Psyllid ID: psy8301

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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-------
Protein Sequence
MFQSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQNSNGKNVFKIKHIFTRKTKPTSAQATIGCPEAKKIGRKPETDFPAEEHNIFVPNFDQSDFLDNKWEDIDILDELHDQYVPNCTDIML
Secondary Structure (PSIPRED)
cccccccccccccccHHHHHHHHHHHHccccccHHHHHHHHHHccccccHHHHHHHccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHcHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mfqshragkmrtngiQSQVFELERKFQHirylspteremlgkeinlsptqvKIWFQNRRYKQKRLQAMnqnsngknvfKIKHIftrktkptsaqatigcpeakkigrkpetdfpaeehnifvpnfdqsdfldnkwedidildelhdqyvpnctdiml
Flexible Loop (DISEMBL)
mfqshragkmrtngiqsqvFELERKFQHIRYLSPTeremlgkeinlsptqvkiWFQNRRYKQKRLqamnqnsngknvFKIKHIFtrktkptsaqatigcpeakkigrKPETDFPAEEHNIFVPNFDQSDFLDNKWEDIDILDElhdqyvpnctdiml
Low Complexity Region (SEG)
MFQSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQNSNGKNVFKIKHIFTRKTKPTSAQATIGCPEAKKIGRKPETDFPAEEHNIFVPNFDQSDFLDNKWEDIDILDELHDQYVPNCTDIML
Disordered region (IsUnstruct)
******************VFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ*************NVFKIKHIFTR*******************************HNIFVPNFDQSDFLDNKWEDIDILDELHDQYVPNCTD***
Disordered Region (DISOPRED)
*************GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRY*******************************************************************************************C*****
Disordered Region (DISEMBL)
***********TNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQNSNGKNVFKIKHIFTRKTKPTSAQATIGCPEAKKIGRKPETDFPAEEHNIFVPNFDQSDFLDNKWEDIDILDELHDQYVPNCTDIML
Disordered Region (DISPRO)
********KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ*************************************KIGRKPETDFPAEEHNIFVP**********************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MFQSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQNSNGKNVFKIKHIFTRKTKPTSAQATIGCPEAKKIGRKPETDFPAEEHNIFVPNFDQSDFLDNKWEDIDILDELHDQYVPNCTDIML
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

No hits with e-value below 0.001 by BLAST

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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	157
ZFIN|ZDB-GENE-050217-3	237	nkx2.2b "NK2 transcription fac	0.407	0.270	0.567	1.6e-13
ZFIN|ZDB-GENE-080204-54	282	hmx1 "H6 homeo box 1" [Danio r	0.566	0.315	0.446	2.8e-13
WB|WBGene00000449	263	ceh-27 [Caenorhabditis elegans	0.662	0.395	0.419	3.4e-13
UNIPROTKB|H2L2F8	170	ceh-27 "Protein CEH-27, isofor	0.662	0.611	0.419	3.4e-13
UNIPROTKB|Q9XVN4	263	ceh-27 "Protein CEH-27, isofor	0.662	0.395	0.419	3.4e-13
UNIPROTKB|F1SC87	269	HHEX "Uncharacterized protein"	0.433	0.252	0.471	3.6e-13
RGD|1308443	248	Nkx2-2 "NK2 homeobox 2" [Rattu	0.388	0.245	0.562	5.6e-13
UNIPROTKB|E1BBE1	273	NKX2-2 "Uncharacterized protei	0.388	0.223	0.562	6.9e-13
UNIPROTKB|E2RNP4	273	NKX2-2 "Uncharacterized protei	0.388	0.223	0.562	6.9e-13
UNIPROTKB|O95096	273	NKX2-2 "Homeobox protein Nkx-2	0.388	0.223	0.562	6.9e-13

ZFIN|ZDB-GENE-050217-3 nkx2.2b "NK2 transcription factor related 2b" [Danio rerio (taxid:7955)]

 Score = 176 (67.0 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 38/67 (56%), Positives = 47/67 (70%)

Query:     4 SHRAGKMRTNGI---QSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRY 60
             S  +GK R   I   ++Q FELER+F+  RYLS  ERE L K ++L+PTQVKIWFQN RY
Sbjct:    89 SEDSGKKRKRRILFSKTQTFELERRFRQQRYLSAPEREHLAKLLHLTPTQVKIWFQNHRY 148

Query:    61 KQKRLQA 67
             K KR +A
Sbjct:   149 KVKRARA 155

GO:0003677 "DNA binding" evidence=IEA

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

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0021514 "ventral spinal cord interneuron differentiation" evidence=IGI

GO:0021508 "floor plate formation" evidence=IMP

ZFIN|ZDB-GENE-080204-54 hmx1 "H6 homeo box 1" [Danio rerio (taxid:7955)]

 Score = 175 (66.7 bits), Expect = 2.8e-13, P = 2.8e-13
 Identities = 42/94 (44%), Positives = 56/94 (59%)

Query:     4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
             S R  K RT   +SQVF+LE  F   RYLS +ER  L   ++L+ TQVKIWFQNRR K K
Sbjct:   147 SARKKKTRTVFSRSQVFQLESTFDMKRYLSSSERAGLAASLHLTETQVKIWFQNRRNKWK 206

Query:    64 R-----LQAMNQNSNGKNVFKIKHIFTRKTKPTS 92
             R     L+A+N N N + + ++  ++  K  P S
Sbjct:   207 RQLAADLEAVNFNHNSQRIVRVPILYHDKATPMS 240

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

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0043010 "camera-type eye development" evidence=IMP

WB|WBGene00000449 ceh-27 [Caenorhabditis elegans (taxid:6239)]

 Score = 173 (66.0 bits), Expect = 3.4e-13, P = 3.4e-13
 Identities = 47/112 (41%), Positives = 61/112 (54%)

Query:    18 QVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQNSNGKNV 77
             QV  LERKFQ  RYLS  +RE L K INLS TQVKIWFQN+RYK KR Q   +  +G   
Sbjct:   109 QVHVLERKFQINRYLSAADRENLAKSINLSATQVKIWFQNQRYKCKR-QEKEKKMDG-GC 166

Query:    78 FKIKHIFTRKTKPTSAQATIGCPEAKKIGRKPETDFPAEEHNIFVPNFDQSD 129
             ++     T   +   +  ++G   +   G K E D   E+   F+P+   SD
Sbjct:   167 YRDSDRDTDSDRDNDSSGSLG---SSMSGIKKEED---EDRKPFMPSAVSSD 212

GO:0005634 "nucleus" evidence=IEA;ISS

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

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

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

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0010171 "body morphogenesis" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0034243 "regulation of transcription elongation from RNA polymerase II promoter" evidence=ISS

GO:0000981 "sequence-specific DNA binding RNA polymerase II transcription factor activity" evidence=ISS

UNIPROTKB|H2L2F8 ceh-27 "Protein CEH-27, isoform b" [Caenorhabditis elegans (taxid:6239)]

 Score = 173 (66.0 bits), Expect = 3.4e-13, P = 3.4e-13
 Identities = 47/112 (41%), Positives = 61/112 (54%)

Query:    18 QVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQNSNGKNV 77
             QV  LERKFQ  RYLS  +RE L K INLS TQVKIWFQN+RYK KR Q   +  +G   
Sbjct:    16 QVHVLERKFQINRYLSAADRENLAKSINLSATQVKIWFQNQRYKCKR-QEKEKKMDG-GC 73

Query:    78 FKIKHIFTRKTKPTSAQATIGCPEAKKIGRKPETDFPAEEHNIFVPNFDQSD 129
             ++     T   +   +  ++G   +   G K E D   E+   F+P+   SD
Sbjct:    74 YRDSDRDTDSDRDNDSSGSLG---SSMSGIKKEED---EDRKPFMPSAVSSD 119

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

UNIPROTKB|Q9XVN4 ceh-27 "Protein CEH-27, isoform a" [Caenorhabditis elegans (taxid:6239)]

 Score = 173 (66.0 bits), Expect = 3.4e-13, P = 3.4e-13
 Identities = 47/112 (41%), Positives = 61/112 (54%)

Query:    18 QVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQNSNGKNV 77
             QV  LERKFQ  RYLS  +RE L K INLS TQVKIWFQN+RYK KR Q   +  +G   
Sbjct:   109 QVHVLERKFQINRYLSAADRENLAKSINLSATQVKIWFQNQRYKCKR-QEKEKKMDG-GC 166

Query:    78 FKIKHIFTRKTKPTSAQATIGCPEAKKIGRKPETDFPAEEHNIFVPNFDQSD 129
             ++     T   +   +  ++G   +   G K E D   E+   F+P+   SD
Sbjct:   167 YRDSDRDTDSDRDNDSSGSLG---SSMSGIKKEED---EDRKPFMPSAVSSD 212

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

UNIPROTKB|F1SC87 HHEX "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 156 (60.0 bits), Expect = 3.6e-13, Sum P(2) = 3.6e-13
 Identities = 33/70 (47%), Positives = 45/70 (64%)

Query:     6 RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65
             + G++R +    Q  ELE+KF+  +YLSP ER+ L K + LS  QVK WFQNRR K +RL
Sbjct:   138 KGGQVRFSN--DQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRL 195

Query:    66 QAMNQNSNGK 75
             +  N  +N K
Sbjct:   196 KQENPQNNKK 205

GO:0005634 "nucleus" evidence=IEA

GO:0090009 "primitive streak formation" evidence=IEA

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

GO:0071103 "DNA conformation change" evidence=IEA

GO:0070491 "repressing transcription factor binding" evidence=IEA

GO:0070365 "hepatocyte differentiation" evidence=IEA

GO:0061017 "hepatoblast differentiation" evidence=IEA

GO:0061011 "hepatic duct development" evidence=IEA

GO:0061010 "gall bladder development" evidence=IEA

GO:0061009 "common bile duct development" evidence=IEA

GO:0060431 "primary lung bud formation" evidence=IEA

GO:0048853 "forebrain morphogenesis" evidence=IEA

GO:0048568 "embryonic organ development" evidence=IEA

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

GO:0044212 "transcription regulatory region DNA binding" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

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

GO:0035264 "multicellular organism growth" evidence=IEA

GO:0035050 "embryonic heart tube development" evidence=IEA

GO:0034504 "protein localization to nucleus" evidence=IEA

GO:0032993 "protein-DNA complex" evidence=IEA

GO:0031016 "pancreas development" evidence=IEA

GO:0030878 "thyroid gland development" evidence=IEA

GO:0030183 "B cell differentiation" evidence=IEA

GO:0030177 "positive regulation of Wnt receptor signaling pathway" evidence=IEA

GO:0022027 "interkinetic nuclear migration" evidence=IEA

GO:0016973 "poly(A)+ mRNA export from nucleus" evidence=IEA

GO:0008301 "DNA binding, bending" evidence=IEA

GO:0008190 "eukaryotic initiation factor 4E binding" evidence=IEA

GO:0007492 "endoderm development" evidence=IEA

GO:0007165 "signal transduction" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0002573 "myeloid leukocyte differentiation" evidence=IEA

GO:0001701 "in utero embryonic development" evidence=IEA

GO:0001570 "vasculogenesis" evidence=IEA

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

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

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

RGD|1308443 Nkx2-2 "NK2 homeobox 2" [Rattus norvegicus (taxid:10116)]

 Score = 171 (65.3 bits), Expect = 5.6e-13, P = 5.6e-13
 Identities = 36/64 (56%), Positives = 44/64 (68%)

Query:     7 AGKMRTNGI---QSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
             AGK R   +   ++Q +ELER+F+  RYLS  ERE L   I L+PTQVKIWFQN RYK K
Sbjct:   125 AGKKRKRRVLFSKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKMK 184

Query:    64 RLQA 67
             R +A
Sbjct:   185 RARA 188

GO:0001159 "core promoter proximal region DNA binding" evidence=ISO

GO:0003323 "type B pancreatic cell development" evidence=ISO

GO:0003326 "pancreatic A cell fate commitment" evidence=ISO

GO:0003327 "type B pancreatic cell fate commitment" evidence=ISO

GO:0003329 "pancreatic PP cell fate commitment" evidence=ISO

GO:0003674 "molecular_function" evidence=ND

GO:0003682 "chromatin binding" evidence=ISO

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

GO:0003713 "transcription coactivator activity" evidence=ISO

GO:0005622 "intracellular" evidence=ISO

GO:0005634 "nucleus" evidence=ISO;IDA

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

GO:0007224 "smoothened signaling pathway" evidence=ISO

GO:0007399 "nervous system development" evidence=ISO

GO:0008134 "transcription factor binding" evidence=ISO

GO:0009749 "response to glucose stimulus" evidence=IEP

GO:0014003 "oligodendrocyte development" evidence=ISO

GO:0014070 "response to organic cyclic compound" evidence=IEP

GO:0021522 "spinal cord motor neuron differentiation" evidence=ISO

GO:0021529 "spinal cord oligodendrocyte cell differentiation" evidence=ISO

GO:0021530 "spinal cord oligodendrocyte cell fate specification" evidence=ISO

GO:0021554 "optic nerve development" evidence=IEP

GO:0030154 "cell differentiation" evidence=ISO

GO:0031018 "endocrine pancreas development" evidence=ISO

GO:0032570 "response to progesterone stimulus" evidence=IEP

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

GO:0045595 "regulation of cell differentiation" evidence=ISO

GO:0045597 "positive regulation of cell differentiation" evidence=ISO

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

GO:0045666 "positive regulation of neuron differentiation" evidence=ISO

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

GO:0048468 "cell development" evidence=ISO

GO:0048565 "digestive tract development" evidence=ISO

GO:0048665 "neuron fate specification" evidence=ISO

GO:0048708 "astrocyte differentiation" evidence=ISO

GO:0048714 "positive regulation of oligodendrocyte differentiation" evidence=ISO

GO:0051091 "positive regulation of sequence-specific DNA binding transcription factor activity" evidence=ISO

GO:0060580 "ventral spinal cord interneuron fate determination" evidence=ISO

UNIPROTKB|E1BBE1 NKX2-2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 171 (65.3 bits), Expect = 6.9e-13, P = 6.9e-13
 Identities = 36/64 (56%), Positives = 44/64 (68%)

Query:     7 AGKMRTNGI---QSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
             AGK R   +   ++Q +ELER+F+  RYLS  ERE L   I L+PTQVKIWFQN RYK K
Sbjct:   125 AGKKRKRRVLFSKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKMK 184

Query:    64 RLQA 67
             R +A
Sbjct:   185 RARA 188

GO:0005634 "nucleus" evidence=IEA

GO:0060580 "ventral spinal cord interneuron fate determination" evidence=IEA

GO:0051091 "positive regulation of sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0048714 "positive regulation of oligodendrocyte differentiation" evidence=IEA

GO:0048708 "astrocyte differentiation" evidence=IEA

GO:0048665 "neuron fate specification" evidence=IEA

GO:0048565 "digestive tract development" evidence=IEA

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

GO:0045666 "positive regulation of neuron differentiation" evidence=IEA

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

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

GO:0021530 "spinal cord oligodendrocyte cell fate specification" evidence=IEA

GO:0021522 "spinal cord motor neuron differentiation" evidence=IEA

GO:0014003 "oligodendrocyte development" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0007224 "smoothened signaling pathway" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

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

GO:0003682 "chromatin binding" evidence=IEA

GO:0003329 "pancreatic PP cell fate commitment" evidence=IEA

GO:0003327 "type B pancreatic cell fate commitment" evidence=IEA

GO:0003326 "pancreatic A cell fate commitment" evidence=IEA

GO:0003323 "type B pancreatic cell development" evidence=IEA

GO:0001159 "core promoter proximal region DNA binding" evidence=IEA

UNIPROTKB|E2RNP4 NKX2-2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 171 (65.3 bits), Expect = 6.9e-13, P = 6.9e-13
 Identities = 36/64 (56%), Positives = 44/64 (68%)

Query:     7 AGKMRTNGI---QSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
             AGK R   +   ++Q +ELER+F+  RYLS  ERE L   I L+PTQVKIWFQN RYK K
Sbjct:   125 AGKKRKRRVLFSKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKMK 184

Query:    64 RLQA 67
             R +A
Sbjct:   185 RARA 188

GO:0005634 "nucleus" evidence=IEA

GO:0060580 "ventral spinal cord interneuron fate determination" evidence=IEA

GO:0051091 "positive regulation of sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0048714 "positive regulation of oligodendrocyte differentiation" evidence=IEA

GO:0048708 "astrocyte differentiation" evidence=IEA

GO:0048665 "neuron fate specification" evidence=IEA

GO:0048565 "digestive tract development" evidence=IEA

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

GO:0045666 "positive regulation of neuron differentiation" evidence=IEA

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

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

GO:0021530 "spinal cord oligodendrocyte cell fate specification" evidence=IEA

GO:0021522 "spinal cord motor neuron differentiation" evidence=IEA

GO:0014003 "oligodendrocyte development" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0007224 "smoothened signaling pathway" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

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

GO:0003682 "chromatin binding" evidence=IEA

GO:0003329 "pancreatic PP cell fate commitment" evidence=IEA

GO:0003327 "type B pancreatic cell fate commitment" evidence=IEA

GO:0003326 "pancreatic A cell fate commitment" evidence=IEA

GO:0003323 "type B pancreatic cell development" evidence=IEA

GO:0001159 "core promoter proximal region DNA binding" evidence=IEA

UNIPROTKB|O95096 NKX2-2 "Homeobox protein Nkx-2.2" [Homo sapiens (taxid:9606)]

 Score = 171 (65.3 bits), Expect = 6.9e-13, P = 6.9e-13
 Identities = 36/64 (56%), Positives = 44/64 (68%)

Query:     7 AGKMRTNGI---QSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
             AGK R   +   ++Q +ELER+F+  RYLS  ERE L   I L+PTQVKIWFQN RYK K
Sbjct:   125 AGKKRKRRVLFSKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKMK 184

Query:    64 RLQA 67
             R +A
Sbjct:   185 RARA 188

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

GO:0003323 "type B pancreatic cell development" evidence=IEA

GO:0003326 "pancreatic A cell fate commitment" evidence=IEA

GO:0003327 "type B pancreatic cell fate commitment" evidence=IEA

GO:0003329 "pancreatic PP cell fate commitment" evidence=IEA

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

GO:0007224 "smoothened signaling pathway" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0014003 "oligodendrocyte development" evidence=IEA

GO:0021522 "spinal cord motor neuron differentiation" evidence=IEA

GO:0021530 "spinal cord oligodendrocyte cell fate specification" evidence=IEA

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

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

GO:0045666 "positive regulation of neuron differentiation" evidence=IEA

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

GO:0048565 "digestive tract development" evidence=IEA

GO:0048665 "neuron fate specification" evidence=IEA

GO:0048708 "astrocyte differentiation" evidence=IEA

GO:0048714 "positive regulation of oligodendrocyte differentiation" evidence=IEA

GO:0060580 "ventral spinal cord interneuron fate determination" evidence=IEA

GO:0051091 "positive regulation of sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0001159 "core promoter proximal region DNA binding" evidence=ISS

GO:0003682 "chromatin binding" evidence=ISS

GO:0003713 "transcription coactivator activity" evidence=ISS

GO:0007420 "brain development" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0031018 "endocrine pancreas development" evidence=TAS

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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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	157
pfam00046	57	pfam00046, Homeobox, Homeobox domain	7e-19
smart00389	57	smart00389, HOX, Homeodomain	6e-17
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	3e-16
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	5e-09

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

 Score = 74.8 bits (185), Expect = 7e-19
 Identities = 28/56 (50%), Positives = 37/56 (66%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
          + RT     Q+ ELE++F+  RY S  ERE L K++ L+  QVK+WFQNRR K KR
Sbjct: 2  RKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57

Length = 57

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 70.0 bits (172), Expect = 6e-17
 Identities = 28/55 (50%), Positives = 36/55 (65%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
          + RT+    Q+ ELE++FQ   Y S  ERE L K++ LS  QVK+WFQNRR K K
Sbjct: 3  RKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

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

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

 Score = 68.0 bits (167), Expect = 3e-16
 Identities = 29/58 (50%), Positives = 37/58 (63%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
          + RT     Q+ ELE++F+   Y S  ERE L KE+ L+  QVKIWFQNRR K KR +
Sbjct: 2  RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59

Length = 59

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

 Score = 51.7 bits (124), Expect = 5e-09
 Identities = 29/93 (31%), Positives = 44/93 (47%), Gaps = 5/93 (5%)

Query: 6   RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65
           ++ + RT   Q  V  LER+F+   Y S   R  L   +N+ P  V+IWFQN+R K+K+ 
Sbjct: 52  KSKRRRTTDEQLMV--LEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKK 109

Query: 66  Q--AMNQNSNGKNVFKIKHIFTRKTKPTSAQAT 96
           +   + Q    +     K I +  T   S   T
Sbjct: 110 RSGKVEQRPGEEEADLAK-IGSLSTGQISIIET 141

Length = 156

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	157
KOG0484|consensus	125		99.9
KOG2251|consensus	228		99.88
KOG0494|consensus	332		99.85
KOG0488|consensus	309		99.83
KOG0843|consensus	197		99.81
KOG0850|consensus	245		99.8
KOG0489|consensus	261		99.79
KOG0842|consensus	307		99.79
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.77
KOG0485|consensus	268		99.76
KOG0492|consensus	246		99.74
KOG0491|consensus	194		99.69
KOG0487|consensus	308		99.68
KOG0490|consensus	235		99.68
KOG0486|consensus	351		99.67
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.66
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.66
KOG0848|consensus	317		99.66
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.65
KOG0493|consensus	342		99.64
COG5576	156	Homeodomain-containing transcription factor [Trans	99.6
KOG0844|consensus	408		99.56
KOG4577|consensus	383		99.55
KOG0483|consensus	198		99.53
KOG3802|consensus	398		99.48
KOG0849|consensus	354		99.48
KOG0847|consensus	288		99.47
KOG0775|consensus	304		99.26
KOG1168|consensus	385		99.0
KOG0774|consensus	334		98.88
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.72
KOG2252|consensus	558		98.62
KOG0490|consensus	235		98.52
KOG1146|consensus	1406		97.9
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	97.07
KOG3623|consensus	1007		96.74
KOG0773|consensus	342		96.64
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	95.22
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	89.23
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	87.25
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	87.08
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	85.15
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	83.77
PRK03975	141	tfx putative transcriptional regulator; Provisiona	82.99
PF10668	60	Phage_terminase: Phage terminase small subunit; In	80.6

>KOG0484|consensus

Probab=99.90  E-value=1.3e-23  Score=141.75  Aligned_cols=66  Identities=32%  Similarity=0.526  Sum_probs=62.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhh
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN   69 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~   69 (157)
                      ++|+||-||+||+.||..||+.|...+||++.+|++||.++.|+|.+|||||||||+|.|+++...
T Consensus        14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a   79 (125)
T KOG0484|consen   14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAA   79 (125)
T ss_pred             HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHH
Confidence            578899999999999999999999999999999999999999999999999999999999987653

>KOG2251|consensus

Probab=99.88  E-value=2.3e-22  Score=152.28  Aligned_cols=66  Identities=32%  Similarity=0.468  Sum_probs=63.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhh
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN   69 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~   69 (157)
                      +||.||.||+|+..|+++||..|.+.+|||+..|++||.+|+|.+.+|+|||+|||+|+|+++...
T Consensus        34 pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   34 PRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             chhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            688999999999999999999999999999999999999999999999999999999999988764

>KOG0494|consensus

Probab=99.85  E-value=1.5e-21  Score=150.96  Aligned_cols=83  Identities=25%  Similarity=0.374  Sum_probs=71.6

Q ss_pred             CCCCCCCC-CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhhcCCCCCCccccc
Q psy8301           3 QSHRAGKM-RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQNSNGKNVFKIK   81 (157)
Q Consensus         3 ~~~~~rr~-Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~~~~~~~~~~~~~   81 (157)
                      +++++||. ||.||..|++.||+.|+..+||++..|+-||.++.|.|.+|+|||||||+||||.++.........++...
T Consensus       136 kkk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~sT~maeygly  215 (332)
T KOG0494|consen  136 KKKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGSTIMAEYGLY  215 (332)
T ss_pred             ccccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcchhhhhhccc
Confidence            34545555 99999999999999999999999999999999999999999999999999999999887777666666554


Q ss_pred             cccc
Q psy8301          82 HIFT   85 (157)
Q Consensus        82 ~~~~   85 (157)
                      ....
T Consensus       216 Gamv  219 (332)
T KOG0494|consen  216 GAMV  219 (332)
T ss_pred             chhh
Confidence            4433

>KOG0488|consensus

Probab=99.83  E-value=3.9e-20  Score=149.22  Aligned_cols=65  Identities=43%  Similarity=0.627  Sum_probs=62.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhh
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM   68 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~   68 (157)
                      ++|+|+.||.||..|+..||+.|++..|.+..+|.+||..|||+..||++||||||+||||+...
T Consensus       169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~  233 (309)
T KOG0488|consen  169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE  233 (309)
T ss_pred             CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence            57888999999999999999999999999999999999999999999999999999999998766

>KOG0843|consensus

Probab=99.81  E-value=6.1e-20  Score=135.21  Aligned_cols=68  Identities=41%  Similarity=0.665  Sum_probs=63.3

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhh
Q psy8301           2 FQSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN   69 (157)
Q Consensus         2 ~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~   69 (157)
                      ++..+.||.||.|+.+|+..||..|+.++|-...+|+.||..|+|++.||+|||||||.|.||.....
T Consensus        97 ~~~~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~  164 (197)
T KOG0843|consen   97 LRSMRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED  164 (197)
T ss_pred             ccccCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence            45567899999999999999999999999999999999999999999999999999999999877654

>KOG0850|consensus

Probab=99.80  E-value=4.3e-19  Score=135.22  Aligned_cols=66  Identities=42%  Similarity=0.603  Sum_probs=62.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhh
Q psy8301           3 QSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM   68 (157)
Q Consensus         3 ~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~   68 (157)
                      +.+|-|+.||+++.-||..|.+.|++++|.-..+|.+||..|||+..||+|||||||.|.||..+.
T Consensus       118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~  183 (245)
T KOG0850|consen  118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQ  183 (245)
T ss_pred             CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhc
Confidence            467888999999999999999999999999999999999999999999999999999999998874

>KOG0489|consensus

Probab=99.79  E-value=7.8e-20  Score=144.78  Aligned_cols=65  Identities=35%  Similarity=0.604  Sum_probs=61.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhhc
Q psy8301           6 RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQ   70 (157)
Q Consensus         6 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~~   70 (157)
                      +.||.||.||..|+..||+.|..|+|.+...|.+||..|.|+|+||+|||||||+||||..+...
T Consensus       158 ~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~  222 (261)
T KOG0489|consen  158 KSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS  222 (261)
T ss_pred             CCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence            46899999999999999999999999999999999999999999999999999999999776543

>KOG0842|consensus

Probab=99.79  E-value=1e-19  Score=145.25  Aligned_cols=70  Identities=51%  Similarity=0.749  Sum_probs=64.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhhcCCC
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQNSN   73 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~~~~~   73 (157)
                      ++++||+|..|+..|+-.||+.|.+++|.+..+|++||..|.|+++||+|||||||.|.||+++......
T Consensus       150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~  219 (307)
T KOG0842|consen  150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA  219 (307)
T ss_pred             cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence            4577888999999999999999999999999999999999999999999999999999999887655543

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.77  E-value=1.5e-18  Score=107.07  Aligned_cols=57  Identities=47%  Similarity=0.609  Sum_probs=55.1

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           8 GKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         8 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      ||.|+.|+.+|+..|+..|..++||+..+++.||..+||+..+|++||+|+|+++|+
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence            578999999999999999999999999999999999999999999999999999886

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

>KOG0485|consensus

Probab=99.76  E-value=2.6e-18  Score=129.96  Aligned_cols=67  Identities=49%  Similarity=0.652  Sum_probs=61.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhhcC
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQN   71 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~~~   71 (157)
                      -++||.||+|+..|+..||..|+..+|.+..+|..||.+|.|+|.||+|||||||.||||+-.....
T Consensus       102 ~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~e  168 (268)
T KOG0485|consen  102 DRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLE  168 (268)
T ss_pred             cccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhh
Confidence            3578899999999999999999999999999999999999999999999999999999997655433

>KOG0492|consensus

Probab=99.74  E-value=2.5e-18  Score=129.30  Aligned_cols=68  Identities=47%  Similarity=0.674  Sum_probs=61.0

Q ss_pred             CCCC-CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhh
Q psy8301           2 FQSH-RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN   69 (157)
Q Consensus         2 ~~~~-~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~   69 (157)
                      |+++ -.|++||.||..||..||+.|...+|.++++|.+++..|.|++.||+|||||||+|.||.+..+
T Consensus       138 LrKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae  206 (246)
T KOG0492|consen  138 LRKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAE  206 (246)
T ss_pred             hcccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHH
Confidence            4444 4566799999999999999999999999999999999999999999999999999999866543

>KOG0491|consensus

Probab=99.69  E-value=3.5e-17  Score=119.06  Aligned_cols=69  Identities=48%  Similarity=0.650  Sum_probs=62.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhhcCCCC
Q psy8301           6 RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQNSNG   74 (157)
Q Consensus         6 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~~~~~~   74 (157)
                      ++++-||+|+..|+..|++.|+..+|.+..+|.+||..|+|+++||+.||||||+|.||+....+....
T Consensus        99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p~nS  167 (194)
T KOG0491|consen   99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQPKNS  167 (194)
T ss_pred             HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCCCCC
Confidence            456779999999999999999999999999999999999999999999999999999998876654433

>KOG0487|consensus

Probab=99.68  E-value=2.4e-17  Score=131.75  Aligned_cols=66  Identities=39%  Similarity=0.626  Sum_probs=61.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhh
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN   69 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~   69 (157)
                      .++.|++|-.+|..|+..||+.|-.|.|.+...|.+|++.|+|+++||+|||||||+|.||..+..
T Consensus       232 ~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~  297 (308)
T KOG0487|consen  232 ARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN  297 (308)
T ss_pred             ccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence            356788899999999999999999999999999999999999999999999999999999977543

>KOG0490|consensus

Probab=99.68  E-value=7.1e-17  Score=124.87  Aligned_cols=135  Identities=21%  Similarity=0.274  Sum_probs=97.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhhcCCCCCCccccccc
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQNSNGKNVFKIKHI   83 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~~~~~~~~~~~~~~~   83 (157)
                      ..++||.|+.|+..|++.|+++|+..+||+...++.||..+++++..|+|||||||+||++++................ 
T Consensus        57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~~~~~~~~~~~~~~~~-  135 (235)
T KOG0490|consen   57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEERPLPEGENLPDLSGTA-  135 (235)
T ss_pred             hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhccccccccCCCCCCCC-
Confidence            4567899999999999999999999999999999999999999999999999999999999764111111110000000 


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCccccCCCCCCCCcCCCCCCCCchhHHHhhhccC
Q psy8301          84 FTRKTKPTSAQATIGCPEAKKIGRKPETDFPAEEHNIFVPNFDQSDFLDNKWEDIDILDELHDQYV  149 (157)
Q Consensus        84 ~~~~~~p~s~~~~~~~p~~~~~~~~~~~~~~~~q~~~~~~~f~~~~~s~s~~p~~~~~~~l~~~~~  149 (157)
                           .................+..+.+.+...+...+...|..+.+     |+....+.|+....
T Consensus       136 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----P~~~~~~~l~~~~~  191 (235)
T KOG0490|consen  136 -----PPSASRDKLDKGPSNKKPRRPRTTFTENQLEVLETVFRATPK-----PDADDREQLAEETG  191 (235)
T ss_pred             -----CccccccccccCCCccccCCCccccccchhHhhhhcccCCCC-----CchhhHHHHHHhcC
Confidence                 000001111122223445556677888888999999999999     99999999887554

>KOG0486|consensus

Probab=99.67  E-value=1.8e-17  Score=131.29  Aligned_cols=66  Identities=33%  Similarity=0.499  Sum_probs=61.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhhc
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQ   70 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~~   70 (157)
                      +|+||.||.|+..|+..||.+|+++.||+...|+++|--++|+|.+|+|||+|||+|||+.+....
T Consensus       110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~  175 (351)
T KOG0486|consen  110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ  175 (351)
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence            378899999999999999999999999999999999999999999999999999999999775543

>smart00389 HOX Homeodomain

Probab=99.66  E-value=2.5e-16  Score=96.41  Aligned_cols=55  Identities=47%  Similarity=0.626  Sum_probs=52.1

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHH
Q psy8301           8 GKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ   62 (157)
Q Consensus         8 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~   62 (157)
                      ++.|+.|+..|+.+|+..|..++||+..++..||..+||+..+|++||+|+|++.
T Consensus         1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~   55 (56)
T smart00389        1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKW   55 (56)
T ss_pred             CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhcc
Confidence            3567889999999999999999999999999999999999999999999999875

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

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.66  E-value=8.3e-17  Score=99.27  Aligned_cols=52  Identities=17%  Similarity=0.277  Sum_probs=50.2

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCC----CCHHHHHHHHHHhCCChhHHHHHHHHHH
Q psy8301           8 GKMRTNGIQSQVFELERKFQHIRY----LSPTEREMLGKEINLSPTQVKIWFQNRR   59 (157)
Q Consensus         8 rr~Rt~~t~~q~~~Le~~F~~~~~----p~~~~r~~La~~l~l~~~~VqvWFqNrR   59 (157)
                      ||.||.||.+|+..|+..|+.++|    |+..++++||..+||++.+|+|||||.+
T Consensus         2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            789999999999999999999999    9999999999999999999999999953

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.

>KOG0848|consensus

Probab=99.66  E-value=7.2e-17  Score=125.47  Aligned_cols=63  Identities=37%  Similarity=0.569  Sum_probs=58.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhh
Q psy8301           7 AGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN   69 (157)
Q Consensus         7 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~   69 (157)
                      +-+-|.++|..|.-.||+.|..++|..+..+.+||..|||+|+||+|||||||||+||..+..
T Consensus       199 kDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk  261 (317)
T KOG0848|consen  199 KDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK  261 (317)
T ss_pred             ccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence            345588999999999999999999999999999999999999999999999999999876654

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

Probab=99.65  E-value=5.8e-16  Score=95.57  Aligned_cols=56  Identities=52%  Similarity=0.702  Sum_probs=53.7

Q ss_pred             CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         9 r~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      +.|+.|+..++.+|+++|..++||+..++..||..+||++.+|++||+|+|++.++
T Consensus         2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~   57 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR   57 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence            56789999999999999999999999999999999999999999999999999876

>KOG0493|consensus

Probab=99.64  E-value=2.1e-16  Score=122.66  Aligned_cols=59  Identities=39%  Similarity=0.609  Sum_probs=56.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301           7 AGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus         7 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      -||+||.||.+||..|+..|+.|+|.....|.+||.+|||.|.||+|||||+|+|-||.
T Consensus       246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs  304 (342)
T KOG0493|consen  246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS  304 (342)
T ss_pred             hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence            35889999999999999999999999999999999999999999999999999998883

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.60  E-value=1.5e-15  Score=111.46  Aligned_cols=63  Identities=33%  Similarity=0.529  Sum_probs=58.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      +..++.|++.+..|+.+|++.|+.++||+..+|..|+..++|+++.|||||||+|++.|+...
T Consensus        49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~  111 (156)
T COG5576          49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRS  111 (156)
T ss_pred             CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcc
Confidence            456788999999999999999999999999999999999999999999999999999988554

>KOG0844|consensus

Probab=99.56  E-value=8.2e-16  Score=121.64  Aligned_cols=61  Identities=38%  Similarity=0.589  Sum_probs=58.3

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhh
Q psy8301           8 GKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM   68 (157)
Q Consensus         8 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~   68 (157)
                      ||-||.||.+|+..||+.|-+..|-+...|.+||..|+|.|..|+|||||||+|+||++..
T Consensus       182 RRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla  242 (408)
T KOG0844|consen  182 RRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA  242 (408)
T ss_pred             HHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence            6789999999999999999999999999999999999999999999999999999998754

>KOG4577|consensus

Probab=99.55  E-value=4.3e-15  Score=116.82  Aligned_cols=62  Identities=32%  Similarity=0.420  Sum_probs=58.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhh
Q psy8301           7 AGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM   68 (157)
Q Consensus         7 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~   68 (157)
                      .||+||++|..||+.|+.+|...+.|-...||+|+..+||.-++|||||||||||.||.++.
T Consensus       167 nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD  228 (383)
T KOG4577|consen  167 NKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD  228 (383)
T ss_pred             cCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence            57999999999999999999999999999999999999999999999999999999986543

>KOG0483|consensus

Probab=99.53  E-value=6.8e-15  Score=111.61  Aligned_cols=61  Identities=36%  Similarity=0.520  Sum_probs=55.8

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhh
Q psy8301           8 GKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM   68 (157)
Q Consensus         8 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~   68 (157)
                      .+.+.+|+.+|...||..|+...|.....+..||..|||..+||.||||||||+||..+..
T Consensus        51 ~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE  111 (198)
T KOG0483|consen   51 KGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLE  111 (198)
T ss_pred             ccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhh
Confidence            3455689999999999999999999999999999999999999999999999999975543

>KOG3802|consensus

Probab=99.48  E-value=5.6e-15  Score=120.72  Aligned_cols=62  Identities=29%  Similarity=0.390  Sum_probs=58.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ   66 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~   66 (157)
                      .|+||+||.|......+||+.|.+|+.|+..++..||..|+|...+|+|||+|||.|.||..
T Consensus       292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~  353 (398)
T KOG3802|consen  292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT  353 (398)
T ss_pred             ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence            36788899999999999999999999999999999999999999999999999999999844

>KOG0849|consensus

Probab=99.48  E-value=2.2e-13  Score=112.14  Aligned_cols=65  Identities=37%  Similarity=0.469  Sum_probs=61.3

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhh
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM   68 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~   68 (157)
                      +++.+|.||.|+..|+..|++.|+.++||++..|+.||.++++++..|+|||+|||++|+|....
T Consensus       173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~  237 (354)
T KOG0849|consen  173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD  237 (354)
T ss_pred             cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence            46678889999999999999999999999999999999999999999999999999999997743

>KOG0847|consensus

Probab=99.47  E-value=3.6e-14  Score=107.83  Aligned_cols=64  Identities=38%  Similarity=0.694  Sum_probs=59.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhh
Q psy8301           6 RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN   69 (157)
Q Consensus         6 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~   69 (157)
                      +++..|.+|+..|+..|+..|++.+|+...+|.+||-.+|+++.+|+|||||||.||||....+
T Consensus       166 ~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaE  229 (288)
T KOG0847|consen  166 QRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAE  229 (288)
T ss_pred             cccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccc
Confidence            4456688999999999999999999999999999999999999999999999999999976544

>KOG0775|consensus

Probab=99.26  E-value=3.2e-11  Score=94.43  Aligned_cols=51  Identities=29%  Similarity=0.416  Sum_probs=47.2

Q ss_pred             CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301          14 GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus        14 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      |...-...|+.+|..++||+..++.+||+++||+..||-+||+|||+++|-
T Consensus       183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa  233 (304)
T KOG0775|consen  183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA  233 (304)
T ss_pred             hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence            555567799999999999999999999999999999999999999999994

>KOG1168|consensus

Probab=99.00  E-value=7.6e-11  Score=93.13  Aligned_cols=61  Identities=26%  Similarity=0.379  Sum_probs=57.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301           6 RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ   66 (157)
Q Consensus         6 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~   66 (157)
                      .+||+||.+-......||++|..++.|+...+..+|++|+|...+|+|||+|+|+|.||..
T Consensus       308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~  368 (385)
T KOG1168|consen  308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK  368 (385)
T ss_pred             ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence            4678899999999999999999999999999999999999999999999999999988854

>KOG0774|consensus

Probab=98.88  E-value=3e-09  Score=83.08  Aligned_cols=61  Identities=30%  Similarity=0.376  Sum_probs=55.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHhh---hcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301           7 AGKMRTNGIQSQVFELERKFQ---HIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus         7 ~rr~Rt~~t~~q~~~Le~~F~---~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      .||+|..|+..-.++|..+|.   .++||+...+++||.+.+++..||-.||.|.|-+.+|.-.
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~  251 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMG  251 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhh
Confidence            467788999999999999994   6889999999999999999999999999999999887443

>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants []

Probab=98.72  E-value=2.1e-08  Score=57.35  Aligned_cols=34  Identities=41%  Similarity=0.618  Sum_probs=28.8

Q ss_pred             hcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301          28 HIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYK   61 (157)
Q Consensus        28 ~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k   61 (157)
                      .++||+..+++.||..+||+..||..||-|.|.+
T Consensus         7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR   40 (40)
T PF05920_consen    7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR   40 (40)
T ss_dssp             TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence            4789999999999999999999999999998864

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

>KOG2252|consensus

Probab=98.62  E-value=7.3e-08  Score=82.08  Aligned_cols=56  Identities=23%  Similarity=0.224  Sum_probs=52.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHH
Q psy8301           7 AGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ   62 (157)
Q Consensus         7 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~   62 (157)
                      .||+|.+||..|+..|.+.|+.+++|+....+.|+.+|+|....|.+||-|-|.+.
T Consensus       420 ~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  420 TKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             CCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            56779999999999999999999999999999999999999999999999987764

>KOG0490|consensus

Probab=98.52  E-value=1.2e-07  Score=73.12  Aligned_cols=64  Identities=30%  Similarity=0.454  Sum_probs=59.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      ..+.++.|+.+...|+..|...|..+++|+...++.|+..+|+++..|++||+|+|++.++...
T Consensus       150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            3567788999999999999999999999999999999999999999999999999999998554

>KOG1146|consensus

Probab=97.90  E-value=2.1e-05  Score=73.08  Aligned_cols=62  Identities=26%  Similarity=0.358  Sum_probs=57.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301           6 RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus         6 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      .+|+.||.++..||.++...|+...||...+.|.|...+++..++|++||||-|+|.++...
T Consensus       902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~  963 (1406)
T KOG1146|consen  902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL  963 (1406)
T ss_pred             hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence            35678999999999999999999999999999999999999999999999999999888655

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

Probab=97.07  E-value=0.00074  Score=41.15  Aligned_cols=41  Identities=24%  Similarity=0.383  Sum_probs=30.8

Q ss_pred             HHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHH
Q psy8301          19 VFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRR   59 (157)
Q Consensus        19 ~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR   59 (157)
                      ...|+++|...+++.......|..+.+|+..+|+.||-.+.
T Consensus        10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~   50 (56)
T PF11569_consen   10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM   50 (56)
T ss_dssp             -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred             hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence            45699999999999999999999999999999999997553

>KOG3623|consensus

Probab=96.74  E-value=0.0048  Score=54.99  Aligned_cols=49  Identities=16%  Similarity=0.267  Sum_probs=45.4

Q ss_pred             HHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301          19 VFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus        19 ~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      +..|+.+|..|..|+..+...+|...||+.+.|+.||.++++.......
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~r  616 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVER  616 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhcc
Confidence            7789999999999999999999999999999999999999999877553

>KOG0773|consensus

Probab=96.64  E-value=0.0012  Score=54.16  Aligned_cols=57  Identities=28%  Similarity=0.268  Sum_probs=48.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHh-h--hcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHH
Q psy8301           7 AGKMRTNGIQSQVFELERKF-Q--HIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK   63 (157)
Q Consensus         7 ~rr~Rt~~t~~q~~~Le~~F-~--~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~r   63 (157)
                      ..|++..+......+|+.+. +  ..+||+..+...||..+||+..+|-+||-|.|.+.-
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w  298 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLW  298 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccC
Confidence            45566789999999999883 3  357999999999999999999999999999987733

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

Probab=95.22  E-value=0.059  Score=32.36  Aligned_cols=47  Identities=13%  Similarity=0.266  Sum_probs=34.4

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHH
Q psy8301           8 GKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRR   59 (157)
Q Consensus         8 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR   59 (157)
                      ||.|..+|-++...+-..++...     ....||..+|++..+|..|..|+.
T Consensus         1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~   47 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD   47 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred             CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence            46788999999776666677665     578899999999999999998853

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

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

Probab=89.23  E-value=2.1  Score=24.71  Aligned_cols=46  Identities=9%  Similarity=0.047  Sum_probs=34.0

Q ss_pred             CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHH
Q psy8301          13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK   63 (157)
Q Consensus        13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~r   63 (157)
                      .+++.+..+|...|...     ..-.++|..+|++...|+.+...-..|-|
T Consensus         4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~kLR   49 (50)
T PF04545_consen    4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKKLR   49 (50)
T ss_dssp             TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence            46788889998888333     46788999999999999988865444433

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

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

Probab=87.25  E-value=1.8  Score=27.11  Aligned_cols=45  Identities=13%  Similarity=0.236  Sum_probs=29.1

Q ss_pred             CCCCCCCHHHHHHHHHHh-hhcCCCCHHHHHHHHHHhCCChhHHHHHHHHH
Q psy8301           9 KMRTNGIQSQVFELERKF-QHIRYLSPTEREMLGKEINLSPTQVKIWFQNR   58 (157)
Q Consensus         9 r~Rt~~t~~q~~~Le~~F-~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNr   58 (157)
                      +.|..|+.++...+-..+ ...     .....+|..+|++...+..|-+--
T Consensus         2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l~~W~~~~   47 (76)
T PF01527_consen    2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTLYNWRKQY   47 (76)
T ss_dssp             -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccccHHHHHH
Confidence            457889999966555444 433     578889999999999999998643

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

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

Probab=87.08  E-value=1.2  Score=26.79  Aligned_cols=40  Identities=18%  Similarity=0.104  Sum_probs=32.2

Q ss_pred             CCHHHHHHHHHHhhhcCC--CCHHHHHHHHHHhCCChhHHHH
Q psy8301          14 GIQSQVFELERKFQHIRY--LSPTEREMLGKEINLSPTQVKI   53 (157)
Q Consensus        14 ~t~~q~~~Le~~F~~~~~--p~~~~r~~La~~l~l~~~~Vqv   53 (157)
                      +|+.|.++|..+|+..=|  |-.....+||..+|++...+.-
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~   42 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSE   42 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence            578999999999886543  6667788999999999876543

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

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

Probab=85.15  E-value=3.2  Score=23.23  Aligned_cols=44  Identities=11%  Similarity=0.043  Sum_probs=32.2

Q ss_pred             CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301          13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYK   61 (157)
Q Consensus        13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k   61 (157)
                      .+++.+..++...|...     ....++|..+|++...|..|...-+.+
T Consensus        10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~   53 (55)
T cd06171          10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK   53 (55)
T ss_pred             hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            35677777777766422     356778999999999999998755443

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

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

Probab=83.77  E-value=5  Score=23.33  Aligned_cols=42  Identities=12%  Similarity=0.039  Sum_probs=27.3

Q ss_pred             CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHH
Q psy8301          14 GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRY   60 (157)
Q Consensus        14 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~   60 (157)
                      +++.+..++.-.|-     ....-.++|..+|++...|+.|...-|.
T Consensus        11 L~~~~r~i~~l~~~-----~g~s~~eIa~~l~~s~~~v~~~l~ra~~   52 (54)
T PF08281_consen   11 LPERQREIFLLRYF-----QGMSYAEIAEILGISESTVKRRLRRARK   52 (54)
T ss_dssp             S-HHHHHHHHHHHT-----S---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH-----HCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence            45566666655443     3357889999999999999999975443

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

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=82.99  E-value=6.7  Score=28.38  Aligned_cols=50  Identities=10%  Similarity=0.038  Sum_probs=39.9

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301          12 TNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus        12 t~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      ..+++.|..+|... ...     ....++|..+|++...|..|-++-+.+.++...
T Consensus         5 ~~Lt~rqreVL~lr-~~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~   54 (141)
T PRK03975          5 SFLTERQIEVLRLR-ERG-----LTQQEIADILGTSRANVSSIEKRARENIEKARE   54 (141)
T ss_pred             cCCCHHHHHHHHHH-HcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            57899999999773 222     357789999999999999999988887776544

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

Probab=80.60  E-value=1.7  Score=26.89  Aligned_cols=22  Identities=9%  Similarity=0.385  Sum_probs=18.8

Q ss_pred             HHHHHHHHHhCCChhHHHHHHH
Q psy8301          35 TEREMLGKEINLSPTQVKIWFQ   56 (157)
Q Consensus        35 ~~r~~La~~l~l~~~~VqvWFq   56 (157)
                      ..-.+||.+||+++.+|+.|=.
T Consensus        23 i~lkdIA~~Lgvs~~tIr~WK~   44 (60)
T PF10668_consen   23 IKLKDIAEKLGVSESTIRKWKS   44 (60)
T ss_pred             ccHHHHHHHHCCCHHHHHHHhh
Confidence            4567789999999999999964

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

---

Homologous Structure Templates

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	157
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	2e-23
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	2e-23
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	3e-23
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	3e-23
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	3e-23
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	5e-23
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	3e-22
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	4e-22
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	5e-21
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	1e-20
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	2e-18
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	1e-17
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	2e-17
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	2e-16
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	6e-16
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	4e-15
1e3o_C	160	Octamer-binding transcription factor 1; transcript	1e-14
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	1e-14
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	3e-14
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	6e-14
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	6e-13
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	7e-13
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	9e-13
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	1e-12
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	2e-12
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	2e-12
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	3e-12
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	4e-12
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	5e-12
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	7e-12
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	9e-12
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	1e-11
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	1e-11
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	1e-11
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	4e-11
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	4e-11
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	1e-10
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	2e-10
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	4e-10
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	4e-10
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	4e-10
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	4e-10
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	4e-10
1uhs_A	72	HOP, homeodomain only protein; structural genomics	7e-10
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	9e-10
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	1e-09
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	2e-09
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	3e-09
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	4e-09
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	9e-09
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	9e-09
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	2e-08
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	9e-08
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	2e-06
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	2e-06
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	6e-06
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	3e-05
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	3e-05
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	9e-05
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	9e-05
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	2e-04
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	3e-04
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	4e-04
1lfb_A	99	Liver transcription factor (LFB1); transcription r	5e-04

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

 Score = 86.6 bits (215), Expect = 2e-23
 Identities = 34/58 (58%), Positives = 41/58 (70%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
          K R    Q+QV+ELER+F+  +YLS  ERE L   I+L+PTQVKIWFQN RYK KR  
Sbjct: 4  KRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61

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

 Score = 86.2 bits (214), Expect = 2e-23
 Identities = 28/58 (48%), Positives = 37/58 (63%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
          KMRT   Q+Q+  L+ +FQ  +YLS  + + L   +NLS  QVK WFQN+R K KR Q
Sbjct: 5  KMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRWQ 62

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

 Score = 86.4 bits (214), Expect = 3e-23
 Identities = 34/64 (53%), Positives = 42/64 (65%)

Query: 3  QSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ 62
            ++  K R    ++Q +ELER+F+  RYLS  ERE L   I L+PTQVKIWFQN RYK 
Sbjct: 5  LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKT 64

Query: 63 KRLQ 66
          KR Q
Sbjct: 65 KRAQ 68

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

 Score = 85.8 bits (213), Expect = 3e-23
 Identities = 30/57 (52%), Positives = 37/57 (64%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65
          K RT    +Q+  LERKF+  +YLS  ER      ++L+ TQVKIWFQNRR K KRL
Sbjct: 2  KPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL 58

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

 Score = 85.4 bits (212), Expect = 3e-23
 Identities = 32/55 (58%), Positives = 39/55 (70%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
          K R    Q+QV+ELER+F+  RYLS  ER+ L   + L+ TQVKIWFQNRRYK K
Sbjct: 4  KPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

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

 Score = 85.1 bits (211), Expect = 5e-23
 Identities = 33/62 (53%), Positives = 41/62 (66%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68
             ++   +QV ELERKF H +YLS  ER  L K + L+ TQVKIWFQNRRYK KR Q  
Sbjct: 6  HHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLS 65

Query: 69 NQ 70
          ++
Sbjct: 66 SE 67

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

 Score = 83.7 bits (207), Expect = 3e-22
 Identities = 27/61 (44%), Positives = 35/61 (57%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68
          K RT    +Q+  L  +FQ  +YLS  + + L   +NLS  QVK WFQN+R K KR Q  
Sbjct: 24 KTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQKN 83

Query: 69 N 69
          N
Sbjct: 84 N 84

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

 Score = 82.7 bits (205), Expect = 4e-22
 Identities = 25/49 (51%), Positives = 33/49 (67%)

Query: 16 QSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
          +SQV ELER+F   +YL+  ER  L K + ++  QVK WFQNRR K +R
Sbjct: 6  RSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRR 54

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

 Score = 80.1 bits (198), Expect = 5e-21
 Identities = 26/64 (40%), Positives = 35/64 (54%)

Query: 3  QSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ 62
                K RT     Q+  L+R+FQ  +YL+  ER  L   + L+ TQVKIWFQN+R K 
Sbjct: 3  SGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKI 62

Query: 63 KRLQ 66
          K+  
Sbjct: 63 KKSG 66

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

 Score = 79.9 bits (197), Expect = 1e-20
 Identities = 26/64 (40%), Positives = 39/64 (60%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68
          K RT+  + QV ELE++F   +YL+  ER  L + + ++  QVK WFQNRR K +R  A 
Sbjct: 19 KPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAE 78

Query: 69 NQNS 72
           + +
Sbjct: 79 EREA 82

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

 Score = 73.6 bits (181), Expect = 2e-18
 Identities = 27/56 (48%), Positives = 34/56 (60%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
            +      Q  ELE+KF+  +YLSP ER+ L K + LS  QVK WFQNRR K +R
Sbjct: 9  GGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64

>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 = 71.5 bits (176), Expect = 1e-17
 Identities = 16/61 (26%), Positives = 34/61 (55%)

Query: 3  QSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ 62
          +  ++ K +++        LE  F+  + L+  E+E + K+  ++P QV++WF N+R + 
Sbjct: 1  KKEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS 60

Query: 63 K 63
          K
Sbjct: 61 K 61

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

 Score = 71.4 bits (175), Expect = 2e-17
 Identities = 23/58 (39%), Positives = 35/58 (60%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
          + RT   + Q+  LE++F+  +YLS  +R  L + + LS  QVK W+QNRR K K+  
Sbjct: 19 RSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSG 76

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

 Score = 69.0 bits (169), Expect = 2e-16
 Identities = 18/71 (25%), Positives = 30/71 (42%)

Query: 4  SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
          S  A   +      Q+  L+  F   ++   +E E L K   LS  +V+ WF +RRY  +
Sbjct: 5  SSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCR 64

Query: 64 RLQAMNQNSNG 74
           L+      + 
Sbjct: 65 NLKGSRSGPSS 75

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

 Score = 67.1 bits (164), Expect = 6e-16
 Identities = 23/65 (35%), Positives = 35/65 (53%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68
          + RT    SQ+ ELE+ F   RYL+      L  ++ L   QVKIWF+NRR + K     
Sbjct: 4  RTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ 63

Query: 69 NQNSN 73
          +++ +
Sbjct: 64 HKDQS 68

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

 Score = 67.3 bits (164), Expect = 4e-15
 Identities = 20/67 (29%), Positives = 27/67 (40%)

Query: 1   MFQSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRY 60
           +    R  K RT+        LE  F      S  E   L   + L    V++WF NRR 
Sbjct: 93  IAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQ 152

Query: 61  KQKRLQA 67
           K+KR+  
Sbjct: 153 KEKRMTP 159

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

 Score = 66.5 bits (162), Expect = 1e-14
 Identities = 16/65 (24%), Positives = 34/65 (52%)

Query: 1   MFQSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRY 60
           +    R  K RT+   +    LE+ F   +  +  +  ++ +++N+    +++WF NRR 
Sbjct: 95  IEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQ 154

Query: 61  KQKRL 65
           K+KR+
Sbjct: 155 KEKRI 159

>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 = 65.8 bits (160), Expect = 1e-14
 Identities = 20/58 (34%), Positives = 30/58 (51%)

Query: 9   KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
           K RT    +    LER F      S  E   + +E+NL    V++WF NRR ++KR++
Sbjct: 89  KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRVK 146

>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 = 62.7 bits (153), Expect = 3e-14
 Identities = 22/54 (40%), Positives = 33/54 (61%)

Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
          RT     Q+  L+R+F   RYL+   R+ L  E+ L+  Q+KIWF+N+R K K+
Sbjct: 7  RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

>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 = 61.6 bits (150), Expect = 6e-14
 Identities = 22/58 (37%), Positives = 34/58 (58%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
          + RT   + Q+  LE++F    Y+S   R  L  ++NL  + +K+WFQNRR K KR +
Sbjct: 3  RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQR 60

>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 = 60.3 bits (146), Expect = 6e-13
 Identities = 27/56 (48%), Positives = 36/56 (64%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
           +RTN    Q+ ELE++F   +YLS   R  +   + L+ TQVKIWFQNRR KQK+
Sbjct: 36 GLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91

>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 = 59.3 bits (144), Expect = 7e-13
 Identities = 17/56 (30%), Positives = 24/56 (42%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
            RT     Q+  L+  F    Y    E E L   +NL    + +WFQN R K ++
Sbjct: 9  SSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64

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

 Score = 59.0 bits (143), Expect = 9e-13
 Identities = 14/68 (20%), Positives = 30/68 (44%), Gaps = 1/68 (1%)

Query: 7  AGKMRTNGIQSQVFELERKFQHI-RYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65
          + +  +   + QV  LE  F  + ++  PT   ++  E  L+  Q + WF+ R  + +R 
Sbjct: 2  SAQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 61

Query: 66 QAMNQNSN 73
          + +     
Sbjct: 62 EGLPSECR 69

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

 Score = 60.8 bits (147), Expect = 1e-12
 Identities = 16/62 (25%), Positives = 26/62 (41%)

Query: 3   QSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ 62
           +  +  K RT+     +  L   F+     +  E   + KE+N     V++WF NRR   
Sbjct: 89  EPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTL 148

Query: 63  KR 64
           K 
Sbjct: 149 KN 150

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

 Score = 58.2 bits (141), Expect = 2e-12
 Identities = 23/56 (41%), Positives = 35/56 (62%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
          + RT   ++Q+ ELE++F   +Y+S   R  L   +NL+   +KIWFQNRR K K+
Sbjct: 5  RTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60

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

 Score = 58.5 bits (141), Expect = 2e-12
 Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 3/68 (4%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68
          K +T   Q QV  LE  F    + +  E + L  E  LS  ++  WF  RR  +  ++  
Sbjct: 18 KEKT---QGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQA 74

Query: 69 NQNSNGKN 76
            +S G  
Sbjct: 75 VLDSMGSG 82

>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 = 3e-12
 Identities = 15/64 (23%), Positives = 30/64 (46%), Gaps = 3/64 (4%)

Query: 1  MFQSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRY 60
          M   H   + +T   + Q+  L+  F   ++    E   L +   L+ +++K WF + RY
Sbjct: 1  MAHHHHHHRKKT---KEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRY 57

Query: 61 KQKR 64
          + +R
Sbjct: 58 RCQR 61

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

 Score = 57.6 bits (139), Expect = 4e-12
 Identities = 23/73 (31%), Positives = 39/73 (53%)

Query: 1  MFQSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRY 60
          M       K R    + Q+ ELER++   ++++  +R  +    NLS  QV IWFQNRR 
Sbjct: 1  MSHMLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRV 60

Query: 61 KQKRLQAMNQNSN 73
          K+K++    + ++
Sbjct: 61 KEKKVINKLKTTS 73

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

 Score = 57.1 bits (138), Expect = 5e-12
 Identities = 21/56 (37%), Positives = 32/56 (57%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
          + R    + Q  ELE++F    YL+   R  +   ++L+  Q+KIWFQNRR K K+
Sbjct: 22 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKK 77

>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 = 57.1 bits (138), Expect = 7e-12
 Identities = 14/64 (21%), Positives = 30/64 (46%)

Query: 3  QSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ 62
          +  R  ++RT     Q+  L +K+      +    + +  E+ L    V++WFQN R ++
Sbjct: 13 EPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARE 72

Query: 63 KRLQ 66
          ++  
Sbjct: 73 RKSG 76

>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 = 56.3 bits (136), Expect = 9e-12
 Identities = 22/58 (37%), Positives = 33/58 (56%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
          + R    + Q  ELE++F   RYL+   R  +   ++L+  Q+KIWFQNRR K K+  
Sbjct: 4  RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61

>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 75

 Score = 56.4 bits (136), Expect = 1e-11
 Identities = 14/66 (21%), Positives = 22/66 (33%), Gaps = 3/66 (4%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68
          K R      Q+  LE  F         E + L  E  ++  ++  WF  RR K    +  
Sbjct: 12 KERA---PEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETK 68

Query: 69 NQNSNG 74
              + 
Sbjct: 69 KSGPSS 74

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

 Score = 56.0 bits (135), Expect = 1e-11
 Identities = 20/64 (31%), Positives = 34/64 (53%)

Query: 3  QSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ 62
                K R    + Q+ ELER++   ++++  +R  +    +LS  Q+ IWFQNRR K+
Sbjct: 3  SGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKE 62

Query: 63 KRLQ 66
          K+  
Sbjct: 63 KKSG 66

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

 Score = 56.4 bits (136), Expect = 1e-11
 Identities = 23/56 (41%), Positives = 35/56 (62%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
          + RT+  + Q  ELE++F   RYL+   R  +   ++L+  Q+KIWFQNRR K K+
Sbjct: 30 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 85

>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 = 54.9 bits (132), Expect = 4e-11
 Identities = 24/58 (41%), Positives = 34/58 (58%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
          K R    + Q  ELE++F    YL+   R  + + +NL+  QVKIWFQNRR K K++ 
Sbjct: 15 KKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKIN 72

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

 Score = 57.0 bits (137), Expect = 4e-11
 Identities = 16/56 (28%), Positives = 25/56 (44%)

Query: 9   KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
           + RT+      + LE  F      S  +   +  ++ L    V++WF NRR K KR
Sbjct: 98  RKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKR 153

>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 = 53.5 bits (129), Expect = 1e-10
 Identities = 12/64 (18%), Positives = 25/64 (39%)

Query: 3  QSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ 62
                + RT     Q+  L + F      S  + + +  +  L    +K WF+N  +K+
Sbjct: 3  SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKE 62

Query: 63 KRLQ 66
          ++  
Sbjct: 63 RQSG 66

>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 = 53.2 bits (128), Expect = 2e-10
 Identities = 15/74 (20%), Positives = 30/74 (40%)

Query: 3  QSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ 62
                +MRT+    Q+  ++  F         + + L ++  L+   +++WFQN R K 
Sbjct: 3  SGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKF 62

Query: 63 KRLQAMNQNSNGKN 76
          +R     +N     
Sbjct: 63 RRNLLRQENGGVSG 76

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

 Score = 52.7 bits (126), Expect = 4e-10
 Identities = 11/67 (16%), Positives = 25/67 (37%), Gaps = 3/67 (4%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68
          K +T     Q+  L+  F +   L+  E   L  +  L+  ++  WF  ++  +   +  
Sbjct: 16 KEKT---AEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEK 72

Query: 69 NQNSNGK 75
           +     
Sbjct: 73 MEIDESN 79

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

 Score = 51.9 bits (125), Expect = 4e-10
 Identities = 18/58 (31%), Positives = 30/58 (51%)

Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68
                 Q+ ELE+ F    Y     RE L  +I L+  ++++WFQNRR K ++ + +
Sbjct: 3  HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEKV 60

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

 Score = 54.5 bits (130), Expect = 4e-10
 Identities = 11/73 (15%), Positives = 26/73 (35%)

Query: 1   MFQSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRY 60
             + +   K R      Q   L   F+  +  S   +  + +++ L  + V  +F N R 
Sbjct: 91  KDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARR 150

Query: 61  KQKRLQAMNQNSN 73
           +       + + +
Sbjct: 151 RSLDKWLEHHHHH 163

>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 = 52.0 bits (125), Expect = 4e-10
 Identities = 17/61 (27%), Positives = 29/61 (47%)

Query: 10 MRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN 69
          +RT   + Q+  L   +          +E L +   LSP  +++WFQN+R K K+   M 
Sbjct: 6  VRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSIMM 65

Query: 70 Q 70
          +
Sbjct: 66 K 66

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

 Score = 51.9 bits (125), Expect = 4e-10
 Identities = 23/60 (38%), Positives = 33/60 (55%)

Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQ 70
          RT   Q+Q+  LE  F+   Y      E L +++NL   +++IWFQNRR K KR    +Q
Sbjct: 5  RTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRESQ 64

>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 = 51.6 bits (124), Expect = 7e-10
 Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 1/63 (1%)

Query: 11 RTNGIQSQVFELERKFQHI-RYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN 69
               + QV  LE  F  + ++  PT   ++  E  L+  Q + WF+ R  + +R + + 
Sbjct: 5  AATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLP 64

Query: 70 QNS 72
             
Sbjct: 65 SEC 67

>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus} Length = 80

 Score = 51.3 bits (123), Expect = 9e-10
 Identities = 23/64 (35%), Positives = 35/64 (54%)

Query: 10 MRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN 69
           RT   ++Q+  LE  F   RY     RE +  +INL  ++V++WF+NRR K ++ Q   
Sbjct: 10 ERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQ 69

Query: 70 QNSN 73
          QN  
Sbjct: 70 QNGG 73

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

 Score = 50.4 bits (121), Expect = 1e-09
 Identities = 20/61 (32%), Positives = 33/61 (54%)

Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQ 70
          RT+    Q+ +LE  FQ  RY   + RE +    NL+  +V++WF+NRR K ++ +    
Sbjct: 7  RTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEFIV 66

Query: 71 N 71
           
Sbjct: 67 T 67

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

 Score = 50.9 bits (122), Expect = 2e-09
 Identities = 20/66 (30%), Positives = 34/66 (51%)

Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQ 70
          RT+  Q Q+  LE++F+   Y     RE L  +I+L   ++++WF NRR K +R + +  
Sbjct: 11 RTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRN 70

Query: 71 NSNGKN 76
                
Sbjct: 71 QRRQSG 76

>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 = 49.8 bits (119), Expect = 3e-09
 Identities = 12/57 (21%), Positives = 22/57 (38%), Gaps = 1/57 (1%)

Query: 9  KMRTNGIQSQVFELERKFQHI-RYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
          + RT      +  L+     +  Y        L  +++L    +  +FQN+RY  K 
Sbjct: 9  RSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH 65

>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 = 49.6 bits (119), Expect = 4e-09
 Identities = 20/59 (33%), Positives = 32/59 (54%)

Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN 69
          RT     Q+  LE  FQ  +Y     RE L ++++L   +V++WF+NRR K +R    +
Sbjct: 11 RTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGPSS 69

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

 Score = 49.3 bits (117), Expect = 9e-09
 Identities = 15/77 (19%), Positives = 26/77 (33%), Gaps = 15/77 (19%)

Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEIN---------------LSPTQVKIWF 55
          R    +  +  +E  F   +Y    +RE +    N               ++  +V  WF
Sbjct: 11 RFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWF 70

Query: 56 QNRRYKQKRLQAMNQNS 72
           NRR + KR   +    
Sbjct: 71 ANRRKEIKRRANIAAIL 87

>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 = 48.9 bits (117), Expect = 9e-09
 Identities = 21/56 (37%), Positives = 33/56 (58%)

Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
          RT    SQ+ ELER F+  +Y     RE L +  NL+  ++++WFQNRR + ++  
Sbjct: 22 RTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH 77

>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 = 47.9 bits (114), Expect = 2e-08
 Identities = 12/48 (25%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 17 SQVFELERKFQHI-RYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
               LE+ F  + +Y      + L K+++ S  +++ WF++RR + K
Sbjct: 18 EPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 65

>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 = 46.7 bits (110), Expect = 9e-08
 Identities = 16/63 (25%), Positives = 25/63 (39%)

Query: 4  SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
             +          Q+  L+  F   ++ SP E + L KE  L+ T +  WF + RY  K
Sbjct: 22 KSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWK 81

Query: 64 RLQ 66
             
Sbjct: 82 NGN 84

>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 76

 Score = 42.7 bits (100), Expect = 2e-06
 Identities = 12/59 (20%), Positives = 23/59 (38%)

Query: 8  GKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
          G       + Q+  L+  F   ++    + + L +   L   ++  WF + RY  K  Q
Sbjct: 4  GSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ 62

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

 Score = 42.1 bits (99), Expect = 2e-06
 Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 22 LERKFQHI-RYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
          LE+ F  I ++      E L K+++     ++ WF+ RR ++K
Sbjct: 15 LEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 57

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

 Score = 40.7 bits (96), Expect = 6e-06
 Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 2/42 (4%)

Query: 26 FQHIR--YLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65
           ++I   YL     E L K  +LS  Q+K W  NRR K+K +
Sbjct: 18 AKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI 59

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

 Score = 39.4 bits (92), Expect = 3e-05
 Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 2/53 (3%)

Query: 26 FQHIR--YLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQNSNGKN 76
           ++I   YL     E L K  +LS  Q+K W   RR K+K +    + ++  +
Sbjct: 22 AKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITIAPELADLLS 74

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

 Score = 39.5 bits (92), Expect = 3e-05
 Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 2/40 (5%)

Query: 26 FQHIR--YLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
           ++I   YL     E L K  +LS  Q+K W  NRR K+K
Sbjct: 47 AKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK 86

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

 Score = 38.2 bits (89), Expect = 9e-05
 Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 4/52 (7%)

Query: 26 FQHIR--YLSPTEREMLGKEINLSPTQVKIWFQN--RRYKQKRLQAMNQNSN 73
          ++H    Y S  E+ +L ++ +LS  QV  WF N  RR     L+   ++ N
Sbjct: 25 YEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRKDGKDPN 76

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

 Score = 37.7 bits (88), Expect = 9e-05
 Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 4/49 (8%)

Query: 26 FQHIR--YLSPTEREMLGKEINLSPTQVKIWFQN--RRYKQKRLQAMNQ 70
          FQH+   Y S  +++ L ++  L+  QV  WF N  RR  Q  +   N+
Sbjct: 18 FQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQSNR 66

>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 = 37.4 bits (87), Expect = 2e-04
 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 4/53 (7%)

Query: 26 FQHIR--YLSPTEREMLGKEINLSPTQVKIWFQN--RRYKQKRLQAMNQNSNG 74
          ++H    Y S  E++ML ++ NLS  Q+  WF N  RR     LQ    + +G
Sbjct: 27 YKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQRRNDPSG 79

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

 Score = 38.5 bits (88), Expect = 3e-04
 Identities = 15/75 (20%), Positives = 25/75 (33%), Gaps = 21/75 (28%)

Query: 11  RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEIN---------------------LSPT 49
           R     +    L + +   +  S  ERE L +E N                     ++  
Sbjct: 146 RFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEV 205

Query: 50  QVKIWFQNRRYKQKR 64
           +V  WF NRR ++  
Sbjct: 206 RVYNWFANRRKEEAF 220

>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 = 38.3 bits (88), Expect = 4e-04
 Identities = 15/75 (20%), Positives = 26/75 (34%), Gaps = 21/75 (28%)

Query: 11  RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEIN---------------------LSPT 49
           R     +    L + ++  +  S  ERE L +E N                     ++  
Sbjct: 119 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 178

Query: 50  QVKIWFQNRRYKQKR 64
           +V  WF NRR ++  
Sbjct: 179 RVYNWFANRRKEEAF 193

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

 Score = 36.7 bits (84), Expect = 5e-04
 Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 21/83 (25%)

Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEIN---------------------LSPT 49
          R     +    L + ++  +  S  ERE L +E N                     ++  
Sbjct: 13 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 72

Query: 50 QVKIWFQNRRYKQKRLQAMNQNS 72
          +V  WF NRR ++     +  ++
Sbjct: 73 RVYNWFANRRKEEAFRHKLAMDT 95

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	157
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.87
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.87
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.87
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.87
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.87
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.87
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.87
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.87
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.87
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.87
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.86
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.86
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.86
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.86
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.86
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.86
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.86
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.86
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.86
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.86
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.86
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.86
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.86
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.86
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.86
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.86
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.85
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.85
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.85
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.85
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.85
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.85
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.85
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.84
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.84
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.84
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.84
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.84
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.84
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.84
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.83
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.83
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.83
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.82
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.82
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.82
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.82
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.82
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.82
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.81
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.81
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.81
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.81
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.81
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.8
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.8
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.8
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.8
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.79
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.79
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.79
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.79
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.78
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.78
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.78
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.78
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.78
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.76
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.75
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.75
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.73
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.69
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.64
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.6
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.59
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.57
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.43
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.68
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	95.72
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	93.2
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	90.14
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	86.86
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	86.57
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	86.16
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	85.4
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	84.96
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	83.0
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	82.55
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	82.47

>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=99.87  E-value=5e-22  Score=129.14  Aligned_cols=66  Identities=52%  Similarity=0.776  Sum_probs=61.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhh
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN   69 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~   69 (157)
                      +++.+|.||.|+..|+..||..|..++||+..++++||..+||++.+|+|||||||+|+|+.....
T Consensus         6 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~~   71 (77)
T 1nk2_P            6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEK   71 (77)
T ss_dssp             SCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhccc
Confidence            456788999999999999999999999999999999999999999999999999999999866543

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

Probab=99.87  E-value=3e-22  Score=131.11  Aligned_cols=64  Identities=33%  Similarity=0.461  Sum_probs=60.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      .++.||.|+.|+..|+.+||..|..++||+..++++||..+||++.+|++||||||+|+|+...
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~   67 (80)
T 2dms_A            4 GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQ   67 (80)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHH
Confidence            3567889999999999999999999999999999999999999999999999999999999553

>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=99.87  E-value=7e-22  Score=129.24  Aligned_cols=64  Identities=22%  Similarity=0.302  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhh
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM   68 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~   68 (157)
                      .+.||.||.|+..|+.+||..|..++||+..++++||..+||++.+|++||||||+|+|+....
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (80)
T 2dmq_A            5 SSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLR   68 (80)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHH
Confidence            4578899999999999999999999999999999999999999999999999999999997654

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

Probab=99.87  E-value=4e-22  Score=124.85  Aligned_cols=59  Identities=39%  Similarity=0.621  Sum_probs=55.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301           7 AGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus         7 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      .+|.|+.|+..|+.+||..|..++||+..++++||..+||++.+|++||||||+|+|+.
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   61 (63)
T 2h1k_A            3 NKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE   61 (63)
T ss_dssp             --CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhh
Confidence            57889999999999999999999999999999999999999999999999999999985

>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=99.87  E-value=2.5e-22  Score=124.97  Aligned_cols=58  Identities=38%  Similarity=0.631  Sum_probs=53.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           7 AGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         7 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      .||.||.|+..|+..||..|..++||+..++++||..+||++.+|++||||||+|+|+
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            5788999999999999999999999999999999999999999999999999999986

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

Probab=99.87  E-value=6.6e-22  Score=125.66  Aligned_cols=63  Identities=37%  Similarity=0.538  Sum_probs=59.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhh
Q psy8301           7 AGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN   69 (157)
Q Consensus         7 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~   69 (157)
                      .||.||.|+..|+.+||..|..++||+..+++.||..+||++.+|++||||||+|+|+.....
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~~   64 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQH   64 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhccc
Confidence            578899999999999999999999999999999999999999999999999999999976543

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

Probab=99.87  E-value=5.5e-22  Score=129.84  Aligned_cols=66  Identities=30%  Similarity=0.526  Sum_probs=61.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhhc
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQ   70 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~~   70 (157)
                      .+.+|.||.|+..|+.+||..|..++||+..++++||..+||++.+|+|||||||+|+|+......
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~~   70 (80)
T 2cue_A            5 SSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRN   70 (80)
T ss_dssp             CSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhhh
Confidence            456789999999999999999999999999999999999999999999999999999999776543

>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=99.87  E-value=9.7e-22  Score=127.77  Aligned_cols=66  Identities=36%  Similarity=0.554  Sum_probs=61.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhh
Q psy8301           3 QSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM   68 (157)
Q Consensus         3 ~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~   68 (157)
                      ..++.+|.|+.|+..|+.+||..|..++||+..++++||..+||++.+|+|||||||+|+|+....
T Consensus         9 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k~   74 (77)
T 1puf_A            9 HARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             CCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhhh
Confidence            345678899999999999999999999999999999999999999999999999999999997654

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

Probab=99.87  E-value=6e-22  Score=121.97  Aligned_cols=57  Identities=51%  Similarity=0.724  Sum_probs=55.4

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           8 GKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         8 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      ||.|+.|+..|+.+||..|..++||+..++++||..+||++.+|++||||||+|+|+
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            578999999999999999999999999999999999999999999999999999987

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

Probab=99.87  E-value=3.6e-22  Score=130.70  Aligned_cols=62  Identities=37%  Similarity=0.592  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      .++.+|.||.|+..|+.+||..|..++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus        14 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~   75 (80)
T 2dmt_A           14 AKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKS   75 (80)
T ss_dssp             CCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcc
Confidence            45678899999999999999999999999999999999999999999999999999999983

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

Probab=99.86  E-value=7.7e-22  Score=125.97  Aligned_cols=61  Identities=33%  Similarity=0.513  Sum_probs=58.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      .+.+|.|+.|+..|+.+||..|..++||+..++++||..+||++.+|++||||||+|+|+.
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~   65 (70)
T 2dmu_A            5 SSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRS   65 (70)
T ss_dssp             TSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehcccccccccccc
Confidence            4567899999999999999999999999999999999999999999999999999999984

>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=99.86  E-value=9.3e-22  Score=129.02  Aligned_cols=64  Identities=33%  Similarity=0.551  Sum_probs=59.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      +++.+|.|+.|+..|+.+|+..|..++||+..++.+||..+||++.+|++||||||+|+|+...
T Consensus        15 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~   78 (81)
T 1fjl_A           15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   78 (81)
T ss_dssp             --CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhcc
Confidence            4567889999999999999999999999999999999999999999999999999999999664

>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=99.86  E-value=4e-22  Score=126.69  Aligned_cols=61  Identities=36%  Similarity=0.581  Sum_probs=58.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301           7 AGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus         7 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      +||.||.|+..|+..||..|..++||+..++++||..+||++.+|++||||||+|+|+...
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~   62 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK   62 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhcc
Confidence            4688999999999999999999999999999999999999999999999999999999553

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

Probab=99.86  E-value=6.5e-22  Score=125.69  Aligned_cols=61  Identities=56%  Similarity=0.814  Sum_probs=58.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301           7 AGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus         7 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      +||.||.|+..|+..||..|..++||+..++.+||..+||++.+|++||+|||+|+|+...
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~   62 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK   62 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhh
Confidence            5688999999999999999999999999999999999999999999999999999999553

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

Probab=99.86  E-value=7.5e-22  Score=122.40  Aligned_cols=58  Identities=38%  Similarity=0.603  Sum_probs=55.5

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301           8 GKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus         8 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      ||.||.|+..|+..||..|..++||+..++++||..+||++.+|++||||||+|+|++
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   59 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHhHhhcc
Confidence            5789999999999999999999999999999999999999999999999999999984

>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=99.86  E-value=4.2e-22  Score=127.23  Aligned_cols=61  Identities=33%  Similarity=0.544  Sum_probs=58.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      .+.||.|+.|+..|+.+||..|..++||+..++++||..+||++.+|++||||||+|+|+.
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~   65 (70)
T 2cra_A            5 SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKS   65 (70)
T ss_dssp             CCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSS
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhccc
Confidence            4678899999999999999999999999999999999999999999999999999999883

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

Probab=99.86  E-value=1.2e-21  Score=131.83  Aligned_cols=66  Identities=39%  Similarity=0.608  Sum_probs=61.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhh
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN   69 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~   69 (157)
                      +.+.||.||.|+..|+..||..|..++||+..++++||..+||++.+|+|||||||+|+|+.....
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~   79 (93)
T 3a01_A           14 PPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEE   79 (93)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHH
Confidence            456788999999999999999999999999999999999999999999999999999999976543

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

Probab=99.86  E-value=3.3e-22  Score=124.79  Aligned_cols=59  Identities=46%  Similarity=0.589  Sum_probs=52.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           6 RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         6 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      +.+|.||.|+..|+.+||..|..++||+..++++||..+||++.+|++||||||+|+|+
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   60 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR   60 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGG
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhh
Confidence            35788999999999999999999999999999999999999999999999999999987

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

Probab=99.86  E-value=6.8e-22  Score=129.22  Aligned_cols=62  Identities=23%  Similarity=0.363  Sum_probs=59.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      +++.+|.||.|+.+|+.+|+..|..++||+..++++||..+||++.+|++||||||+|+|+.
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   75 (80)
T 2da3_A           14 PQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKS   75 (80)
T ss_dssp             CCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhh
Confidence            45678899999999999999999999999999999999999999999999999999999983

>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=99.86  E-value=8.1e-22  Score=125.84  Aligned_cols=61  Identities=20%  Similarity=0.286  Sum_probs=58.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      .+.+|.||.|+..|+.+||..|..++||+..++++||..+||++.+|++||||||+|+|+.
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   65 (70)
T 2da1_A            5 SSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQS   65 (70)
T ss_dssp             CCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhh
Confidence            4678899999999999999999999999999999999999999999999999999999984

>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=99.86  E-value=6.2e-22  Score=123.09  Aligned_cols=60  Identities=27%  Similarity=0.467  Sum_probs=48.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHH
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK   63 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~r   63 (157)
                      +++.+|.|+.|+..|+.+|+..|..++||+..++++||..+||++.+|++||+|||+++|
T Consensus         2 k~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            2 KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             ----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            466788999999999999999999999999999999999999999999999999999975

>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=99.86  E-value=6.1e-22  Score=125.05  Aligned_cols=60  Identities=27%  Similarity=0.412  Sum_probs=57.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301           6 RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus         6 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      +.+|.||.|+..|+..||..|..++||+..++++||..+||++.+|++||||||+|+|+.
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   61 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR   61 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHH
Confidence            467899999999999999999999999999999999999999999999999999998873

>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=99.86  E-value=2.3e-21  Score=123.78  Aligned_cols=62  Identities=44%  Similarity=0.608  Sum_probs=58.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ   66 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~   66 (157)
                      .+.++.|+.|+..|+.+||..|..++||+..++++||..+||++.+|++||||||+|+|+..
T Consensus         5 ~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~   66 (70)
T 2e1o_A            5 SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSG   66 (70)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCC
Confidence            35678899999999999999999999999999999999999999999999999999999853

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

Probab=99.86  E-value=3e-21  Score=124.26  Aligned_cols=61  Identities=23%  Similarity=0.346  Sum_probs=57.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhh-cCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301           7 AGKMRTNGIQSQVFELERKFQH-IRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus         7 ~rr~Rt~~t~~q~~~Le~~F~~-~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      .++.||.|+..|+.+||..|.. ++||+..++++||..+||++.+|++||||||+|+|+...
T Consensus         2 ~~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~~   63 (73)
T 2hi3_A            2 SAQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   63 (73)
T ss_dssp             CCSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhcc
Confidence            4577999999999999999995 999999999999999999999999999999999999764

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

Probab=99.86  E-value=9.6e-22  Score=125.49  Aligned_cols=61  Identities=28%  Similarity=0.353  Sum_probs=58.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      .+.+|.||.|+..|+.+||..|..++||+..++++||..+||++.+|++||||||+|+|+.
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   65 (70)
T 2da2_A            5 SSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKS   65 (70)
T ss_dssp             CCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhc
Confidence            4678899999999999999999999999999999999999999999999999999999883

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

Probab=99.86  E-value=3e-22  Score=132.17  Aligned_cols=63  Identities=41%  Similarity=0.538  Sum_probs=59.3

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ   66 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~   66 (157)
                      +.+.+|.||.|+..|+.+||..|..++||+..++++||..+||++.+|+|||||||+|+|+..
T Consensus        19 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   81 (84)
T 2kt0_A           19 PVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQ   81 (84)
T ss_dssp             CSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHh
Confidence            456788999999999999999999999999999999999999999999999999999998843

>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=99.85  E-value=5.6e-22  Score=125.98  Aligned_cols=62  Identities=32%  Similarity=0.503  Sum_probs=58.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301           6 RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus         6 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      +.+|.||.|+..|+..||..|..++||+..++++||..+||++.+|++||||||+|+|+...
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~   63 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREE   63 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhh
Confidence            36788999999999999999999999999999999999999999999999999999999654

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

Probab=99.85  E-value=1e-21  Score=128.55  Aligned_cols=62  Identities=23%  Similarity=0.280  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhc----CCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHI----RYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~----~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      .++.+|.||.|+.+|+.+||.+|..+    +||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus         5 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~   70 (80)
T 2da4_A            5 SSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLM   70 (80)
T ss_dssp             CCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhc
Confidence            35678899999999999999999999    999999999999999999999999999999999984

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

Probab=99.85  E-value=1.1e-21  Score=126.75  Aligned_cols=65  Identities=32%  Similarity=0.483  Sum_probs=60.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301           3 QSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus         3 ~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      ...+++|.||.|+..|+.+|+..|..++||+..++++||..+||++.+|++||+|||+|+|+...
T Consensus         5 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r   69 (75)
T 2m0c_A            5 NKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRER   69 (75)
T ss_dssp             CCSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHh
Confidence            34567888999999999999999999999999999999999999999999999999999998443

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

Probab=99.85  E-value=2.2e-21  Score=124.88  Aligned_cols=61  Identities=36%  Similarity=0.579  Sum_probs=58.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      .+.+|.|+.|+..|+..||..|..++||+..++++||..+||++.+|++||||||+|+|+.
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   65 (73)
T 2l7z_A            5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKV   65 (73)
T ss_dssp             SCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHH
Confidence            4578899999999999999999999999999999999999999999999999999999984

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

Probab=99.85  E-value=7.9e-22  Score=125.94  Aligned_cols=60  Identities=43%  Similarity=0.603  Sum_probs=57.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      .+.+|.|+.|+..|+.+||..|..++||+..++++||..+||++.+|++||||||+|+|+
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   64 (70)
T 2djn_A            5 SSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK   64 (70)
T ss_dssp             CCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcc
Confidence            467889999999999999999999999999999999999999999999999999999887

>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=99.85  E-value=4.4e-21  Score=123.09  Aligned_cols=60  Identities=23%  Similarity=0.320  Sum_probs=56.8

Q ss_pred             CCCCCCCCHHHHHHHHHHhhh-cCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301           8 GKMRTNGIQSQVFELERKFQH-IRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus         8 rr~Rt~~t~~q~~~Le~~F~~-~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      .+.|+.|+..|+.+||..|.. ++||+..++++||..+||++.+|++||||||+|+|+...
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~~   62 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   62 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhcc
Confidence            467899999999999999996 999999999999999999999999999999999999664

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

Probab=99.85  E-value=2.6e-21  Score=118.86  Aligned_cols=57  Identities=56%  Similarity=0.841  Sum_probs=54.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHH
Q psy8301           7 AGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK   63 (157)
Q Consensus         7 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~r   63 (157)
                      ++|.|+.|+..|+..|+..|..++||+..++++||..+||++.+|++||||||+|+|
T Consensus         2 ~rr~Rt~~t~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~k   58 (58)
T 3rkq_A            2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK   58 (58)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHC
T ss_pred             cCCCCCCcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhhccCC
Confidence            467899999999999999999999999999999999999999999999999999975

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

Probab=99.84  E-value=2.2e-21  Score=120.24  Aligned_cols=58  Identities=31%  Similarity=0.488  Sum_probs=50.7

Q ss_pred             CCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301          10 MRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus        10 ~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      .|+.||..|+..||..|..++||+..++++||..+||++.+|++||||||+|+|+..+
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~k   59 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK   59 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC----
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhcc
Confidence            4799999999999999999999999999999999999999999999999999998653

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

Probab=99.84  E-value=3.5e-21  Score=121.87  Aligned_cols=60  Identities=37%  Similarity=0.448  Sum_probs=57.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301           7 AGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ   66 (157)
Q Consensus         7 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~   66 (157)
                      .||.|+.|+..|+.+||..|..++||+..+++.||..+||++.+|++||+|||+|+|+..
T Consensus         1 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~   60 (67)
T 2k40_A            1 GRRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSH   60 (67)
T ss_dssp             CCCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSC
T ss_pred             CcCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhc
Confidence            368899999999999999999999999999999999999999999999999999999843

>1wh5_A ZF-HD homeobox family protein; structural genomics, zinc finger homeobox family protein, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} SCOP: a.4.1.1

Probab=99.84  E-value=9.8e-22  Score=128.70  Aligned_cols=60  Identities=13%  Similarity=0.133  Sum_probs=56.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhh----cCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQH----IRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~----~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      +++||.||.|+.+|+..||..|+.    ++||+..++++||..+||++.+|+|||||||+|+|+
T Consensus        15 ~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           15 GIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            467889999999999999999999    999999999999999999999999999999999764

>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=99.84  E-value=3.1e-21  Score=126.59  Aligned_cols=61  Identities=34%  Similarity=0.543  Sum_probs=54.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      .+.+|.||.|+..|+..||..|..++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus        18 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   78 (81)
T 1b8i_A           18 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE   78 (81)
T ss_dssp             ------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhh
Confidence            3567889999999999999999999999999999999999999999999999999999984

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

Probab=99.84  E-value=4.9e-21  Score=117.19  Aligned_cols=54  Identities=48%  Similarity=0.743  Sum_probs=51.0

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301          12 TNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus        12 t~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      |.|+..|+..||..|..++||+..++++||..+||++.+|++||||||+|+|++
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~   55 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ   55 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhhccc
Confidence            689999999999999999999999999999999999999999999999999984

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

Probab=99.84  E-value=4e-21  Score=127.88  Aligned_cols=61  Identities=38%  Similarity=0.610  Sum_probs=54.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      .+.+|.||.|+..|+.+||..|..++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus        26 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~   86 (88)
T 2r5y_A           26 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   86 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhh
Confidence            3567899999999999999999999999999999999999999999999999999999984

>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=99.84  E-value=7.5e-21  Score=122.78  Aligned_cols=59  Identities=19%  Similarity=0.278  Sum_probs=55.4

Q ss_pred             CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301           9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus         9 r~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      ..|+.||.+|+.+|++.|..++||+..++++||..+||++.+|+|||||||+|+|+...
T Consensus         5 ~~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~l   63 (76)
T 2ecc_A            5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQL   63 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHHH
Confidence            45678999999999999999999999999999999999999999999999999998543

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

Probab=99.83  E-value=9.1e-21  Score=128.32  Aligned_cols=62  Identities=44%  Similarity=0.655  Sum_probs=56.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301           6 RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus         6 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      +.++.||.|+..|+..||..|..++||+..++++||..+||++.+|+|||||||+|+|+...
T Consensus        33 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   94 (97)
T 1b72_A           33 SPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   94 (97)
T ss_dssp             ----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhc
Confidence            45788999999999999999999999999999999999999999999999999999999664

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

Probab=99.83  E-value=2.4e-20  Score=125.79  Aligned_cols=64  Identities=23%  Similarity=0.329  Sum_probs=60.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhC---------------CChhHHHHHHHHHHHHHHHHHhh
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEIN---------------LSPTQVKIWFQNRRYKQKRLQAM   68 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~---------------l~~~~VqvWFqNrR~k~rr~~~~   68 (157)
                      ++.||.|+.|+..|+.+||..|..++||+..++++||..+|               |++.+|++||||||+|+|+....
T Consensus         5 ~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~~   83 (95)
T 2cuf_A            5 SSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANI   83 (95)
T ss_dssp             SCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhhc
Confidence            56788999999999999999999999999999999999999               99999999999999999997764

>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=99.83  E-value=1.4e-21  Score=127.88  Aligned_cols=60  Identities=18%  Similarity=0.245  Sum_probs=55.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhh-----cCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQH-----IRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~-----~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      ..++||.||.|+.+|+..|| .|..     ++||+..++++||..+||++.+|+|||||||+|+|+
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           14 GGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            34678899999999999999 7999     999999999999999999999999999999999764

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

Probab=99.82  E-value=2e-20  Score=120.58  Aligned_cols=61  Identities=23%  Similarity=0.370  Sum_probs=57.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301           6 RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ   66 (157)
Q Consensus         6 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~   66 (157)
                      ..++.|+.|+..|+..||..|..++||+..++++||..+||++.+|++||||||+|+|+..
T Consensus         5 ~~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   65 (74)
T 2ly9_A            5 DSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSK   65 (74)
T ss_dssp             CCCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTT
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhC
Confidence            3567899999999999999999999999999999999999999999999999999999843

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

Probab=99.82  E-value=2.2e-20  Score=120.77  Aligned_cols=59  Identities=20%  Similarity=0.277  Sum_probs=55.5

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301           8 GKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ   66 (157)
Q Consensus         8 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~   66 (157)
                      .+.|+.||..|+.+||..|..++||+..++++||..+||++.+|++||||||+|+|+..
T Consensus         8 ~~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~   66 (75)
T 2da5_A            8 PTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEE   66 (75)
T ss_dssp             SCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSS
T ss_pred             CCCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhh
Confidence            45677899999999999999999999999999999999999999999999999999944

>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=99.82  E-value=5.6e-20  Score=118.17  Aligned_cols=61  Identities=18%  Similarity=0.200  Sum_probs=57.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQH---IRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~---~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      .+.++.|+.|+..|+.+|+.+|..   ++||+..++++||..+||++.+|++||+|||+|+++.
T Consensus         5 ~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~   68 (73)
T 1x2n_A            5 SSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQS   68 (73)
T ss_dssp             SSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhcccc
Confidence            457788999999999999999987   9999999999999999999999999999999999984

>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=99.82  E-value=3.5e-20  Score=116.00  Aligned_cols=58  Identities=19%  Similarity=0.233  Sum_probs=55.3

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhh-cCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQH-IRYLSPTEREMLGKEINLSPTQVKIWFQNRRYK   61 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~-~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k   61 (157)
                      .+++||.||.|+.+|+.+|+..|+. ++||+...|+.||..+||++++|+|||||||.-
T Consensus         4 ~~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~   62 (71)
T 1wi3_A            4 GSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYH   62 (71)
T ss_dssp             CCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceee
Confidence            4568899999999999999999999 999999999999999999999999999999975

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

Probab=99.82  E-value=1.1e-20  Score=122.55  Aligned_cols=60  Identities=28%  Similarity=0.471  Sum_probs=56.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301           7 AGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ   66 (157)
Q Consensus         7 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~   66 (157)
                      ..+.|+.|+..|+.+||..|..++||+..++++||..+||++.+|++||||||+|+|+..
T Consensus         8 ~~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~   67 (76)
T 2dn0_A            8 ASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLK   67 (76)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCC
T ss_pred             CCCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhc
Confidence            456799999999999999999999999999999999999999999999999999998843

>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=99.82  E-value=5.7e-20  Score=118.15  Aligned_cols=60  Identities=28%  Similarity=0.347  Sum_probs=56.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHh---hhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301           7 AGKMRTNGIQSQVFELERKF---QHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ   66 (157)
Q Consensus         7 ~rr~Rt~~t~~q~~~Le~~F---~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~   66 (157)
                      .||.|+.|+..|+.+|+.+|   ..++||+..+++.||..+||++.+|++||+|||+|+|+..
T Consensus         1 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~   63 (73)
T 1puf_B            1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccccc
Confidence            36789999999999999999   9999999999999999999999999999999999999843

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

Probab=99.81  E-value=4.2e-20  Score=122.97  Aligned_cols=54  Identities=17%  Similarity=0.310  Sum_probs=52.2

Q ss_pred             CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301          13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ   66 (157)
Q Consensus        13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~   66 (157)
                      .||..|+.+||..|..++||+..+|++||..+||++.+|+|||||||+|||+.+
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~   70 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE   70 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCC
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHH
Confidence            899999999999999999999999999999999999999999999999999844

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

Probab=99.81  E-value=3.4e-20  Score=125.29  Aligned_cols=61  Identities=26%  Similarity=0.378  Sum_probs=55.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      ...+|.|+.|+..|+.+||..|..++||+..++++||..+||++.+|++||||||+|+|+.
T Consensus        23 ~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~   83 (96)
T 3nar_A           23 SGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNG   83 (96)
T ss_dssp             ----CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhh
Confidence            4567889999999999999999999999999999999999999999999999999999984

>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=99.81  E-value=1e-19  Score=123.47  Aligned_cols=66  Identities=26%  Similarity=0.279  Sum_probs=61.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHh---------------------CCChhHHHHHHHHHHHHH
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEI---------------------NLSPTQVKIWFQNRRYKQ   62 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l---------------------~l~~~~VqvWFqNrR~k~   62 (157)
                      .++.||.|+.|++.|+.+||..|..++||+..+|++||..+                     +|++.+|++||||||+++
T Consensus         3 ~~~~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k~   82 (102)
T 2da6_A            3 SGSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEE   82 (102)
T ss_dssp             TCCSCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHHH
Confidence            45678999999999999999999999999999999999999                     799999999999999999


Q ss_pred             HHHHhhh
Q psy8301          63 KRLQAMN   69 (157)
Q Consensus        63 rr~~~~~   69 (157)
                      ++.....
T Consensus        83 kr~~~~~   89 (102)
T 2da6_A           83 AFRQKLA   89 (102)
T ss_dssp             HHHHHHH
T ss_pred             HHhhHhh
Confidence            9876543

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

Probab=99.81  E-value=1.7e-20  Score=117.65  Aligned_cols=59  Identities=24%  Similarity=0.299  Sum_probs=56.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHh---hhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           6 RAGKMRTNGIQSQVFELERKF---QHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         6 ~~rr~Rt~~t~~q~~~Le~~F---~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      ..++.|+.|+..|+.+|+.+|   ..++||+..++++||..+||++.+|++||+|+|+|+|+
T Consensus         2 ~~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A            2 SGHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             CCCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            467889999999999999999   99999999999999999999999999999999999875

>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=99.81  E-value=8.9e-20  Score=112.94  Aligned_cols=55  Identities=35%  Similarity=0.362  Sum_probs=53.1

Q ss_pred             CCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301          10 MRTNGIQSQVFELERKFQH---IRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus        10 ~Rt~~t~~q~~~Le~~F~~---~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      +|+.|+..|+.+|+.+|..   ++||+..++++||..+||++.+|++||+|||+|+|+
T Consensus         1 rr~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk   58 (60)
T 1k61_A            1 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             CCCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CcCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHccccc
Confidence            3689999999999999999   999999999999999999999999999999999986

>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=99.80  E-value=8.1e-20  Score=121.28  Aligned_cols=59  Identities=32%  Similarity=0.313  Sum_probs=55.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHH
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQH---IRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK   63 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~---~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~r   63 (157)
                      .++++.|+.|+..|+.+|+.+|..   ++||+..++++||..+||++.+|++||+|||+|+|
T Consensus        25 ~~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k   86 (87)
T 1mnm_C           25 STKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK   86 (87)
T ss_dssp             ESSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcc
Confidence            456677999999999999999999   99999999999999999999999999999999987

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

Probab=99.80  E-value=1.3e-19  Score=120.16  Aligned_cols=60  Identities=27%  Similarity=0.337  Sum_probs=56.3

Q ss_pred             CCCCCCCCHHHHHHHHHHh---hhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301           8 GKMRTNGIQSQVFELERKF---QHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus         8 rr~Rt~~t~~q~~~Le~~F---~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      ||.|+.|+..|+.+|+.+|   ..++||+..++++||..+||++.+|++||+|||+|+|+...
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~   64 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG   64 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGG
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhccc
Confidence            6789999999999999999   89999999999999999999999999999999999998543

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

Probab=99.80  E-value=3.3e-20  Score=119.08  Aligned_cols=59  Identities=22%  Similarity=0.316  Sum_probs=55.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHh-hhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           6 RAGKMRTNGIQSQVFELERKF-QHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         6 ~~rr~Rt~~t~~q~~~Le~~F-~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      ...+.|++++..|+..||..| ..++||+..++++||..+||++.+|+|||||||+|+|+
T Consensus         7 ~g~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~   66 (72)
T 2cqx_A            7 GGIKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKP   66 (72)
T ss_dssp             CCCCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCC
Confidence            455677889999999999999 99999999999999999999999999999999999986

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

Probab=99.80  E-value=3.7e-19  Score=117.17  Aligned_cols=63  Identities=27%  Similarity=0.250  Sum_probs=58.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQH---IRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~---~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      .++++.|+.|+..|+.+|+.+|..   ++||+..++++||..+||++.+|++||+|+|+|+++...
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            456788999999999999999987   599999999999999999999999999999999988554

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

Probab=99.79  E-value=2.6e-19  Score=112.06  Aligned_cols=53  Identities=23%  Similarity=0.394  Sum_probs=50.4

Q ss_pred             CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301          14 GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ   66 (157)
Q Consensus        14 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~   66 (157)
                      -+.+|+..||..|..++||+..++++||..+||++.+|++||||||+|||+..
T Consensus        11 ~~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg~   63 (66)
T 3nau_A           11 KTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGI   63 (66)
T ss_dssp             CCHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhccC
Confidence            37899999999999999999999999999999999999999999999999853

>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=99.79  E-value=1.1e-19  Score=131.41  Aligned_cols=61  Identities=34%  Similarity=0.446  Sum_probs=55.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      .+++||.||.|+..|+..||..|..++||+..++++||..+||++.+|+|||||||+|+|+
T Consensus        84 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr  144 (146)
T 1au7_A           84 NERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR  144 (146)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhc
Confidence            3567888999999999999999999999999999999999999999999999999999987

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

Probab=99.79  E-value=1.2e-19  Score=133.70  Aligned_cols=63  Identities=32%  Similarity=0.364  Sum_probs=51.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ   66 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~   66 (157)
                      .+++||.||.|+..|+..||..|..++||+..+|++||..+||++.+|+|||||||+|+|+..
T Consensus        96 ~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~  158 (164)
T 2xsd_C           96 QGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMT  158 (164)
T ss_dssp             ----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSC
T ss_pred             cccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhcc
Confidence            356788999999999999999999999999999999999999999999999999999999843

>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=99.79  E-value=2.2e-19  Score=130.52  Aligned_cols=61  Identities=26%  Similarity=0.371  Sum_probs=58.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      +.++||.|+.|+..|+..||..|..++||+..++++||..+||++.+|+|||||||+|+||
T Consensus        90 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           90 PSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            3567889999999999999999999999999999999999999999999999999999986

>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=99.78  E-value=1.7e-19  Score=132.41  Aligned_cols=60  Identities=27%  Similarity=0.483  Sum_probs=54.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      .++||.||.|+..|+.+||..|..++||+..++++||..+||++.+|+|||||||+|+||
T Consensus        99 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr  158 (160)
T 1e3o_C           99 SRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR  158 (160)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTS
T ss_pred             CCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhc
Confidence            467889999999999999999999999999999999999999999999999999999987

>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=99.78  E-value=2.7e-19  Score=117.78  Aligned_cols=58  Identities=31%  Similarity=0.310  Sum_probs=53.5

Q ss_pred             CCCCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301           8 GKMRTNGIQSQVFELERKFQH---IRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus         8 rr~Rt~~t~~q~~~Le~~F~~---~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      ++.|++|+..|+.+|+.+|..   ++||+..++++||..+||++.+|++||||||+|+|+.
T Consensus         3 ~krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~   63 (83)
T 1le8_B            3 PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTI   63 (83)
T ss_dssp             --CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHcccccc
Confidence            355677999999999999999   9999999999999999999999999999999999884

>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=99.78  E-value=3.2e-19  Score=118.91  Aligned_cols=57  Identities=26%  Similarity=0.382  Sum_probs=53.0

Q ss_pred             CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301          11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus        11 Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      +..||..|+.+||..|..++||+..++++||..+||++.+|+|||||||+|+|+.+.
T Consensus        17 ~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~   73 (89)
T 2dmp_A           17 FKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQ   73 (89)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCS
T ss_pred             cccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhH
Confidence            344999999999999999999999999999999999999999999999999988443

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

Probab=99.78  E-value=1.2e-19  Score=115.35  Aligned_cols=55  Identities=60%  Similarity=0.916  Sum_probs=52.1

Q ss_pred             CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301          12 TNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ   66 (157)
Q Consensus        12 t~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~   66 (157)
                      ...+..|+..||..|..++||+..+|.+||..+||++++|+|||||||+|+|+..
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~   63 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ   63 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSS
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhh
Confidence            4689999999999999999999999999999999999999999999999998843

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

Probab=99.78  E-value=1.7e-19  Score=122.33  Aligned_cols=61  Identities=23%  Similarity=0.304  Sum_probs=52.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHH------------------hC---CChhHHHHHHHHHHHHH
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKE------------------IN---LSPTQVKIWFQNRRYKQ   62 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~------------------l~---l~~~~VqvWFqNrR~k~   62 (157)
                      +++.||.|+.|+..|+.+||..|..++||+..+|++||..                  +|   |++.+|++||||||+++
T Consensus         6 ~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k~   85 (99)
T 1lfb_A            6 TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEE   85 (99)
T ss_dssp             -------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHHH
Confidence            4677889999999999999999999999999999999999                  88   99999999999999987


Q ss_pred             HH
Q psy8301          63 KR   64 (157)
Q Consensus        63 rr   64 (157)
                      ++
T Consensus        86 k~   87 (99)
T 1lfb_A           86 AF   87 (99)
T ss_dssp             SC
T ss_pred             HH
Confidence            65

>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=99.76  E-value=5.9e-19  Score=128.85  Aligned_cols=61  Identities=26%  Similarity=0.361  Sum_probs=57.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      .++||.||.|+..|+..||..|..++||+..++++||..+||++.+|+|||||||+|+||.
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             cCCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            3567889999999999999999999999999999999999999999999999999999973

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

Probab=99.75  E-value=8.1e-19  Score=110.10  Aligned_cols=55  Identities=18%  Similarity=0.197  Sum_probs=50.7

Q ss_pred             CCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301          10 MRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus        10 ~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      .+...+..|+..||..|..++||+..++++||..+||++++|+|||||||+|.++
T Consensus         6 ~~~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~   60 (64)
T 2e19_A            6 SGQPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS   60 (64)
T ss_dssp             SCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSC
T ss_pred             CCCCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCC
Confidence            3456789999999999999999999999999999999999999999999998554

>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=99.75  E-value=8e-19  Score=109.74  Aligned_cols=50  Identities=22%  Similarity=0.352  Sum_probs=46.5

Q ss_pred             CHHHHHHHHHHh-hhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301          15 IQSQVFELERKF-QHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus        15 t~~q~~~Le~~F-~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      ...|+..||+.| ..++||+..+|.+||..+||++++|+|||||||+|+|+
T Consensus         8 ~~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~   58 (64)
T 1x2m_A            8 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   58 (64)
T ss_dssp             SSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             CchHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCC
Confidence            356899999999 67999999999999999999999999999999999876

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

Probab=99.73  E-value=2e-18  Score=127.02  Aligned_cols=61  Identities=18%  Similarity=0.138  Sum_probs=54.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      .+.||.||.|+..|+..|+..|..++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus        95 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~  155 (164)
T 2d5v_A           95 NTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDK  155 (164)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhcccccc
Confidence            3568899999999999999999999999999999999999999999999999999998873

>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=99.69  E-value=4.6e-17  Score=102.91  Aligned_cols=54  Identities=19%  Similarity=0.172  Sum_probs=49.6

Q ss_pred             CCCCHHHHHHHHHHhh---hcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301          12 TNGIQSQVFELERKFQ---HIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus        12 t~~t~~q~~~Le~~F~---~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      ..|+.+|+.+|+.+|.   .++||+..++++||..+||++.+|++||+|+|+|+++.
T Consensus         3 g~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~   59 (67)
T 3k2a_A            3 GIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQP   59 (67)
T ss_dssp             ---CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSC
T ss_pred             CcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHH
Confidence            3699999999999999   99999999999999999999999999999999999873

>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=99.64  E-value=6.1e-17  Score=121.91  Aligned_cols=60  Identities=25%  Similarity=0.298  Sum_probs=53.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhC---------------------CChhHHHHHHHHHHHHHH
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEIN---------------------LSPTQVKIWFQNRRYKQK   63 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~---------------------l~~~~VqvWFqNrR~k~r   63 (157)
                      ++.||.|+.|+..|+.+|+..|..++||+..+|++||..++                     |++.+|++||||||++++
T Consensus       113 ~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~~k  192 (194)
T 1ic8_A          113 KKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEA  192 (194)
T ss_dssp             ----CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHHCC
T ss_pred             ccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhhhh
Confidence            56789999999999999999999999999999999999999                     999999999999999865


Q ss_pred             H
Q psy8301          64 R   64 (157)
Q Consensus        64 r   64 (157)
                      .
T Consensus       193 ~  193 (194)
T 1ic8_A          193 F  193 (194)
T ss_dssp             -
T ss_pred             c
Confidence            3

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

Probab=99.60  E-value=9.5e-16  Score=116.85  Aligned_cols=58  Identities=26%  Similarity=0.319  Sum_probs=53.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhC---------------------CChhHHHHHHHHHHHH
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEIN---------------------LSPTQVKIWFQNRRYK   61 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~---------------------l~~~~VqvWFqNrR~k   61 (157)
                      +++.||.|+.|++.|+.+|+.+|..++||+..+|++||..+|                     |++.+|++||+|||++
T Consensus       139 ~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~~  217 (221)
T 2h8r_A          139 NKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKE  217 (221)
T ss_dssp             ---CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHTT
T ss_pred             cCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhhh
Confidence            467889999999999999999999999999999999999988                     8999999999999975

>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=99.59  E-value=2.6e-15  Score=94.44  Aligned_cols=46  Identities=17%  Similarity=0.241  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301          16 QSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYK   61 (157)
Q Consensus        16 ~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k   61 (157)
                      .+|+..|+.+|..+++|+..++..||..+||+.++|+|||+|||+.
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~   59 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVY   59 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhcccc
Confidence            5789999999999999999999999999999999999999999974

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

Probab=99.57  E-value=1.1e-14  Score=96.31  Aligned_cols=58  Identities=24%  Similarity=0.202  Sum_probs=53.3

Q ss_pred             CCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhh
Q psy8301          12 TNGIQSQVFELERKFQH---IRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN   69 (157)
Q Consensus        12 t~~t~~q~~~Le~~F~~---~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~   69 (157)
                      ..|+.++..+|+.+|..   ++||+..++++||..+||++.||++||+|+|.|+++.....
T Consensus        10 ~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~~~   70 (89)
T 2lk2_A           10 HMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRK   70 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHHHh
Confidence            46899999999999987   99999999999999999999999999999999998866544

>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=99.43  E-value=4.6e-14  Score=115.54  Aligned_cols=55  Identities=27%  Similarity=0.462  Sum_probs=51.9

Q ss_pred             CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHH
Q psy8301           9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK   63 (157)
Q Consensus         9 r~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~r   63 (157)
                      +.|+.++..|+..|++.|..++||+..+|++||..+||+++||++||||||+|+|
T Consensus       367 ~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          367 AAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            4467899999999999999999999999999999999999999999999999864

>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=98.68  E-value=3.8e-10  Score=62.45  Aligned_cols=21  Identities=52%  Similarity=0.795  Sum_probs=18.1

Q ss_pred             hHHHHHHHHHHHHHHHHHhhh
Q psy8301          49 TQVKIWFQNRRYKQKRLQAMN   69 (157)
Q Consensus        49 ~~VqvWFqNrR~k~rr~~~~~   69 (157)
                      +||+|||||||+|||+.....
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~   21 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFND   21 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHH
T ss_pred             CCceeccHHHHHHHHHHhHHH
Confidence            479999999999999977653

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

Probab=95.72  E-value=0.018  Score=35.73  Aligned_cols=42  Identities=29%  Similarity=0.370  Sum_probs=37.9

Q ss_pred             CHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHH
Q psy8301          15 IQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQ   56 (157)
Q Consensus        15 t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFq   56 (157)
                      ++.-.+.|+.+|...+.........|..+.+|+..+|+.||-
T Consensus        14 ~p~~~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa   55 (70)
T 2ys9_A           14 PPPDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFD   55 (70)
T ss_dssp             CCCCCHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHH
T ss_pred             CCCcchHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHH
Confidence            334467899999999999999999999999999999999995

>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=93.20  E-value=0.0015  Score=43.16  Aligned_cols=70  Identities=14%  Similarity=0.160  Sum_probs=40.5

Q ss_pred             HhCCChhHHHHHHHHHHHHHHHHHhhhcCCCCCCcccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCccccCC
Q psy8301          43 EINLSPTQVKIWFQNRRYKQKRLQAMNQNSNGKNVFKIKHIFTRKTKPTSAQATIGCPEAKKIGRKPETDFPAEEHNIFV  122 (157)
Q Consensus        43 ~l~l~~~~VqvWFqNrR~k~rr~~~~~~~~~~~~~~~~~~~~~~~~~p~s~~~~~~~p~~~~~~~~~~~~~~~~q~~~~~  122 (157)
                      .++.+..+|..||++.|..-+...                        .      ..+ .........+.|+..|...|.
T Consensus         2 ~~~~~~~~~~~W~~~~r~~~~~~~------------------------~------~~~-~~~~~rr~Rt~ft~~Ql~~Le   50 (97)
T 1b72_A            2 EPNTPTARTFDWMKVKRNPPKTAK------------------------V------SEP-GLGSPSGLRTNFTTRQLTELE   50 (97)
T ss_dssp             ------CCCCGGGGC---------------------------------------------------CCCCCCHHHHHHHH
T ss_pred             CCCCCCcccccccccccCCCCCCC------------------------C------CCC-CCCCCCCCCcCcCHHHHHHHH
Confidence            356777888899999887633210                        0      000 112344556889999999999


Q ss_pred             CCCCCCcCCCCCCCCchhHHHhhhcc
Q psy8301         123 PNFDQSDFLDNKWEDIDILDELHDQY  148 (157)
Q Consensus       123 ~~f~~~~~s~s~~p~~~~~~~l~~~~  148 (157)
                      ..|..+.|     |+...+++|+..+
T Consensus        51 ~~F~~~~y-----p~~~~r~~LA~~l   71 (97)
T 1b72_A           51 KEFHFNKY-----LSRARRVEIAATL   71 (97)
T ss_dssp             HHHTTCSS-----CCHHHHHHHHHHH
T ss_pred             HHHhccCC-----CCHHHHHHHHHHh
Confidence            99999999     9999999999875

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

Probab=90.14  E-value=1.3  Score=27.79  Aligned_cols=46  Identities=7%  Similarity=0.206  Sum_probs=33.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHH
Q psy8301           7 AGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQN   57 (157)
Q Consensus         7 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqN   57 (157)
                      +++.+..|+.++.......+.. ..    ...++|..+|++...|..|...
T Consensus        16 ~~~~~~~ys~e~k~~~v~~~~~-g~----s~~~iA~~~gIs~sTl~rW~k~   61 (87)
T 2elh_A           16 GKRPLRSLTPRDKIHAIQRIHD-GE----SKASVARDIGVPESTLRGWCKN   61 (87)
T ss_dssp             CSSCCSSCCHHHHHHHHHHHHH-TC----CHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHC-CC----CHHHHHHHHCcCHHHHHHHHHH
Confidence            4456778999886554455543 22    3568899999999999999853

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

Probab=86.86  E-value=2.4  Score=28.24  Aligned_cols=49  Identities=12%  Similarity=0.201  Sum_probs=37.3

Q ss_pred             CCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301          10 MRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYK   61 (157)
Q Consensus        10 ~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k   61 (157)
                      .|..+|.++...+-..+..+....   ..++|..+|++...|..|..++...
T Consensus         4 ~r~~~t~e~K~~iv~~~~~~g~~~---~~~~A~~~gvs~stl~~~~~~~~~~   52 (131)
T 1hlv_A            4 KRRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNKRAI   52 (131)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTHHHH
T ss_pred             cceeCCHHHHHHHHHHHHHCCCCc---HHHHHHHhCCCHHHHHHHHhchhhh
Confidence            567899999877766665554443   3468999999999999999876654

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

Probab=86.57  E-value=1.1  Score=26.00  Aligned_cols=46  Identities=11%  Similarity=0.198  Sum_probs=31.6

Q ss_pred             CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHH
Q psy8301          11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQN   57 (157)
Q Consensus        11 Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqN   57 (157)
                      |..|+.+........+.. .........++|..+|++...|..|.+.
T Consensus         3 r~~ys~efK~~~~~~~~~-g~s~~~~~~~vA~~~gIs~~tl~~W~~~   48 (59)
T 2glo_A            3 RRIFTPHFKLQVLESYRN-DNDCKGNQRATARKYNIHRRQIQKWLQC   48 (59)
T ss_dssp             CCCCCHHHHHHHHHHHHH-CTTTTTCHHHHHHHTTSCHHHHHHHHTT
T ss_pred             CCcCCHHHHHHHHHHHHc-CCCcchHHHHHHHHHCcCHHHHHHHHHH
Confidence            457888887666544443 3321112668999999999999999753

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

Probab=86.16  E-value=3.8  Score=25.69  Aligned_cols=48  Identities=6%  Similarity=0.009  Sum_probs=36.1

Q ss_pred             CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301          14 GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ   66 (157)
Q Consensus        14 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~   66 (157)
                      ++..+..+|.-.|-..     ..-.++|..+|++...|+.+...-|.+.|+.-
T Consensus        38 L~~~~r~vl~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l   85 (92)
T 3hug_A           38 LSAEHRAVIQRSYYRG-----WSTAQIATDLGIAEGTVKSRLHYAVRALRLTL   85 (92)
T ss_dssp             SCHHHHHHHHHHHTSC-----CCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            5677777777654332     25778999999999999999987777766644

>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=85.40  E-value=0.15  Score=31.83  Aligned_cols=41  Identities=12%  Similarity=0.208  Sum_probs=35.4

Q ss_pred             CCCCCCCCCCCCcCccccCCCCCCCCcCCCCCCCCchhHHHhhhcc
Q psy8301         103 KKIGRKPETDFPAEEHNIFVPNFDQSDFLDNKWEDIDILDELHDQY  148 (157)
Q Consensus       103 ~~~~~~~~~~~~~~q~~~~~~~f~~~~~s~s~~p~~~~~~~l~~~~  148 (157)
                      ........+.|+..|..+|...|..++|     |+...+++|+.++
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~f~~~~y-----p~~~~r~~La~~l   54 (80)
T 2da3_A           14 PQRDKRLRTTITPEQLEILYQKYLLDSN-----PTRKMLDHIAHEV   54 (80)
T ss_dssp             CCCCTTCCSSCCTTTHHHHHHHHHHCSS-----CCHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCC-----CCHHHHHHHHHHH
Confidence            3445667788999999999999999999     9999999999875

>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=84.96  E-value=0.16  Score=32.14  Aligned_cols=39  Identities=15%  Similarity=0.239  Sum_probs=33.9

Q ss_pred             CCCCCCCCCCCcCccccCCCCCCC-----CcCCCCCCCCchhHHHhhhcc
Q psy8301         104 KIGRKPETDFPAEEHNIFVPNFDQ-----SDFLDNKWEDIDILDELHDQY  148 (157)
Q Consensus       104 ~~~~~~~~~~~~~q~~~~~~~f~~-----~~~s~s~~p~~~~~~~l~~~~  148 (157)
                      .......+.|+..|...|. .|..     ++|     |+...+++|+...
T Consensus        15 ~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~y-----p~~~~r~~La~~l   58 (80)
T 1wh7_A           15 GTTKRFRTKFTAEQKEKML-AFAERLGWRIQK-----HDDVAVEQFCAET   58 (80)
T ss_dssp             CCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCS-----STTHHHHHHHHHS
T ss_pred             CCCCCCCccCCHHHHHHHH-HHHHHcCcCCCC-----CCHHHHHHHHHHh
Confidence            3455677899999999999 8999     999     9999999999875

>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=83.00  E-value=0.13  Score=32.26  Aligned_cols=40  Identities=18%  Similarity=0.211  Sum_probs=35.2

Q ss_pred             CCCCCCCCCCCcCccccCCCCCCCCcCCCCCCCCchhHHHhhhcc
Q psy8301         104 KIGRKPETDFPAEEHNIFVPNFDQSDFLDNKWEDIDILDELHDQY  148 (157)
Q Consensus       104 ~~~~~~~~~~~~~q~~~~~~~f~~~~~s~s~~p~~~~~~~l~~~~  148 (157)
                      .......+.|+..|...|...|..++|     |+...+++|+..+
T Consensus        15 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~y-----p~~~~r~~LA~~l   54 (80)
T 2dmt_A           15 KKGRRSRTVFTELQLMGLEKRFEKQKY-----LSTPDRIDLAESL   54 (80)
T ss_dssp             CCCCCSCCCCCHHHHHHHHHHHHHCSS-----CCHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCC-----CCHHHHHHHHHHh
Confidence            445667788999999999999999999     9999999999875

>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=82.55  E-value=0.098  Score=32.42  Aligned_cols=40  Identities=18%  Similarity=0.268  Sum_probs=36.1

Q ss_pred             CCCCCCCCCCCcCccccCCCCCCC-CcCCCCCCCCchhHHHhhhcc
Q psy8301         104 KIGRKPETDFPAEEHNIFVPNFDQ-SDFLDNKWEDIDILDELHDQY  148 (157)
Q Consensus       104 ~~~~~~~~~~~~~q~~~~~~~f~~-~~~s~s~~p~~~~~~~l~~~~  148 (157)
                      +....+.+.++..|+.++..+|+. +.+     |+..++++|+.+.
T Consensus         5 ~~~kR~RT~~s~eQL~~Lqs~f~~~~~y-----Pd~~~r~~La~~t   45 (71)
T 1wi3_A            5 SSGPRSRTKISLEALGILQSFIHDVGLY-----PDQEAIHTLSAQL   45 (71)
T ss_dssp             CCCCCCCCCCCSHHHHHHHHHHHHHCSC-----CCHHHHHHHHHHS
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHhcCCC-----CCHHHHHHHHHHh
Confidence            456677899999999999999999 999     9999999999875

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

Probab=82.47  E-value=0.22  Score=31.39  Aligned_cols=42  Identities=14%  Similarity=0.256  Sum_probs=36.2

Q ss_pred             CCCCCCCCCCCCcCccccCCCCCCCCcCCCCCCCCchhHHHhhhccC
Q psy8301         103 KKIGRKPETDFPAEEHNIFVPNFDQSDFLDNKWEDIDILDELHDQYV  149 (157)
Q Consensus       103 ~~~~~~~~~~~~~~q~~~~~~~f~~~~~s~s~~p~~~~~~~l~~~~~  149 (157)
                      ........+.|+..|...|...|..+.|     |+...+++|+..+.
T Consensus        19 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~y-----p~~~~r~~La~~l~   60 (84)
T 2kt0_A           19 PVKKQKTRTVFSSTQLCVLNDRFQRQKY-----LSLQQMQELSNILN   60 (84)
T ss_dssp             CSCSCCCSSCCCHHHHHHHHHHHHHSSS-----CCHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCC-----CCHHHHHHHHHHcC
Confidence            3445667788999999999999999999     99999999998763

---

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	157
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	7e-17
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	9e-17
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	1e-16
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	2e-15
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	4e-15
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	7e-15
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	1e-14
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	1e-14
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	8e-14
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	2e-13
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	2e-13
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	3e-13
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	3e-13
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	4e-13
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	4e-13
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	1e-12
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	1e-12
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	1e-12
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	2e-12
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	2e-12
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	8e-12
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	1e-11
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	1e-11
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	3e-11
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	3e-11
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	4e-11
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	7e-11
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	1e-10
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	2e-10
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	2e-09
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	6e-09
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	6e-09

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-a9
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.7 bits (168), Expect = 7e-17
 Identities = 24/58 (41%), Positives = 34/58 (58%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
          K R    + Q  ELE++F    YL+   R  + + +NL+  QVKIWFQNRR K K++ 
Sbjct: 15 KKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKIN 72

>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 = 67.9 bits (166), Expect = 9e-17
 Identities = 22/54 (40%), Positives = 32/54 (59%)

Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
          R    + Q  ELE++F   RYL+   R  +   ++L+  Q+KIWFQNRR K K+
Sbjct: 1  RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 54

>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 = 67.9 bits (166), Expect = 1e-16
 Identities = 20/63 (31%), Positives = 35/63 (55%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68
          + RT+  Q Q+  LE++F+   Y     RE L  +I+L   ++++WF NRR K +R + +
Sbjct: 3  RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL 62

Query: 69 NQN 71
             
Sbjct: 63 RNQ 65

>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 = 64.5 bits (157), Expect = 2e-15
 Identities = 20/56 (35%), Positives = 34/56 (60%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
          K R    + Q+ ELER++   ++++  +R  +    +LS  Q+ IWFQNRR K+K+
Sbjct: 3  KKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 58

>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 = 63.4 bits (154), Expect = 4e-15
 Identities = 20/58 (34%), Positives = 30/58 (51%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
          K RT    +    LER F      S  E   + +E+NL    V++WF NRR ++KR++
Sbjct: 1  KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRVK 58

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein prh
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.9 bits (153), Expect = 7e-15
 Identities = 27/54 (50%), Positives = 34/54 (62%)

Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
          +      Q  ELE+KF+  +YLSP ER+ L K + LS  QVK WFQNRR K +R
Sbjct: 4  QVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 57

>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 = 62.2 bits (151), Expect = 1e-14
 Identities = 22/53 (41%), Positives = 31/53 (58%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYK 61
          + RT     Q+  L+R+F   RYL+   R+ L  E+ L+  Q+KIWFQN R K
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>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 = 62.6 bits (152), Expect = 1e-14
 Identities = 17/62 (27%), Positives = 30/62 (48%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68
          ++RT   + Q+  L   +          +E L +   LSP  +++WFQN+R K K+   M
Sbjct: 5  RVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSIM 64

Query: 69 NQ 70
           +
Sbjct: 65 MK 66

>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 = 60.3 bits (146), Expect = 8e-14
 Identities = 30/57 (52%), Positives = 37/57 (64%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65
          K RT    +Q+  LERKF+  +YLS  ER      ++L+ TQVKIWFQNRR K KRL
Sbjct: 2  KPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL 58

>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 = 59.5 bits (144), Expect = 2e-13
 Identities = 22/56 (39%), Positives = 33/56 (58%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
          + RT   + Q+  LE++F    Y+S   R  L  ++NL  + +K+WFQNRR K KR
Sbjct: 1  RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 56

>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 = 60.4 bits (146), Expect = 2e-13
 Identities = 27/63 (42%), Positives = 37/63 (58%)

Query: 4  SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
                +RTN    Q+ ELE++F   +YLS   R  +   + L+ TQVKIWFQNRR KQK
Sbjct: 24 LGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQK 83

Query: 64 RLQ 66
          + +
Sbjct: 84 KRE 86

>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 = 59.2 bits (143), Expect = 3e-13
 Identities = 34/58 (58%), Positives = 41/58 (70%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
          K R    Q+QV+ELER+F+  +YLS  ERE L   I+L+PTQVKIWFQN RYK KR  
Sbjct: 4  KRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61

>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 = 58.3 bits (141), Expect = 3e-13
 Identities = 10/49 (20%), Positives = 19/49 (38%)

Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRR 59
          R      Q   L   F+  +  S   +  + +++ L  + V  +F N R
Sbjct: 2  RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>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 = 58.8 bits (142), Expect = 4e-13
 Identities = 21/56 (37%), Positives = 34/56 (60%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
          + RT    SQ+ ELER F+  +Y     RE L +  NL+  ++++WFQNRR + ++
Sbjct: 4  RSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK 59

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 52

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.2 bits (141), Expect = 4e-13
 Identities = 12/48 (25%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 18 QVFELERKFQHI-RYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
              LE+ F  I ++      E L K+++     ++ WF+ RR ++K 
Sbjct: 4  PNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 51

>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 = 57.6 bits (139), Expect = 1e-12
 Identities = 23/64 (35%), Positives = 34/64 (53%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68
          + RT    SQ+ ELE+ F   RYL+      L  ++ L   QVKIWF+NRR + K     
Sbjct: 3  RTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ 62

Query: 69 NQNS 72
          +++ 
Sbjct: 63 HKDQ 66

>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 = 57.8 bits (139), Expect = 1e-12
 Identities = 34/58 (58%), Positives = 40/58 (68%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
          K R    ++Q +ELER+F+  RYLS  ERE L   I L+PTQVKIWFQN RYK KR Q
Sbjct: 11 KRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ 68

>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 = 57.1 bits (138), Expect = 1e-12
 Identities = 19/53 (35%), Positives = 24/53 (45%), Gaps = 3/53 (5%)

Query: 16 QSQVFELERKF---QHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65
          +  V  LE  F       YL     E L K  +LS  Q+K W  NRR K+K +
Sbjct: 7  KENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI 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 = 56.9 bits (137), Expect = 2e-12
 Identities = 20/58 (34%), Positives = 34/58 (58%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
          + RT+    Q+ +LE  FQ  RY   + RE +    NL+  +V++WF+NRR K ++ +
Sbjct: 3  RQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 60

>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-12
 Identities = 15/53 (28%), Positives = 31/53 (58%)

Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
          +++        LE+ F+  + L+  E+E + K+  ++P QV++WF N+R + K
Sbjct: 1  KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53

>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 = 55.4 bits (133), Expect = 8e-12
 Identities = 14/65 (21%), Positives = 27/65 (41%), Gaps = 1/65 (1%)

Query: 9  KMRTNGIQSQVFELERKFQH-IRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA 67
          +      + QV  LE  F    ++  PT   ++  E  L+  Q + WF+ R  + +R + 
Sbjct: 3  EGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG 62

Query: 68 MNQNS 72
          +    
Sbjct: 63 LPSEC 67

>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 = 55.0 bits (132), Expect = 1e-11
 Identities = 16/56 (28%), Positives = 25/56 (44%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
          + RT+      + LE  F      S  +   +  ++ L    V++WF NRR K KR
Sbjct: 10 RKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR 65

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.6 bits (131), Expect = 1e-11
 Identities = 14/55 (25%), Positives = 31/55 (56%)

Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65
          RT+   +    LE+ F   +  +  +  ++ +++N+    +++WF NRR K+KR+
Sbjct: 2  RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI 56

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-containing protein 1, HMBOX1 (Flj21616)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.3 bits (130), Expect = 3e-11
 Identities = 15/71 (21%), Positives = 25/71 (35%), Gaps = 15/71 (21%)

Query: 9  KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEIN---------------LSPTQVKI 53
            R    +  +  +E  F   +Y    +RE +    N               ++  +V  
Sbjct: 2  GSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYN 61

Query: 54 WFQNRRYKQKR 64
          WF NRR + KR
Sbjct: 62 WFANRRKEIKR 72

>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 = 53.6 bits (129), Expect = 3e-11
 Identities = 12/43 (27%), Positives = 25/43 (58%), Gaps = 1/43 (2%)

Query: 22 LERKFQHI-RYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
          LE+ F  + +Y      + L K+++ S  +++ WF++RR + K
Sbjct: 16 LEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 80

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 53.9 bits (129), Expect = 4e-11
 Identities = 10/64 (15%), Positives = 19/64 (29%), Gaps = 2/64 (3%)

Query: 3  QSHRAGKMRTNGIQSQVFE--LERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRY 60
           + +  + +    Q +      ER    I+       E    E  +    +KIW  N + 
Sbjct: 15 GTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKN 74

Query: 61 KQKR 64
              
Sbjct: 75 SGPS 78

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Length = 73

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.0 bits (127), Expect = 7e-11
 Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 3/69 (4%)

Query: 9  KMRTNGIQSQVFELERKFQHI---RYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65
          + R N  +     L   F       Y S   +E L K+  ++ +QV  WF N+R + K+ 
Sbjct: 3  RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN 62

Query: 66 QAMNQNSNG 74
              Q    
Sbjct: 63 IGKFQEEAN 71

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Length = 62

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (126), Expect = 1e-10
 Identities = 11/59 (18%), Positives = 21/59 (35%), Gaps = 3/59 (5%)

Query: 9  KMRTNGIQSQVFELERKF---QHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
            R    +     +           Y +  E++ +  + NL+  QV  WF N R +  +
Sbjct: 4  NKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQ 62

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.0 bits (124), Expect = 2e-10
 Identities = 12/57 (21%), Positives = 22/57 (38%), Gaps = 1/57 (1%)

Query: 9  KMRTNGIQSQVFELERKFQHI-RYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
          + RT      +  L+     +  Y        L  +++L    +  +FQN+RY  K 
Sbjct: 9  RSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH 65

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Length = 78

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Rat (Rattus rattus) [TaxId: 10117]

 Score = 49.4 bits (117), Expect = 2e-09
 Identities = 15/77 (19%), Positives = 26/77 (33%), Gaps = 21/77 (27%)

Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEIN---------------------LSPT 49
          R     +    L + ++  +  S  ERE L +E N                     ++  
Sbjct: 1  RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 50 QVKIWFQNRRYKQKRLQ 66
          +V  WF NRR ++    
Sbjct: 61 RVYNWFANRRKEEAFRH 77

>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 = 48.2 bits (114), Expect = 6e-09
 Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 5/73 (6%)

Query: 4  SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
          S  +GK +T   + Q+  L+  F   ++    + + L +   L   ++  WF + RY  K
Sbjct: 3  SGSSGKRKT---KEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALK 59

Query: 64 R--LQAMNQNSNG 74
             L+    N++G
Sbjct: 60 HGQLKWFRDNASG 72

>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 = 47.8 bits (113), Expect = 6e-09
 Identities = 9/51 (17%), Positives = 21/51 (41%)

Query: 16 QSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
            Q+  L+  F +   L+  E   L  +  L+  ++  WF  ++  +   +
Sbjct: 13 AEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE 63

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	157
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.9
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.9
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.9
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.89
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.89
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.89
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.89
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.89
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.88
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.88
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.88
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.88
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.88
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.87
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.86
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.86
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.85
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.85
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.85
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.84
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.83
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.82
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.8
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.78
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.78
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.77
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.77
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.74
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.73
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.73
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.7
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.69
d1hlva1	66	DNA-binding domain of centromere binding protein B	91.64
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	90.0
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	88.56
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	88.38
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	83.61
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	82.79
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	82.74
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	81.17

>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=99.90  E-value=1.2e-24  Score=132.59  Aligned_cols=58  Identities=34%  Similarity=0.587  Sum_probs=55.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           7 AGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         7 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      .||.||.||..|+.+||..|..++||+..++++||..+||++.+|+|||||||+|+||
T Consensus         1 Grr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           1 GRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            3678999999999999999999999999999999999999999999999999999874

>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=99.90  E-value=4.2e-24  Score=130.34  Aligned_cols=57  Identities=51%  Similarity=0.724  Sum_probs=55.4

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           8 GKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         8 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      ||.|+.||+.|+.+||..|+.++||+..++++||..+||++.+|++||||||+|+||
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            578999999999999999999999999999999999999999999999999999987

>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=99.90  E-value=8.8e-24  Score=132.37  Aligned_cols=61  Identities=38%  Similarity=0.548  Sum_probs=57.9

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhh
Q psy8301           8 GKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM   68 (157)
Q Consensus         8 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~   68 (157)
                      ||.||+||..|+.+||..|+.++||+..++.+||..|||++.+|+|||||||+|+|++...
T Consensus         2 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~~   62 (67)
T d1zq3p1           2 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ   62 (67)
T ss_dssp             SCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhhh
Confidence            5779999999999999999999999999999999999999999999999999999986654

>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=99.89  E-value=1.1e-23  Score=128.01  Aligned_cols=57  Identities=47%  Similarity=0.679  Sum_probs=55.1

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           8 GKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         8 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      |+.|+.||+.|+.+||..|+.++||+..++++||..+||++.+|+|||||||+++||
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k~kk   57 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR   57 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhhccC
Confidence            478999999999999999999999999999999999999999999999999999986

>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=99.89  E-value=1.1e-23  Score=127.91  Aligned_cols=56  Identities=39%  Similarity=0.640  Sum_probs=54.7

Q ss_pred             CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         9 r~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      |.||.||+.|+.+||..|..++||+..++++||..+||++.+|+|||||||+|+|+
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk   56 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR   56 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhc
Confidence            57999999999999999999999999999999999999999999999999999997

>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=99.89  E-value=1.9e-23  Score=134.09  Aligned_cols=65  Identities=37%  Similarity=0.556  Sum_probs=60.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhh
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM   68 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~   68 (157)
                      .+..||.||+|+.+|+.+||..|..++||+..++++||..+||++++|+|||||||+|+|+....
T Consensus        10 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~   74 (77)
T d1pufa_          10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHH
Confidence            44567889999999999999999999999999999999999999999999999999999986654

>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=99.89  E-value=1.7e-23  Score=130.33  Aligned_cols=62  Identities=34%  Similarity=0.565  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301           6 RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus         6 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      |+||.||.|+.+|+.+||..|..++||+..++++||..+||++.+|++||||+|+|+|+...
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~   62 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   62 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhccc
Confidence            46788999999999999999999999999999999999999999999999999999998654

>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=99.89  E-value=1.5e-23  Score=126.51  Aligned_cols=55  Identities=40%  Similarity=0.658  Sum_probs=53.6

Q ss_pred             CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301          11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus        11 Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      ||.||..|+..||..|..++||+..++++||..+||++++|+|||||||+|+|++
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk~   55 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   55 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhhc
Confidence            7999999999999999999999999999999999999999999999999999983

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.88  E-value=1.9e-23  Score=125.14  Aligned_cols=53  Identities=42%  Similarity=0.659  Sum_probs=51.6

Q ss_pred             CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301           9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYK   61 (157)
Q Consensus         9 r~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k   61 (157)
                      |.||.||..|+..||..|+.++||+..++++||..+||++.+|+|||||||+|
T Consensus         1 R~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~lgL~~~qV~vWFqNrRaK   53 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK   53 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             CCCccCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChHHhhhcccccCCC
Confidence            57999999999999999999999999999999999999999999999999986

>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=99.88  E-value=4.7e-23  Score=129.36  Aligned_cols=61  Identities=33%  Similarity=0.562  Sum_probs=57.9

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhh
Q psy8301           8 GKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM   68 (157)
Q Consensus         8 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~   68 (157)
                      ||.||+||..|+.+|+..|..++||+..++++||..+||++.+|++||||+|+|+|+....
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~   62 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL   62 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhhh
Confidence            6789999999999999999999999999999999999999999999999999999986543

>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=99.88  E-value=3.6e-23  Score=129.86  Aligned_cols=60  Identities=57%  Similarity=0.830  Sum_probs=57.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301           7 AGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ   66 (157)
Q Consensus         7 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~   66 (157)
                      +||.||.||+.|+.+|+..|..++||+..++++||..+||++.+|++||||+|+|+|+..
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~   61 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA   61 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhcc
Confidence            467899999999999999999999999999999999999999999999999999999843

>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=99.88  E-value=8e-23  Score=129.42  Aligned_cols=60  Identities=23%  Similarity=0.320  Sum_probs=56.5

Q ss_pred             CCCCCCCCHHHHHHHHHHhhh-cCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301           8 GKMRTNGIQSQVFELERKFQH-IRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus         8 rr~Rt~~t~~q~~~Le~~F~~-~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      ++.|++||.+|+.+||..|.. ++||+...+++||..+||++++|+|||||||+|+|+...
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~~   62 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   62 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhccC
Confidence            578999999999999999986 789999999999999999999999999999999999653

>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=99.88  E-value=2.3e-23  Score=127.80  Aligned_cols=58  Identities=34%  Similarity=0.530  Sum_probs=56.2

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301           8 GKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus         8 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      ||.||+||.+|+.+|+..|..++||+..+++.||..+||++.+|++||+|+|+|+|+.
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            6789999999999999999999999999999999999999999999999999999985

>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=99.87  E-value=1.3e-22  Score=133.31  Aligned_cols=62  Identities=44%  Similarity=0.655  Sum_probs=56.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301           6 RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA   67 (157)
Q Consensus         6 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~   67 (157)
                      +.+|.|+.||..|+.+||..|..++||+..++++||..+||++.+|+|||||||+|+|+...
T Consensus        26 ~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~~   87 (88)
T d1b72a_          26 SPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   87 (88)
T ss_dssp             ----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhcc
Confidence            45788999999999999999999999999999999999999999999999999999998653

>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=99.86  E-value=2.9e-23  Score=133.35  Aligned_cols=61  Identities=54%  Similarity=0.840  Sum_probs=58.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      +.+++|.||+||.+|+.+|+..|..++||+..++++||..+||++.+|+|||||||+|+|+
T Consensus         6 p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   66 (77)
T d1vnda_           6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR   66 (77)
T ss_dssp             SSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHH
Confidence            4567889999999999999999999999999999999999999999999999999999876

>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=99.86  E-value=2.5e-22  Score=125.27  Aligned_cols=59  Identities=27%  Similarity=0.432  Sum_probs=56.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           6 RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         6 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      +.+|.||.|+.+|+.+|+..|..++||+..++++||..+||++.+|++||+|+|++.|+
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk   60 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKK   60 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSS
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHH
Confidence            46789999999999999999999999999999999999999999999999999999776

>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=99.85  E-value=2.3e-22  Score=125.72  Aligned_cols=59  Identities=27%  Similarity=0.367  Sum_probs=56.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           6 RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         6 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      .+||.||.|+..|+.+|+..|..++||+..++++||..+||++.+|++||||+|+++|+
T Consensus         7 ~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk   65 (67)
T d1ocpa_           7 ARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR   65 (67)
T ss_dssp             CSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSS
T ss_pred             ccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhc
Confidence            34678999999999999999999999999999999999999999999999999999876

>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=99.85  E-value=1.3e-21  Score=127.01  Aligned_cols=61  Identities=25%  Similarity=0.345  Sum_probs=57.2

Q ss_pred             CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhC---------------CChhHHHHHHHHHHHHHHHHHhh
Q psy8301           8 GKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEIN---------------LSPTQVKIWFQNRRYKQKRLQAM   68 (157)
Q Consensus         8 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~---------------l~~~~VqvWFqNrR~k~rr~~~~   68 (157)
                      ||.|+.|+++|+.+||.+|..++||+..+|++||..+|               |++.+|++||||||+|+|+....
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~~   76 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANI   76 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhhH
Confidence            57899999999999999999999999999999999875               99999999999999999996654

>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=99.85  E-value=8.8e-22  Score=119.82  Aligned_cols=56  Identities=36%  Similarity=0.458  Sum_probs=54.2

Q ss_pred             CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         9 r~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      |.||.|+.+|+.+|+..|..++||+..++.+||..+||++.+|++||||+|+++|+
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr   56 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR   56 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHh
Confidence            56899999999999999999999999999999999999999999999999999876

>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=99.84  E-value=1.2e-21  Score=117.21  Aligned_cols=53  Identities=28%  Similarity=0.520  Sum_probs=51.3

Q ss_pred             CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHH
Q psy8301          11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK   63 (157)
Q Consensus        11 Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~r   63 (157)
                      ||.||++|+.+|+..|..++||+..++++||..+||++.+|++||||||+|.|
T Consensus         1 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~K   53 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   53 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTTC
T ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhccC
Confidence            79999999999999999999999999999999999999999999999999854

>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=99.83  E-value=5.2e-21  Score=115.94  Aligned_cols=55  Identities=25%  Similarity=0.490  Sum_probs=53.5

Q ss_pred             CCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301          10 MRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus        10 ~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      .||.|+.+|+.+||..|..++||+..++++||..+||++.+|++||||+|+++|+
T Consensus         1 kRT~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk   55 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR   55 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTS
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHc
Confidence            4899999999999999999999999999999999999999999999999999986

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=7.7e-21  Score=120.18  Aligned_cols=60  Identities=20%  Similarity=0.222  Sum_probs=55.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhh-hcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQ-HIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~-~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      ...+|.|+.|+.+|+.+|+.+|. .++||+..++++||..+||++.+|++||||+|++.|+
T Consensus         5 ~~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk   65 (71)
T d1wi3a_           5 SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             CCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhcc
Confidence            34678899999999999999997 5899999999999999999999999999999999775

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=1.4e-20  Score=111.19  Aligned_cols=50  Identities=20%  Similarity=0.167  Sum_probs=48.9

Q ss_pred             CCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHH
Q psy8301          10 MRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRR   59 (157)
Q Consensus        10 ~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR   59 (157)
                      +||.||..|+.+||+.|..++||+..++++||..+||++++|++||||||
T Consensus         1 PRt~ft~~Q~~~Le~~F~~n~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1           1 PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             CCSCCCHHHHHHHHHHTTSSCSSTHHHHHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhhcCCcCc
Confidence            58999999999999999999999999999999999999999999999987

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=3.3e-19  Score=113.15  Aligned_cols=57  Identities=28%  Similarity=0.380  Sum_probs=54.1

Q ss_pred             CCCCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301           8 GKMRTNGIQSQVFELERKFQH---IRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus         8 rr~Rt~~t~~q~~~Le~~F~~---~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      ||.|+.|+.+|+.+|+.+|..   ++||+..++++||..+||++.+|++||+|+|+|.++
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~   61 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   61 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcc
Confidence            577899999999999999974   889999999999999999999999999999999887

>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=99.78  E-value=1.6e-19  Score=115.40  Aligned_cols=52  Identities=17%  Similarity=0.325  Sum_probs=49.5

Q ss_pred             CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301          13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus        13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      .+|.+|+.+|+..|..++||+..++++||..+||++.+|++||||||++.++
T Consensus        10 ~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~   61 (76)
T d2ecba1          10 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKAL   61 (76)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHS
T ss_pred             CCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHH
Confidence            3589999999999999999999999999999999999999999999998766

>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=99.77  E-value=4.5e-20  Score=119.10  Aligned_cols=59  Identities=17%  Similarity=0.187  Sum_probs=54.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhhh----cCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHH
Q psy8301           5 HRAGKMRTNGIQSQVFELERKFQH----IRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK   63 (157)
Q Consensus         5 ~~~rr~Rt~~t~~q~~~Le~~F~~----~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~r   63 (157)
                      .++||.||.||.+|+..|+.+|+.    ++||+..++++||..+||++.+|+|||||+|++++
T Consensus        15 ~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k   77 (80)
T d1wh7a_          15 GTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGP   77 (80)
T ss_dssp             CCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSC
T ss_pred             cCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCC
Confidence            456789999999999999999986    78999999999999999999999999999997644

>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=99.77  E-value=6.8e-19  Score=112.49  Aligned_cols=57  Identities=18%  Similarity=0.279  Sum_probs=53.5

Q ss_pred             CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301           9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL   65 (157)
Q Consensus         9 r~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~   65 (157)
                      ..++.+|.+|+.+|+..|..++||+..++++||..+||++.+|++||+|+|+++|+.
T Consensus         5 s~~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~   61 (76)
T d2ecca1           5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhc
Confidence            345678999999999999999999999999999999999999999999999999983

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=3.9e-19  Score=105.51  Aligned_cols=50  Identities=22%  Similarity=0.363  Sum_probs=46.3

Q ss_pred             CHHHHHHHHHHhhh-cCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301          15 IQSQVFELERKFQH-IRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus        15 t~~q~~~Le~~F~~-~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      |.+|..+||..|.. ++||+..++++||..+||++++|++||||||+++|+
T Consensus         1 T~~q~~iLE~~F~~~~~~P~~~~~~~LA~~~~ls~~qV~~WFqNrR~k~k~   51 (52)
T d1x2ma1           1 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   51 (52)
T ss_dssp             SSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             ChhHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccCc
Confidence            46789999999987 689999999999999999999999999999999764

>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=99.73  E-value=9.3e-19  Score=112.09  Aligned_cols=54  Identities=28%  Similarity=0.310  Sum_probs=51.4

Q ss_pred             CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhC---------------------CChhHHHHHHHHHHHHHHH
Q psy8301          11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEIN---------------------LSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus        11 Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~---------------------l~~~~VqvWFqNrR~k~rr   64 (157)
                      |++|++.|+.+|+..|+.++||+..+|+.||..++                     |++.+|++||+|||++.|+
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr   75 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAF   75 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSC
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHH
Confidence            78999999999999999999999999999999994                     8999999999999999776

>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=99.73  E-value=1.4e-18  Score=105.68  Aligned_cols=55  Identities=24%  Similarity=0.375  Sum_probs=51.0

Q ss_pred             CCCCCCCHHHHHHHHHHhhh-cCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHH
Q psy8301           9 KMRTNGIQSQVFELERKFQH-IRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK   63 (157)
Q Consensus         9 r~Rt~~t~~q~~~Le~~F~~-~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~r   63 (157)
                      +.+++++.++..+||.+|.. ++||+..++++||..+||++++|++||+|||+++|
T Consensus         3 k~~~~~k~~~~~iLE~~F~~~~~yPs~~~~~~LA~~lgls~~qV~~WFqNrR~k~r   58 (59)
T d2cqxa1           3 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK   58 (59)
T ss_dssp             CCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCccccHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccC
Confidence            56788899999999999986 68999999999999999999999999999999975

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.70  E-value=3.5e-17  Score=99.81  Aligned_cols=52  Identities=37%  Similarity=0.402  Sum_probs=48.4

Q ss_pred             CCCHHHHHHHHHHhhhc---CCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301          13 NGIQSQVFELERKFQHI---RYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus        13 ~~t~~q~~~Le~~F~~~---~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      +|+.+|+.+|+.+|..+   +||+..++++||..+||++.+|++||+|+|+|.|.
T Consensus         4 Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           4 RFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             SCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            49999999999999764   79999999999999999999999999999998764

>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=99.69  E-value=5.4e-17  Score=99.53  Aligned_cols=57  Identities=19%  Similarity=0.219  Sum_probs=52.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHH
Q psy8301           7 AGKMRTNGIQSQVFELERKFQH---IRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK   63 (157)
Q Consensus         7 ~rr~Rt~~t~~q~~~Le~~F~~---~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~r   63 (157)
                      .|+.|+.|+.+++.+|+.+|..   ++||+..++..||..+||+..+|++||+|+|+|-.
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            3566789999999999999985   78999999999999999999999999999998753

>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=91.64  E-value=0.35  Score=28.08  Aligned_cols=48  Identities=13%  Similarity=0.214  Sum_probs=36.6

Q ss_pred             CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301          11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYK   61 (157)
Q Consensus        11 Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k   61 (157)
                      |..+|-.+...+-..++.++...   ..++|..+|+....|..|.+|+..-
T Consensus         5 Rk~LT~~eK~~ii~~~e~g~k~s---q~eIA~~fGv~~STvs~IlKnK~ki   52 (66)
T d1hlva1           5 RRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNKRAI   52 (66)
T ss_dssp             SCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTHHHH
T ss_pred             cccCCHHHHHHHHHHHHcCCcch---HHHHHHHhCCChhHHHHHHHHHHHH
Confidence            44588888666667777765433   5678999999999999999986543

>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=90.00  E-value=0.012  Score=34.89  Aligned_cols=38  Identities=18%  Similarity=0.427  Sum_probs=33.9

Q ss_pred             CCCCCCCCCcCccccCCCCCCCCcCCCCCCCCchhHHHhhhcc
Q psy8301         106 GRKPETDFPAEEHNIFVPNFDQSDFLDNKWEDIDILDELHDQY  148 (157)
Q Consensus       106 ~~~~~~~~~~~q~~~~~~~f~~~~~s~s~~p~~~~~~~l~~~~  148 (157)
                      |..+.+.|+..|..+|...|..++|     |+.+++++|+..+
T Consensus         1 grR~Rt~ft~~Ql~~Le~~F~~n~y-----P~~~~r~~LA~~l   38 (68)
T d2cuea1           1 GQRNRTSFTQEQIEALEKEFERTHY-----PDVFARERLAAKI   38 (68)
T ss_dssp             SCCCCCCSCHHHHHHHHHHHTTCSS-----CCHHHHHHHHHHT
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHcCC-----CCHHHHHHHHHHh
Confidence            3456788999999999999999999     9999999999865

>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=88.56  E-value=0.02  Score=31.56  Aligned_cols=36  Identities=11%  Similarity=0.154  Sum_probs=32.2

Q ss_pred             CCCCCCcCccccCCCCCCCCcCCCCCCCCchhHHHhhhccC
Q psy8301         109 PETDFPAEEHNIFVPNFDQSDFLDNKWEDIDILDELHDQYV  149 (157)
Q Consensus       109 ~~~~~~~~q~~~~~~~f~~~~~s~s~~p~~~~~~~l~~~~~  149 (157)
                      |.+.++..|..+|...|..+++     |+...+++|+..+.
T Consensus         1 PRt~ft~~Q~~~Le~~F~~n~~-----P~~~~~~~LA~~l~   36 (50)
T d1s7ea1           1 PRLVFTDVQRRTLHAIFKENKR-----PSKELQITISQQLG   36 (50)
T ss_dssp             CCSCCCHHHHHHHHHHTTSSCS-----STHHHHHHHHTTSC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCC-----CCHHHHHHHHHHHC
Confidence            4577889999999999999999     99999999998764

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=88.38  E-value=0.45  Score=25.65  Aligned_cols=40  Identities=10%  Similarity=0.118  Sum_probs=33.9

Q ss_pred             CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHH
Q psy8301          11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWF   55 (157)
Q Consensus        11 Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWF   55 (157)
                      +..+|++|+....+.+....     ...++|..+|++...|-.||
T Consensus         3 ~~~lt~~q~~~a~~l~~~G~-----s~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_           3 PRAINKHEQEQISRLLEKGH-----PRQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             CCSSCHHHHHHHHHHHHTTC-----CHHHHHHHHTCCHHHHHHHS
T ss_pred             CCcCCHHHHHHHHHHHHCCC-----CHHHHHHHHCcCHHHHHhhC
Confidence            35789999999999987643     47889999999999998887

>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=83.61  E-value=0.024  Score=32.45  Aligned_cols=38  Identities=13%  Similarity=0.217  Sum_probs=33.7

Q ss_pred             CCCCCCCCCcCccccCCCCCCCCcCCCCCCCCchhHHHhhhcc
Q psy8301         106 GRKPETDFPAEEHNIFVPNFDQSDFLDNKWEDIDILDELHDQY  148 (157)
Q Consensus       106 ~~~~~~~~~~~q~~~~~~~f~~~~~s~s~~p~~~~~~~l~~~~  148 (157)
                      |....+.|+..|..+|...|..++|     |+.+.+++|+..+
T Consensus         1 Grr~Rt~ft~~Q~~~Le~~F~~~~y-----p~~~~r~~LA~~l   38 (58)
T d2craa1           1 GRKKRIPYSKGQLRELEREYAANKF-----ITKDKRRKISAAT   38 (58)
T ss_dssp             CCCSCCCSCHHHHHHHHHHHHHCSS-----CCHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCC-----CCHHHHHHHHHHc
Confidence            3456678999999999999999999     9999999999865

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=82.79  E-value=2.3  Score=23.85  Aligned_cols=47  Identities=9%  Similarity=0.009  Sum_probs=35.2

Q ss_pred             CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301          13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus        13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      .+++.+..++.-.|-..     ..-+++|..+|+++..|+.....-+.+-|+
T Consensus        21 ~L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~~~ra~~~Lr~   67 (71)
T d1rp3a2          21 KLPEREKLVIQLIFYEE-----LPAKEVAKILETSVSRVSQLKAKALERLRE   67 (71)
T ss_dssp             TSCHHHHHHHHHHHTSC-----CCHHHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhHh-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            36677777777766443     367889999999999999988766655554

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=82.74  E-value=2.3  Score=23.82  Aligned_cols=46  Identities=7%  Similarity=-0.093  Sum_probs=33.0

Q ss_pred             CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301          14 GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR   64 (157)
Q Consensus        14 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr   64 (157)
                      +++.+..++.-.|-...     .-.++|..+|++...|+++.+.-|.+-|.
T Consensus        19 Lp~~~r~v~~l~~~~~~-----s~~eIA~~lgis~~tv~~~l~ra~~~Lr~   64 (68)
T d1or7a1          19 LPEDLRMAITLRELDGL-----SYEEIAAIMDCPVGTVRSRIFRAREAIDN   64 (68)
T ss_dssp             SCHHHHHHHHHHHTTCC-----CHHHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            45556666665544432     46788999999999999999876666554

>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=81.17  E-value=0.054  Score=30.97  Aligned_cols=36  Identities=14%  Similarity=0.330  Sum_probs=32.0

Q ss_pred             CCCCCCCcCccccCCCCCCCCcCCCCCCCCchhHHHhhhcc
Q psy8301         108 KPETDFPAEEHNIFVPNFDQSDFLDNKWEDIDILDELHDQY  148 (157)
Q Consensus       108 ~~~~~~~~~q~~~~~~~f~~~~~s~s~~p~~~~~~~l~~~~  148 (157)
                      ...+.++..|..+|...|..++|     |+..++++|+...
T Consensus         3 r~Rt~ft~~Q~~~Le~~F~~~~y-----P~~~~r~~LA~~l   38 (60)
T d1yz8p1           3 RQRTHFTSQQLQQLEATFQRNRY-----PDMSTREEIAVWT   38 (60)
T ss_dssp             CSCCCCCHHHHHHHHHHHTTCSS-----CCTTTTTHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHHHHcCC-----CChHHHHHHHHHH
Confidence            34577899999999999999999     9999999999875