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= psy5355
(76 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 49.3 bits (116), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 22/43 (51%), Positives = 35/43 (81%)
Query: 13 RPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
R +S Q+ AL++ F++T+YLA PERA+LA +LG+T++QVK+
Sbjct: 11 RTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKI 53
>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 = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 33/52 (63%)
Query: 9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPER 60
++ R FS Q++ LE+ F+Q +YL+ PER +LA L +T +QVK+ R
Sbjct: 2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNR 53
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 46.2 bits (108), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 31/47 (65%)
Query: 9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
++ R FS Q++ LE+ F+Q KYL+ PER LA + +T +QVK+
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKI 48
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 45.8 bits (107), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 33/51 (64%)
Query: 5 KDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
K K + +R F+ Q+ LEK FE+ KYL+ P+R LA +LG+++ QVK
Sbjct: 13 KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKT 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 = 45.8 bits (107), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 24/48 (50%), Positives = 31/48 (64%)
Query: 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
K+K R +F+ Q+ LEK F + KYLA ERA LA L MT++QVK
Sbjct: 16 KRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKT 63
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 45.8 bits (107), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/46 (50%), Positives = 29/46 (63%)
Query: 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPER 60
+FS Q+ LE+ F + KYLA ERA LA AL MT++QVK R
Sbjct: 3 SFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNR 48
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 33/53 (62%)
Query: 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPER 60
K + R F+ +Q+ LEK F KYL+ ER+++A+AL ++E QVK+ R
Sbjct: 6 KSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNR 58
>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 = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/41 (48%), Positives = 26/41 (63%)
Query: 20 QIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPER 60
Q+ LE+ F KYL+ PERA LA L +TE+QVK+ R
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNR 55
>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 = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 30/48 (62%)
Query: 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
KK+ R F+ Q + LE+ F Q +YL+ PER LA + +T +QVK+
Sbjct: 8 KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKI 55
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/40 (52%), Positives = 25/40 (62%)
Query: 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
FS Q LEK FE KYL+ PER +LA L ++E QVK
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKT 53
>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 = 19/43 (44%), Positives = 30/43 (69%)
Query: 13 RPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
R F+ Q+ ALE+ F Q +YL+ ERA+ + +L +TE+QVK+
Sbjct: 4 RTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKI 46
>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 = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 28/51 (54%)
Query: 10 KHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPER 60
K TR ++ Q+ LEK F KY++ P R +LA L +TE +K+ R
Sbjct: 4 KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNR 54
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 29/48 (60%)
Query: 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
KK+ R F+ Q + LE+ F Q +YL+ PER L + +T +QVK+
Sbjct: 11 KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKI 58
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 29/52 (55%)
Query: 9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPER 60
+K R T++ Q LEK F +YL R ++A+AL +TE Q+K+ R
Sbjct: 3 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNR 54
>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 = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 10 KHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVT-GPERAKL 63
K R FS +Q+ L++ F + +YL R +L+ LG+ E+Q+K+ ERAK+
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKI 56
>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 = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 28/47 (59%)
Query: 9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+K R T++ Q LEK F +YL R ++A+AL +TE Q+K+
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKI 48
>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 = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 28/47 (59%)
Query: 9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+K R T++ Q LEK F +YL R ++A+AL +TE Q+K+
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKI 48
>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 = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 28/46 (60%)
Query: 10 KHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
K R FS +Q+ L++ F + +YL R +L+ LG+ E+Q+K+
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKI 49
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 29/53 (54%)
Query: 10 KHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPERAK 62
+ TR TF+ QI LE+ F Q +YL P A L+ L + +QVK+ R +
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRR 55
>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 = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 28/46 (60%)
Query: 10 KHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
K R FS +Q+ L++ F + +YL R +L+ LG+ E+Q+K+
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKI 49
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 28/52 (53%)
Query: 9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPER 60
++ R T++ Q LEK F YL R ++A+AL +TE Q+K+ R
Sbjct: 20 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNR 71
>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 = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 28/46 (60%)
Query: 10 KHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
K R FS +Q+ L++ F + +YL R +L+ LG+ E+Q+K+
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKI 47
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 28/46 (60%)
Query: 10 KHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
K R FS +Q+ L++ F + +YL R +L+ LG+ E+Q+K+
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKI 47
>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 = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 27/51 (52%)
Query: 10 KHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPER 60
K TR T++ Q LEK F +Y+ R +A AL ++E Q+K+ R
Sbjct: 4 KRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNR 54
>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 = 0.001, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 13 RPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVT-GPERAKL 63
R FS +Q+ L++ F + +YL R +L+ LG+ E+Q+K+ +RAK+
Sbjct: 3 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKI 54
>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 = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 33/54 (61%), Gaps = 2/54 (3%)
Query: 2 NSDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
N++ + K++ R +++ Q LEK F +YL R ++A+AL +TE Q+K+
Sbjct: 23 NANGETKRQ--RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKI 74
>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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 31/48 (64%)
Query: 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
K++ +R TFS Q+ LE+ FE+T+Y R +LA +TE++++V
Sbjct: 17 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQV 64
>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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 27/45 (60%)
Query: 10 KHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVK 54
K R FS +Q+ L++ F + +YL R +L+ LG+ E+QVK
Sbjct: 5 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVK 49
>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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 26/46 (56%)
Query: 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPER 60
T++ Q LEK F +YL R ++A+AL +TE Q+K+ R
Sbjct: 2 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNR 47
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 27/43 (62%)
Query: 13 RPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
R FS +Q+ L++ F + +YL R +L+ LG+ E+Q+K+
Sbjct: 3 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKI 45
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 27/46 (58%)
Query: 10 KHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
K R FS +Q+ ++ F + +YL R +L+ LG+ E+Q+K+
Sbjct: 4 KRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKI 49
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 26/43 (60%)
Query: 13 RPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
R F+ +Q+ LEK F KYL+ R ++A L + E+QVK+
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKI 80
>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 = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 26/46 (56%)
Query: 10 KHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ R F+ Q+ LEK F + Y++ P R +LA L + ES +KV
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKV 47
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 30/53 (56%)
Query: 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPER 60
KK+ R TF+ Q+ LEK F++T Y R +LA +TE++V+V R
Sbjct: 8 KKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNR 60
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 34.7 bits (78), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 27/48 (56%)
Query: 7 AKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVK 54
KK+ TR FS Q+ L F++ KYL+ + +L+ L ++ QVK
Sbjct: 20 VKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVK 67
>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 = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 30/48 (62%)
Query: 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
K++ R TF+ Q+ LEK F +T Y R +LA +G+TE++++V
Sbjct: 5 KQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQV 52
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 33.9 bits (76), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 29/46 (63%)
Query: 10 KHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ R +F+ +QI ALEK FE+T Y R +LA + + E++++V
Sbjct: 8 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQV 53
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 33.9 bits (76), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 30/47 (63%)
Query: 9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
++ +R TF+ +Q+ LE+ FE+T Y R +LA +TE++V+V
Sbjct: 2 QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQV 48
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 33.1 bits (74), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 28/48 (58%)
Query: 13 RPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPER 60
R TF+ Q+ LEK F +T Y R +LA +G+TE++++V R
Sbjct: 3 RTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNR 50
>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 = 32.7 bits (73), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 28/47 (59%)
Query: 9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
++ R F+ QQ+ LE TF++ +Y R ++A +TE++V+V
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRV 49
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 32.3 bits (72), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 23/48 (47%)
Query: 13 RPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPER 60
R ++ Q LEK F YL R ++A L +TE QVK+ R
Sbjct: 17 RCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNR 64
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 27/46 (58%)
Query: 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPER 60
TF+ Q+ LEK F +T Y R +LA +G+TE++++V R
Sbjct: 5 TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNR 50
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 23/48 (47%)
Query: 13 RPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPER 60
R ++ Q LEK F YL R ++A L +TE QVK+ R
Sbjct: 5 RCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNR 52
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 27/47 (57%)
Query: 9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
++ R F+ QQ+ LE TF++ Y R ++A +TE++V+V
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRV 49
>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 = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 27/46 (58%)
Query: 9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVK 54
K+ R FS Q+ AL+ F++ KYL+ + +L+ L ++ QVK
Sbjct: 3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVK 48
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 30.8 bits (68), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
++H R F+ +Q+ ALE F++TKY R +LA + + E +V+V
Sbjct: 8 RRH-RTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEV 53
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 29.3 bits (64), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 26 KTFEQTKYLAGPERAKLAYALGMTESQVKVT-GPERAKL 63
+ F + +YL R +L+ LG+ E+Q+K+ +RAK+
Sbjct: 3 REFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKI 41
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 26/46 (56%)
Query: 10 KHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ R TF+ Q+ LE F +T+Y R ++A + + ES+V+V
Sbjct: 8 RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQV 53
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
0.309 0.123 0.330
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,917,969
Number of Sequences: 62578
Number of extensions: 55443
Number of successful extensions: 152
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 50
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 84
Number of HSP's gapped (non-prelim): 68
length of query: 76
length of database: 14,973,337
effective HSP length: 45
effective length of query: 31
effective length of database: 12,157,327
effective search space: 376877137
effective search space used: 376877137
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 45 (21.9 bits)