L~~~a~kRke~ep  412 (558)
T KOG2252|consen  336 KAELKRYSIPQAIFAERVL--CRSQGTLSDLLRNPKPWSKLKS-GRETFRRMANWLEEPEFQRLMSALRKKACKRKEQEP  412 (558)
T ss_pred             HHHHhhcCCcHHHHHHHHh--hcccchHHHHhhCCCchhhhcc-ccHHHHHHHHHhcCHHHHHHHHHHHHHHhhhcccCC
Confidence            3477777665666777664  667766542  24677776654 5667777777775444444 2223222         


Q ss_pred             ----hhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHh
Q psy5541         105 ----FLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRY  166 (301)
Q Consensus       105 ----~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~  166 (301)
                          ....||.|.+|+..|++.|...|   ..+++|+.+..+.|+.+|+|....|.|||-|.|+|.
T Consensus       413 ~~d~~~~~KKPRlVfTd~QkrTL~aiF---ke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  413 TDDKMLQTKKPRLVFTDIQKRTLQAIF---KENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             CccccccCCCceeeecHHHHHHHHHHH---hcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence                22357889999999999999999   999999999999999999999999999999999996

>KOG0490|consensus

Probab=98.86  E-value=1.4e-09  Score=97.16  Aligned_cols=64  Identities=23%  Similarity=0.250  Sum_probs=59.7

Q ss_pred             hhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         105 FLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       105 ~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      ..++|+.|+.|+..++.+|++.|   ...+||+...++.||..+++++..|+|||||+|++|+++..
T Consensus        57 ~~~~rr~rt~~~~~ql~~ler~f---~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~  120 (235)
T KOG0490|consen   57 KFSKRCARCKFTISQLDELERAF---EKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER  120 (235)
T ss_pred             hccccccCCCCCcCHHHHHHHhh---cCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence            34568899999999999999999   89999999999999999999999999999999999999764

>KOG0849|consensus

Probab=98.73  E-value=5.1e-08  Score=93.01  Aligned_cols=62  Identities=32%  Similarity=0.641  Sum_probs=58.3

Q ss_pred             cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhh
Q psy5541         108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGK  172 (301)
Q Consensus       108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~  172 (301)
                      .+|.|++|+..|+..|+++|   .+++||....|+.||.++++++..|.+||+|||.|++|....
T Consensus       176 ~rr~rtsft~~Q~~~le~~f---~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~  237 (354)
T KOG0849|consen  176 GRRNRTSFSPSQLEALEECF---QRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD  237 (354)
T ss_pred             ccccccccccchHHHHHHHh---cCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence            56678999999999999999   999999999999999999999999999999999999998643

>KOG0490|consensus

Probab=97.51  E-value=9.5e-05  Score=65.87  Aligned_cols=62  Identities=27%  Similarity=0.590  Sum_probs=57.4

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      +.++.|+.+...++..+...|   ...++|+...+..|+..+|++...|.+||+|+|.+.++...
T Consensus       152 ~~~~~~~~~~~~~~~~~~~~~---~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  152 KPRRPRTTFTENQLEVLETVF---RATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             ccCCCccccccchhHhhhhcc---cCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            456778999999999999999   99999999999999999999999999999999999998654

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

Probab=96.86  E-value=0.0004  Score=48.40  Aligned_cols=42  Identities=29%  Similarity=0.569  Sum_probs=30.5

Q ss_pred             HHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHH
Q psy5541         120 SEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRI  164 (301)
Q Consensus       120 ~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~  164 (301)
                      +..|+++|   ..+.++.+.+-..|..+++|+..||+.||--++.
T Consensus        10 ~~pL~~Yy---~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~   51 (56)
T PF11569_consen   10 IQPLEDYY---LKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ   51 (56)
T ss_dssp             -HHHHHHH---HHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred             hHHHHHHH---HHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence            45599999   7888999999999999999999999999976543

>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2

Probab=96.76  E-value=0.0028  Score=43.55  Aligned_cols=36  Identities=25%  Similarity=0.295  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHh
Q psy5541          25 YRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLRE   60 (301)
Q Consensus        25 ~~~kl~qv~~~~~~el~ky~~~~~~f~~~~~~~l~~   60 (301)
                      -+++||+||+.||.+|.+|++...+...+.+.+++.
T Consensus         7 ~dpELDqFMeaYc~~L~kykeeL~~p~~EA~~f~~~   42 (52)
T PF03791_consen    7 ADPELDQFMEAYCDMLVKYKEELQRPFQEAMEFCRE   42 (52)
T ss_pred             CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            367899999999999999999999988888877743

KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus

>KOG1146|consensus

Probab=96.69  E-value=0.0011  Score=71.14  Aligned_cols=61  Identities=21%  Similarity=0.275  Sum_probs=57.6

Q ss_pred             cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      .|+.|+.++..++.++...|   ....||...+.+.|-..+++..+.|.+||+|.|.|.||...
T Consensus       903 r~a~~~~~~d~qlk~i~~~~---~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~  963 (1406)
T KOG1146|consen  903 RRAYRTQESDLQLKIIKACY---EAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL  963 (1406)
T ss_pred             hhhhccchhHHHHHHHHHHH---hhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence            57789999999999999999   99999999999999999999999999999999999998754

>PF07526 POX: Associated with HOX; InterPro: IPR006563 This domain in found exclusively in plant proteins, associated with HOX domains which may suggest these proteins are homeodomain transcription factors

Probab=94.94  E-value=0.099  Score=43.57  Aligned_cols=65  Identities=15%  Similarity=0.294  Sum_probs=47.1

Q ss_pred             CCCChHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhh--cCCCCCChHHHHHHHHHHhhhhhHHH
Q psy5541          19 AIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQ--SRTRPITPKEIERMVQIIHRKFSSIQ   87 (301)
Q Consensus        19 ~le~~~~~~kl~qv~~~~~~el~ky~~~~~~f~~~~~~~l~~q--~~~~~l~~~~~~~~~~~~~~~f~~~~   87 (301)
                      ..+..+++.|..+|+.+..++.++|+++|.++...+.+|-.--  +...+++.-.+..    |.+.|..++
T Consensus        69 ~~~~~e~q~kK~KLl~mL~eVd~RY~qY~~Qmq~VvssFe~vaG~gaA~~YtalAlqa----mSrhFR~LR  135 (140)
T PF07526_consen   69 PAERQELQRKKAKLLSMLDEVDRRYRQYYDQMQAVVSSFEAVAGLGAAAPYTALALQA----MSRHFRCLR  135 (140)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchhhHHHHHHH----HHHHHHHHH
Confidence            3567789999999999999999999999999999999885433  3333444444444    445554443

>KOG0773|consensus

Probab=94.51  E-value=0.02  Score=54.43  Aligned_cols=109  Identities=28%  Similarity=0.382  Sum_probs=76.0

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhhhhhHHHHHHhhhHHHHHHHhhhhhhhcCCCCC
Q psy5541          34 TIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRR  113 (301)
Q Consensus        34 ~~~~~el~ky~~~~~~f~~~~~~~l~~q~~~~~l~~~~~~~~~~~~~~~f~~~~~~l~~~~~~~~~~l~~~~~~~rr~R~  113 (301)
                      ..+...+...+.+|++||.....++.......++..-  .         +                 .........+++.
T Consensus        49 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~--~---------~-----------------~~~~~~~~~~~~~  100 (342)
T KOG0773|consen   49 LASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRS--P---------A-----------------SLSPPEDKGARRG  100 (342)
T ss_pred             cccccccccchhHHhHHhhccccccccccCcCccccc--c---------c-----------------cccCccccccccc
Confidence            3344466666777888888777776555554432110  0         0                 0000111224455


Q ss_pred             CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      ..+.+. ..|..|...|..++||+..++..++..++|+..+|.+||.|.|++.++...
T Consensus       101 n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~  157 (342)
T KOG0773|consen  101 NATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELK  157 (342)
T ss_pred             cccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccC
Confidence            666666 778889999999999999999999999999999999999999999887543

>smart00574 POX domain associated with HOX domains

Probab=94.33  E-value=0.15  Score=42.19  Aligned_cols=42  Identities=14%  Similarity=0.255  Sum_probs=36.8

Q ss_pred             CCCChHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHh
Q psy5541          19 AIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLRE   60 (301)
Q Consensus        19 ~le~~~~~~kl~qv~~~~~~el~ky~~~~~~f~~~~~~~l~~   60 (301)
                      .+|..+++.|..+|+.+..++.++|+++|.++...+.+|-.-
T Consensus        69 ~~~r~e~q~kk~kLl~mL~eVd~RY~qY~~qmq~v~ssFe~v  110 (140)
T smart00574       69 TAERQELQRKKAKLLSMLEEVDRRYKHYYEQMQTVVSSFDQA  110 (140)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            446678999999999999999999999999999998888543

>PF00157 Pou: Pou domain - N-terminal to homeobox domain; InterPro: IPR000327 POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain

Probab=92.04  E-value=0.047  Score=40.45  Aligned_cols=56  Identities=21%  Similarity=0.347  Sum_probs=39.0

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhcCCCCCChHHH-HHHHHHHhhhhhHHHHHHhhhHH
Q psy5541          39 ELEKYEQACSEFTTHVMNLLREQSRTRPITPKEI-ERMVQIIHRKFSSIQMQLKQSTC   95 (301)
Q Consensus        39 el~ky~~~~~~f~~~~~~~l~~q~~~~~l~~~~~-~~~~~~~~~~f~~~~~~l~~~~~   95 (301)
                      .++..+++++.|+.++|.++.+|.+++..-.... ..++++.+++|+.++..++ ++|
T Consensus         5 ~~~ele~Fa~~fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~L~LS~k-n~~   61 (75)
T PF00157_consen    5 DLKELEQFAKEFKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEALQLSFK-NMC   61 (75)
T ss_dssp             HHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHTTTSCHH-HHH
T ss_pred             CHHHHHHHHHHHHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHhcccCHH-HHH
Confidence            3455666699999999999999998764322222 2467888999999988877 444

The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system [] and the development of an organism []. Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) [, ], and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1). The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (IPR000327 from INTERPRO), while the C-terminal subunit is a homeobox domain (IPR007103 from INTERPRO). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions []. The subdomains are connected by a flexible linker [, , ]. In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [, ]. This entry represents the POU-specific subunit of the POU domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3D1N_O 1AU7_A 3L1P_A 2XSD_C 1O4X_A 1HF0_B 1GT0_C 1POU_A 1CQT_B 1E3O_C ....

>KOG3623|consensus

Probab=91.71  E-value=0.18  Score=51.79  Aligned_cols=48  Identities=23%  Similarity=0.477  Sum_probs=44.1

Q ss_pred             HHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541         120 SEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI  170 (301)
Q Consensus       120 ~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~  170 (301)
                      +..|..+|   ..|+.|+..+-..+|.+.||..+.|+.||.+++.......
T Consensus       568 ~sllkayy---aln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~  615 (1007)
T KOG3623|consen  568 TSLLKAYY---ALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE  615 (1007)
T ss_pred             HHHHHHHH---HhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence            77889999   9999999999999999999999999999999999876543

>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=91.70  E-value=0.3  Score=33.63  Aligned_cols=47  Identities=23%  Similarity=0.355  Sum_probs=33.2

Q ss_pred             CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhH
Q psy5541         109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKR  163 (301)
Q Consensus       109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR  163 (301)
                      ||+|..++-++...+-..+   ...+     -...||+.+|++..+|..|..|+.
T Consensus         1 krkR~~LTl~eK~~iI~~~---e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~   47 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRL---EEGE-----SKRDIAREFGVSRSTVSTILKNKD   47 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHH---HCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred             CCCCccCCHHHHHHHHHHH---HcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence            4788899988877776666   4444     477899999999999999998853

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	301
1b72_B	87	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		3e-35
1puf_B	73	Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo		1e-34
1lfu_P	82	Nmr Solution Stucture Of The Extended Pbx Homeodoma		5e-34
1b8i_B	63	Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX		9e-31
1du6_A	64	Solution Structure Of The Truncated Pbx Homeodomain		5e-25
1x2n_A	73	Solution Structure Of The Homeobox Domain Of Human		1e-08
3k2a_A	67	Crystal Structure Of The Homeobox Domain Of Human H		9e-08
2dmn_A	83	The Solution Structure Of The Homeobox Domain Of Hu		2e-07
4egc_A	559	Crystal Structure Of Mbp-fused Human Six1 Bound To		5e-06
2lk2_A	89	Solution Nmr Structure Of Homeobox Domain (171-248)		2e-05
3d1n_I	151	Structure Of Human Brn-5 Transcription Factor In Co		5e-04
1apl_C	83	Crystal Structure Of A Mat-Alpha2 Homeodomain-Opera		9e-04

>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Length = 87

Iteration: 1
 Score =  145 bits (366), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 66/73 (90%), Positives = 71/73 (97%)
Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
           ARRKRRNF+KQA+EILNEYFYSHLSNPYPSEEAKEELA+KC IT+SQVSNWFGNKRIRYK
Sbjct: 1   ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 168 KNIGKAQEEANLY 180
           KNIGK QEEAN+Y
Sbjct: 61  KNIGKFQEEANIY 73

>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To Dna Length = 73

Iteration: 1
 Score =  143 bits (361), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 66/73 (90%), Positives = 71/73 (97%)
Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
           ARRKRRNF+KQA+EILNEYFYSHLSNPYPSEEAKEELA+KC IT+SQVSNWFGNKRIRYK
Sbjct: 1   ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 168 KNIGKAQEEANLY 180
           KNIGK QEEAN+Y
Sbjct: 61  KNIGKFQEEANIY 73

>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain Bound To Dna Length = 82

Iteration: 1
 Score =  141 bits (355), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 65/73 (89%), Positives = 70/73 (95%)
Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
           ARRKRRNF+KQA+EILNEYFYSHLSNPYPSEEAKEELA+K  IT+SQVSNWFGNKRIRYK
Sbjct: 2   ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYK 61
Query: 168 KNIGKAQEEANLY 180
           KNIGK QEEAN+Y
Sbjct: 62  KNIGKFQEEANIY 74

>pdb|1B8I|B Chain B, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX Length = 63

Iteration: 1
 Score =  130 bits (327), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 61/63 (96%), Positives = 62/63 (98%)
Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
           ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKC IT+SQVSNWFGNKRIRYK
Sbjct: 1   ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYK 60
Query: 168 KNI 170
           KNI
Sbjct: 61  KNI 63

>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain Length = 64

Iteration: 1
 Score =  111 bits (278), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 50/57 (87%), Positives = 55/57 (96%)
Query: 113 RNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN 169
           R+ +KQA+EILNEYFYSHLSNPYPSEEAKEELA+KC IT+SQVSNWFGNKRIRYKKN
Sbjct: 8   RHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN 64

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 38/58 (65%)
Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIR 165
            + KR    K A+ ++  + + H+ +PYP+E+ K+++A + N+TL QV+NWF N R R
Sbjct: 7   GKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRR 64

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 24/51 (47%), Positives = 35/51 (68%)
Query: 115 FSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIR 165
           F K A+ I   + + HL++PYPSEE K++LA+   +T+ QV+NWF N R R
Sbjct: 5   FPKVATNIXRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRR 55

>pdb|2DMN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human Homeobox Protein Tgif2lx Length = 83

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 37/58 (63%)
Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIR 165
            ++++ N   ++ +IL ++ Y H    YPSEE K+ L+ K N++L Q+SNWF N R R
Sbjct: 7   GKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRR 64

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/51 (47%), Positives = 33/51 (64%), Gaps = 3/51 (5%)
Query: 115 FSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIR 165
           F +++  +L E+ Y+H  NPYPS   K ELA    +T +QVSNWF N+R R
Sbjct: 501 FKEKSRGVLREW-YAH--NPYPSPREKRELAEATGLTTTQVSNWFKNRRQR 548

>pdb|2LK2|A Chain A, Solution Nmr Structure Of Homeobox Domain (171-248) Of Human Homeobox Protein Tgif1, Northeast Structural Genomics Consortium Target Hr4411b Length = 89

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/49 (40%), Positives = 32/49 (65%)
Query: 117 KQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIR 165
           K++ +IL ++ Y H  N YPSE+ K  L+++ +++  QV NWF N R R
Sbjct: 14  KESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRR 62

>pdb|3D1N|I Chain I, Structure Of Human Brn-5 Transcription Factor In Complex With Corticotrophin-Releasing Hormone Gene Promoter Length = 151

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 25/97 (25%), Positives = 47/97 (48%), Gaps = 3/97 (3%)
Query: 67  ITPKEIERMVQIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEY 126
           ITPK  +++  ++ +  +  +++ ++        +       R++R +F+ QA E LN Y
Sbjct: 52  ITPKSAQKLKPVLEKWLNEAELRNQEGQQNLXEFVGGEPSKKRKRRTSFTPQAIEALNAY 111
Query: 127 FYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKR 163
           F     NP P+ +   E A++ N     V  WF N+R
Sbjct: 112 FEK---NPLPTGQEITEXAKELNYDREVVRVWFSNRR 145

>pdb|1APL|C Chain C, Crystal Structure Of A Mat-Alpha2 Homeodomain-Operator Complex Suggests A General Model For Homeodomain-Dna Interactions Length = 83

Iteration: 1
 Score = 40.8 bits (94), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 115 FSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQ 174
           F+K+   IL  +F  ++ NPY   +  E L +  +++  Q+ NW  N+R R +K I  A 
Sbjct: 9   FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR-RKEKTITIAP 67
Query: 175 EEANL 179
           E A+L
Sbjct: 68  ELADL 72

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	301
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	1e-36
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	6e-35
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	2e-30
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	6e-25
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	1e-24
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	2e-24
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	4e-24
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	2e-23
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	4e-23
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	9e-23
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	7e-14
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	2e-11
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	2e-11
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	3e-11
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	2e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	2e-09
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	2e-09
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	4e-09
1lfb_A	99	Liver transcription factor (LFB1); transcription r	5e-09
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	7e-09
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	1e-08
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	1e-08
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	1e-08
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	2e-08
1e3o_C	160	Octamer-binding transcription factor 1; transcript	7e-08
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	1e-07
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	1e-07
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	2e-07
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	2e-07
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	2e-07
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	4e-07
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	5e-07
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	6e-07
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	7e-07
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	8e-07
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	1e-06
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	2e-06
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	2e-06
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	2e-06
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	2e-06
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	4e-06
1uhs_A	72	HOP, homeodomain only protein; structural genomics	4e-06
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	8e-06
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	9e-06
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	1e-05
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	1e-05
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	2e-05
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	4e-05
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	5e-05
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	1e-04
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	2e-04
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	2e-04
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	2e-04
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	2e-04
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	3e-04
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	3e-04
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	4e-04
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	4e-04
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	5e-04
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	6e-04
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	7e-04

>1b72_B Protein (PBX1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1 PDB: 1lfu_P Length = 87

 Score =  125 bits (315), Expect = 1e-36
 Identities = 72/85 (84%), Positives = 78/85 (91%)

Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
           ARRKRRNF+KQA+EILNEYFYSHLSNPYPSEEAKEELA+KC IT+SQVSNWFGNKRIRYK
Sbjct: 1   ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60

Query: 168 KNIGKAQEEANLYAAKKAAGASPYS 192
           KNIGK QEEAN+YAAK A  A+  S
Sbjct: 61  KNIGKFQEEANIYAAKTAVTATNVS 85

>1puf_B PRE-B-cell leukemia transcription factor-1; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Homo sapiens} SCOP: a.4.1.1 PDB: 1b8i_B* 2r5y_B* 2r5z_B* Length = 73

 Score =  120 bits (303), Expect = 6e-35
 Identities = 66/73 (90%), Positives = 71/73 (97%)

Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
           ARRKRRNF+KQA+EILNEYFYSHLSNPYPSEEAKEELA+KC IT+SQVSNWFGNKRIRYK
Sbjct: 1   ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60

Query: 168 KNIGKAQEEANLY 180
           KNIGK QEEAN+Y
Sbjct: 61  KNIGKFQEEANIY 73

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

 Score =  108 bits (272), Expect = 2e-30
 Identities = 50/62 (80%), Positives = 56/62 (90%)

Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
              + R+ +KQA+EILNEYFYSHLSNPYPSEEAKEELA+KC IT+SQVSNWFGNKRIRYK
Sbjct: 3   GHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 62

Query: 168 KN 169
           KN
Sbjct: 63  KN 64

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

 Score = 93.9 bits (234), Expect = 6e-25
 Identities = 25/66 (37%), Positives = 39/66 (59%)

Query: 112 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171
              F K A+ I+  + + HL++PYPSEE K++LA+   +T+ QV+NWF N R R  + + 
Sbjct: 2   SGIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMI 61

Query: 172 KAQEEA 177
                A
Sbjct: 62  DQSNRA 67

>2dmn_A Homeobox protein TGIF2LX; TGFB-induced factor 2-like protein, X-linked TGF(beta) induced transcription factor 2-like protein, TGIF-like on the X; NMR {Homo sapiens} Length = 83

 Score = 93.7 bits (233), Expect = 1e-24
 Identities = 23/68 (33%), Positives = 41/68 (60%)

Query: 107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRY 166
             ++++ N   ++ +IL ++ Y H    YPSEE K+ L+ K N++L Q+SNWF N R R 
Sbjct: 6   SGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRI 65

Query: 167 KKNIGKAQ 174
             ++ + +
Sbjct: 66  LPDMLQQR 73

>1x2n_A Homeobox protein pknox1; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 73

 Score = 92.8 bits (231), Expect = 2e-24
 Identities = 22/63 (34%), Positives = 40/63 (63%)

Query: 107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRY 166
             + KR    K A+ ++  + + H+ +PYP+E+ K+++A + N+TL QV+NWF N R R 
Sbjct: 6   SGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRI 65

Query: 167 KKN 169
            ++
Sbjct: 66  LQS 68

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

 Score = 92.6 bits (230), Expect = 4e-24
 Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 1/84 (1%)

Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
                    K++ +IL ++ Y H  N YPSE+ K  L+++ +++  QV NWF N R R  
Sbjct: 5   HHHHSHMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLL 64

Query: 168 KN-IGKAQEEANLYAAKKAAGASP 190
            + + K  ++ N +   +      
Sbjct: 65  PDMLRKDGKDPNQFTISRRGAKIS 88

>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 = 89.7 bits (223), Expect = 2e-23
 Identities = 16/58 (27%), Positives = 30/58 (51%)

Query: 111 KRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           +   F+K+   IL  +F  ++ NPY   +  E L +  +++  Q+ NW  N+R + K 
Sbjct: 1   RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

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

 Score = 89.9 bits (223), Expect = 4e-23
 Identities = 16/59 (27%), Positives = 30/59 (50%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
             +   F+K+   IL  +F  ++ NPY   +  E L +  +++  Q+ NW  N+R + K
Sbjct: 28  PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK 86

>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 = 88.7 bits (220), Expect = 9e-23
 Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 1/79 (1%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
             +   F+K+   IL  +F  ++ NPY   +  E L +  +++  Q+ NW   +R   +K
Sbjct: 3   PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARR-AKEK 61

Query: 169 NIGKAQEEANLYAAKKAAG 187
            I  A E A+L + +  A 
Sbjct: 62  TITIAPELADLLSGEPLAK 80

>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 = 65.4 bits (159), Expect = 7e-14
 Identities = 23/85 (27%), Positives = 34/85 (40%), Gaps = 18/85 (21%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCN---------------ITLS 153
           R  R  + K+   ++  YF     N YP E  +EE+A  CN               +T  
Sbjct: 8   RGSRFTWRKECLAVMESYFNE---NQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSL 64

Query: 154 QVSNWFGNKRIRYKKNIGKAQEEAN 178
           +V NWF N+R   K+    A    +
Sbjct: 65  KVYNWFANRRKEIKRRANIAAILES 89

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

 Score = 57.8 bits (140), Expect = 2e-11
 Identities = 13/68 (19%), Positives = 24/68 (35%), Gaps = 3/68 (4%)

Query: 107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRY 166
            A   +   S +    L   F     N +P +   E L +   ++  +V  WF ++R   
Sbjct: 7   GASIYKNKKSHEQLSALKGSF---CRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHC 63

Query: 167 KKNIGKAQ 174
           +   G   
Sbjct: 64  RNLKGSRS 71

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

 Score = 57.5 bits (139), Expect = 2e-11
 Identities = 13/64 (20%), Positives = 24/64 (37%), Gaps = 3/64 (4%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
               R  +K+    L   F   L + +P +     L     +  S++  WF + R R ++
Sbjct: 5   HHHHRKKTKEQIAHLKASF---LQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR 61

Query: 169 NIGK 172
            I  
Sbjct: 62  GIVH 65

>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 71

 Score = 57.1 bits (138), Expect = 3e-11
 Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 2/61 (3%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
            R R   S +A  IL  +   H    YP +EA   L+ + ++    +  +F N+R   K 
Sbjct: 8   PRSRTKISLEALGILQSFI--HDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH 65

Query: 169 N 169
           +
Sbjct: 66  S 66

>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 = 54.5 bits (132), Expect = 2e-10
 Identities = 23/60 (38%), Positives = 32/60 (53%), Gaps = 3/60 (5%)

Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
           + + + + S QA   L E F         + + KEE+A+KC IT  QV  WF NKR+R K
Sbjct: 5   SPKGKSSISPQARAFLEEVFRRK---QSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61

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

 Score = 60.3 bits (145), Expect = 2e-10
 Identities = 35/176 (19%), Positives = 57/176 (32%), Gaps = 46/176 (26%)

Query: 16  LLHAIEHSDYRAKLAQIRTIYQQELEKYEQACSEF------TTHVMNLLREQSRTRPITP 69
           L   IE S        +  +   E  K     S F       T +++L+           
Sbjct: 355 LTTIIESS--------LNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDV-----IK 401

Query: 70  KEIERMVQIIHRKFSSIQMQLKQST-------------CEAVMILRSRFLDARRKRRNFS 116
            ++  +V  +H+  S ++ Q K+ST              E    L    +D     + F 
Sbjct: 402 SDVMVVVNKLHKY-SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFD 460

Query: 117 KQ--ASEILNEYFYS----HLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRY 166
                   L++YFYS    HL N    E  +  L R   +       +   K IR+
Sbjct: 461 SDDLIPPYLDQYFYSHIGHHLKNIEHPE--RMTLFRMVFLDF----RFLEQK-IRH 509

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

 Score = 45.2 bits (106), Expect = 2e-05
 Identities = 48/339 (14%), Positives = 98/339 (28%), Gaps = 103/339 (30%)

Query: 24  DYRAKLAQIRTIYQQ---ELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQIIH 80
           +Y+  ++ I+T  +Q       Y +             R  +  +      + R      
Sbjct: 90  NYKFLMSPIKTEQRQPSMMTRMYIEQRD----------RLYNDNQVFAKYNVSR-----L 134

Query: 81  RKFSSIQ---MQLKQS-------------TCEAVMILRSRFLDARRKRR----NFSKQAS 120
           + +  ++   ++L+ +             T  A+ +  S  +  +   +    N     S
Sbjct: 135 QPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNS 194

Query: 121 -----EILNEYFY----------SHLSN-PYPSEEAKEELAR--------KCNITLSQVS 156
                E+L +  Y           H SN        + EL R         C + L  V 
Sbjct: 195 PETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQ 254

Query: 157 NW-----FGNK-RI----RYKKNIGKAQEEANLYAAKKAAGASPYSMGASTPMMSPAPDS 206
           N      F    +I    R+K+                AA  +  S+   +  ++P  + 
Sbjct: 255 NAKAWNAFNLSCKILLTTRFKQVT----------DFLSAATTTHISLDHHSMTLTP-DEV 303

Query: 207 VG-YSKEANLYAAK---KAAGASPY--SM-GASTPMMSPAPDSVGYSSMEDRMHNTNMLP 259
                K  +        +    +P   S+       +     +        +  N + L 
Sbjct: 304 KSLLLKYLDCRPQDLPREVLTTNPRRLSIIAE---SIRDGLATWDNW----KHVNCDKLT 356

Query: 260 NYIEGANDINT-DPQGPRK--QDISDILQQILNITDQSL 295
             IE  + +N  +P   RK    +S +     +I    L
Sbjct: 357 TIIE--SSLNVLEPAEYRKMFDRLS-VFPPSAHIPTILL 392

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

 Score = 55.8 bits (133), Expect = 2e-09
 Identities = 26/161 (16%), Positives = 50/161 (31%), Gaps = 34/161 (21%)

Query: 28  KLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQIIHRKFSSIQ 87
           K  +   +Y   + K  +   +F   V      QS          ++++ +         
Sbjct: 72  KTQKRAALYTWYVRKQREILRQFNQTV------QSSGNMTDKSSQDQLLFLFPEFSQQSH 125

Query: 88  MQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARK 147
              +     +    +      RR R  +   + +IL + +        PS+E +E L  +
Sbjct: 126 GPGQSDDACSEPTNKKM----RRNRFKWGPASQQILYQAY---DRQKNPSKEEREALVEE 178

Query: 148 CN---------------------ITLSQVSNWFGNKRIRYK 167
           CN                     +T  +V NWF N+R    
Sbjct: 179 CNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEEA 219

>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 = 54.3 bits (130), Expect = 2e-09
 Identities = 26/102 (25%), Positives = 50/102 (49%), Gaps = 3/102 (2%)

Query: 67  ITPKEIERMVQIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEY 126
           ITPK  +++  ++ +  +  +++ ++     +  +       R++R +F+ QA E LN Y
Sbjct: 52  ITPKSAQKLKPVLEKWLNEAELRNQEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEALNAY 111

Query: 127 FYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           F     NP P+ +   E+A++ N     V  WF N+R   K 
Sbjct: 112 F---EKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN 150

>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 = 51.4 bits (123), Expect = 4e-09
 Identities = 13/71 (18%), Positives = 27/71 (38%), Gaps = 3/71 (4%)

Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
              K +  + +    L   F     NP P +E  + L  +  +T  ++ +WF  +R +  
Sbjct: 7   GPTKYKERAPEQLRALESSF---AQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVN 63

Query: 168 KNIGKAQEEAN 178
               K    ++
Sbjct: 64  AEETKKSGPSS 74

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

 Score = 52.1 bits (124), Expect = 5e-09
 Identities = 19/81 (23%), Positives = 30/81 (37%), Gaps = 24/81 (29%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCN------------------- 149
           RR R  +   + +IL + +        PS+E +E L  +CN                   
Sbjct: 10  RRNRFKWGPASQQILFQAYER---QKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGS 66

Query: 150 --ITLSQVSNWFGNKRIRYKK 168
             +T  +V NWF N+R     
Sbjct: 67  NLVTEVRVYNWFANRRKEEAF 87

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

 Score = 53.7 bits (128), Expect = 7e-09
 Identities = 19/80 (23%), Positives = 30/80 (37%), Gaps = 24/80 (30%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCN------------------- 149
           RR R  +   + +IL + +        PS+E +E L  +CN                   
Sbjct: 116 RRNRFKWGPASQQILFQAY---ERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGS 172

Query: 150 --ITLSQVSNWFGNKRIRYK 167
             +T  +V NWF N+R    
Sbjct: 173 NLVTEVRVYNWFANRRKEEA 192

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

 Score = 50.1 bits (120), Expect = 1e-08
 Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 2/72 (2%)

Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
           + +     ++   EIL   F  +  N +P       +A +  +T  Q   WF  +   ++
Sbjct: 2   SAQTVSGPTEDQVEILEYNF--NKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 59

Query: 168 KNIGKAQEEANL 179
           ++ G   E  ++
Sbjct: 60  RSEGLPSECRSV 71

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

 Score = 52.6 bits (125), Expect = 1e-08
 Identities = 24/146 (16%), Positives = 55/146 (37%), Gaps = 19/146 (13%)

Query: 37  QQELEKYEQACSEFTTHVMNLLR--------------EQSRTRPITPKEIERMVQIIHRK 82
             EL++Y    + F   V+   +              +    R    +  + + +   ++
Sbjct: 14  TTELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPEFQR 73

Query: 83  FSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKE 142
            S++++   +   +     R      ++ R  F+      L+  F  +     PS+E + 
Sbjct: 74  MSALRLAACKRKEQEHGKDRGN--TPKKPRLVFTDVQRRTLHAIFKEN---KRPSKELQI 128

Query: 143 ELARKCNITLSQVSNWFGNKRIRYKK 168
            ++++  + LS VSN+F N R R   
Sbjct: 129 TISQQLGLELSTVSNFFMNARRRSLD 154

>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 = 50.1 bits (120), Expect = 1e-08
 Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 3/61 (4%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           R  R  F+     +L ++F +   N YP ++  E+L+   N+    +  WF N R + +K
Sbjct: 8   RSSRTRFTDYQLRVLQDFFDA---NAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64

Query: 169 N 169
           +
Sbjct: 65  S 65

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

 Score = 49.3 bits (118), Expect = 2e-08
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 3/61 (4%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           +R R   +     +L +YF     N  PSEE  +E+A K  +    + +WF N   + ++
Sbjct: 8   KRPRTRITDDQLRVLRQYF---DINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQ 64

Query: 169 N 169
           +
Sbjct: 65  S 65

>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 = 50.3 bits (120), Expect = 7e-08
 Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 3/60 (5%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           R+KR +        L + F   + N  P+ E    +A + N+    +  WF N+R + K+
Sbjct: 102 RKKRTSIETNIRVALEKSF---MENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 158

>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 = 49.6 bits (118), Expect = 1e-07
 Identities = 20/102 (19%), Positives = 39/102 (38%), Gaps = 8/102 (7%)

Query: 67  ITPKEIERMVQIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEY 126
           ++ K   ++  I+ +     +        +     R R     ++R   S  A + L  +
Sbjct: 51  LSFKNACKLKAILSKWLEEAEQVGALYNEKVGANERKR-----KRRTTISIAAKDALERH 105

Query: 127 FYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           F     +  PS +    +A + N+    V  WF N+R R K+
Sbjct: 106 F---GEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 144

>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 = 47.0 bits (112), Expect = 1e-07
 Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 3/66 (4%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
            R R   +++    L   + +   NP P    KE+L     ++   +  WF NKR + KK
Sbjct: 4   TRVRTVLNEKQLHTLRTCYAA---NPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKK 60

Query: 169 NIGKAQ 174
                +
Sbjct: 61  RSIMMK 66

>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 = 49.0 bits (116), Expect = 2e-07
 Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 3/63 (4%)

Query: 107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRY 166
             +RKR +   +    L   F   L +P PS +    +A +  +    V  WF N+R + 
Sbjct: 95  ARKRKRTSIENRVRWSLETMF---LKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKG 151

Query: 167 KKN 169
           K++
Sbjct: 152 KRS 154

>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 = 46.7 bits (111), Expect = 2e-07
 Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 3/61 (4%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           +R R   + +  EIL + +   L +  P+ +  + +A +  +    V  WF N R R +K
Sbjct: 18  KRLRTTITPEQLEILYQKY---LLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERK 74

Query: 169 N 169
           +
Sbjct: 75  S 75

>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 = 46.7 bits (111), Expect = 2e-07
 Identities = 12/67 (17%), Positives = 31/67 (46%), Gaps = 3/67 (4%)

Query: 103 SRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNK 162
                 +    N   + ++ L + F S     YP E+  + L+++ + ++ ++  WF ++
Sbjct: 4   GSSGGIKDSPVN-KVEPNDTLEKVFVSV--TKYPDEKRLKGLSKQLDWSVRKIQCWFRHR 60

Query: 163 RIRYKKN 169
           R + K +
Sbjct: 61  RNQDKPS 67

>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 = 45.8 bits (109), Expect = 4e-07
 Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 3/66 (4%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           RR R  F++   E+L   F     N YP  +  E+LA+K N+ L ++  WF N+R + K+
Sbjct: 2   RRPRTAFTQNQIEVLENVFRV---NCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKR 58

Query: 169 NIGKAQ 174
           +  ++Q
Sbjct: 59  SHRESQ 64

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

 Score = 47.7 bits (113), Expect = 5e-07
 Identities = 17/60 (28%), Positives = 24/60 (40%), Gaps = 3/60 (5%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           R+KR +        L  +F   L  P PS      LA    +    V  WF N+R + K+
Sbjct: 100 RKKRTSIEVGVKGALESHF---LKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKR 156

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

 Score = 45.2 bits (107), Expect = 6e-07
 Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 5/76 (6%)

Query: 103 SRFLDARRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGN 161
           S  L+ R+KR  ++K Q  E+  EY      N + +++ +  ++   N++  QV+ WF N
Sbjct: 2   SHMLEGRKKRVPYTKVQLKELEREYAT----NKFITKDKRRRISATTNLSERQVTIWFQN 57

Query: 162 KRIRYKKNIGKAQEEA 177
           +R++ KK I K +  +
Sbjct: 58  RRVKEKKVINKLKTTS 73

>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens} Length = 96

 Score = 45.9 bits (108), Expect = 7e-07
 Identities = 13/61 (21%), Positives = 28/61 (45%), Gaps = 3/61 (4%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
             K    + +   +L   F   +   +PS E  ++LA++  +  + + +WFG+ R  +K 
Sbjct: 26  TGKICKKTPEQLHMLKSAF---VRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKN 82

Query: 169 N 169
            
Sbjct: 83  G 83

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

 Score = 45.4 bits (107), Expect = 8e-07
 Identities = 12/80 (15%), Positives = 34/80 (42%), Gaps = 3/80 (3%)

Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
           A +K +  ++   +IL + F   L + +P++   + L  +  ++  ++ +WF  +R    
Sbjct: 13  APQKFKEKTQGQVKILEDSF---LKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRD 69

Query: 168 KNIGKAQEEANLYAAKKAAG 187
                  +      +  ++G
Sbjct: 70  SMEQAVLDSMGSGKSGPSSG 89

>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 = 45.0 bits (106), Expect = 1e-06
 Identities = 16/86 (18%), Positives = 36/86 (41%), Gaps = 7/86 (8%)

Query: 105 FLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRI 164
           F   + K +  + +   +L   F   L++   ++E    L  +  +T  ++  WF  K  
Sbjct: 10  FTPQKFKEK--TAEQLRVLQASF---LNSSVLTDEELNRLRAQTKLTRREIDAWFTEK-- 62

Query: 165 RYKKNIGKAQEEANLYAAKKAAGASP 190
           +  K + + + E +   A  ++G S 
Sbjct: 63  KKSKALKEEKMEIDESNAGSSSGPSS 88

>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 = 44.2 bits (104), Expect = 2e-06
 Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 3/60 (5%)

Query: 110 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN 169
              +  +K+   IL  +F   L   +   E  ++L +   +   ++  WFG+ R   K  
Sbjct: 5   SSGKRKTKEQLAILKSFF---LQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG 61

>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 = 43.8 bits (104), Expect = 2e-06
 Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 3/61 (4%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           RR+R +F+ Q  + L   F     N YP    +EE+A   N+T ++V  WF N+R +++K
Sbjct: 4   RRQRTHFTSQQLQQLEATF---QRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60

Query: 169 N 169
            
Sbjct: 61  R 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 = 43.9 bits (104), Expect = 2e-06
 Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 3/61 (4%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           RR+R  F++   ++L   F       YP    +EE+A K N+  S+V  WF N+R + ++
Sbjct: 8   RRERTTFTRAQLDVLEALF---AKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQ 64

Query: 169 N 169
            
Sbjct: 65  Q 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 = 44.0 bits (104), Expect = 2e-06
 Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 3/66 (4%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           +R R +F       +  YF     N  P  +  ++LA+K  +T   +  WF N R ++++
Sbjct: 8   KRMRTSFKHHQLRTMKSYFAI---NHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRR 64

Query: 169 NIGKAQ 174
           N+ + +
Sbjct: 65  NLLRQE 70

>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 = 42.7 bits (101), Expect = 4e-06
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 5/62 (8%)

Query: 109 RRKRRNFSKQASEILNEYF-YSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
           RR R  F+ +  E L   F  +     YP    +E+LARK ++   +V  WF N+R +++
Sbjct: 8   RRHRTIFTDEQLEALENLFQETK----YPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 63

Query: 168 KN 169
           ++
Sbjct: 64  RS 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 = 42.8 bits (101), Expect = 4e-06
 Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
                   ++   EIL   F  +  N +P       +A +  +T  Q   WF  +   ++
Sbjct: 1   GSEGAATMTEDQVEILEYNF--NKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 58

Query: 168 KN 169
           ++
Sbjct: 59  RS 60

>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 = 42.1 bits (99), Expect = 8e-06
 Identities = 18/67 (26%), Positives = 37/67 (55%), Gaps = 5/67 (7%)

Query: 103 SRFLDARRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGN 161
           S     R+KR  +SK Q  E+  EY      N + +++ + +++   +++  Q++ WF N
Sbjct: 2   SSGSSGRKKRIPYSKGQLRELEREYAA----NKFITKDKRRKISAATSLSERQITIWFQN 57

Query: 162 KRIRYKK 168
           +R++ KK
Sbjct: 58  RRVKEKK 64

>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 = 42.4 bits (100), Expect = 9e-06
 Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 3/60 (5%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           RR R  FS    + L   F       YP    +EELA++ N+T +++  WF N+R R +K
Sbjct: 19  RRSRTTFSASQLDELERAF---ERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK 75

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

 Score = 41.6 bits (98), Expect = 1e-05
 Identities = 18/62 (29%), Positives = 36/62 (58%), Gaps = 5/62 (8%)

Query: 109 RRKRRNFSKQASEILNEYF-YSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
           +R R +F+++  E L + F  +H    YP   A+E LA K ++  +++  WF N+R +++
Sbjct: 8   QRNRTSFTQEQIEALEKEFERTH----YPDVFARERLAAKIDLPEARIQVWFSNRRAKWR 63

Query: 168 KN 169
           + 
Sbjct: 64  RE 65

>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 = 41.8 bits (98), Expect = 1e-05
 Identities = 22/63 (34%), Positives = 36/63 (57%), Gaps = 5/63 (7%)

Query: 107 DARRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIR 165
             R+KR  ++K Q  E+  E+ +    N Y + + + E+AR  N+T  QV  WF N+R++
Sbjct: 12  STRKKRCPYTKHQTLELEKEFLF----NMYLTRDRRYEVARLLNLTERQVKIWFQNRRMK 67

Query: 166 YKK 168
            KK
Sbjct: 68  MKK 70

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

 Score = 41.8 bits (97), Expect = 2e-05
 Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 24/77 (31%)

Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCN------------------ 149
           + R R  +   + +IL + +        PS+E +E L  +CN                  
Sbjct: 6   SGRNRFKWGPASQQILYQAYDR---QKNPSKEEREALVEECNRAECLQRGVSPSKAHGLG 62

Query: 150 ---ITLSQVSNWFGNKR 163
              +T  +V NWF N+R
Sbjct: 63  SNLVTEVRVYNWFANRR 79

>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 = 40.0 bits (94), Expect = 4e-05
 Identities = 18/65 (27%), Positives = 35/65 (53%), Gaps = 5/65 (7%)

Query: 106 LDARRKRRNFS-KQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRI 164
           +  +R R  FS +Q + +  E+      N Y +E  +++L+ +  +  +Q+  WF NKR 
Sbjct: 1   MAEKRPRTAFSSEQLARLKREFNE----NRYLTERRRQQLSSELGLNEAQIKIWFKNKRA 56

Query: 165 RYKKN 169
           + KK+
Sbjct: 57  KIKKS 61

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

 Score = 39.8 bits (93), Expect = 5e-05
 Identities = 11/53 (20%), Positives = 25/53 (47%), Gaps = 2/53 (3%)

Query: 111 KRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKR 163
              + + Q + IL E  ++     +P E+  E L+++ +  +  +  WF  +R
Sbjct: 3   SGSSGTAQPNAIL-EKVFTA-ITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRR 53

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

 Score = 38.5 bits (90), Expect = 1e-04
 Identities = 22/69 (31%), Positives = 30/69 (43%), Gaps = 4/69 (5%)

Query: 109 RRKRRN-FSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
           RRKRR  FS+     L   F       Y S   +E LA   ++T +QV  WF N R + K
Sbjct: 2   RRKRRVLFSQAQVYELERRF---KQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMK 58

Query: 168 KNIGKAQEE 176
           +       +
Sbjct: 59  RQAKDKAAQ 67

>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 = 38.7 bits (90), Expect = 2e-04
 Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 5/82 (6%)

Query: 88  MQLKQSTCEAVMILRSRFLDARRKRRNF-SKQASEILNEYFYSHLSNPYPSEEAKEELAR 146
           M++K++  +   +           R NF ++Q +E+  E+ +    N Y S   + E+A 
Sbjct: 14  MKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHF----NKYLSRARRVEIAA 69

Query: 147 KCNITLSQVSNWFGNKRIRYKK 168
              +  +QV  WF N+R++ KK
Sbjct: 70  TLELNETQVKIWFQNRRMKQKK 91

>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 = 37.8 bits (88), Expect = 2e-04
 Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 5/70 (7%)

Query: 109 RRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
           RR R  F+  Q +E+   +        Y +     +L+ K  +  +QV  WF N+R R+K
Sbjct: 3   RRTRTTFTSSQIAELEQHFLQ----GRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58

Query: 168 KNIGKAQEEA 177
               + ++++
Sbjct: 59  IQSDQHKDQS 68

>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 = 37.8 bits (88), Expect = 2e-04
 Identities = 17/61 (27%), Positives = 35/61 (57%), Gaps = 5/61 (8%)

Query: 109 RRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
           +R R+ +++ Q  E+  E+ +    N Y +   + E+A   ++T  Q+  WF N+R+++K
Sbjct: 3   KRGRQTYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 58

Query: 168 K 168
           K
Sbjct: 59  K 59

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

 Score = 37.6 bits (88), Expect = 2e-04
 Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 4/61 (6%)

Query: 108 ARRKRRN-FSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRY 166
            RRK R  FS+     L   F       Y S   +++LA    +T +QV  WF N+R + 
Sbjct: 1   GRRKPRVLFSQAQVYELERRF---KQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKS 57

Query: 167 K 167
           K
Sbjct: 58  K 58

>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 = 38.0 bits (87), Expect = 3e-04
 Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 108 ARRKRRNFSKQASEILNEYFYSHLSN-PYPSEEAKEELARKCNITLSQVSNWFGNKRIRY 166
           A + R  FS +    L +Y+ + +++      E  E +A + N+    V  W GN+R +Y
Sbjct: 8   ALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKY 67

Query: 167 KK 168
           + 
Sbjct: 68  RL 69

>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 = 37.2 bits (87), Expect = 3e-04
 Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 3/58 (5%)

Query: 112 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN 169
              F+    E L + F       YP    +EELA K  +T +++  WF N+R +++K 
Sbjct: 3   HMTFTSFQLEELEKAFSR---THYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

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

 Score = 36.8 bits (86), Expect = 4e-04
 Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 3/60 (5%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           R+ R  F+      L   F       Y S   + E +   ++T +QV  WF N+R + K+
Sbjct: 1   RKPRTPFTTAQLLALERKFRQ---KQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

 Score = 37.4 bits (87), Expect = 4e-04
 Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 3/60 (5%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           R+ R  +S      L   F       Y +   + ELA    +T +QV  WF NKR + KK
Sbjct: 8   RKPRTIYSSFQLAALQRRFQK---TQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64

>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 = 36.6 bits (85), Expect = 5e-04
 Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 5/61 (8%)

Query: 109 RRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
           RR R  F++ Q   +  E++       Y S   + ELA + N+  S +  WF N+R++ K
Sbjct: 2   RRYRTAFTRDQLGRLEKEFYK----ENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDK 57

Query: 168 K 168
           +
Sbjct: 58  R 58

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

 Score = 36.6 bits (85), Expect = 6e-04
 Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 5/63 (7%)

Query: 107 DARRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIR 165
             +R R  +++ Q  E+  E+ +    N Y S   + ELA   N+T   +  WF N+R++
Sbjct: 2   SNKRTRTAYTRAQLLELEKEFLF----NKYISRPRRVELAVMLNLTERHIKIWFQNRRMK 57

Query: 166 YKK 168
           +KK
Sbjct: 58  WKK 60

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

 Score = 36.5 bits (85), Expect = 7e-04
 Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 3/60 (5%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           ++ R  FS+     L + F       Y S +  +EL+   N++  QV  WF N+R++ K+
Sbjct: 4   QKMRTVFSQAQLCALKDRFQK---QKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	301
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.78
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.78
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.78
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.78
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.78
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.77
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.76
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.75
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.75
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.72
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.71
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.71
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.7
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.7
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.7
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.7
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.7
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.7
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.7
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.7
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.69
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.69
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.69
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.69
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.69
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.69
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.69
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.69
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.68
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.68
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.68
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.68
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.68
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.68
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.68
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.68
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.68
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.68
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.67
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.67
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.67
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.67
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.67
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.67
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.67
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.66
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.66
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.66
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.66
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.66
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.66
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.66
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.65
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.65
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.64
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.64
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.63
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.62
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.62
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.62
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.62
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.61
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.6
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.6
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.58
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.57
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.56
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.55
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.55
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.54
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.54
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.51
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.48
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.31
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.3
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.23
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.13
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.4
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	95.1

>1b72_B Protein (PBX1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1 PDB: 1lfu_P

Probab=99.78  E-value=2.1e-19  Score=136.70  Aligned_cols=69  Identities=91%  Similarity=1.376  Sum_probs=63.8

Q ss_pred             CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHHHHH
Q psy5541         109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEA  177 (301)
Q Consensus       109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~~~~  177 (301)
                      ||+|+.|+..|+.+|+.||.+|..++||+..++..||..+||++.||+|||+|||+|+|+.......+.
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~~~~~   70 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEA   70 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGGGHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhccccccccc
Confidence            688999999999999999999999999999999999999999999999999999999999887665543

>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=99.78  E-value=3.1e-20  Score=154.69  Aligned_cols=126  Identities=24%  Similarity=0.337  Sum_probs=91.8

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhcCCCCCChHHH-HHHHHHHhhhhhHHHHHHhhhHHHHHHHhh----------------
Q psy5541          40 LEKYEQACSEFTTHVMNLLREQSRTRPITPKEI-ERMVQIIHRKFSSIQMQLKQSTCEAVMILR----------------  102 (301)
Q Consensus        40 l~ky~~~~~~f~~~~~~~l~~q~~~~~l~~~~~-~~~~~~~~~~f~~~~~~l~~~~~~~~~~l~----------------  102 (301)
                      |+..+++++.|+.+.|.++.+|++++....... ..++++..++|..++..++ +.|..-..|.                
T Consensus         2 ~~~l~~fa~~~k~~ri~lg~tQ~~vg~al~~l~g~~~Sqtti~rfe~l~ls~k-nm~kLkPlL~~wl~e~e~~~~~~~~~   80 (146)
T 1au7_A            2 MRALEQFANEFKVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFENLQLSFK-NACKLKAILSKWLEEAEQVGALYNEK   80 (146)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHTTSSCCCHHHHHHHHTTCSBHH-HHHHHHHHHHHHHHHCCC--------
T ss_pred             ccHHHHHHHHHHHHHHhccCcHHhhhhhcchhccCCCCcchHHHHhccCCChH-HHHhcchHHHHHHHHhhcccCccCcc
Confidence            345566799999999999999887653221111 1235666777777666554 3343221111                


Q ss_pred             -hhhhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541         103 -SRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN  169 (301)
Q Consensus       103 -~~~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~  169 (301)
                       ....++||+|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.||+|||||||+|+||.
T Consensus        81 ~~~~~~~rr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           81 VGANERKRKRRTTISIAAKDALERHF---GEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             --------CCCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             cCCCCCCCCCCcCccHHHHHHHHHHH---HHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence             1123467789999999999999999   899999999999999999999999999999999999985

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

Probab=99.78  E-value=3e-20  Score=157.59  Aligned_cols=127  Identities=22%  Similarity=0.292  Sum_probs=88.6

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhcCCCCCChHHH-HHHHHHHhhhhhHHHHHHhhhHHHHHHHhh-----------------
Q psy5541          41 EKYEQACSEFTTHVMNLLREQSRTRPITPKEI-ERMVQIIHRKFSSIQMQLKQSTCEAVMILR-----------------  102 (301)
Q Consensus        41 ~ky~~~~~~f~~~~~~~l~~q~~~~~l~~~~~-~~~~~~~~~~f~~~~~~l~~~~~~~~~~l~-----------------  102 (301)
                      +..+++++.|+.+.|.+..+|++++....... ..+.++.+++|+.++..++ +.|..-..+.                 
T Consensus        13 ~~l~~fa~~fk~~ri~lg~tQ~~vg~alg~l~g~~~Sqtti~rFE~l~ls~k-n~~klkPlL~~wl~eae~~~~~~~~~~   91 (164)
T 2xsd_C           13 DDLEQFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFK-NMCKLKPLLNKWLEETDSSSGSPTNLD   91 (164)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHTTCSBHH-HHHHHHHHHHHHHHHHCC---------
T ss_pred             hHHHHHHHHHHHHHhhcCCcccccccccccccCCCcCcchhhhhhccCCCHH-HHHHcchhHHHHHhhhccccCCCcccc
Confidence            34456699999999999999988664322211 1235666777776666554 3343221111                 


Q ss_pred             --hhhhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         103 --SRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       103 --~~~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                        ....++||+|+.|+..|+.+|+.+|   ..++||+..+|..||..+||++.||+|||||||+|+||...
T Consensus        92 ~~~~~~~~rr~Rt~ft~~Ql~~LE~~F---~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~  159 (164)
T 2xsd_C           92 KIAAQGRKRKKRTSIEVGVKGALESHF---LKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTP  159 (164)
T ss_dssp             --------------CCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC
T ss_pred             cccccccCCCCceeccHHHHHHHHHHH---hcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhccC
Confidence              0123467789999999999999999   99999999999999999999999999999999999999764

>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=99.78  E-value=8.7e-20  Score=153.42  Aligned_cols=124  Identities=21%  Similarity=0.295  Sum_probs=95.8

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhcCCCCCChHHHH-HHHHHHhhhhhHHHHHHhhhHHHHHHHhhhhh--------------
Q psy5541          41 EKYEQACSEFTTHVMNLLREQSRTRPITPKEIE-RMVQIIHRKFSSIQMQLKQSTCEAVMILRSRF--------------  105 (301)
Q Consensus        41 ~ky~~~~~~f~~~~~~~l~~q~~~~~l~~~~~~-~~~~~~~~~f~~~~~~l~~~~~~~~~~l~~~~--------------  105 (301)
                      +..+++++.|+.+.|.++.+|.+++........ .++++.+++|+.++..++ ++|.. .++..+|              
T Consensus        10 ~~l~~fa~~fk~~ri~lg~tq~~vg~al~~l~G~~~Sqtti~rfE~l~ls~~-nm~kL-kPlL~~Wl~eae~~~~~~~~~   87 (155)
T 3l1p_A           10 KELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTISRFEALQLSLK-NMSKL-RPLLEKWVEEADNNENLQEIS   87 (155)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHTTCSCHH-HHHHH-HHHHHHHHHHHTTCHHHHHSS
T ss_pred             HHHHHHHHHHHhhhheecccHHHHHHHHHhhcCcccccccccccccccCChh-hHhhc-chHHHHHhhhhhcccCccccc
Confidence            344445999999999999999887743333222 355777888888777665 33432 2221111              


Q ss_pred             ------hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541         106 ------LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN  169 (301)
Q Consensus       106 ------~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~  169 (301)
                            .++||+|+.|+..|+..|+.+|   ..++||+..++..||..+||++.||+|||||||+|+||.
T Consensus        88 ~~~~~~~~~rr~Rt~ft~~Q~~~Le~~F---~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A           88 KSETLVQARKRKRTSIENRVRWSLETMF---LKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             CC---CCCSCCCCCCCCHHHHHHHHTTT---TTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             cccccccCCCCCCcccCHHHHHHHHHHH---ccCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence                  1467889999999999999999   999999999999999999999999999999999999984

>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=99.78  E-value=1.7e-19  Score=151.05  Aligned_cols=126  Identities=23%  Similarity=0.367  Sum_probs=85.9

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhcCCCCCChHH-HHHHHHHHhhhhhHHHH--------------HHhhhHHH-------H
Q psy5541          40 LEKYEQACSEFTTHVMNLLREQSRTRPITPKE-IERMVQIIHRKFSSIQM--------------QLKQSTCE-------A   97 (301)
Q Consensus        40 l~ky~~~~~~f~~~~~~~l~~q~~~~~l~~~~-~~~~~~~~~~~f~~~~~--------------~l~~~~~~-------~   97 (301)
                      ++..+++++.|+.+.|.++.+|++++...... ...++++.+++|..+..              |+.+....       .
T Consensus         3 ~~~~~~fa~~f~~~ri~lg~tQ~~vg~al~~l~g~~~Sqsti~rfe~l~ls~kn~~klkPll~~Wl~e~e~~~~~~~~~~   82 (151)
T 3d1n_I            3 MEEIREFAKNFKIRRLSLGLTQTQVGQAMTATEGPAYSQSAISRFEKLDITPKSAQKLKPVLEKWLNEAELRNQEGQQNL   82 (151)
T ss_dssp             HHHHHHHHHHHHHHHHTTTCCHHHHHHHHSCSSSCCCCHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHHHHHHHHCSTTH
T ss_pred             HHHHHHHHHHHHHHHhhcCCCcccHHHhhccccCCCCCccccccccCCCCChhHHHHhchhHHHHHHHHHhccccCcccc
Confidence            45556679999999999988887653110000 00122333334433222              22111100       0


Q ss_pred             HHHhhhhhhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541          98 VMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK  168 (301)
Q Consensus        98 ~~~l~~~~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk  168 (301)
                      .........++||+|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.||+|||||||+|+||
T Consensus        83 ~~~~~~~~~~~rr~Rt~ft~~q~~~Le~~F---~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           83 MEFVGGEPSKKRKRRTSFTPQAIEALNAYF---EKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             HHHHCSSCCCCCCCCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             cccCCCCCCCCCCCCcccCHHHHHHHHHHH---HhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            011112234567889999999999999999   88999999999999999999999999999999999987

>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=99.77  E-value=2.7e-19  Score=131.70  Aligned_cols=68  Identities=91%  Similarity=1.385  Sum_probs=63.8

Q ss_pred             CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHHHH
Q psy5541         109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEE  176 (301)
Q Consensus       109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~~~  176 (301)
                      ||+|+.|+..|+.+|+.||.+|..++||+..++..||..+||++.||+|||+|+|+|+|+.......+
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~~~~e   69 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEE   69 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTTTTTH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccccccccccc
Confidence            68899999999999999999999999999999999999999999999999999999999987765544

>2dmn_A Homeobox protein TGIF2LX; TGFB-induced factor 2-like protein, X-linked TGF(beta) induced transcription factor 2-like protein, TGIF-like on the X; NMR {Homo sapiens}

Probab=99.76  E-value=6.3e-19  Score=133.01  Aligned_cols=66  Identities=35%  Similarity=0.636  Sum_probs=61.8

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      .+++++|+.|+.+++.+|+.||.+|..+|||+..+|..||..+||++.||+|||||+|+|+|+...
T Consensus         5 ~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~   70 (83)
T 2dmn_A            5 SSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDML   70 (83)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHH
Confidence            356788999999999999999999999999999999999999999999999999999999998754

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

Probab=99.75  E-value=4e-19  Score=127.41  Aligned_cols=63  Identities=79%  Similarity=1.245  Sum_probs=59.9

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN  169 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~  169 (301)
                      .++++|+.|+.+++.+|+.||.+|..++||+..++..||..+||++.||+|||+|+|+|+||.
T Consensus         2 ~~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~   64 (64)
T 1du6_A            2 SGHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN   64 (64)
T ss_dssp             CCCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSCC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhccC
Confidence            357889999999999999999999999999999999999999999999999999999999873

>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=1.1e-18  Score=128.34  Aligned_cols=65  Identities=34%  Similarity=0.684  Sum_probs=61.4

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      +.+++|+.|+..++.+|+.||..|..++||+..++..||..+||++.||+|||+|+|+|+|+...
T Consensus         6 ~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~   70 (73)
T 1x2n_A            6 SGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSGP   70 (73)
T ss_dssp             SSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhcccccc
Confidence            45788999999999999999998889999999999999999999999999999999999999764

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

Probab=99.72  E-value=1.6e-18  Score=146.41  Aligned_cols=126  Identities=21%  Similarity=0.312  Sum_probs=82.1

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhcCCCCCChHHH-HHHHHHHhhhhhHHHHHHhhhHHHHHHH------------------
Q psy5541          40 LEKYEQACSEFTTHVMNLLREQSRTRPITPKEI-ERMVQIIHRKFSSIQMQLKQSTCEAVMI------------------  100 (301)
Q Consensus        40 l~ky~~~~~~f~~~~~~~l~~q~~~~~l~~~~~-~~~~~~~~~~f~~~~~~l~~~~~~~~~~------------------  100 (301)
                      ++..++++..|..+.+.++.+|+.++....... ..+.++..++|..++..++ .+|..-..                  
T Consensus         6 ~~~~~~~~~~~k~~r~~lg~tQ~~vg~~lg~l~g~~~sq~ti~rfE~l~lS~k-nm~klkPlL~~WL~e~e~~~~~~~~~   84 (160)
T 1e3o_C            6 LEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFK-NMSKLKPLLEKWLNDAEANLSSDSSL   84 (160)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHHTCSCHH-HHHHHHHHHHHHHHHHC---------
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHhhccccCCCcCccccccccccCCChH-HHHhcchhHHHHHHhhhcccccCCCC
Confidence            345566688899999888777765442211100 0112333444444332222 11111000                  


Q ss_pred             -----h----hhhhhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541         101 -----L----RSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN  169 (301)
Q Consensus       101 -----l----~~~~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~  169 (301)
                           .    .....++||+|+.|+..|+.+|+.+|   ..++||+..+|..||..+||++.||+|||||||+|+||.
T Consensus        85 ~s~~~~~~~~~~~~~~~rr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C           85 SSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSF---MENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             -------------------CCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCcCCCCCCCCCCCCcCccccCHHHHHHHHHHH---hhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence                 0    01123567899999999999999999   899999999999999999999999999999999999985

>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=99.71  E-value=9e-18  Score=118.78  Aligned_cols=59  Identities=27%  Similarity=0.566  Sum_probs=55.7

Q ss_pred             CCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541         111 KRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN  169 (301)
Q Consensus       111 ~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~  169 (301)
                      +|+.|+.+|+.+|+.||..|..++||+..++..||..+||++.||++||+|||+|+|+.
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            46899999999999999777779999999999999999999999999999999999974

>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=99.71  E-value=5.8e-18  Score=120.22  Aligned_cols=59  Identities=31%  Similarity=0.522  Sum_probs=53.1

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK  168 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk  168 (301)
                      +.+|+|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||++||+|||+|+||
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            2 AEKRPRTAFSSEQLARLKREF---NENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             -----CCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCHHHHHHHHHHH---HccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            357899999999999999999   89999999999999999999999999999999999987

>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=99.70  E-value=9.3e-18  Score=121.49  Aligned_cols=60  Identities=40%  Similarity=0.714  Sum_probs=53.8

Q ss_pred             CCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhh
Q psy5541         113 RNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGK  172 (301)
Q Consensus       113 ~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~  172 (301)
                      ..|+++++.+|+.||.+|..+|||+..+|..||..+||++.||+|||+|+|+|+||+...
T Consensus         3 g~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~   62 (67)
T 3k2a_A            3 GIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMID   62 (67)
T ss_dssp             ---CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC--
T ss_pred             CcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHHH
Confidence            579999999999999999999999999999999999999999999999999999997654

>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=99.70  E-value=1.2e-17  Score=125.95  Aligned_cols=63  Identities=24%  Similarity=0.476  Sum_probs=57.6

Q ss_pred             CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      +++|+.|+.+|+.+|+.||..|..++||+..++..||..+||++.||+|||||||+|+|+...
T Consensus         3 ~krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~~   65 (83)
T 1le8_B            3 PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITI   65 (83)
T ss_dssp             --CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHcccccccc
Confidence            355667999999999999988888999999999999999999999999999999999999754

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

Probab=99.70  E-value=2.3e-17  Score=123.52  Aligned_cols=64  Identities=27%  Similarity=0.544  Sum_probs=59.9

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhH
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKA  173 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~  173 (301)
                      +.+++|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||+|||||||+|+||.....
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~   69 (80)
T 2cue_A            6 SGQRNRTSFTQEQIEALEKEF---ERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLR   69 (80)
T ss_dssp             SSCCCCCCSCHHHHHHHHHHH---TTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCccCHHHHHHHHHHH---hccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhh
Confidence            467899999999999999999   9999999999999999999999999999999999999976543

>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=99.70  E-value=5.6e-18  Score=122.18  Aligned_cols=62  Identities=26%  Similarity=0.409  Sum_probs=58.6

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      +++++|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||++||+|||+|+|+...
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F---~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   63 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCY---AANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI   63 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHH---HHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHH---hcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHHhh
Confidence            467899999999999999999   88999999999999999999999999999999999998753

>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=99.70  E-value=9.4e-18  Score=123.81  Aligned_cols=59  Identities=20%  Similarity=0.420  Sum_probs=55.8

Q ss_pred             CCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         110 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       110 r~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      .+|+.|+.+|+.+|+.+|   ..++||+..+|++||..|||++.||+|||+|+|+|+|+...
T Consensus         5 ~~r~kfT~~Ql~~Le~~F---~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~l   63 (76)
T 2ecc_A            5 SSGKRKTKEQLAILKSFF---LQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQL   63 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCHHHHHHHHHHH---HHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHHH
Confidence            467889999999999999   89999999999999999999999999999999999999754

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

Probab=99.70  E-value=1e-17  Score=119.74  Aligned_cols=59  Identities=32%  Similarity=0.542  Sum_probs=55.7

Q ss_pred             cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541         108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN  169 (301)
Q Consensus       108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~  169 (301)
                      .+++|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.||++||+|||+|+||.
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   61 (63)
T 2h1k_A            3 NKRTRTAYTRAQLLELEKEF---LFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE   61 (63)
T ss_dssp             --CCCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCHHHHHHHHHHH---hcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhh
Confidence            47899999999999999999   899999999999999999999999999999999999986

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

Probab=99.70  E-value=1.4e-17  Score=117.02  Aligned_cols=57  Identities=28%  Similarity=0.468  Sum_probs=55.1

Q ss_pred             CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541         109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK  168 (301)
Q Consensus       109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk  168 (301)
                      |++|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||++||+|||+|+||
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKF---RQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHH---HHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHH---hcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            5789999999999999999   89999999999999999999999999999999999987

>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=99.70  E-value=1.7e-17  Score=126.19  Aligned_cols=62  Identities=26%  Similarity=0.537  Sum_probs=58.0

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK  168 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk  168 (301)
                      +++++|+.|+.+|+.+|+.||..|..++||+..+|..||..+||++.||+|||+|||+|+|.
T Consensus        26 ~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k~   87 (87)
T 1mnm_C           26 TKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   87 (87)
T ss_dssp             SSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccC
Confidence            45677899999999999999988888999999999999999999999999999999999874

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

Probab=99.69  E-value=1.3e-17  Score=121.72  Aligned_cols=62  Identities=31%  Similarity=0.607  Sum_probs=58.5

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      +.+|+|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||++||+|||+|+||...
T Consensus         6 ~~rr~Rt~ft~~q~~~Le~~F---~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2dmu_A            6 SGRRHRTIFTDEQLEALENLF---QETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP   67 (70)
T ss_dssp             SSCCCCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTST
T ss_pred             CCCCCCCCCCHHHHHHHHHHH---HccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccCC
Confidence            467899999999999999999   88999999999999999999999999999999999999653

>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=99.69  E-value=9.3e-18  Score=122.46  Aligned_cols=62  Identities=23%  Similarity=0.460  Sum_probs=58.5

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      +.+++|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.||+|||||||+|+||...
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (70)
T 2cra_A            6 SGRKKRIPYSKGQLRELEREY---AANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGP   67 (70)
T ss_dssp             CCCCSCCCSCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSCT
T ss_pred             CCCCCCCcCCHHHHHHHHHHH---HhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccCC
Confidence            467899999999999999999   89999999999999999999999999999999999999653

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

Probab=99.69  E-value=1.5e-17  Score=121.30  Aligned_cols=61  Identities=31%  Similarity=0.428  Sum_probs=58.2

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI  170 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~  170 (301)
                      +.+++|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||++||+|||+|+||..
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2djn_A            6 SGRKPRTIYSSFQLAALQRRF---QKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSG   66 (70)
T ss_dssp             CCCCSSCSSCHHHHHHHHHHH---TTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHH---cCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccC
Confidence            467899999999999999999   9999999999999999999999999999999999999864

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

Probab=99.69  E-value=3.1e-17  Score=118.98  Aligned_cols=61  Identities=30%  Similarity=0.453  Sum_probs=58.2

Q ss_pred             cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      ++++|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.+|+|||+|||+|+|+...
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~   62 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHF---LQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD   62 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHH---TTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCcCHHHHHHHHHHH---hcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhc
Confidence            47899999999999999999   99999999999999999999999999999999999999754

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

Probab=99.69  E-value=1.1e-17  Score=119.13  Aligned_cols=59  Identities=29%  Similarity=0.476  Sum_probs=52.8

Q ss_pred             cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541         108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN  169 (301)
Q Consensus       108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~  169 (301)
                      ++++|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.+|++||+|||+|+||.
T Consensus         3 ~rr~Rt~ft~~q~~~Le~~F---~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A            3 KQKMRTVFSQAQLCALKDRF---QKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             -----CCCCHHHHHHHHHHH---HHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             CCCCCCCCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            46889999999999999999   899999999999999999999999999999999999985

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

Probab=99.69  E-value=2.1e-17  Score=119.50  Aligned_cols=61  Identities=34%  Similarity=0.639  Sum_probs=57.9

Q ss_pred             cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      +|++|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||++||+|||+|+|+...
T Consensus         1 ~rr~Rt~ft~~q~~~Le~~F---~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~   61 (67)
T 2k40_A            1 GRRPRTAFTQNQIEVLENVF---RVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR   61 (67)
T ss_dssp             CCCCSCCCCHHHHHHHHHHH---TTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCC
T ss_pred             CcCCCCCCCHHHHHHHHHHH---HhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhch
Confidence            36889999999999999999   99999999999999999999999999999999999998754

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

Probab=99.69  E-value=1.6e-17  Score=117.51  Aligned_cols=58  Identities=31%  Similarity=0.533  Sum_probs=55.3

Q ss_pred             CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541         109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN  169 (301)
Q Consensus       109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~  169 (301)
                      |++|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||++||+|+|+|+||+
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEF---YKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   59 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHH---HHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHH---HHcCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHhHhhcc
Confidence            5789999999999999999   889999999999999999999999999999999999985

>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=99.69  E-value=1.5e-17  Score=121.32  Aligned_cols=63  Identities=25%  Similarity=0.495  Sum_probs=59.0

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      .+.+++|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||++||+|||+|+||...
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F---~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2da2_A            5 SSGRSSRTRFTDYQLRVLQDFF---DANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGP   67 (70)
T ss_dssp             CCSCCCCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHH---HcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhccc
Confidence            3567899999999999999999   88999999999999999999999999999999999999654

>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=99.68  E-value=1.5e-17  Score=120.63  Aligned_cols=62  Identities=34%  Similarity=0.595  Sum_probs=58.7

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      +++++|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.||++||+|||+|+|+...
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~   63 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATF---QRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREE   63 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHH---TTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHH---HccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhh
Confidence            357899999999999999999   99999999999999999999999999999999999999754

>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=99.68  E-value=1.4e-17  Score=124.68  Aligned_cols=63  Identities=27%  Similarity=0.431  Sum_probs=58.8

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      .+.+|+|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||+|||||||+|+||...
T Consensus        15 ~~~rr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~~   77 (80)
T 2dmt_A           15 KKGRRSRTVFTELQLMGLEKRF---EKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGP   77 (80)
T ss_dssp             CCCCCSCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCCS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHH---HhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcccC
Confidence            3467889999999999999999   89999999999999999999999999999999999999653

>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=99.68  E-value=1.3e-17  Score=118.31  Aligned_cols=58  Identities=40%  Similarity=0.575  Sum_probs=48.1

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK  167 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~k  167 (301)
                      +.+++|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||+|||+|||+|+|
T Consensus         4 k~rr~Rt~ft~~q~~~Le~~f---~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            4 KSPKGKSSISPQARAFLEEVF---RRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             --------CCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCHHHHHHHHHHH---HhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            457889999999999999999   8889999999999999999999999999999999975

>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=99.68  E-value=2.5e-17  Score=120.16  Aligned_cols=62  Identities=23%  Similarity=0.439  Sum_probs=58.3

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      +.+++|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||++||+|||+|+|+...
T Consensus         6 ~~~r~R~~ft~~q~~~Le~~F---~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2e1o_A            6 SGKGGQVRFSNDQTIELEKKF---ETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGP   67 (70)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHH---HcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCCC
Confidence            457889999999999999999   89999999999999999999999999999999999999653

>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=99.68  E-value=1.3e-17  Score=121.69  Aligned_cols=63  Identities=25%  Similarity=0.455  Sum_probs=59.0

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      .+.+++|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||++||+|||+|+||...
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F---~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2da1_A            5 SSGKRPRTRITDDQLRVLRQYF---DINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGP   67 (70)
T ss_dssp             CCCCSCSCCCCHHHHHHHHHHH---HHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHH---HHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhcc
Confidence            3567899999999999999999   89999999999999999999999999999999999999754

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

Probab=99.68  E-value=2.1e-17  Score=121.63  Aligned_cols=63  Identities=27%  Similarity=0.541  Sum_probs=59.4

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      .+++++|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.||++||||||+|+||...
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   67 (73)
T 2l7z_A            5 LEGRKKRVPYTKVQLKELEREY---ATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVIN   67 (73)
T ss_dssp             SCCCCCCCCSCHHHHHHHHHHH---HHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHH---hhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHhc
Confidence            4568899999999999999999   89999999999999999999999999999999999999754

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

Probab=99.68  E-value=2e-17  Score=123.82  Aligned_cols=61  Identities=26%  Similarity=0.432  Sum_probs=57.4

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCC----CCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSN----PYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN  169 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~----~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~  169 (301)
                      .+++++|+.|+.+|+.+|+.+|   ..+    +||+..++.+||..+||++.||+|||||||+|+|+.
T Consensus         6 ~~~rr~Rt~ft~~Q~~~Le~~F---~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~   70 (80)
T 2da4_A            6 SGALQDRTQFSDRDLATLKKYW---DNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLM   70 (80)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHH---TTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHH---HhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhc
Confidence            3567889999999999999999   788    999999999999999999999999999999999985

>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=99.68  E-value=1.8e-17  Score=120.27  Aligned_cols=61  Identities=26%  Similarity=0.490  Sum_probs=57.8

Q ss_pred             cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      ++++|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.||++||||||+|+||...
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~   62 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEF---HFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK   62 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHH---HHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCcCHHHHHHHHHHH---ccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhcc
Confidence            36889999999999999999   89999999999999999999999999999999999999754

>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=99.68  E-value=2.7e-17  Score=123.02  Aligned_cols=62  Identities=26%  Similarity=0.542  Sum_probs=58.6

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      +.||+|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||+|||+|||+|+||...
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (80)
T 2dmq_A            6 SGKRMRTSFKHHQLRTMKSYF---AINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLL   67 (80)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHH---HHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHH
Confidence            467899999999999999999   89999999999999999999999999999999999999753

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

Probab=99.68  E-value=5.1e-17  Score=113.82  Aligned_cols=57  Identities=32%  Similarity=0.463  Sum_probs=54.6

Q ss_pred             cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhh
Q psy5541         108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK  167 (301)
Q Consensus       108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~k  167 (301)
                      ++++|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.||++||||||+|+|
T Consensus         2 ~rr~Rt~~t~~q~~~Le~~F---~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~k   58 (58)
T 3rkq_A            2 RRKPRVLFSQAQVYELERRF---KQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK   58 (58)
T ss_dssp             CCCCCCCCCHHHHHHHHHHH---TTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHC
T ss_pred             cCCCCCCcCHHHHHHHHHHH---HHcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhhccCC
Confidence            46789999999999999999   9999999999999999999999999999999999976

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

Probab=99.67  E-value=3e-17  Score=122.87  Aligned_cols=63  Identities=30%  Similarity=0.560  Sum_probs=59.2

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      .+.+|+|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.+|+|||+|||+|+|+...
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~   67 (80)
T 2dms_A            5 SSGRRERTTFTRAQLDVLEALF---AKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQ   67 (80)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHH---HccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHH
Confidence            3567899999999999999999   89999999999999999999999999999999999999754

>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=99.67  E-value=3.7e-17  Score=121.51  Aligned_cols=63  Identities=30%  Similarity=0.431  Sum_probs=58.6

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      .+++++|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.||+|||||||+|+|+...
T Consensus         7 ~~~rr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~   69 (77)
T 1nk2_P            7 NKKRKRRVLFTKAQTYELERRF---RQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQN   69 (77)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHH---HHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCccCCHHHHHHHHHHH---hhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhc
Confidence            3467889999999999999999   89999999999999999999999999999999999998644

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

Probab=99.67  E-value=3.3e-17  Score=118.89  Aligned_cols=61  Identities=31%  Similarity=0.462  Sum_probs=58.0

Q ss_pred             cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      ++++|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.+|++||+|||+|+|+...
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~   62 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRF---KQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK   62 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHH---HHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCccCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhh
Confidence            46889999999999999999   89999999999999999999999999999999999999754

>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=99.67  E-value=3.5e-17  Score=122.73  Aligned_cols=63  Identities=33%  Similarity=0.564  Sum_probs=58.5

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      .+++++|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.||++||+|||+|+||...
T Consensus        16 ~~~rr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~   78 (81)
T 1fjl_A           16 RKQRRSRTTFSASQLDELERAF---ERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   78 (81)
T ss_dssp             -CCCCCCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHH---HHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhcc
Confidence            3567889999999999999999   88999999999999999999999999999999999999753

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

Probab=99.67  E-value=2.9e-17  Score=126.44  Aligned_cols=67  Identities=24%  Similarity=0.500  Sum_probs=60.5

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHHH
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQE  175 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~~  175 (301)
                      .+++++|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||+|||||||+|+|+......+
T Consensus        15 ~~~rr~Rt~ft~~Ql~~Le~~F---~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~~   81 (93)
T 3a01_A           15 PKRKKPRTSFTRIQVAELEKRF---HKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEERE   81 (93)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHH---HHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC--
T ss_pred             CCCCCCCcCCCHHHHHHHHHHH---HcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHHHH
Confidence            3567889999999999999999   899999999999999999999999999999999999998765443

>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=99.67  E-value=1.9e-17  Score=123.81  Aligned_cols=62  Identities=24%  Similarity=0.424  Sum_probs=58.4

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI  170 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~  170 (301)
                      .+++|+|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||+|||||||+|+||..
T Consensus        15 ~~~rr~Rt~ft~~Ql~~Le~~f---~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   76 (80)
T 2da3_A           15 QRDKRLRTTITPEQLEILYQKY---LLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSG   76 (80)
T ss_dssp             CCCTTCCSSCCTTTHHHHHHHH---HHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHH---HhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhc
Confidence            3467889999999999999999   8899999999999999999999999999999999999964

>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=99.67  E-value=5.1e-17  Score=120.73  Aligned_cols=62  Identities=35%  Similarity=0.523  Sum_probs=58.5

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      +.+++|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.||++||||||+|+|+...
T Consensus        12 ~~rr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k   73 (77)
T 1puf_A           12 STRKKRCPYTKHQTLELEKEF---LFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINK   73 (77)
T ss_dssp             TTSCCCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHH---hccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhh
Confidence            457889999999999999999   89999999999999999999999999999999999999754

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

Probab=99.66  E-value=3.5e-17  Score=123.51  Aligned_cols=63  Identities=29%  Similarity=0.474  Sum_probs=58.9

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      .+++++|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.||+|||||||+|+||..+
T Consensus        20 ~~~rr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k   82 (84)
T 2kt0_A           20 VKKQKTRTVFSSTQLCVLNDRF---QRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK   82 (84)
T ss_dssp             SCSCCCSSCCCHHHHHHHHHHH---HHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhh
Confidence            3567889999999999999999   89999999999999999999999999999999999998653

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

Probab=99.66  E-value=7.8e-17  Score=122.75  Aligned_cols=61  Identities=26%  Similarity=0.528  Sum_probs=55.4

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI  170 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~  170 (301)
                      +.+|+|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.||+|||||||+|+||..
T Consensus        27 ~~rr~Rt~ft~~Ql~~Le~~F---~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   87 (88)
T 2r5y_A           27 ETKRQRTSYTRYQTLELEKEF---HFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH   87 (88)
T ss_dssp             ----CCCCCCHHHHHHHHHHH---TTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCcCHHHHHHHHHHH---hccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhhc
Confidence            457899999999999999999   9999999999999999999999999999999999999864

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

Probab=99.66  E-value=6.5e-17  Score=122.60  Aligned_cols=60  Identities=33%  Similarity=0.590  Sum_probs=56.5

Q ss_pred             CCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         112 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       112 R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      ...|+++++.+|+.||.+|..+|||+..+|.+||..|||++.||+|||+|+|+|+|+...
T Consensus         9 ~~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~   68 (89)
T 2lk2_A            9 SHMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDML   68 (89)
T ss_dssp             CCCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHH
Confidence            346899999999999999999999999999999999999999999999999999998754

>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=99.66  E-value=4.2e-17  Score=122.36  Aligned_cols=61  Identities=30%  Similarity=0.522  Sum_probs=54.5

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI  170 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~  170 (301)
                      +.+|+|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.||+|||+|||+|+||..
T Consensus        19 ~~rr~Rt~ft~~Ql~~Le~~F---~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   79 (81)
T 1b8i_A           19 LRRRGRQTYTRYQTLELEKEF---HTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEI   79 (81)
T ss_dssp             -----CCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCcccCHHHHHHHHHHH---hcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhc
Confidence            457889999999999999999   8999999999999999999999999999999999999974

>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=99.66  E-value=8.9e-17  Score=117.86  Aligned_cols=59  Identities=19%  Similarity=0.328  Sum_probs=56.1

Q ss_pred             CCCCCCCCHHHHHHHHhHhhcCCC-CCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541         109 RRKRRNFSKQASEILNEYFYSHLS-NPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI  170 (301)
Q Consensus       109 rr~R~~~~~~q~~~L~~~f~~h~~-~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~  170 (301)
                      .++|+.|+..|+.+|+.+|   .. ++||+..++..||..+||++.||++||+|||+|+||..
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F---~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~   61 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNF---NKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHH---HSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHH---HccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhc
Confidence            4789999999999999999   85 99999999999999999999999999999999999964

>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=99.66  E-value=3.1e-17  Score=122.81  Aligned_cols=59  Identities=12%  Similarity=0.205  Sum_probs=55.8

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCC----CCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLS----NPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK  168 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~----~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk  168 (301)
                      ++||+|+.|+.+|+..|+.+|   ..    ++||+..+|.+||..+||++.||+|||||||+|+|+
T Consensus        16 ~~rR~Rt~ft~~Ql~~Le~~f---~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           16 IRKRHRTKFTAEQKERMLALA---ERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CSCCCSCCCCHHHHHHHHHHH---HHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCccCCHHHHHHHHHHH---HhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            467889999999999999999   66    999999999999999999999999999999999886

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

Probab=99.66  E-value=4.8e-17  Score=115.05  Aligned_cols=57  Identities=30%  Similarity=0.512  Sum_probs=50.4

Q ss_pred             CCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541         111 KRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI  170 (301)
Q Consensus       111 ~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~  170 (301)
                      .|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||++||+|||+|+||..
T Consensus         2 ~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~   58 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAF---SRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE   58 (60)
T ss_dssp             ---CCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC---
T ss_pred             CCcccCHHHHHHHHHHH---HcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhc
Confidence            57899999999999999   8899999999999999999999999999999999999864

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

Probab=99.65  E-value=1.3e-16  Score=117.36  Aligned_cols=59  Identities=19%  Similarity=0.296  Sum_probs=56.2

Q ss_pred             CCCCCCCCHHHHHHHHhHhhcCC-CCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541         109 RRKRRNFSKQASEILNEYFYSHL-SNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI  170 (301)
Q Consensus       109 rr~R~~~~~~q~~~L~~~f~~h~-~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~  170 (301)
                      +++|+.|+.+|+.+|+.+|   . .++||+..++..||..+||++.||++||+|||+|+||..
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F---~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~   62 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNF---NKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   62 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHH---HHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHH---HhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhc
Confidence            5789999999999999999   8 599999999999999999999999999999999999965

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

Probab=99.65  E-value=7.4e-17  Score=112.55  Aligned_cols=54  Identities=28%  Similarity=0.556  Sum_probs=50.8

Q ss_pred             CCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541         113 RNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN  169 (301)
Q Consensus       113 ~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~  169 (301)
                      +.|+.+|+..|+.+|   ..++||+..++..||..+||++.||++||+|||+|+||.
T Consensus         2 T~ft~~Ql~~Le~~F---~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~   55 (56)
T 3a03_A            2 TSFSRSQVLELERRF---LRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ   55 (56)
T ss_dssp             --CCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHH---HhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhhccc
Confidence            579999999999999   899999999999999999999999999999999999985

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

Probab=99.64  E-value=8.7e-17  Score=118.62  Aligned_cols=63  Identities=32%  Similarity=0.548  Sum_probs=58.8

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      .++++.|+.|+..++.+|+.+|   ..++||+..++..||..+||++.+|++||+|||+|+||...
T Consensus         7 ~~~rr~Rt~ft~~q~~~Le~~F---~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r   69 (75)
T 2m0c_A            7 GKKRRNRTTFTSYQLEELEKVF---QKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRER   69 (75)
T ss_dssp             SCCCSCSCSSCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHH---HhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHh
Confidence            3467889999999999999999   89999999999999999999999999999999999999654

>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=99.64  E-value=1.8e-16  Score=122.93  Aligned_cols=62  Identities=29%  Similarity=0.426  Sum_probs=56.1

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      +.+++|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.||+|||||||+|+||...
T Consensus        33 ~~rr~Rt~ft~~Ql~~Le~~F---~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   94 (97)
T 1b72_A           33 SPSGLRTNFTTRQLTELEKEF---HFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   94 (97)
T ss_dssp             ----CCCCCCHHHHHHHHHHH---TTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCcCcCHHHHHHHHHHH---hccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhc
Confidence            457889999999999999999   99999999999999999999999999999999999999754

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

Probab=99.63  E-value=1.9e-16  Score=116.60  Aligned_cols=63  Identities=19%  Similarity=0.357  Sum_probs=58.8

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      .+.++.|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||++||||||+|+||...
T Consensus         4 ~~~~~~Rt~ft~~Ql~~Le~~F---~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   66 (74)
T 2ly9_A            4 PDSFGIRAKKTKEQLAELKVSY---LKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKS   66 (74)
T ss_dssp             CCCCCTTCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTTC
T ss_pred             CCCCCCCcCCCHHHHHHHHHHH---HHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhCc
Confidence            3457889999999999999999   89999999999999999999999999999999999999653

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

Probab=99.62  E-value=1.1e-16  Score=118.60  Aligned_cols=62  Identities=21%  Similarity=0.419  Sum_probs=57.8

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      +..+.|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||++||+|||+|+||...
T Consensus         7 ~~~~~R~~ft~~Ql~~Le~~F---~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~   68 (76)
T 2dn0_A            7 GASIYKNKKSHEQLSALKGSF---CRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKG   68 (76)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHH---HHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCS
T ss_pred             CCCCCCccCCHHHHHHHHHHH---hcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhcc
Confidence            445678999999999999999   99999999999999999999999999999999999999653

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

Probab=99.62  E-value=3.2e-16  Score=119.36  Aligned_cols=57  Identities=16%  Similarity=0.297  Sum_probs=53.5

Q ss_pred             CCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         112 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       112 R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      ...|+.+|+.+|+.+|   ..++||+..+|.+||..|||+++||+|||||||+|+||...
T Consensus        15 ~k~~t~~Ql~~Le~~F---~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~   71 (89)
T 2ecb_A           15 FKEKTAEQLRVLQASF---LNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEE   71 (89)
T ss_dssp             CCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCS
T ss_pred             hccCCHHHHHHHHHHH---HhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHH
Confidence            3489999999999999   99999999999999999999999999999999999998654

>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=99.62  E-value=2.5e-16  Score=116.44  Aligned_cols=60  Identities=20%  Similarity=0.412  Sum_probs=56.1

Q ss_pred             CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      .++|+.|+.+|+.+|+..|   ..++||+..++..||..+||++.||++||+|||+|+|+...
T Consensus         8 ~~kr~~~t~~Ql~~Le~~F---~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (75)
T 2da5_A            8 PTKYKERAPEQLRALESSF---AQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEET   67 (75)
T ss_dssp             SCCCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSC
T ss_pred             CCCCccCCHHHHHHHHHHH---hccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhh
Confidence            3567789999999999999   99999999999999999999999999999999999999754

>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=99.62  E-value=1.1e-16  Score=119.84  Aligned_cols=58  Identities=16%  Similarity=0.241  Sum_probs=54.3

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCC-----CCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLS-----NPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK  168 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~-----~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk  168 (301)
                      ++||+|+.|+.+|+..|+ .|   ..     ++||+..+|.+||..+||++.||+|||||||+|+|+
T Consensus        16 ~~rR~Rt~ft~~Ql~~Le-~F---~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           16 TTKRFRTKFTAEQKEKML-AF---AERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CSSCCCCCCCHHHHHHHH-HH---HHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCccCCHHHHHHHH-HH---HHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            467889999999999999 78   55     999999999999999999999999999999999886

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

Probab=99.61  E-value=3.2e-16  Score=121.05  Aligned_cols=63  Identities=35%  Similarity=0.677  Sum_probs=59.1

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcC---------------CCchhhhhhhhhhHHHhhhhh
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCN---------------ITLSQVSNWFGNKRIRYKKNI  170 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~---------------L~~~qV~~WFqNrR~r~kk~~  170 (301)
                      .+++|.|+.|+..|+.+|+.+|   ..++||+..+++.||..+|               |++.+|++||||||+|+|+..
T Consensus         5 ~~~rr~R~~ft~~ql~~Le~~F---~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~   81 (95)
T 2cuf_A            5 SSGRGSRFTWRKECLAVMESYF---NENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRA   81 (95)
T ss_dssp             SCCCCCSCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHH---hcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHh
Confidence            3567899999999999999999   8899999999999999999               999999999999999999975


Q ss_pred             h
Q psy5541         171 G  171 (301)
Q Consensus       171 ~  171 (301)
                      .
T Consensus        82 ~   82 (95)
T 2cuf_A           82 N   82 (95)
T ss_dssp             H
T ss_pred             h
Confidence            4

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

Probab=99.60  E-value=4.2e-16  Score=120.63  Aligned_cols=64  Identities=22%  Similarity=0.426  Sum_probs=57.7

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhH
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKA  173 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~  173 (301)
                      ..+++|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.||++||||||+|+||...+-
T Consensus        24 ~~~r~Rt~ft~~Ql~~Le~~F---~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~lk~   87 (96)
T 3nar_A           24 GSTGKICKKTPEQLHMLKSAF---VRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNLKW   87 (96)
T ss_dssp             ---CCSSSSCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTCCHH
T ss_pred             CCCCCCccCCHHHHHHHHHHH---HHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhcccH
Confidence            356789999999999999999   8999999999999999999999999999999999999976543

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

Probab=99.60  E-value=4e-16  Score=111.43  Aligned_cols=51  Identities=22%  Similarity=0.504  Sum_probs=49.4

Q ss_pred             CHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541         116 SKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN  169 (301)
Q Consensus       116 ~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~  169 (301)
                      +++|+..|+..|   ..++||+..++.+||..|||+++||++||+|||.|+|+.
T Consensus        12 ~~~Ql~~LE~~F---~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg   62 (66)
T 3nau_A           12 TKEQIAHLKASF---LQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRG   62 (66)
T ss_dssp             CHHHHHHHHHHH---HGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHH---hcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhcc
Confidence            689999999999   999999999999999999999999999999999999975

>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=99.58  E-value=2.3e-15  Score=116.82  Aligned_cols=62  Identities=27%  Similarity=0.464  Sum_probs=58.1

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHc---------------------CCCchhhhhhhhhhHHH
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKC---------------------NITLSQVSNWFGNKRIR  165 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~---------------------~L~~~qV~~WFqNrR~r  165 (301)
                      ++||.|+.|+..++.+|+.+|   ..++||+..+|++||..+                     +|++.+|.|||||||+|
T Consensus         5 ~~Rr~Rt~ft~~ql~~Le~~F---~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k   81 (102)
T 2da6_A            5 SSGRNRFKWGPASQQILYQAY---DRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKE   81 (102)
T ss_dssp             CSCCCCCCCCHHHHHHHHHHH---TTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCccCCHHHHHHHHHHH---cCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHH
Confidence            467899999999999999999   999999999999999999                     79999999999999999


Q ss_pred             hhhhhh
Q psy5541         166 YKKNIG  171 (301)
Q Consensus       166 ~kk~~~  171 (301)
                      +|+...
T Consensus        82 ~kr~~~   87 (102)
T 2da6_A           82 EAFRQK   87 (102)
T ss_dssp             HHHHHH
T ss_pred             HHHhhH
Confidence            988644

>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=99.57  E-value=1.5e-15  Score=108.38  Aligned_cols=59  Identities=25%  Similarity=0.439  Sum_probs=55.3

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCC-CCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLS-NPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK  168 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~-~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk  168 (301)
                      ++||.||.|+.+|+.+|+..|   .. ++||+..+|+.||.+|||++++|++||||+|--.+.
T Consensus         6 ~~kR~RT~~s~eQL~~Lqs~f---~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~~~~   65 (71)
T 1wi3_A            6 SGPRSRTKISLEALGILQSFI---HDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             CCCCCCCCCCSHHHHHHHHHH---HHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             CCCCCCccCCHHHHHHHHHHH---HhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceeeecC
Confidence            568899999999999999999   88 999999999999999999999999999999986554

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

Probab=99.56  E-value=3.9e-16  Score=132.18  Aligned_cols=63  Identities=27%  Similarity=0.346  Sum_probs=54.7

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      .++||+|+.|+..|+.+|+.+|   ..++||+..+|..||..+||++.||+|||||||+|+|+...
T Consensus        95 ~~~rr~Rt~ft~~q~~~Le~~F---~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~  157 (164)
T 2d5v_A           95 NTPKKPRLVFTDVQRRTLHAIF---KENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWL  157 (164)
T ss_dssp             -----CCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC--
T ss_pred             CCCCCCCCcCCHHHHHHHHHHH---hcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccCC
Confidence            3467899999999999999999   88899999999999999999999999999999999998643

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

Probab=99.55  E-value=3.6e-15  Score=106.85  Aligned_cols=55  Identities=24%  Similarity=0.375  Sum_probs=51.4

Q ss_pred             CCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541         111 KRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK  168 (301)
Q Consensus       111 ~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk  168 (301)
                      .+..+.++|+..|+.+|   ..++||+..+|..||..+||+++||++||||||+|.++
T Consensus         6 ~~~~p~~~Ql~~Le~~F---~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~   60 (64)
T 2e19_A            6 SGQPPLKNLLSLLKAYY---ALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS   60 (64)
T ss_dssp             SCCCCCHHHHHHHHHHH---TTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSC
T ss_pred             CCCCccHHHHHHHHHHH---hcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCC
Confidence            34567799999999999   99999999999999999999999999999999999876

>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=99.55  E-value=2.6e-15  Score=114.56  Aligned_cols=58  Identities=17%  Similarity=0.408  Sum_probs=53.8

Q ss_pred             CCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         111 KRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       111 ~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      ++..|+.+|+.+|+.+|   ..++||+..++..||..+||++.||+|||||||+|+|+...
T Consensus        16 k~k~~t~~Ql~~Le~~F---~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~   73 (89)
T 2dmp_A           16 KFKEKTQGQVKILEDSF---LKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQ   73 (89)
T ss_dssp             CCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCS
T ss_pred             ccccCCHHHHHHHHHHH---ccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhH
Confidence            34459999999999999   89999999999999999999999999999999999998754

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

Probab=99.54  E-value=3.6e-15  Score=115.87  Aligned_cols=63  Identities=27%  Similarity=0.417  Sum_probs=53.9

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHH------------------cC---CCchhhhhhhhhhHH
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARK------------------CN---ITLSQVSNWFGNKRI  164 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~------------------~~---L~~~qV~~WFqNrR~  164 (301)
                      .++||.|+.|+..|+.+|+.+|   ..++||+..+|++||..                  +|   |++.+|+|||||||+
T Consensus         7 ~k~rr~Rt~ft~~Ql~~LE~~F---~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~   83 (99)
T 1lfb_A            7 KKGRRNRFKWGPASQQILFQAY---ERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRK   83 (99)
T ss_dssp             ------CCCCCHHHHHHHHHHH---TTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCcCHHHHHHHHHHH---hcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHH
Confidence            3567889999999999999999   99999999999999999                  88   999999999999999


Q ss_pred             Hhhhhhh
Q psy5541         165 RYKKNIG  171 (301)
Q Consensus       165 r~kk~~~  171 (301)
                      +.|+...
T Consensus        84 k~k~k~~   90 (99)
T 1lfb_A           84 EEAFRHK   90 (99)
T ss_dssp             TTSCCC-
T ss_pred             HHHHhch
Confidence            9887654

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

Probab=99.54  E-value=2.7e-15  Score=108.96  Aligned_cols=56  Identities=27%  Similarity=0.392  Sum_probs=52.5

Q ss_pred             CCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         113 RNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       113 ~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      ..++..|+..|+..|   ..++||+..+|.+||..+||+++||++||||||+|+||...
T Consensus         9 ~~~t~~ql~~LE~~F---~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~~   64 (69)
T 2l9r_A            9 SHMSHTQVIELERKF---SHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQL   64 (69)
T ss_dssp             CCCCHHHHHHHHHHH---HHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSSS
T ss_pred             CcCCHHHHHHHHHHH---hcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhhh
Confidence            457899999999999   99999999999999999999999999999999999998653

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

Probab=99.51  E-value=4.5e-15  Score=108.79  Aligned_cols=61  Identities=16%  Similarity=0.342  Sum_probs=54.7

Q ss_pred             cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541         108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI  170 (301)
Q Consensus       108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~  170 (301)
                      ..++|+.++.+|+.+||..|.  ..++||+..++.+||..+||++.||++||||||+|+|+..
T Consensus         8 g~k~r~r~~~~ql~~LE~~F~--~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~~   68 (72)
T 2cqx_A            8 GIKDSPVNKVEPNDTLEKVFV--SVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSG   68 (72)
T ss_dssp             CCCCCCCSCSCSTTHHHHHHH--HTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSCC
T ss_pred             CCCCCCCCCHHHHHHHHHHHH--hcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCCC
Confidence            456777888999999999994  4578999999999999999999999999999999999854

>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=99.48  E-value=2.4e-14  Score=102.18  Aligned_cols=51  Identities=24%  Similarity=0.410  Sum_probs=46.0

Q ss_pred             HHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541         118 QASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI  170 (301)
Q Consensus       118 ~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~  170 (301)
                      .++.+||..|.  ..+.||+..+|.+||.++||+++||++||||||+|+|+..
T Consensus        10 ~~~~~LE~~F~--~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~~~   60 (64)
T 1x2m_A           10 QPNAILEKVFT--AITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPSG   60 (64)
T ss_dssp             CHHHHHHHHHH--TTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCCSS
T ss_pred             hHHHHHHHHHH--HcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCCCC
Confidence            46899999993  3489999999999999999999999999999999998753

>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=99.31  E-value=7.8e-13  Score=94.95  Aligned_cols=46  Identities=17%  Similarity=0.431  Sum_probs=44.0

Q ss_pred             HHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHH
Q psy5541         117 KQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIR  165 (301)
Q Consensus       117 ~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r  165 (301)
                      ++|+..|+.+|   ..+++|+.+++..||..+||++++|++||||||++
T Consensus        14 k~ql~~Lk~yF---~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~   59 (71)
T 2da7_A           14 KDHMSVLKAYY---AMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVY   59 (71)
T ss_dssp             THHHHHHHHHH---HHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHH---HhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhcccc
Confidence            67899999999   99999999999999999999999999999999974

>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=99.30  E-value=3.1e-13  Score=117.01  Aligned_cols=60  Identities=32%  Similarity=0.545  Sum_probs=53.5

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcC---------------------CCchhhhhhhhhhHH
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCN---------------------ITLSQVSNWFGNKRI  164 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~---------------------L~~~qV~~WFqNrR~  164 (301)
                      .++||.|+.|+..|+.+|+.+|   ..++||+..+|++||..++                     |++.+|+|||+|||+
T Consensus       113 ~k~rr~R~~ft~~ql~~Le~~F---~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~  189 (194)
T 1ic8_A          113 KKGRRNRFKWGPASQQILFQAY---ERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRK  189 (194)
T ss_dssp             ----CCCCCCCHHHHHHHHHHH---HHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHH
T ss_pred             ccCCCCCcccCHHHHHHHHHHH---HhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhh
Confidence            4567899999999999999999   8999999999999999999                     999999999999999


Q ss_pred             Hhhh
Q psy5541         165 RYKK  168 (301)
Q Consensus       165 r~kk  168 (301)
                      |.|.
T Consensus       190 ~~k~  193 (194)
T 1ic8_A          190 EEAF  193 (194)
T ss_dssp             HCC-
T ss_pred             hhhc
Confidence            9874

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

Probab=99.23  E-value=3.3e-12  Score=111.95  Aligned_cols=58  Identities=33%  Similarity=0.582  Sum_probs=52.9

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcC---------------------CCchhhhhhhhhhHH
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCN---------------------ITLSQVSNWFGNKRI  164 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~---------------------L~~~qV~~WFqNrR~  164 (301)
                      .+.||.|+.|++.++.+|+.+|   ..++||+..+|++||..+|                     |++.+|+|||+|||+
T Consensus       140 ~k~RR~R~~ft~~ql~~Le~~F---~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~  216 (221)
T 2h8r_A          140 KKMRRNRFKWGPASQQILYQAY---DRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRK  216 (221)
T ss_dssp             --CCCCCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHT
T ss_pred             CCCCCCCcCCCHHHHHHHHHHH---HcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhh
Confidence            4567889999999999999999   8999999999999999988                     899999999999998


Q ss_pred             Hh
Q psy5541         165 RY  166 (301)
Q Consensus       165 r~  166 (301)
                      +.
T Consensus       217 ~~  218 (221)
T 2h8r_A          217 EE  218 (221)
T ss_dssp             TC
T ss_pred             hh
Confidence            74

>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=99.13  E-value=1.3e-11  Score=117.23  Aligned_cols=55  Identities=40%  Similarity=0.545  Sum_probs=51.9

Q ss_pred             CCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhh
Q psy5541         110 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK  167 (301)
Q Consensus       110 r~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~k  167 (301)
                      +.++.|+..++..|++.|   ..++||+..+|.+||.+|||+++||+|||||||+|+|
T Consensus       367 ~~~~~~~~~q~~~Le~~f---~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          367 AAAAAISPQARAFLEQVF---RRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHCSSCHHHHHHHHHHH---HHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhcchHHHHHHHHH---hcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            456789999999999999   9999999999999999999999999999999999976

>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=98.40  E-value=4.7e-08  Score=61.57  Aligned_cols=20  Identities=35%  Similarity=0.816  Sum_probs=17.7

Q ss_pred             hhhhhhhhhhHHHhhhhhhh
Q psy5541         153 SQVSNWFGNKRIRYKKNIGK  172 (301)
Q Consensus       153 ~qV~~WFqNrR~r~kk~~~~  172 (301)
                      +||+|||||||+|+||....
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~   20 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFN   20 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHH
T ss_pred             CCceeccHHHHHHHHHHhHH
Confidence            58999999999999998654

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

Probab=95.10  E-value=0.009  Score=42.49  Aligned_cols=41  Identities=20%  Similarity=0.401  Sum_probs=36.6

Q ss_pred             HHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhh
Q psy5541         117 KQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFG  160 (301)
Q Consensus       117 ~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFq  160 (301)
                      +.-.+.|+++|   ..+....+.+...|+.+++|+..||+.||-
T Consensus        15 p~~~e~L~~Yy---~~hk~L~EeDl~~L~~kskms~qqvkdwFa   55 (70)
T 2ys9_A           15 PPDIQPLERYW---AAHQQLRETDIPQLSQASRLSTQQVLDWFD   55 (70)
T ss_dssp             CCCCHHHHHHH---HHTCCCCTTHHHHHHHHTTCCHHHHHHHHH
T ss_pred             CCcchHHHHHH---HHhcccchhhHHHHHHHhCCCHHHHHHHHH
Confidence            34457899999   778889999999999999999999999994

---

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	301
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	8e-23
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	1e-20
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	3e-17
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	3e-12
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	4e-12
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	4e-12
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	5e-12
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	7e-12
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	1e-11
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	1e-11
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	2e-11
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	2e-11
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	5e-11
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	7e-11
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	8e-11
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	2e-10
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	4e-10
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	4e-10
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	5e-10
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	6e-10
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	2e-09
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	2e-09
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	2e-09
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	3e-09
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	6e-09
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	9e-09
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	2e-08
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	9e-08
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	1e-07
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	2e-07
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	6e-07
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	1e-05

>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 = 87.7 bits (217), Expect = 8e-23
 Identities = 66/73 (90%), Positives = 71/73 (97%)

Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
           ARRKRRNF+KQA+EILNEYFYSHLSNPYPSEEAKEELA+KC IT+SQVSNWFGNKRIRYK
Sbjct: 1   ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60

Query: 168 KNIGKAQEEANLY 180
           KNIGK QEEAN+Y
Sbjct: 61  KNIGKFQEEANIY 73

>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 = 81.3 bits (201), Expect = 1e-20
 Identities = 22/61 (36%), Positives = 39/61 (63%)

Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
            + KR    K A+ ++  + + H+ +PYP+E+ K+++A + N+TL QV+NWF N R R  
Sbjct: 2   GKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRIL 61

Query: 168 K 168
           +
Sbjct: 62  Q 62

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 72.1 bits (177), Expect = 3e-17
 Identities = 16/58 (27%), Positives = 30/58 (51%)

Query: 111 KRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           +   F+K+   IL  +F  ++ NPY   +  E L +  +++  Q+ NW  N+R + K 
Sbjct: 1   RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 52

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.6 bits (142), Expect = 3e-12
 Identities = 12/54 (22%), Positives = 27/54 (50%), Gaps = 2/54 (3%)

Query: 116 SKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN 169
           + Q + IL + F +     +P E+  E L+++ +  +  +  WF  +R + K +
Sbjct: 1   TAQPNAILEKVFTAI--TKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPS 52

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.3 bits (141), Expect = 4e-12
 Identities = 17/68 (25%), Positives = 35/68 (51%), Gaps = 3/68 (4%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           +R R +F+++  E L + F       YP   A+E LA K ++  +++  WF N+R ++++
Sbjct: 2   QRNRTSFTQEQIEALEKEF---ERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRR 58

Query: 169 NIGKAQEE 176
                 + 
Sbjct: 59  EEKLRNQR 66

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein prh
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.3 bits (141), Expect = 4e-12
 Identities = 14/60 (23%), Positives = 29/60 (48%), Gaps = 3/60 (5%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           +  +  FS   +  L + F    +  Y S   ++ LA+   ++  QV  WF N+R ++++
Sbjct: 1   KGGQVRFSNDQTIELEKKF---ETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 57

>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 = 58.5 bits (141), Expect = 5e-12
 Identities = 13/72 (18%), Positives = 27/72 (37%), Gaps = 2/72 (2%)

Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
                   ++   EIL   F  +  N +P       +A +  +T  Q   WF  +   ++
Sbjct: 1   GSEGAATMTEDQVEILEYNF--NKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 58

Query: 168 KNIGKAQEEANL 179
           ++ G   E  ++
Sbjct: 59  RSEGLPSECRSV 70

>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 = 57.5 bits (139), Expect = 7e-12
 Identities = 11/58 (18%), Positives = 29/58 (50%), Gaps = 2/58 (3%)

Query: 110 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
           +       + ++ L + F S     YP E+  + L+++ + ++ ++  WF ++R + K
Sbjct: 3   KDSPVNKVEPNDTLEKVFVSV--TKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 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 = 57.4 bits (138), Expect = 1e-11
 Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 2/61 (3%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
            R R   S +A  IL  + +      YP +EA   L+ + ++    +  +F N+R   K 
Sbjct: 8   PRSRTKISLEALGILQSFIHDV--GLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH 65

Query: 169 N 169
           +
Sbjct: 66  S 66

>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 = 57.1 bits (138), Expect = 1e-11
 Identities = 22/60 (36%), Positives = 35/60 (58%), Gaps = 3/60 (5%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           R+KR  ++K  +  L + F   L N Y + + + E+AR  N+T  QV  WF N+R++ KK
Sbjct: 14  RKKRCPYTKHQTLELEKEF---LFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 53

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 56.4 bits (136), Expect = 2e-11
 Identities = 22/56 (39%), Positives = 30/56 (53%), Gaps = 3/56 (5%)

Query: 112 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
           + + S QA   L + F         + + KEE+A+KC IT  QV  WF NKR+R K
Sbjct: 1   KSSISPQARAFLEQVF---RRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53

>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 = 56.4 bits (136), Expect = 2e-11
 Identities = 13/60 (21%), Positives = 34/60 (56%), Gaps = 3/60 (5%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           R+KR  +SK     L   + ++    + +++ + +++   +++  Q++ WF N+R++ KK
Sbjct: 2   RKKRIPYSKGQLRELEREYAAN---KFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 58

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.2 bits (135), Expect = 5e-11
 Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 3/81 (3%)

Query: 88  MQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARK 147
           M++K++  +   +           R NF+ +    L         N Y S   + E+A  
Sbjct: 7   MKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELE---KEFHFNKYLSRARRVEIAAT 63

Query: 148 CNITLSQVSNWFGNKRIRYKK 168
             +  +QV  WF N+R++ KK
Sbjct: 64  LELNETQVKIWFQNRRMKQKK 84

>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 = 55.4 bits (133), Expect = 7e-11
 Identities = 8/61 (13%), Positives = 19/61 (31%), Gaps = 1/61 (1%)

Query: 109 RRKRRNFSKQASEILNEYFY-SHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
           +R R  F+ +  E +  +            + A E+   +  +    +  W  N +    
Sbjct: 18  KRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGP 77

Query: 168 K 168
            
Sbjct: 78  S 78

>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 = 54.8 bits (132), Expect = 8e-11
 Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 3/60 (5%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
            R R   +++    L   +    +NP P    KE+L     ++   +  WF NKR + KK
Sbjct: 4   TRVRTVLNEKQLHTLRTCY---AANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKK 60

>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 = 53.8 bits (129), Expect = 2e-10
 Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 3/60 (5%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           RR R  FS    + L   F       YP    +EELA++ N+T +++  WF N+R R +K
Sbjct: 3   RRSRTTFSASQLDELERAF---ERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK 59

>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 = 52.6 bits (126), Expect = 4e-10
 Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 3/60 (5%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           RR+R +F+ Q  + L   F     N YP    +EE+A   N+T ++V  WF N+R +++K
Sbjct: 2   RRQRTHFTSQQLQQLEATF---QRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 58

>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 = 53.1 bits (127), Expect = 4e-10
 Identities = 25/84 (29%), Positives = 35/84 (41%), Gaps = 20/84 (23%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCN---------------ITLS 153
           R  R  + K+   ++  YF     N YP E  +EE+A  CN               +T  
Sbjct: 1   RGSRFTWRKECLAVMESYF---NENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSL 57

Query: 154 QVSNWFGNKRIRYKK--NIGKAQE 175
           +V NWF N+R   K+  NI    E
Sbjct: 58  KVYNWFANRRKEIKRRANIAAILE 81

>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 = 52.1 bits (125), Expect = 5e-10
 Identities = 15/57 (26%), Positives = 31/57 (54%), Gaps = 3/57 (5%)

Query: 112 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           R+ +++  +  L + F     N Y +   + E+A   ++T  Q+  WF N+R+++KK
Sbjct: 1   RQTYTRYQTLELEKEF---HFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 54

>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 = 52.2 bits (125), Expect = 6e-10
 Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 3/69 (4%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           RR R  F+      L ++F   L   Y +     +L+ K  +  +QV  WF N+R R+K 
Sbjct: 2   RRTRTTFTSSQIAELEQHF---LQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKI 58

Query: 169 NIGKAQEEA 177
              + ++++
Sbjct: 59  QSDQHKDQS 67

>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 = 51.1 bits (122), Expect = 2e-09
 Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 3/59 (5%)

Query: 110 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           ++R   S  A + L  +F  H     PS +    +A + N+    V  WF N+R R K+
Sbjct: 1   KRRTTISIAAKDALERHFGEH---SKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 56

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.7 bits (121), Expect = 2e-09
 Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 3/60 (5%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           R+ R  F+      L   F       Y S   + E +   ++T +QV  WF N+R + K+
Sbjct: 1   RKPRTPFTTAQLLALERKF---RQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 50.3 bits (120), Expect = 2e-09
 Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 3/59 (5%)

Query: 110 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           R R  F++     L + F       Y S   + ELA + N+  S +  WF N+R++ K+
Sbjct: 1   RYRTAFTRDQLGRLEKEF---YKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 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 = 50.7 bits (121), Expect = 3e-09
 Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 3/61 (4%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           R++R  FS+     L   F       Y S   +E LA   ++T +QV  WF N R + K+
Sbjct: 3   RKRRVLFSQAQVYELERRF---KQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKR 59

Query: 169 N 169
            
Sbjct: 60  Q 60

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 53

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

 Score = 49.1 bits (117), Expect = 6e-09
 Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 3/56 (5%)

Query: 110 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIR 165
           R R  FS +    L   F     N Y +E  +++L+ +  +  +Q+  WF N R +
Sbjct: 1   RPRTAFSSEQLARLKREF---NENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>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 = 49.2 bits (117), Expect = 9e-09
 Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 3/60 (5%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           +RKR +   +    L   F      P PS +    +A +  +    V  WF N+R + K+
Sbjct: 9   KRKRTSIENRVRWSLETMFLKC---PKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR 65

>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 = 47.9 bits (114), Expect = 2e-08
 Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 3/52 (5%)

Query: 112 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKR 163
           R  F+      L+  F     N  PS+E +  ++++  + LS VSN+F N R
Sbjct: 2   RLVFTDVQRRTLHAIF---KENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>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 = 46.6 bits (110), Expect = 9e-08
 Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 3/60 (5%)

Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           R++R  F+K  +  L   F       Y S   +E LA    +T +QV  WF N R + K+
Sbjct: 10  RKRRVLFTKAQTYELERRF---RQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.7 bits (108), Expect = 1e-07
 Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 3/58 (5%)

Query: 111 KRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
           KR +        L + F  +     P+ E    +A + N+    +  WF N+R + K+
Sbjct: 1   KRTSIETNIRVALEKSFMEN---QKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 55

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Length = 78

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Rat (Rattus rattus) [TaxId: 10117]

 Score = 45.9 bits (108), Expect = 2e-07
 Identities = 17/78 (21%), Positives = 28/78 (35%), Gaps = 24/78 (30%)

Query: 112 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCN---------------------I 150
           R  +   + +IL + +        PS+E +E L  +CN                     +
Sbjct: 1   RFKWGPASQQILFQAYER---QKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLV 57

Query: 151 TLSQVSNWFGNKRIRYKK 168
           T  +V NWF N+R     
Sbjct: 58  TEVRVYNWFANRRKEEAF 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 = 44.3 bits (104), Expect = 6e-07
 Identities = 11/69 (15%), Positives = 27/69 (39%), Gaps = 3/69 (4%)

Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
             +K +  + +   +L   F   L++   ++E    L  +  +T  ++  WF  K+    
Sbjct: 4   TPQKFKEKTAEQLRVLQASF---LNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKA 60

Query: 168 KNIGKAQEE 176
               K + +
Sbjct: 61  LKEEKMEID 69

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-leucine zipper protein Homez
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.9 bits (95), Expect = 1e-05
 Identities = 12/69 (17%), Positives = 26/69 (37%), Gaps = 3/69 (4%)

Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
           +    +  +K+   IL  +    L   +   E  ++L +   +   ++  WFG+ R   K
Sbjct: 3   SGSSGKRKTKEQLAILKSF---FLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALK 59

Query: 168 KNIGKAQEE 176
               K   +
Sbjct: 60  HGQLKWFRD 68

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	301
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.79
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.77
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.75
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.75
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.75
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.74
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.74
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.74
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.74
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.73
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.72
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.72
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.72
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.72
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.72
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.71
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.71
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.7
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.7
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.69
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.69
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.68
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.67
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.67
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.65
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.62
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.58
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.58
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.57
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.55
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.54
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.5
d1e3oc2	75	Oct-1 {Human (Homo sapiens) [TaxId: 9606]}	95.51
d1au7a2	72	Pit-1 {Rat (Rattus norvegicus) [TaxId: 10116]}	95.26
d1hlva1	66	DNA-binding domain of centromere binding protein B	83.47

>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=99.79  E-value=3.6e-20  Score=134.66  Aligned_cols=67  Identities=91%  Similarity=1.387  Sum_probs=62.4

Q ss_pred             CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHHH
Q psy5541         109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQE  175 (301)
Q Consensus       109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~~  175 (301)
                      ||+|+.|+++++.+|+.||.+|..+|||+..++++||..+||++.||+|||+|+|+|.|+.......
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~~~~~~   68 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQE   68 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTTTTT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccchhhHh
Confidence            6789999999999999999999999999999999999999999999999999999999987655444

>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=99.77  E-value=8.9e-20  Score=126.45  Aligned_cols=58  Identities=24%  Similarity=0.518  Sum_probs=55.6

Q ss_pred             cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541         108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK  168 (301)
Q Consensus       108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk  168 (301)
                      +||+|+.|+.+|+.+|+..|   ..++||+..++.+||..+||++.||++||||||+|+||
T Consensus         1 Grr~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           1 GRKKRIPYSKGQLRELEREY---AANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCCSCCCSCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCHHHHHHHHHHH---hhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            36889999999999999999   89999999999999999999999999999999999986

>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=99.75  E-value=4.5e-19  Score=121.78  Aligned_cols=55  Identities=27%  Similarity=0.532  Sum_probs=53.6

Q ss_pred             CCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541         112 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN  169 (301)
Q Consensus       112 R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~  169 (301)
                      |+.|+.+|+.+|+.+|   ..++||+..++.+||..+||++.+|+|||||||+|+||+
T Consensus         1 Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk~   55 (56)
T d9anta_           1 RQTYTRYQTLELEKEF---HFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   55 (56)
T ss_dssp             CCCCCHHHHHHHHHHH---TTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCcCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhhc
Confidence            7899999999999999   999999999999999999999999999999999999985

>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=99.75  E-value=5.6e-19  Score=126.02  Aligned_cols=60  Identities=30%  Similarity=0.459  Sum_probs=57.3

Q ss_pred             CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      ||+|+.|+.+|+.+|+..|   ..++||+..++..||..+||++.+|+|||||||+|+|+...
T Consensus         2 rr~Rt~ft~~Ql~~Le~~F---~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~   61 (67)
T d1zq3p1           2 RRTRTTFTSSQIAELEQHF---LQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD   61 (67)
T ss_dssp             SCCSCCCCHHHHHHHHHHH---TTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHH---HHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhh
Confidence            6789999999999999999   99999999999999999999999999999999999998654

>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=99.75  E-value=3.4e-19  Score=123.71  Aligned_cols=57  Identities=28%  Similarity=0.468  Sum_probs=55.2

Q ss_pred             CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541         109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK  168 (301)
Q Consensus       109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk  168 (301)
                      ||+|+.|+.+|+.+|+..|   ..++||+..++.+||..+||++.+|++||||+|+|+||
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F---~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKF---RQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHH---HHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHH---HHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            5789999999999999999   89999999999999999999999999999999999997

>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=99.74  E-value=5.4e-19  Score=122.18  Aligned_cols=57  Identities=25%  Similarity=0.502  Sum_probs=55.0

Q ss_pred             CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541         109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK  168 (301)
Q Consensus       109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk  168 (301)
                      |++|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||++||||||+|+||
T Consensus         1 k~~R~~ft~~Q~~~Le~~F---~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k~kk   57 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKF---ETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR   57 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhhccC
Confidence            4789999999999999999   99999999999999999999999999999999999986

>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=99.74  E-value=5.2e-19  Score=122.26  Aligned_cols=57  Identities=30%  Similarity=0.515  Sum_probs=54.9

Q ss_pred             CCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541         110 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN  169 (301)
Q Consensus       110 r~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~  169 (301)
                      |+|+.|+.+|+.+|+..|   ..++||+..++.+||..+||++.||++||||+|+|+||+
T Consensus         1 R~Rt~fT~~Ql~~Le~~F---~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk~   57 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEF---YKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   57 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHH---HHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCHHHHHHHHHHH---HHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhcC
Confidence            578999999999999999   999999999999999999999999999999999999974

>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=99.74  E-value=1.2e-18  Score=122.33  Aligned_cols=60  Identities=37%  Similarity=0.759  Sum_probs=56.8

Q ss_pred             cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhh
Q psy5541         108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK  167 (301)
Q Consensus       108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~k  167 (301)
                      +|++|+.|+++++.+|+.||.+|..+|||+..++..||..+||+..||++||+|+|+|..
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            367788999999999999999999999999999999999999999999999999999864

>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=99.74  E-value=8e-19  Score=124.53  Aligned_cols=62  Identities=34%  Similarity=0.584  Sum_probs=58.2

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      ++||.|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||++||||+|+|+|+...
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F---~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~   62 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAF---ERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   62 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHH---HHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhccc
Confidence            357889999999999999999   89999999999999999999999999999999999998643

>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=99.73  E-value=2.3e-18  Score=123.14  Aligned_cols=62  Identities=27%  Similarity=0.562  Sum_probs=58.3

Q ss_pred             cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhh
Q psy5541         108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGK  172 (301)
Q Consensus       108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~  172 (301)
                      +||+|+.|+.+|+.+|+..|   ..++||+..++..||..+||++.+|++||+|+|+|+|+....
T Consensus         1 grR~Rt~ft~~Ql~~Le~~F---~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~   62 (68)
T d2cuea1           1 GQRNRTSFTQEQIEALEKEF---ERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL   62 (68)
T ss_dssp             SCCCCCCSCHHHHHHHHHHH---TTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCCHHHHHHHHHHH---HHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhhh
Confidence            36789999999999999999   999999999999999999999999999999999999986543

>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=99.72  E-value=2.3e-18  Score=120.24  Aligned_cols=55  Identities=29%  Similarity=0.610  Sum_probs=53.2

Q ss_pred             CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541         114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK  168 (301)
Q Consensus       114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk  168 (301)
                      +|+.+++.+|+.||.+|..+|||+..++..||..+||+..||++||+|+|+|.|+
T Consensus         4 Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           4 RFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             SCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            4999999999999999999999999999999999999999999999999999876

>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=99.72  E-value=1.6e-18  Score=126.77  Aligned_cols=61  Identities=36%  Similarity=0.529  Sum_probs=57.9

Q ss_pred             cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      +||+|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.||+|||||||+|+|+...
T Consensus        13 ~rr~Rt~ft~~Ql~~Le~~F---~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~   73 (77)
T d1pufa_          13 TRKKRCPYTKHQTLELEKEF---LFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINK   73 (77)
T ss_dssp             TSCCCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHH---HHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHH
Confidence            46789999999999999999   99999999999999999999999999999999999998654

>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=99.72  E-value=1.2e-18  Score=121.81  Aligned_cols=58  Identities=36%  Similarity=0.654  Sum_probs=56.2

Q ss_pred             CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541         109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN  169 (301)
Q Consensus       109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~  169 (301)
                      ||+|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.+|++||+|+|+|+|+.
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F---~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATF---QRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHH---TTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHH---HHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            6789999999999999999   999999999999999999999999999999999999985

>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=99.72  E-value=1.4e-18  Score=118.27  Aligned_cols=53  Identities=28%  Similarity=0.508  Sum_probs=51.2

Q ss_pred             CCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHH
Q psy5541         110 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIR  165 (301)
Q Consensus       110 r~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r  165 (301)
                      |+|+.|+.+|+.+|+..|   ..++||+..++.+||..+||++.||++||||||+|
T Consensus         1 R~Rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~LA~~lgL~~~qV~vWFqNrRaK   53 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREF---NENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK   53 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             CCCccCCHHHHHHHHHHH---HHCCCCCHHHHHHHHHHhCCChHHhhhcccccCCC
Confidence            578999999999999999   99999999999999999999999999999999986

>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=99.72  E-value=2.2e-18  Score=123.19  Aligned_cols=61  Identities=31%  Similarity=0.462  Sum_probs=57.7

Q ss_pred             cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      +||+|+.|+..|+.+|+..|   ..++||+..++..||..+||++.+|++||+|+|.|+|+...
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F---~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~~   62 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRF---KQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK   62 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHH---HHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCCCHHHHHHHHHHH---HHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhccc
Confidence            36789999999999999999   99999999999999999999999999999999999998753

>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=99.71  E-value=2.9e-18  Score=122.16  Aligned_cols=60  Identities=27%  Similarity=0.440  Sum_probs=57.1

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN  169 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~  169 (301)
                      .+||+|+.|+.+|+.+|+.+|   ..++||+..++.+||..+||++.+|++||+|+|+|+||.
T Consensus         7 ~~rr~Rt~~t~~q~~~Le~~F---~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_           7 ARKRKRTSIENRVRWSLETMF---LKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             CSSSCCSSCCHHHHHHHHHHH---SSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             ccCCCCCCCCHHHHHHHHHHH---HHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            357889999999999999999   999999999999999999999999999999999999874

>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=99.71  E-value=4.7e-18  Score=127.43  Aligned_cols=61  Identities=30%  Similarity=0.438  Sum_probs=55.5

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI  170 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~  170 (301)
                      +++|.|+.|+.+|+.+|+.+|   ..++||+..++++||..+||++.+|+|||||+|+|+||..
T Consensus        26 ~~kr~Rt~ft~~Ql~~Le~~F---~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~   86 (88)
T d1b72a_          26 SPSGLRTNFTTRQLTELEKEF---HFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRE   86 (88)
T ss_dssp             ----CCCCCCHHHHHHHHHHH---TTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCCCHHHHHHHHHHH---HhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhc
Confidence            456889999999999999999   9999999999999999999999999999999999999864

>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=99.70  E-value=2.1e-18  Score=122.64  Aligned_cols=62  Identities=26%  Similarity=0.409  Sum_probs=58.6

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      +.+|.|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.+|++||+|+|+|.|+...
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F---~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~~~   63 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCY---AANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI   63 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHH---HHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCCC
T ss_pred             CCCCCCcCcCHHHHHHHHHHH---HHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHHHH
Confidence            467899999999999999999   99999999999999999999999999999999999998653

>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=99.70  E-value=7.4e-18  Score=121.55  Aligned_cols=58  Identities=19%  Similarity=0.349  Sum_probs=55.2

Q ss_pred             CCCCCCCCHHHHHHHHhHhhcCCC-CCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541         109 RRKRRNFSKQASEILNEYFYSHLS-NPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN  169 (301)
Q Consensus       109 rr~R~~~~~~q~~~L~~~f~~h~~-~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~  169 (301)
                      +++|++|+.+|+.+|+..|   .. ++||+..+++.||..+||++++|++||||||+|+||.
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F---~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~   60 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNF---NKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS   60 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHH---HSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHH---HHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhc
Confidence            5789999999999999999   75 7899999999999999999999999999999999985

>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=99.69  E-value=5.2e-18  Score=117.57  Aligned_cols=57  Identities=28%  Similarity=0.426  Sum_probs=54.8

Q ss_pred             CCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541         110 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN  169 (301)
Q Consensus       110 r~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~  169 (301)
                      |+|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.+|++||||+|+|+|+.
T Consensus         1 r~Rt~~s~~q~~~Le~~F---~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr~   57 (58)
T d1au7a1           1 KRRTTISIAAKDALERHF---GEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV   57 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCHHHHHHHHHHH---HHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHhc
Confidence            578999999999999999   899999999999999999999999999999999999874

>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=99.69  E-value=2.3e-18  Score=126.13  Aligned_cols=63  Identities=30%  Similarity=0.431  Sum_probs=58.3

Q ss_pred             hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      .+++|.|++|+.+|+.+|+..|   ..++||+..+++.||..+||++.||++||||+|+|.|+...
T Consensus         7 ~k~rr~Rt~ft~~Q~~~Le~~F---~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   69 (77)
T d1vnda_           7 NKKRKRRVLFTKAQTYELERRF---RQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQN   69 (77)
T ss_dssp             SSSCSSCCCCCTTHHHHHHHHH---HHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHH---HHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHhh
Confidence            3457789999999999999999   99999999999999999999999999999999999998643

>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=99.68  E-value=8.8e-18  Score=114.28  Aligned_cols=53  Identities=42%  Similarity=0.603  Sum_probs=51.2

Q ss_pred             CCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhh
Q psy5541         112 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK  167 (301)
Q Consensus       112 R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~k  167 (301)
                      |+.|+++|+.+|+.+|   ..++||+..++..||..+||++.||++||+|+|+|.|
T Consensus         1 Rt~~s~~q~~~Le~~F---~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~K   53 (53)
T d1le8a_           1 KSSISPQARAFLEQVF---RRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   53 (53)
T ss_dssp             CCCCCHHHHHHHHHHH---HHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTTC
T ss_pred             CCCCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhccC
Confidence            6899999999999999   8999999999999999999999999999999999975

>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=99.67  E-value=1.6e-17  Score=114.59  Aligned_cols=56  Identities=25%  Similarity=0.437  Sum_probs=54.0

Q ss_pred             CCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541         111 KRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN  169 (301)
Q Consensus       111 ~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~  169 (301)
                      +||.|+.+++.+|+.+|   ..++||+..++..||..+||++.||++||+|+|+|+||.
T Consensus         1 kRT~~~~~q~~~Le~~F---~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk~   56 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSF---MENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI   56 (57)
T ss_dssp             CCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCCHHHHHHHHHHH---HhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHcc
Confidence            58999999999999999   889999999999999999999999999999999999984

>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=99.67  E-value=1.4e-17  Score=120.19  Aligned_cols=60  Identities=25%  Similarity=0.429  Sum_probs=56.0

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcCC-CCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSHL-SNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN  169 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h~-~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~  169 (301)
                      ..+++|+.|+.+|+.+|+.+|   . .++||+..++++||..+||++.||++||+|+|+|.|+.
T Consensus         6 ~~~r~R~~~t~~Q~~~Le~~F---~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk~   66 (71)
T d1wi3a_           6 SGPRSRTKISLEALGILQSFI---HDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS   66 (71)
T ss_dssp             CCCCCCCCCCSHHHHHHHHHH---HHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCSS
T ss_pred             CCCCCCccCCHHHHHHHHHHH---HHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhccc
Confidence            457889999999999999999   6 48999999999999999999999999999999999874

>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=99.65  E-value=3.3e-17  Score=121.37  Aligned_cols=60  Identities=37%  Similarity=0.717  Sum_probs=56.1

Q ss_pred             CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcC---------------CCchhhhhhhhhhHHHhhhhhh
Q psy5541         109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCN---------------ITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~---------------L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      ||+|+.|+.+|+.+|+.+|   ..++||+..+|++||..+|               |++.+|+|||||||+|+||...
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F---~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~   75 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYF---NENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRAN   75 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhh
Confidence            5789999999999999999   8999999999999999875               9999999999999999999653

>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=99.62  E-value=1.1e-16  Score=107.44  Aligned_cols=50  Identities=32%  Similarity=0.461  Sum_probs=48.7

Q ss_pred             CCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhH
Q psy5541         111 KRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKR  163 (301)
Q Consensus       111 ~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR  163 (301)
                      +|+.|+.+|+.+|+.+|   ..++||+..++..||..+||++.+|++||||+|
T Consensus         1 PRt~ft~~Q~~~Le~~F---~~n~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1           1 PRLVFTDVQRRTLHAIF---KENKRPSKELQITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             CCSCCCHHHHHHHHHHT---TSSCSSTHHHHHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             CCCCCCHHHHHHHHHHH---HHCCCCCHHHHHHHHHHHCcCHHHhhhcCCcCc
Confidence            58999999999999999   999999999999999999999999999999998

>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=99.58  E-value=4.1e-16  Score=113.76  Aligned_cols=57  Identities=16%  Similarity=0.297  Sum_probs=52.1

Q ss_pred             CCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541         112 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG  171 (301)
Q Consensus       112 R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~  171 (301)
                      +..++.+|+.+|+.+|   ..++||+..+++.||..+||++.+|++||||+|+|.|+...
T Consensus         8 ~k~~T~~Q~~~Le~~F---~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~   64 (76)
T d2ecba1           8 FKEKTAEQLRVLQASF---LNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEE   64 (76)
T ss_dssp             CCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCS
T ss_pred             CCCCCHHHHHHHHHHH---HHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhH
Confidence            3446899999999999   89999999999999999999999999999999999877644

>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=99.58  E-value=6.1e-16  Score=112.84  Aligned_cols=58  Identities=21%  Similarity=0.453  Sum_probs=54.1

Q ss_pred             CCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541         110 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI  170 (301)
Q Consensus       110 r~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~  170 (301)
                      ..++.++.+|+.+|+.+|   ..++||+..++..||..+||++.||++||+|+|+|+|+..
T Consensus         5 s~~~r~T~eQ~~~Le~~F---~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~~   62 (76)
T d2ecca1           5 SSGKRKTKEQLAILKSFF---LQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ   62 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHH---HHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCHHHHHHHHHHH---HHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhch
Confidence            455678999999999999   8899999999999999999999999999999999999854

>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=99.57  E-value=2.6e-16  Score=115.86  Aligned_cols=62  Identities=13%  Similarity=0.190  Sum_probs=54.6

Q ss_pred             hcCCCCCCCCHHHHHHHHhHhhcC-CCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541         107 DARRKRRNFSKQASEILNEYFYSH-LSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK  168 (301)
Q Consensus       107 ~~rr~R~~~~~~q~~~L~~~f~~h-~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk  168 (301)
                      ++||.|+.|+.+|+..|+.+|... ..++||+..++++||..+||++.+|+|||||+|.+.|+
T Consensus        16 ~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          16 TTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            457889999999999998887211 24899999999999999999999999999999998875

>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=99.55  E-value=7.9e-16  Score=103.94  Aligned_cols=50  Identities=24%  Similarity=0.481  Sum_probs=46.1

Q ss_pred             CHHHHHHHHhHhhcCCC-CCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541         116 SKQASEILNEYFYSHLS-NPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK  168 (301)
Q Consensus       116 ~~~q~~~L~~~f~~h~~-~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk  168 (301)
                      +.++..+||.+|   .. ++||+..++..||..+||+++||++||+|||+|.|+
T Consensus         1 T~~q~~iLE~~F---~~~~~~P~~~~~~~LA~~~~ls~~qV~~WFqNrR~k~k~   51 (52)
T d1x2ma1           1 TAQPNAILEKVF---TAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   51 (52)
T ss_dssp             SSCHHHHHHHHH---HTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             ChhHHHHHHHHH---HHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccCc
Confidence            356889999999   65 799999999999999999999999999999999886

>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=99.54  E-value=1.7e-15  Score=110.60  Aligned_cols=56  Identities=30%  Similarity=0.519  Sum_probs=52.6

Q ss_pred             CCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcC---------------------CCchhhhhhhhhhHHHhhhhh
Q psy5541         112 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCN---------------------ITLSQVSNWFGNKRIRYKKNI  170 (301)
Q Consensus       112 R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~---------------------L~~~qV~~WFqNrR~r~kk~~  170 (301)
                      |++|++.|+.+|+.+|   ..++||+..+|+.||+.++                     |++.+|+|||+|||+|.|+..
T Consensus         1 R~~~tp~Ql~~Le~~F---~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr~~   77 (78)
T d1lfba_           1 RFKWGPASQQILFQAY---ERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFRH   77 (78)
T ss_dssp             CCCCCHHHHHHHHHHH---TTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCCC
T ss_pred             CccCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHHhc
Confidence            6789999999999999   9999999999999999995                     899999999999999998853

>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=99.50  E-value=2e-15  Score=104.52  Aligned_cols=55  Identities=20%  Similarity=0.466  Sum_probs=50.4

Q ss_pred             CCCCCCCHHHHHHHHhHhhcCCC-CCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhh
Q psy5541         110 RKRRNFSKQASEILNEYFYSHLS-NPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK  167 (301)
Q Consensus       110 r~R~~~~~~q~~~L~~~f~~h~~-~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~k  167 (301)
                      +.+.++..++..+||.+|   .. ++||+..++..||..+||++.||++||+|||+++|
T Consensus         3 k~~~~~k~~~~~iLE~~F---~~~~~yPs~~~~~~LA~~lgls~~qV~~WFqNrR~k~r   58 (59)
T d2cqxa1           3 KDSPVNKVEPNDTLEKVF---VSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK   58 (59)
T ss_dssp             CCCCCSCSCSTTHHHHHH---HHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCccccHHHHHHH---HHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccC
Confidence            566778888899999999   64 78999999999999999999999999999999976

>d1e3oc2 a.35.1.1 (C:1-75) Oct-1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: POU-specific domain
domain: Oct-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.51  E-value=0.0006  Score=47.19  Aligned_cols=54  Identities=19%  Similarity=0.213  Sum_probs=40.0

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhcCCCCCChHHH-HHHHHHHhhhhhHHHHHHhhhHH
Q psy5541          41 EKYEQACSEFTTHVMNLLREQSRTRPITPKEI-ERMVQIIHRKFSSIQMQLKQSTC   95 (301)
Q Consensus        41 ~ky~~~~~~f~~~~~~~l~~q~~~~~l~~~~~-~~~~~~~~~~f~~~~~~l~~~~~   95 (301)
                      ++.+++++.|+.++|.++.+|.+++....... ..++++++|+|+.++..++ ++|
T Consensus         7 ~Ele~Fa~~fk~rRi~LG~TQ~dVG~al~~l~g~~~SQttIcRFE~l~LS~k-n~~   61 (75)
T d1e3oc2           7 EELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFK-NMS   61 (75)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHHTCSCHH-HHH
T ss_pred             HHHHHHHHHHHHHHHhccccHHHHHHHHHHHcCcchhHHHHHHHHHhccCHH-HHH
Confidence            45555699999999999999998763322222 2457889999999998888 455

>d1au7a2 a.35.1.1 (A:5-76) Pit-1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: POU-specific domain
domain: Pit-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=95.26  E-value=0.00055  Score=46.96  Aligned_cols=55  Identities=20%  Similarity=0.311  Sum_probs=39.3

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhcCCCCCChHHH-HHHHHHHhhhhhHHHHHHhhhHH
Q psy5541          40 LEKYEQACSEFTTHVMNLLREQSRTRPITPKEI-ERMVQIIHRKFSSIQMQLKQSTC   95 (301)
Q Consensus        40 l~ky~~~~~~f~~~~~~~l~~q~~~~~l~~~~~-~~~~~~~~~~f~~~~~~l~~~~~   95 (301)
                      |++.++++++|+.++|.++.+|.+++-...... ..++++++++|+.++..++ ++|
T Consensus         2 L~Ele~Fa~~fk~rRi~LG~TQ~dVG~al~~l~g~~~SQttIcRFE~l~LS~k-n~~   57 (72)
T d1au7a2           2 MRALEQFANEFKVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFENLQLSFK-NAC   57 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHTTSSCCCHHHHHHHHTTCSBHH-HHH
T ss_pred             hHHHHHHHHHHHHHHhccCccHHHHHHHHHHhcCcccchhHHHHHHhcccCHH-HHH
Confidence            345556699999999999999988752211111 2357889999999988887 445

>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=83.47  E-value=0.61  Score=31.03  Aligned_cols=47  Identities=34%  Similarity=0.401  Sum_probs=34.7

Q ss_pred             CCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhH
Q psy5541         111 KRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKR  163 (301)
Q Consensus       111 ~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR  163 (301)
                      +|..|+-+....+-..+   ..++..+   +.+||+.+|+...+|..|..|+.
T Consensus         4 kRk~LT~~eK~~ii~~~---e~g~k~s---q~eIA~~fGv~~STvs~IlKnK~   50 (66)
T d1hlva1           4 KRRQLTFREKSRIIQEV---EENPDLR---KGEIARRFNIPPSTLSTILKNKR   50 (66)
T ss_dssp             SSCCCCHHHHHHHHHHH---HHCTTSC---HHHHHHHHTCCHHHHHHHHHTHH
T ss_pred             ccccCCHHHHHHHHHHH---HcCCcch---HHHHHHHhCCChhHHHHHHHHHH
Confidence            45568877776666666   4444333   56799999999999999998843