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= psy13127
(64 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/52 (50%), Positives = 33/52 (63%), Gaps = 2/52 (3%)
Query: 10 PGFLLQPFRKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTE 61
PG L+ RK +R RT FS SQL +LE AFE+ Y R++LAQ +LTE
Sbjct: 10 PGIALK--RKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTE 59
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/46 (52%), Positives = 30/46 (65%), Gaps = 3/46 (6%)
Query: 18 RKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63
RKP RT F+ +QLL LE F + Y+ AER + + SLSLTETQ
Sbjct: 1 RKP---RTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQ 43
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 22/48 (45%), Positives = 29/48 (60%)
Query: 16 PFRKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63
P K +R RTAF+ QLL+LE F Y+ ER Q+A +L L+E Q
Sbjct: 3 PGGKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQ 50
>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 = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/43 (46%), Positives = 26/43 (60%)
Query: 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63
KR RTAFS QL +L+ F +N Y+ R+QL+ L L E Q
Sbjct: 5 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQ 47
>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 = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/44 (45%), Positives = 26/44 (59%)
Query: 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64
KR RTAFS QL +L+ F +N Y+ R+QL+ L L E Q
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQI 47
>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 = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/44 (45%), Positives = 26/44 (59%)
Query: 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64
KR RTAFS QL +L+ F +N Y+ R+QL+ L L E Q
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQI 47
>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 = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/45 (44%), Positives = 26/45 (57%)
Query: 20 PKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64
KR RTAFS QL +L+ F +N Y+ R+QL+ L L E Q
Sbjct: 1 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQI 45
>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 = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/44 (45%), Positives = 26/44 (59%)
Query: 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64
KR RTAFS QL +L+ F +N Y+ R+QL+ L L E Q
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQI 45
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/44 (45%), Positives = 26/44 (59%)
Query: 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64
KR RTAFS QL +L+ F +N Y+ R+QL+ L L E Q
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQI 45
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 39.3 bits (90), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/39 (46%), Positives = 27/39 (69%)
Query: 25 TAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63
T+FS SQ+L+LE F + Y+ AER LA++L +T+ Q
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQ 40
>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 = 39.3 bits (90), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/46 (45%), Positives = 28/46 (60%)
Query: 16 PFRKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTE 61
P RK +R RT F+ QL +LE AF + HY R++LA + LTE
Sbjct: 2 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTE 47
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/41 (48%), Positives = 26/41 (63%)
Query: 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTE 61
+R RT F+ QL +LE AFE+ HY R++LAQ LTE
Sbjct: 3 RRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTE 43
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 29/46 (63%)
Query: 18 RKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63
+K +R RT F+ QL+ LE FEK Y+ +R LA+SL L++ Q
Sbjct: 15 KKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQ 60
>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 = 38.5 bits (88), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 25/43 (58%)
Query: 22 RIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64
R RTAFS QL +L+ F +N Y+ R+QL+ L L E Q
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQI 43
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 38.5 bits (88), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 19/42 (45%), Positives = 25/42 (59%)
Query: 22 RIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63
R RTAFS QL +L+ F +N Y+ R+QL+ L L E Q
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQ 42
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 25/44 (56%)
Query: 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64
KR RTAFS QL + + F +N Y+ R+QL+ L L E Q
Sbjct: 4 KRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQI 47
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/46 (45%), Positives = 29/46 (63%), Gaps = 3/46 (6%)
Query: 18 RKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63
RKP+ I ++F QL L+ F+K Y+ ER +LA SL LT+TQ
Sbjct: 8 RKPRTIYSSF---QLAALQRRFQKTQYLALPERAELAASLGLTQTQ 50
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 26/43 (60%)
Query: 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63
+R R ++ Q L+LE F NHY+ R ++A +LSLTE Q
Sbjct: 21 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQ 63
>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 = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 28/45 (62%)
Query: 19 KPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63
K K+ RT+F+ Q+ +LE F K Y+ AER LA+ L +T+ Q
Sbjct: 16 KRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQ 60
>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 = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/41 (48%), Positives = 27/41 (65%)
Query: 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTE 61
KR RTA++ +QLL+LE F N Y+ R +LA L+LTE
Sbjct: 4 KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTE 44
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/43 (46%), Positives = 25/43 (58%)
Query: 19 KPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTE 61
K +R RT F+ QL +LE F+K HY R+QLA LTE
Sbjct: 8 KKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTE 50
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 26/44 (59%)
Query: 20 PKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63
P +RT F+ QL +LE F N Y+ A R ++A +L L ETQ
Sbjct: 34 PSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQ 77
>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 = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 27/44 (61%)
Query: 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64
KR RT+++ Q L+LE F N Y+ R ++A +LSLTE Q
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQI 72
>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 = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/42 (45%), Positives = 26/42 (61%)
Query: 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTET 62
+R RTAF+ QL +LE F K +YV R +LA L+L E+
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPES 43
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 27/41 (65%)
Query: 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTE 61
+R RT F+ QL +LE F++NHY + R+++A +LTE
Sbjct: 4 RRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTE 44
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 24/40 (60%)
Query: 22 RIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTE 61
R RT F+ QL +LE AF + HY R++LA + LTE
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTE 40
>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 = 33.9 bits (76), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 24/44 (54%)
Query: 20 PKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63
KR R ++ Q L+LE F N Y+ R +A +LSL+E Q
Sbjct: 3 SKRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQ 46
>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 = 33.5 bits (75), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 25/43 (58%)
Query: 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63
KR R ++ Q L+LE F N Y+ R ++A +LSLTE Q
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQ 45
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 33.5 bits (75), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 25/43 (58%)
Query: 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63
KR R ++ Q L+LE F N Y+ R ++A +LSLTE Q
Sbjct: 4 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQ 46
>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 = 32.3 bits (72), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 24/43 (55%)
Query: 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63
KR R ++ Q L+LE F N Y+ R ++A +L LTE Q
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQ 45
>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 = 32.0 bits (71), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 26/41 (63%)
Query: 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTE 61
+R RT F+ QL +LE F++N Y + R+++A +LTE
Sbjct: 4 RRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTE 44
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 23/41 (56%)
Query: 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTE 61
KR+RT+F QL ++ F NH + KQLAQ LT+
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTK 48
>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 = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 22/38 (57%)
Query: 26 AFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63
++ Q L+LE F N Y+ R ++A +LSLTE Q
Sbjct: 2 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQ 39
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 25/44 (56%)
Query: 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64
+R RT+F+ Q+ LE FE+ HY R++LA + L E +
Sbjct: 8 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARI 51
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 30.0 bits (66), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 23/44 (52%)
Query: 20 PKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63
P+R RT F+ SQ+ +LE F + Y+ L+ L+L Q
Sbjct: 2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQ 45
>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 = 29.3 bits (64), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 27/44 (61%)
Query: 20 PKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63
+++RT FS +QL L+ F+K Y+ + ++L+ L+L+ Q
Sbjct: 3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQ 46
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 28.9 bits (63), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 26/46 (56%)
Query: 18 RKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63
R ++ R ++ Q L+LE F N Y+ R ++A+ L+LTE Q
Sbjct: 11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQ 56
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 28.9 bits (63), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 24 RTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63
R ++ Q L+LE F N Y+ R ++A+ L+LTE Q
Sbjct: 5 RCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQ 44
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 28.9 bits (63), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 21/36 (58%)
Query: 26 AFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTE 61
F+ QL +LE AF + HY R++LA + LTE
Sbjct: 5 TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTE 40
>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 = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 15 QPFRKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLS 58
+P +K KR RT+F+P + L FEKN G E + A+ L+
Sbjct: 89 EPSKKRKR-RTSFTPQAIEALNAYFEKNPLPTGQEITEXAKELN 131
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
0.322 0.136 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,710,442
Number of Sequences: 62578
Number of extensions: 48568
Number of successful extensions: 122
Number of sequences better than 100.0: 40
Number of HSP's better than 100.0 without gapping: 40
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 82
Number of HSP's gapped (non-prelim): 40
length of query: 64
length of database: 14,973,337
effective HSP length: 35
effective length of query: 29
effective length of database: 12,783,107
effective search space: 370710103
effective search space used: 370710103
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)