BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy10638
(140 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 68.2 bits (165), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 30/58 (51%), Positives = 42/58 (72%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
R RT+FT QL LE FE+Q+Y+ P+R+ LA +L L++ QVK W+QNRR+KW+K
Sbjct: 19 RSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSG 76
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 65.1 bits (157), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 31/56 (55%), Positives = 39/56 (69%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
R RT FT EQL LE EF ++Y+ ER +AH L L+E QVK+WFQNRR KW++
Sbjct: 9 RRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKR 64
>pdb|3A01|A Chain A, Crystal Structure Of Aristaless And Clawless
Homeodomains Bo
pdb|3A01|E Chain E, Crystal Structure Of Aristaless And Clawless
Homeodomains Bo
Length = 93
Score = 64.7 bits (156), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 31/58 (53%), Positives = 38/58 (65%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE 96
RT FT Q+ LE F +Q+Y+ ER LA L +T+AQVK WFQNRR KWR+Q E
Sbjct: 21 RTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAE 78
>pdb|1JGG|A Chain A, Even-Skipped Homeodomain Complexed To At-Rich Dna
pdb|1JGG|B Chain B, Even-Skipped Homeodomain Complexed To At-Rich Dna
Length = 60
Score = 62.8 bits (151), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 31/58 (53%), Positives = 40/58 (68%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
R RT FT +QL RLE EF ++ Y+ P R LA LNL E+ +KVWFQNRR+K ++Q
Sbjct: 3 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQR 60
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 62.4 bits (150), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 29/54 (53%), Positives = 36/54 (66%)
Query: 40 TIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
T F+ Q+ LE F RQ+Y+ ER LA L +T+AQVK WFQNRR KWR+Q
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>pdb|1FJL|A Chain A, Homeodomain From The Drosophila Paired Protein Bound To
A Dna Oligonucleotide
pdb|1FJL|B Chain B, Homeodomain From The Drosophila Paired Protein Bound To
A Dna Oligonucleotide
pdb|1FJL|C Chain C, Homeodomain From The Drosophila Paired Protein Bound To
A Dna Oligonucleotide
Length = 81
Score = 61.2 bits (147), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 32/58 (55%), Positives = 38/58 (65%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
R RT F+ QL+ LE FER QY R LA NLTEA+++VWFQNRR + RKQH
Sbjct: 20 RSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH 77
>pdb|2H1K|A Chain A, Crystal Structure Of The Pdx1 Homeodomain In Complex
With Dna
pdb|2H1K|B Chain B, Crystal Structure Of The Pdx1 Homeodomain In Complex
With Dna
Length = 63
Score = 60.8 bits (146), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 30/57 (52%), Positives = 39/57 (68%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
R RT +T QL LE EF +Y+ P R+ LA LNLTE +K+WFQNRR+KW+K+
Sbjct: 5 RTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61
>pdb|2R5Y|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd
Site
pdb|2R5Z|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A DNA SEQUENCE
Derived From The Fkh Gene
Length = 88
Score = 60.5 bits (145), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 29/58 (50%), Positives = 40/58 (68%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
R RT +T Q LE EF +Y+ R+ +AH L+LTE Q+K+WFQNRR+KW+K+H
Sbjct: 30 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH 87
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 59.7 bits (143), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 33/57 (57%), Positives = 36/57 (63%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
R RT FT EQLE LE FER Y R LA LTEA+V+VWF NRR +WRKQ
Sbjct: 4 RSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 58.5 bits (140), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 31/57 (54%), Positives = 39/57 (68%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
R RT FT +QL+ LEA F+R Y R +A NLTEA+V+VWF+NRR KWRK+
Sbjct: 5 RQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61
>pdb|2L7F|P Chain P, Solution Structure Of The Pitx2 Homeodomain
pdb|2LKX|A Chain A, Nmr Structure Of The Homeodomain Of Pitx2 In Complex
With A Taatcc Dna Binding Site
Length = 68
Score = 58.5 bits (140), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 31/57 (54%), Positives = 40/57 (70%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
R RT FT +QL+ LEA F+R +Y R +A NLTEA+V+VWF+NRR KWRK+
Sbjct: 5 RQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 58.5 bits (140), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 32/57 (56%), Positives = 36/57 (63%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
R RT FT QLE LE F R Y R LA + LTEA+++VWFQNRR KWRKQ
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 58.2 bits (139), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 27/56 (48%), Positives = 38/56 (67%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
RTI++ QL L+ F++ QY+ PER LA +L LT+ QVK+WFQN+R K +K
Sbjct: 11 RTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSG 66
>pdb|3A01|B Chain B, Crystal Structure Of Aristaless And Clawless
Homeodomains Bo
pdb|3A01|F Chain F, Crystal Structure Of Aristaless And Clawless
Homeodomains Bo
Length = 67
Score = 58.2 bits (139), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 32/57 (56%), Positives = 36/57 (63%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
R RT FT QLE LE F R Y R LA + LTEA+++VWFQNRR KWRKQ
Sbjct: 8 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 64
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 58.2 bits (139), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 28/51 (54%), Positives = 35/51 (68%)
Query: 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
F+ +Q LE +FE Q+Y+ PER LA L L+E QVK WFQNRR KWR+
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 57.8 bits (138), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 30/57 (52%), Positives = 38/57 (66%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
R RT FT EQ+E LE EFER Y R LA ++L EA+++VWF NRR KWR++
Sbjct: 9 RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE 65
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 56.6 bits (135), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 27/58 (46%), Positives = 39/58 (67%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
R R +T Q LE EF +Y+ R+ +AH L+LTE Q+K+WFQNRR+KW+K++
Sbjct: 5 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 62
>pdb|1AHD|P Chain P, Determination Of The Nmr Solution Structure Of An
Antennapedia Homeodomain-Dna Complex
pdb|2HOA|A Chain A, Structure Determination Of The Antp(C39->s) Homeodomain
From Nuclear Magnetic Resonance Data In Solution Using
A Novel Strategy For The Structure Calculation With The
Programs Diana, Caliba, Habas And Glomsa
Length = 68
Score = 56.6 bits (135), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 27/58 (46%), Positives = 39/58 (67%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
R R +T Q LE EF +Y+ R+ +AH L+LTE Q+K+WFQNRR+KW+K++
Sbjct: 4 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61
>pdb|2L9R|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Homeobox
Protein Nkx-3.1 From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6470a
Length = 69
Score = 55.8 bits (133), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 26/51 (50%), Positives = 35/51 (68%)
Query: 46 QLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE 96
Q+ LE +F Q+Y+ PER +LA L LTE QVK+WFQNRR K +++ L
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLS 65
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 55.8 bits (133), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 31/56 (55%), Positives = 36/56 (64%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
R RT FT QLE LE F++ Y R LA +LTEA+V+VWFQNRR KWRK
Sbjct: 11 RNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRK 66
>pdb|1HOM|A Chain A, Determination Of The Three-Dimensional Structure Of The
Antennapedia Homeodomain From Drosophila In Solution By
1h Nuclear Magnetic Resonance Spectroscopy
Length = 68
Score = 55.8 bits (133), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 27/58 (46%), Positives = 38/58 (65%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
R R +T Q LE EF +Y+ R+ +AH L LTE Q+K+WFQNRR+KW+K++
Sbjct: 4 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 61
>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna
Complex At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|1HDD|D Chain D, Crystal Structure Of An Engrailed Homeodomain-Dna
Complex At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|2JWT|A Chain A, Solution Structure Of Engrailed Homeodomain Wt
Length = 61
Score = 55.5 bits (132), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/56 (48%), Positives = 36/56 (64%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
R RT F+ EQL RL+ EF +Y+ R L+ L L EAQ+K+WFQN+R K +K
Sbjct: 5 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/56 (48%), Positives = 36/56 (64%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
R RT F+ EQL RL+ EF +Y+ R L+ L L EAQ+K+WFQN+R K +K
Sbjct: 3 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58
>pdb|3RKQ|A Chain A, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna
pdb|3RKQ|B Chain B, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna
Length = 58
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 26/51 (50%), Positives = 34/51 (66%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
R +F+ Q+ LE F++Q+Y+ PER LA L LT QVK+WFQNRR K
Sbjct: 6 RVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYK 56
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 25/55 (45%), Positives = 38/55 (69%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
R +F+ Q+ LE F++Q+Y+ PER +LA ++LT QVK+WFQN R K ++Q
Sbjct: 6 RVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 54.7 bits (130), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 29/59 (49%), Positives = 38/59 (64%)
Query: 38 VRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE 96
+RT FT QL LE EF +Y+ R+ +A TL L E QVK+WFQNRR+K +K+ E
Sbjct: 37 LRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE 95
>pdb|1SAN|A Chain A, The Des(1-6)antennapedia Homeodomain: Comparison Of The
Nmr Solution Structure And The Dna Binding Affinity
With The Intact Antennapedia Homeodomain
Length = 62
Score = 54.7 bits (130), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 25/54 (46%), Positives = 37/54 (68%)
Query: 41 IFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
+T Q LE EF +Y+ R+ +AH L+LTE Q+K+WFQNRR+KW+K++
Sbjct: 2 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 55
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 27/54 (50%), Positives = 37/54 (68%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
RT FT QL LE +F ++QY+ ER + +L+LTE QVK+WFQNRR K ++
Sbjct: 4 RTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>pdb|2HDD|A Chain A, Engrailed Homeodomain Q50k Variant Dna Complex
pdb|2HDD|B Chain B, Engrailed Homeodomain Q50k Variant Dna Complex
Length = 61
Score = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 26/56 (46%), Positives = 36/56 (64%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
R RT F+ EQL RL+ EF +Y+ R L+ L L EAQ+K+WF+N+R K +K
Sbjct: 5 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
>pdb|1P7J|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52e
Length = 59
Score = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 27/56 (48%), Positives = 35/56 (62%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
R RT F+ EQL RL+ EF +Y+ R L+ L L EAQ+K+WFQN R K +K
Sbjct: 3 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 29/52 (55%), Positives = 33/52 (63%)
Query: 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
FT QLE LE F R Y R LA + LTEA+++VWFQNRR KWRKQ
Sbjct: 6 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 53.5 bits (127), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 26/53 (49%), Positives = 34/53 (64%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
R RT F+ EQL RL+ EF +Y+ R L+ L L EAQ+K+WFQN+R K
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>pdb|1P7I|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52a
Length = 59
Score = 53.5 bits (127), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 27/56 (48%), Positives = 35/56 (62%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
R RT F+ EQL RL+ EF +Y+ R L+ L L EAQ+K+WFQN R K +K
Sbjct: 3 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 53.5 bits (127), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/56 (46%), Positives = 35/56 (62%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
R RT F+ EQL R + EF +Y+ R L+ L L EAQ+K+WFQN+R K R+
Sbjct: 5 RPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 53.1 bits (126), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 29/57 (50%), Positives = 37/57 (64%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
R RTIFT EQLE LE F+ +Y R LA ++L E +V+VWF+NRR KWR+
Sbjct: 9 RHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRS 65
>pdb|1DU0|A Chain A, Engrailed Homeodomain Q50a Variant Dna Complex
pdb|1DU0|B Chain B, Engrailed Homeodomain Q50a Variant Dna Complex
Length = 57
Score = 52.8 bits (125), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 26/56 (46%), Positives = 35/56 (62%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
R RT F+ EQL RL+ EF +Y+ R L+ L L EAQ+K+WF N+R K +K
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 52.8 bits (125), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 26/57 (45%), Positives = 36/57 (63%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
R R +T Q LE EF Y+ R+ +AH L+LTE Q+K+WFQNRR+K +K+
Sbjct: 22 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE 78
>pdb|1NK2|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES
pdb|1NK3|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, MINIMIZED AVERAGE
Structure
pdb|1VND|A Chain A, VndNK-2 Protein (Homeodomain), Nmr
Length = 77
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/54 (46%), Positives = 34/54 (62%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
R +FT Q LE F +Q+Y+ PER +LA + LT QVK+WFQN R K ++
Sbjct: 13 RVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66
>pdb|2HOS|A Chain A, Phage-selected Homeodomain Bound To Unmodified Dna
pdb|2HOS|B Chain B, Phage-selected Homeodomain Bound To Unmodified Dna
pdb|2HOT|A Chain A, Phage Selected Homeodomain Bound To Modified Dna
pdb|2HOT|B Chain B, Phage Selected Homeodomain Bound To Modified Dna
Length = 63
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/56 (48%), Positives = 34/56 (60%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
R RT F+ EQL RL+ EF +Y+ R L+ L L EAQVK WF+N R K +K
Sbjct: 6 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 49.7 bits (117), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 24/54 (44%), Positives = 33/54 (61%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
R +FT Q LE F +Q+Y+ PER +L + LT QVK+WFQN R K ++
Sbjct: 16 RVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKR 69
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 49.3 bits (116), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 39/61 (63%), Gaps = 3/61 (4%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK---WRKQ 93
+ RT+F+ QL L F+RQ+Y+ + L++ LNL+ QVK WFQN+R+K W+K
Sbjct: 24 KTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQKN 83
Query: 94 H 94
+
Sbjct: 84 N 84
>pdb|1FTZ|A Chain A, Nuclear Magnetic Resonance Solution Structure Of The
Fushi Tarazu Homeodomain From Drosophila And Comparison
With The Antennapedia Homeodomain
Length = 70
Score = 48.9 bits (115), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 36/57 (63%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
R R +T Q LE EF +Y+ R+ +A+ L+L+E Q+K+WFQNRR+K +K
Sbjct: 5 RTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKD 61
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/56 (46%), Positives = 33/56 (58%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
R +T Q LE EF Y+ R +A LNLTE QVK+WFQNRR+K +K +
Sbjct: 5 RCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKMN 60
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/51 (45%), Positives = 30/51 (58%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRR 87
R RT FT Q+ LE F + +Y+ P L+ L L AQVK+WF+NRR
Sbjct: 4 RTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRR 54
>pdb|2VI6|A Chain A, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|B Chain B, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|C Chain C, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|D Chain D, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|E Chain E, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|F Chain F, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|G Chain G, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|H Chain H, Crystal Structure Of The Nanog Homeodomain
Length = 62
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 38/56 (67%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
++RT+F+ QL L+ F++Q+Y+ + L+ LNL+ QVK WFQN+R+K ++
Sbjct: 5 KMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/54 (48%), Positives = 32/54 (59%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
R +T Q LE EF Y+ R +A LNLTE QVK+WFQNRR+K +K
Sbjct: 17 RCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 47.4 bits (111), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 35/54 (64%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
R +T QL+ LE E+ +++ +R ++ T NL+E QV +WFQNRR+K +K
Sbjct: 5 RVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 47.4 bits (111), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 35/54 (64%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
R +T QL+ LE E+ +++ +R ++ T NL+E QV +WFQNRR+K +K
Sbjct: 11 RVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/58 (46%), Positives = 37/58 (63%), Gaps = 6/58 (10%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPE---RLYLAHTLNLTEAQVKVWFQNRRIKWR 91
R RT FT QL+ LEA F + +Y P+ R +A +NL E++V+VWF+NRR K R
Sbjct: 9 RERTTFTRAQLDVLEALFAKTRY---PDIFMREEVALKINLPESRVQVWFKNRRAKCR 63
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/63 (44%), Positives = 36/63 (57%), Gaps = 2/63 (3%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERL-YLAHTLNLTEAQVKVWFQNRRIKWRKQHL 95
R RT FT Q+E LE F Y G + L LA LNL ++++WFQNRR K ++ H
Sbjct: 3 RPRTAFTQNQIEVLENVFRVNCY-PGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61
Query: 96 EFQ 98
E Q
Sbjct: 62 ESQ 64
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 33/55 (60%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
R ++ QL LE E+ +++ +R ++ +L+E Q+ +WFQNRR+K +K
Sbjct: 11 RIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKS 65
>pdb|3D1N|I Chain I, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|J Chain J, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|K Chain K, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|L Chain L, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|M Chain M, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|N Chain N, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|O Chain O, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|P Chain P, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
Length = 151
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 26/49 (53%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRR 87
RT FTP+ +E L A FE+ G E A LN V+VWF NRR
Sbjct: 97 RTSFTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVRVWFSNRR 145
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 25/40 (62%)
Query: 53 EFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
EF +Y+ R L+ L L EAQ+K+WFQN+R K +K
Sbjct: 4 EFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/62 (41%), Positives = 36/62 (58%), Gaps = 10/62 (16%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMV--GPERL---YLAHTLNLTEAQVKVWFQNRRIKWR 91
R+RT TPEQLE L Q+Y++ P R ++AH + L + V+VWFQN R + R
Sbjct: 19 RLRTTITPEQLEIL-----YQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARER 73
Query: 92 KQ 93
K
Sbjct: 74 KS 75
>pdb|3NAR|A Chain A, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And
Homeoboxes Protein 1, Homeodomain 4)
pdb|3NAR|B Chain B, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And
Homeoboxes Protein 1, Homeodomain 4)
Length = 96
Score = 35.8 bits (81), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 27/55 (49%)
Query: 43 TPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEF 97
TPEQL L++ F R Q+ E LA L + WF + R W+ +L++
Sbjct: 33 TPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNLKW 87
>pdb|1MH3|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form I
pdb|1MH4|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form Ii
Length = 421
Score = 35.4 bits (80), Expect = 0.009, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 27/47 (57%)
Query: 43 TPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
+P+ LE F R+Q + E+ +A +T QV+VWF N+R++
Sbjct: 373 SPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 419
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 33.9 bits (76), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 29/51 (56%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
++ +P+ LE F R+Q + E+ +A +T QV+VWF N+R++
Sbjct: 9 KSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 59
>pdb|1YRN|A Chain A, Crystal Structure Of The Mata1MATALPHA2 HOMEODOMAIN
Heterodimer Bound To Dna
pdb|1F43|A Chain A, Solution Structure Of The Mata1 Homeodomain
Length = 61
Score = 33.9 bits (76), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 29/51 (56%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
++ +P+ LE F R+Q + E+ +A +T QV+VWF N+R++
Sbjct: 9 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 59
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 33.9 bits (76), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 29/51 (56%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
++ +P+ LE F R+Q + E+ +A +T QV+VWF N+R++
Sbjct: 1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 51
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 33.5 bits (75), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 27/54 (50%)
Query: 40 TIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
T FT QL L+ F+ Y E L++ LNL + VWFQN R K RK
Sbjct: 12 TRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKS 65
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 33.1 bits (74), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 29/57 (50%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
R+RT F QL +++ F + LA LT+ ++VWFQN R K+R+
Sbjct: 9 RMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRN 65
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 32.0 bits (71), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 22/33 (66%)
Query: 68 LAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQQ 100
LA +T +QV WF N+RI+++K +FQ++
Sbjct: 37 LAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEE 69
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 32.0 bits (71), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 22/33 (66%)
Query: 68 LAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQQ 100
LA +T +QV WF N+RI+++K +FQ++
Sbjct: 37 LAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEE 69
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 31.6 bits (70), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 22/33 (66%)
Query: 68 LAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQQ 100
LA +T +QV WF N+RI+++K +FQ++
Sbjct: 38 LAKKSGITVSQVSNWFGNKRIRYKKNIGKFQEE 70
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 31.6 bits (70), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 41 IFTPEQLERLEAEFERQQYMVGPERLYL-AHTLNLTEAQVKVWFQNRRIKWRKQ 93
T +Q+E LE F + P L L A LTE Q + WF+ R +WR+
Sbjct: 7 TMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60
>pdb|2NZZ|A Chain A, Nmr Structure Analysis Of The Penetratin Conjugated Gas
(374-394) Peptide
pdb|2O00|A Chain A, Nmr Structure Analysis Of The Penetratin Conjugated Gas
(374-394) Peptide
Length = 37
Score = 31.6 bits (70), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 11/16 (68%), Positives = 16/16 (100%)
Query: 78 QVKVWFQNRRIKWRKQ 93
Q+K+WFQNRR+KW+K+
Sbjct: 2 QIKIWFQNRRMKWKKR 17
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of
Human Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 31.2 bits (69), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 23/47 (48%)
Query: 45 EQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR 91
EQL L+ F R Q+ E +L L+ +V+ WF +RR R
Sbjct: 18 EQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCR 64
>pdb|2HI3|A Chain A, Solution Structure Of The Homeodomain-Only Protein Hop
Length = 73
Score = 31.2 bits (69), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 43 TPEQLERLEAEFERQQYMVGPERLYL-AHTLNLTEAQVKVWFQNRRIKWRKQ 93
T +Q+E LE F + P L L A LTE Q + WF+ R +WR+
Sbjct: 10 TEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 61
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 30.8 bits (68), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 11/15 (73%), Positives = 15/15 (100%)
Query: 78 QVKVWFQNRRIKWRK 92
Q+K+WFQNRR+KW+K
Sbjct: 2 QIKIWFQNRRMKWKK 16
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 30.4 bits (67), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 11/15 (73%), Positives = 15/15 (100%)
Query: 78 QVKVWFQNRRIKWRK 92
Q+K+WFQNRR+KW+K
Sbjct: 2 QIKIWFQNRRMKWKK 16
>pdb|2LY9|A Chain A, Solution Nmr Structure Of Homeobox 2 Domain From Human
Zhx1 Repressor, Northeast Structural Genomics
Consortium (Nesg) Target Hr7907f
Length = 74
Score = 30.4 bits (67), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 26/54 (48%)
Query: 38 VRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR 91
+R T EQL L+ + + Q+ E + L LT+ ++K WF + R R
Sbjct: 9 IRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQR 62
>pdb|1BW5|A Chain A, The Nmr Solution Structure Of The Homeodomain Of The Rat
Insulin Gene Enhancer Protein Isl-1, 50 Structures
Length = 66
Score = 30.0 bits (66), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 28/59 (47%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL 95
RVRT+ +QL L + + L L+ ++VWFQN+R K +K+ +
Sbjct: 5 RVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI 63
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 29.3 bits (64), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 68 LAHTLNLTEAQVKVWFQNRRIKWRKQ 93
LA +T +QV WF N+RI+++K
Sbjct: 39 LAKKCGITVSQVSNWFGNKRIRYKKN 64
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 29.3 bits (64), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 23/49 (46%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRR 87
RT + + LE F E + +A LNL + V+VWF NRR
Sbjct: 91 RTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRR 139
>pdb|1B8I|B Chain B, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
pdb|2R5Y|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd
Site
pdb|2R5Z|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A DNA SEQUENCE
Derived From The Fkh Gene
Length = 63
Score = 29.3 bits (64), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 68 LAHTLNLTEAQVKVWFQNRRIKWRKQ 93
LA +T +QV WF N+RI+++K
Sbjct: 37 LARKCGITVSQVSNWFGNKRIRYKKN 62
>pdb|1HF0|A Chain A, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1HF0|B Chain B, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1GT0|C Chain C, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 159
Score = 28.9 bits (63), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 20/40 (50%)
Query: 50 LEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
LE F Q E +A LN+ + ++VWF NRR K
Sbjct: 115 LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQK 154
>pdb|3NAU|A Chain A, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And
Homeoboxes Protein 2, Homeodomain 2)
pdb|3NAU|B Chain B, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And
Homeoboxes Protein 2, Homeodomain 2)
Length = 66
Score = 28.9 bits (63), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 22/45 (48%)
Query: 43 TPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRR 87
T EQ+ L+A F + Q+ E L L +++K WF + R
Sbjct: 12 TKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHR 56
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 20/40 (50%)
Query: 50 LEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
LE F Q + +A LN+ + ++VWF NRR K
Sbjct: 116 LEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQK 155
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 28.1 bits (61), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 20/40 (50%)
Query: 50 LEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
LE F Q E +A LN+ + ++VWF NRR K
Sbjct: 22 LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQK 61
>pdb|1CQT|A Chain A, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
pdb|1CQT|B Chain B, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
Length = 163
Score = 28.1 bits (61), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 20/40 (50%)
Query: 50 LEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
LE F Q E +A LN+ + ++VWF NRR K
Sbjct: 118 LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQK 157
>pdb|1O4X|A Chain A, Ternary Complex Of The Dna Binding Domains Of The Oct1 And
Sox2 Transcription Factors With A 19mer Oligonucleotide
From The Hoxb1 Regulatory Element
Length = 167
Score = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 22/43 (51%)
Query: 50 LEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
LE F Q E +A LN+ + ++VWF NRR K ++
Sbjct: 119 LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 161
>pdb|1OCT|C Chain C, Crystal Structure Of The Oct-1 Pou Domain Bound To An
Octamer Site: Dna Recognition With Tethered Dna-Binding
Modules
Length = 156
Score = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 20/40 (50%)
Query: 50 LEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
LE F Q E +A LN+ + ++VWF NRR K
Sbjct: 111 LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQK 150
>pdb|1HDP|A Chain A, Solution Structure Of A Pou-Specific Homeodomain: 3d-Nmr
Studies Of Human B-Cell Transcription Factor Oct-2
Length = 63
Score = 27.3 bits (59), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 50 LEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
LE F Q E L +A L++ + ++VWF NRR K
Sbjct: 16 LEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQK 55
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 26.9 bits (58), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 14/24 (58%)
Query: 64 ERLYLAHTLNLTEAQVKVWFQNRR 87
E+ LA LT QV WF+NRR
Sbjct: 523 EKRELAEATGLTTTQVSNWFKNRR 546
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 26.9 bits (58), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 67 YLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
++A+ L L + V+VWF NRR K ++
Sbjct: 128 HIANQLGLEKDVVRVWFSNRRQKGKRSS 155
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 26.6 bits (57), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 21/40 (52%)
Query: 50 LEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
LE+ F + E LA +L L + V+VWF NRR K
Sbjct: 114 LESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQK 153
>pdb|2DA5|A Chain A, Solution Structure Of The Second Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 3 (Triple Homeobox 1
Protein)
Length = 75
Score = 26.6 bits (57), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 21/46 (45%)
Query: 44 PEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
PEQL LE+ F + + E L +T ++ WF RR K
Sbjct: 16 PEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKK 61
>pdb|1KZ2|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain Derivative [w6f,W14f]
Length = 16
Score = 25.8 bits (55), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 9/15 (60%), Positives = 15/15 (100%)
Query: 78 QVKVWFQNRRIKWRK 92
Q+K++FQNRR+K++K
Sbjct: 2 QIKIFFQNRRMKFKK 16
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.325 0.136 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,234,430
Number of Sequences: 62578
Number of extensions: 58464
Number of successful extensions: 295
Number of sequences better than 100.0: 90
Number of HSP's better than 100.0 without gapping: 90
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 203
Number of HSP's gapped (non-prelim): 90
length of query: 140
length of database: 14,973,337
effective HSP length: 89
effective length of query: 51
effective length of database: 9,403,895
effective search space: 479598645
effective search space used: 479598645
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 46 (22.3 bits)