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= psy8538
(64 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 42.4 bits (98), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 17/29 (58%), Positives = 25/29 (86%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVRC 33
EFH++RYIT RR+ ++AN+L LSERQ++
Sbjct: 21 EFHFNRYITRRRRIDIANALSLSERQIKI 49
>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 = 39.3 bits (90), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 25/29 (86%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVRC 33
EFH++RY+T RR+ E+A++L L+ERQ++
Sbjct: 46 EFHFNRYLTRRRRIEIAHALSLTERQIKI 74
>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 = 38.9 bits (89), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 25/29 (86%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVRC 33
EFH++RY+T RR+ E+A++L L+ERQ++
Sbjct: 14 EFHFNRYLTRRRRIEIAHALSLTERQIKI 42
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 25/29 (86%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVRC 33
EFH++RY+T RR+ E+A++L L+ERQ++
Sbjct: 21 EFHFNRYLTRRRRIEIAHALSLTERQIKI 49
>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 = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 25/29 (86%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVRC 33
EFH++RY+T RR+ E+A++L L+ERQ++
Sbjct: 20 EFHFNRYLTRRRRIEIAHALSLTERQIKI 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 = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/28 (53%), Positives = 25/28 (89%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVR 32
EFH++RY+T RR+ E+A++L L+ERQ++
Sbjct: 20 EFHFNRYLTRRRRIEIAHALCLTERQIK 47
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 23/29 (79%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVRC 33
EFH + Y+T RR+ E+A++L L+ERQ++
Sbjct: 38 EFHTNHYLTRRRRIEMAHALSLTERQIKI 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 = 33.1 bits (74), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 23/28 (82%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVR 32
EF+ +RY+T RR+ +L++ LGL+E QV+
Sbjct: 22 EFNENRYLTERRRQQLSSELGLNEAQVK 49
>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 = 32.3 bits (72), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 23/29 (79%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVRC 33
EF+ +RY+T RR+ +L++ LGL+E Q++
Sbjct: 21 EFNENRYLTERRRQQLSSELGLNEAQIKI 49
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 32.3 bits (72), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 23/28 (82%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVR 32
EF+ +RY+T RR+ +L++ LGL+E Q++
Sbjct: 4 EFNENRYLTERRRQQLSSELGLNEAQIK 31
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 32.3 bits (72), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 23/28 (82%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVR 32
EF+ +RY+T RR+ +L++ LGL+E Q++
Sbjct: 19 EFNENRYLTERRRQQLSSELGLNEAQIK 46
>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 = 32.0 bits (71), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 23/28 (82%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVR 32
EF+ +RY+T RR+ +L++ LGL+E Q++
Sbjct: 21 EFNENRYLTERRRQQLSSELGLNEAQIK 48
>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 = 32.0 bits (71), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 23/28 (82%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVR 32
EF+ +RY+T RR+ +L++ LGL+E Q++
Sbjct: 19 EFNENRYLTERRRQQLSSELGLNEAQIK 46
>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 = 32.0 bits (71), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 23/28 (82%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVR 32
EF+ +RY+T RR+ +L++ LGL+E Q++
Sbjct: 19 EFNENRYLTERRRQQLSSELGLNEAQIK 46
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 32.0 bits (71), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 23/28 (82%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVR 32
EF+ +RY+T RR+ +L++ LGL+E Q++
Sbjct: 21 EFNENRYLTERRRQQLSSELGLNEAQIK 48
>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 = 32.0 bits (71), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 23/28 (82%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVR 32
EF+ +RY+T RR+ +L++ LGL+E Q++
Sbjct: 17 EFNENRYLTERRRQQLSSELGLNEAQIK 44
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 32.0 bits (71), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 23/28 (82%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVR 32
EF+ +RY+T RR+ +L++ LGL+E Q++
Sbjct: 17 EFNENRYLTERRRQQLSSELGLNEAQIK 44
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 22/29 (75%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVRC 33
EFH+++Y++ R+ E+A +L L+E QV+
Sbjct: 52 EFHFNKYLSRARRVEIAATLELNETQVKI 80
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 30.4 bits (67), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 20/27 (74%)
Query: 6 FHYSRYITIRRKAELANSLGLSERQVR 32
F ++Y+ + +AELA SLGL++ QV+
Sbjct: 26 FQKTQYLALPERAELAASLGLTQTQVK 52
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 28.9 bits (63), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 22/28 (78%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVR 32
EFH +Y+++ ++++A++L LSE QV+
Sbjct: 25 EFHCKKYLSLTERSQIAHALKLSEVQVK 52
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 28.5 bits (62), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 20/28 (71%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVR 32
EF ++ Y+T R+ E+A L L+ERQV+
Sbjct: 19 EFLFNMYLTRDRRYEVARVLNLTERQVK 46
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 20/28 (71%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVR 32
EF ++ Y+T R+ E+A L L+ERQV+
Sbjct: 31 EFLFNMYLTRDRRYEVARLLNLTERQVK 58
>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 = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 20/29 (68%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVRC 33
EF +++YI+ R+ ELA L L+ER ++
Sbjct: 21 EFLFNKYISRPRRVELAVMLNLTERHIKI 49
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 27.3 bits (59), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 20/28 (71%)
Query: 5 EFHYSRYITIRRKAELANSLGLSERQVR 32
+F +Y++I +AE ++SL L+E QV+
Sbjct: 18 KFRQKQYLSIAERAEFSSSLSLTETQVK 45
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 26.6 bits (57), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 6 FHYSRYITIRRKAELANSLGLSERQVRCPHH 36
F +Y++ + +LA SLGLS+ QV+ +
Sbjct: 36 FEKQKYLSTPDRIDLAESLGLSQLQVKTWYQ 66
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 10/27 (37%), Positives = 19/27 (70%)
Query: 6 FHYSRYITIRRKAELANSLGLSERQVR 32
F +Y+++++ EL+N L LS +QV+
Sbjct: 41 FQRQKYLSLQQMQELSNILNLSYKQVK 67
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
0.320 0.131 0.375
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,723,363
Number of Sequences: 62578
Number of extensions: 42401
Number of successful extensions: 207
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 29
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 178
Number of HSP's gapped (non-prelim): 29
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 (21.8 bits)
S2: 45 (21.9 bits)