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= 047986
(134 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 32.3 bits (72), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 6 GLPPRQIAVWYQNRRAREKIHTI 28
GL PR I VW+QN+R ++K +I
Sbjct: 41 GLSPRVIRVWFQNKRCKDKKRSI 63
>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 = 31.6 bits (70), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 16/28 (57%), Positives = 19/28 (67%), Gaps = 1/28 (3%)
Query: 1 LARRLGLPPRQIAVWYQNRRAR-EKIHT 27
LA+R L +I VW+QNRRAR K HT
Sbjct: 51 LAQRTNLTEARIQVWFQNRRARLRKQHT 78
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 31.6 bits (70), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 12/22 (54%), Positives = 17/22 (77%)
Query: 1 LARRLGLPPRQIAVWYQNRRAR 22
LA ++GL +I VW+QNRRA+
Sbjct: 32 LAMKIGLTEARIQVWFQNRRAK 53
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
+A +GL R + VW+QN RARE+
Sbjct: 50 IAHEVGLKKRVVQVWFQNTRARER 73
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 31.2 bits (69), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 6 GLPPRQIAVWYQNRRAREK 24
L RQ+ +W+QNRR +EK
Sbjct: 45 NLSERQVTIWFQNRRVKEK 63
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 30.8 bits (68), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
+AR L L RQ+ +W+QNRR + K
Sbjct: 34 VARVLNLTERQVKIWFQNRRMKMK 57
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 30.8 bits (68), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 7 LPPRQIAVWYQNRRAREK 24
L RQI +W+QNRR +EK
Sbjct: 46 LSERQITIWFQNRRVKEK 63
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 6 GLPPRQIAVWYQNRRAREK 24
L RQ+ +W+QNRR +EK
Sbjct: 39 NLSERQVTIWFQNRRVKEK 57
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 12/22 (54%), Positives = 17/22 (77%)
Query: 1 LARRLGLPPRQIAVWYQNRRAR 22
LA ++GL +I VW+QNRRA+
Sbjct: 32 LAMKIGLTEARIQVWFQNRRAK 53
>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 = 30.0 bits (66), Expect = 0.37, Method: Composition-based stats.
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
+A++ G+ P Q+ VW+ N+R R K
Sbjct: 398 VAKKCGITPLQVRVWFINKRMRSK 421
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 30.0 bits (66), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
+AR L L RQ+ +W+QNRR + K
Sbjct: 46 VARLLNLTERQVKIWFQNRRMKMK 69
>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 = 30.0 bits (66), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
+A L L RQI +W+QNRR + K
Sbjct: 36 IANALSLSERQIKIWFQNRRMKSK 59
>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 = 29.6 bits (65), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 12/22 (54%), Positives = 17/22 (77%)
Query: 1 LARRLGLPPRQIAVWYQNRRAR 22
LA ++GL +I VW+QNRRA+
Sbjct: 39 LAMKIGLTEARIQVWFQNRRAK 60
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 29.6 bits (65), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 1 LARRLGLPPRQIAVWYQNRRAR 22
LA+ L L RQ+ W+QNRRA+
Sbjct: 40 LAKMLQLSERQVKTWFQNRRAK 61
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 29.6 bits (65), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREKIHT 27
L+ +L L Q+ +W++NRR R KI +
Sbjct: 35 LSAKLALGTAQVKIWFKNRRRRHKIQS 61
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 29.3 bits (64), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
+A++ G+ P Q+ VW+ N+R R K
Sbjct: 30 VAKKCGITPLQVRVWFINKRMRSK 53
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 28.9 bits (63), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 13/24 (54%), Positives = 15/24 (62%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
LA LGL Q+ WYQNRR + K
Sbjct: 50 LAESLGLSQLQVKTWYQNRRMKWK 73
>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 = 28.9 bits (63), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
+A L L RQI +W+QNRR + K
Sbjct: 29 IAHALSLTERQIKIWFQNRRMKWK 52
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 28.9 bits (63), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREKIHT 27
L+ LGL QI +W+QN+RA+ K T
Sbjct: 34 LSSELGLNEAQIKIWFQNKRAKIKKST 60
>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 = 28.9 bits (63), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
LA+ L L Q+ +W+QNRR + K
Sbjct: 37 LAKNLKLTETQVKIWFQNRRYKTK 60
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 28.9 bits (63), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
+A++ G+ P Q+ VW+ N+R R K
Sbjct: 38 VAKKCGITPLQVRVWFINKRMRSK 61
>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 = 28.9 bits (63), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
+A++ G+ P Q+ VW+ N+R R K
Sbjct: 38 VAKKCGITPLQVRVWFINKRMRSK 61
>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 = 28.9 bits (63), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 13/24 (54%), Positives = 17/24 (70%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
LA +L LP I VW+QNRR ++K
Sbjct: 34 LAAQLNLPESTIKVWFQNRRMKDK 57
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 28.9 bits (63), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
+A L L RQI +W+QNRR + K
Sbjct: 53 MAHALSLTERQIKIWFQNRRMKLK 76
>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 = 28.9 bits (63), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
+A L L RQI +W+QNRR + K
Sbjct: 61 IAHALSLTERQIKIWFQNRRMKWK 84
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 28.9 bits (63), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
+A L L RQI +W+QNRR + K
Sbjct: 36 IAHALSLTERQIKIWFQNRRMKWK 59
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
LA LGL Q+ +W+QN+R++ K
Sbjct: 40 LAASLGLTQTQVKIWFQNKRSKIK 63
>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 = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 1 LARRLGLPPRQIAVWYQNRRAR 22
L+ LGL QI +W+QN+RA+
Sbjct: 36 LSSELGLNEAQIKIWFQNKRAK 57
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 28.5 bits (62), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 1 LARRLGLPPRQIAVWYQNRRAR 22
LA++ GL R + VW+QN RA+
Sbjct: 40 LAQKTGLTKRVLQVWFQNARAK 61
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 18/24 (75%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
LA++L L +I +W+QNRRA+ K
Sbjct: 34 LAQKLNLELDRIQIWFQNRRAKLK 57
>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 = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
+A L L RQI +W+QNRR + K
Sbjct: 35 IAHALSLTERQIKIWFQNRRMKWK 58
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 5 LGLPPRQIAVWYQNRRAREK 24
L L Q+ +W+QNRRA+ K
Sbjct: 37 LSLTETQVKIWFQNRRAKAK 56
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 28.1 bits (61), Expect = 1.7, Method: Composition-based stats.
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
LA GL Q++ W++NRR R++
Sbjct: 527 LAEATGLTTTQVSNWFKNRRQRDR 550
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 5 LGLPPRQIAVWYQNRRAR 22
LGL QI +W+QN+RA+
Sbjct: 36 LGLNEAQIKIWFQNKRAK 53
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 5 LGLPPRQIAVWYQNRRAR 22
LGL QI +W+QN+RA+
Sbjct: 40 LGLNEAQIKIWFQNKRAK 57
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 17/22 (77%)
Query: 1 LARRLGLPPRQIAVWYQNRRAR 22
LAR++ L ++ VW++NRRA+
Sbjct: 40 LARKVHLREEKVEVWFKNRRAK 61
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 27.7 bits (60), Expect = 2.0, Method: Composition-based stats.
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
L+ LGL QI +W+QN+RA+ K
Sbjct: 19 LSSELGLNEAQIKIWFQNKRAKIK 42
>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 = 27.7 bits (60), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
+A L L RQI +W+QNRR + K
Sbjct: 35 IAHALCLTERQIKIWFQNRRMKWK 58
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 27.7 bits (60), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
+A L L Q+ +W+QNRRA+ K
Sbjct: 40 IAHALKLSEVQVKIWFQNRRAKWK 63
>pdb|2X26|A Chain A, Crystal Structure Of The Periplasmic Aliphatic Sulphonate
Binding Protein Ssua From Escherichia Coli
pdb|2X26|B Chain B, Crystal Structure Of The Periplasmic Aliphatic Sulphonate
Binding Protein Ssua From Escherichia Coli
Length = 308
Score = 27.3 bits (59), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREKIHTIELDYKTIQQELDNVLAENRKLEQEV 53
LA+ +GLP IA Y + R I + + +QQ+ ++ ENR + ++V
Sbjct: 227 LAKTMGLPAPVIAS-YLDHRPPTTIKPVNAEVAALQQQTADLFYENRLVPKKV 278
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 27.3 bits (59), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 1 LARRLGLPPRQIAVWYQNRRAR 22
LA ++ LP +I VW+ NRRA+
Sbjct: 40 LAAKIDLPEARIQVWFSNRRAK 61
>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 = 2.7, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
LA L L R I +W+QNRR + K
Sbjct: 36 LAVMLNLTERHIKIWFQNRRMKWK 59
>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 = 27.3 bits (59), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 1 LARRLGLPPRQIAVWYQNRRAR 22
L+ LGL QI +W+QN RA+
Sbjct: 34 LSSELGLNEAQIKIWFQNERAK 55
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 26.9 bits (58), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 9/22 (40%), Positives = 17/22 (77%)
Query: 1 LARRLGLPPRQIAVWYQNRRAR 22
+A ++ LP ++ VW++NRRA+
Sbjct: 40 VALKINLPESRVQVWFKNRRAK 61
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 26.9 bits (58), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
L+ L LP R I VW+QN R + +
Sbjct: 40 LSNLLNLPTRVIVVWFQNARQKAR 63
>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 = 26.9 bits (58), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 5 LGLPPRQIAVWYQNRRAR 22
LGL QI +W++N+RA+
Sbjct: 40 LGLNEAQIKIWFKNKRAK 57
>pdb|2R7A|A Chain A, Crystal Structure Of A Periplasmic Heme Binding Protein
From Shigella Dysenteriae
pdb|2R7A|B Chain B, Crystal Structure Of A Periplasmic Heme Binding Protein
From Shigella Dysenteriae
pdb|2R7A|C Chain C, Crystal Structure Of A Periplasmic Heme Binding Protein
From Shigella Dysenteriae
pdb|2R7A|D Chain D, Crystal Structure Of A Periplasmic Heme Binding Protein
From Shigella Dysenteriae
pdb|2RG7|A Chain A, Apo- Crystal Structure Of A Periplasmic Heme Binding
Protein From Shigella Dysenteriae
pdb|2RG7|B Chain B, Apo- Crystal Structure Of A Periplasmic Heme Binding
Protein From Shigella Dysenteriae
pdb|2RG7|C Chain C, Apo- Crystal Structure Of A Periplasmic Heme Binding
Protein From Shigella Dysenteriae
pdb|2RG7|D Chain D, Apo- Crystal Structure Of A Periplasmic Heme Binding
Protein From Shigella Dysenteriae
Length = 256
Score = 26.9 bits (58), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 12/49 (24%), Positives = 26/49 (53%)
Query: 63 SQQMLLASNPSATLLPSVSTSGDNDLTSSSSPLNMTCNWEDTGLLPMDE 111
S + L+A+NP ++ S GD + S + + T W++ ++ +D+
Sbjct: 184 SAESLIAANPEVIVVTSQMVDGDINRLRSIAGITHTAAWKNQRIITVDQ 232
>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 = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 5 LGLPPRQIAVWYQNRRAR 22
LGL QI +W+QN RA+
Sbjct: 38 LGLNEAQIKIWFQNARAK 55
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 26.6 bits (57), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 1 LARRLGLPPRQIAVWYQNRRAR 22
LA R L ++ VW+QNRRA+
Sbjct: 42 LAMRTDLTEARVQVWFQNRRAK 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 = 26.6 bits (57), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREKIHTIE 29
LAR L + Q+ W+QNRR + + T E
Sbjct: 50 LARGLKMTDAQVKTWFQNRRTKWRRQTAE 78
>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 = 26.6 bits (57), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
LAR+ G+ Q++ W+ N+R R K
Sbjct: 37 LARKCGITVSQVSNWFGNKRIRYK 60
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 26.2 bits (56), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
+A +L + I VW+ NRR +EK
Sbjct: 134 IAEQLNMEKEVIRVWFSNRRQKEK 157
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 25.8 bits (55), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 1 LARRLGLPPRQIAVWYQNRRAR 22
LA+R L ++ VW+ NRRAR
Sbjct: 35 LAQRAKLTEARVQVWFSNRRAR 56
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 25.8 bits (55), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
+A L L + VW+ NRR REK
Sbjct: 120 MAEELNLEKEVVRVWFCNRRQREK 143
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 25.8 bits (55), Expect = 6.9, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 10 RQIAVWYQNRRAREK 24
RQI +W+QNRR + K
Sbjct: 1 RQIKIWFQNRRMKWK 15
>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 = 25.8 bits (55), Expect = 6.9, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 10 RQIAVWYQNRRAREK 24
RQI +W+QNRR + K
Sbjct: 1 RQIKIWFQNRRMKWK 15
>pdb|2D8D|A Chain A, Structure Of Chorismate Mutase (Form I) From Thermus
Thermophilus Hb8
pdb|2D8D|B Chain B, Structure Of Chorismate Mutase (Form I) From Thermus
Thermophilus Hb8
pdb|2D8E|A Chain A, Structure Of Chorismate Mutase (Form Ii) From Thermus
Thermophilus Hb8
Length = 90
Score = 25.8 bits (55), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 10/61 (16%)
Query: 23 EKIHTIELDYKTIQQELDNVLAENRKLEQEVGMLKHEL-------KKSQQMLL---ASNP 72
E+I + + + +E+ +L+E +L QE+G L+ EL K+ ++ML A NP
Sbjct: 3 ERIQALRKEVDRVNREILRLLSERGRLVQEIGRLQTELGLPHYDPKREEEMLAYLTAENP 62
Query: 73 S 73
Sbjct: 63 G 63
>pdb|1FMH|A Chain A, Nmr Solution Structure Of A Designed Heterodimeric
Leucine Zipper
Length = 33
Score = 25.8 bits (55), Expect = 7.7, Method: Composition-based stats.
Identities = 12/25 (48%), Positives = 18/25 (72%)
Query: 35 IQQELDNVLAENRKLEQEVGMLKHE 59
+++E+ AEN +LEQEV L+HE
Sbjct: 6 LEKEVAQAEAENYQLEQEVAQLEHE 30
>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 = 25.8 bits (55), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
+A +L + I VW+ NRR +EK
Sbjct: 133 IADQLNMEKEVIRVWFSNRRQKEK 156
>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 = 25.8 bits (55), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 5 LGLPPRQIAVWYQNRRAR 22
LGL QI +W+ N+RA+
Sbjct: 36 LGLNEAQIKIWFANKRAK 53
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 25.8 bits (55), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 1 LARRLGLPPRQIAVWYQNRRAREK 24
+A +LGL + VW+ NRR + K
Sbjct: 129 IANQLGLEKDVVRVWFSNRRQKGK 152
>pdb|3T97|C Chain C, Molecular Architecture Of The Transport Channel Of The
Nuclear Pore Complex: Nup62NUP54
pdb|3T97|A Chain A, Molecular Architecture Of The Transport Channel Of The
Nuclear Pore Complex: Nup62NUP54
Length = 64
Score = 25.4 bits (54), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 10/27 (37%), Positives = 20/27 (74%)
Query: 24 KIHTIELDYKTIQQELDNVLAENRKLE 50
++ ++LD K + QELD +L++ ++LE
Sbjct: 20 EVEKVKLDQKRLDQELDFILSQQKELE 46
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
0.313 0.129 0.371
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,847,479
Number of Sequences: 62578
Number of extensions: 135138
Number of successful extensions: 350
Number of sequences better than 100.0: 81
Number of HSP's better than 100.0 without gapping: 75
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 274
Number of HSP's gapped (non-prelim): 82
length of query: 134
length of database: 14,973,337
effective HSP length: 88
effective length of query: 46
effective length of database: 9,466,473
effective search space: 435457758
effective search space used: 435457758
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 46 (22.3 bits)