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= psy10851
(159 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/25 (64%), Positives = 21/25 (84%)
Query: 41 LAKDTGLSVRVVQVWFQNQRAKMKK 65
LA+ TGL+ RV+QVWFQN RAK ++
Sbjct: 40 LAQKTGLTKRVLQVWFQNARAKFRR 64
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 29/45 (64%), Gaps = 3/45 (6%)
Query: 27 SCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAK 71
+C PG + E LA+ L + +Q+WFQN+RAK+K+ R+++
Sbjct: 23 NCYPG---IDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRESQ 64
>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 = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/29 (58%), Positives = 23/29 (79%)
Query: 37 VREALAKDTGLSVRVVQVWFQNQRAKMKK 65
++E L + TGLS RV++VWFQN+R K KK
Sbjct: 32 MKEQLVEMTGLSPRVIRVWFQNKRCKDKK 60
>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 = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 22/29 (75%)
Query: 37 VREALAKDTGLSVRVVQVWFQNQRAKMKK 65
RE LA+ T L+ +QVWFQN+RA+++K
Sbjct: 47 TREELAQRTNLTEARIQVWFQNRRARLRK 75
>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 = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 30/47 (63%), Gaps = 2/47 (4%)
Query: 19 VKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
+LK FN + T + R+ L+ + GL+ +++WFQN+RAK+KK
Sbjct: 14 ARLKREFNEN--RYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 16/32 (50%), Positives = 23/32 (71%)
Query: 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
T ++ + +A + GL RVVQVWFQN RA+ +K
Sbjct: 43 TRKMLDHIAHEVGLKKRVVQVWFQNTRARERK 74
>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 = 36.2 bits (82), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 30/47 (63%), Gaps = 2/47 (4%)
Query: 19 VKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
+LK FN + T + R+ L+ + GL+ +++WFQN+RAK+KK
Sbjct: 16 ARLKREFNEN--RYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 35.8 bits (81), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 30/47 (63%), Gaps = 2/47 (4%)
Query: 19 VKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
+LK FN + T + R+ L+ + GL+ +++WFQN+RAK+KK
Sbjct: 14 ARLKREFNEN--RYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 35.8 bits (81), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 19/38 (50%), Positives = 25/38 (65%)
Query: 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQE 74
RE LA T L+ VQVWFQN+RAK +K +R + Q+
Sbjct: 38 AREQLAMRTDLTEARVQVWFQNRRAKWRKRERFGQMQQ 75
>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 = 35.4 bits (80), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 29/47 (61%), Gaps = 2/47 (4%)
Query: 19 VKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
+LK FN + T + R+ L+ + GL+ +++WFQN RAK+KK
Sbjct: 14 ARLKREFNEN--RYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 35.0 bits (79), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 16/29 (55%), Positives = 20/29 (68%)
Query: 37 VREALAKDTGLSVRVVQVWFQNQRAKMKK 65
RE LA GL+ +QVWFQN+RAK +K
Sbjct: 28 TREELAMKIGLTEARIQVWFQNRRAKWRK 56
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 35.0 bits (79), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 16/29 (55%), Positives = 20/29 (68%)
Query: 37 VREALAKDTGLSVRVVQVWFQNQRAKMKK 65
RE LA GL+ +QVWFQN+RAK +K
Sbjct: 28 TREELAMKIGLTEARIQVWFQNRRAKWRK 56
>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 = 0.021, Method: Compositional matrix adjust.
Identities = 16/29 (55%), Positives = 20/29 (68%)
Query: 37 VREALAKDTGLSVRVVQVWFQNQRAKMKK 65
RE LA GL+ +QVWFQN+RAK +K
Sbjct: 35 TREELAMKIGLTEARIQVWFQNRRAKWRK 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 = 34.3 bits (77), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 30/47 (63%), Gaps = 2/47 (4%)
Query: 19 VKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
+LK FN + T + R+ L+ + GL+ +++WF+N+RAK+KK
Sbjct: 16 ARLKREFNEN--RYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 34.3 bits (77), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 23/35 (65%)
Query: 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68
T R +A+ L+ R V++WFQN+R KMKKI +
Sbjct: 39 TRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINK 73
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 33.9 bits (76), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 24/32 (75%)
Query: 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
T + R+ L+ + GL+ +++WFQN+RAK+KK
Sbjct: 12 TERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43
>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 = 33.5 bits (75), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 29/47 (61%), Gaps = 2/47 (4%)
Query: 19 VKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
+LK FN + T + R+ L+ + GL+ +++WF N+RAK+KK
Sbjct: 12 ARLKREFNEN--RYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 32.7 bits (73), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 21/29 (72%)
Query: 38 REALAKDTGLSVRVVQVWFQNQRAKMKKI 66
R +A+ L+ R V++WFQN+R KMKK+
Sbjct: 31 RYEVARVLNLTERQVKIWFQNRRMKMKKM 59
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 32.7 bits (73), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 28/45 (62%), Gaps = 2/45 (4%)
Query: 19 VKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKM 63
+LK FN + T + R+ L+ + GL+ +++WFQN+RAK+
Sbjct: 12 ARLKREFNEN--RYLTERRRQQLSSELGLNEAQIKIWFQNKRAKI 54
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 32.7 bits (73), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 20/28 (71%)
Query: 38 REALAKDTGLSVRVVQVWFQNQRAKMKK 65
R LA GL+ V++WFQN+R+K+KK
Sbjct: 37 RAELAASLGLTQTQVKIWFQNKRSKIKK 64
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 32.7 bits (73), Expect = 0.100, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 21/34 (61%)
Query: 38 REALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAK 71
R ++ T LS R V +WFQN+R K KK+ K K
Sbjct: 37 RRRISATTNLSERQVTIWFQNRRVKEKKVINKLK 70
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 32.3 bits (72), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 21/34 (61%)
Query: 38 REALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAK 71
R ++ T LS R V +WFQN+R K KK+ K K
Sbjct: 31 RRRISATTNLSERQVTIWFQNRRVKEKKVINKLK 64
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 32.3 bits (72), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 29/47 (61%), Gaps = 2/47 (4%)
Query: 19 VKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
+ K FN + T + R+ L+ + GL+ +++WFQN+RAK+++
Sbjct: 16 ARAKREFNEN--RYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60
>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 = 31.6 bits (70), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 2/47 (4%)
Query: 19 VKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
+LK FN + T + R+ L+ + GL+ V+ WF+N RAK+KK
Sbjct: 17 ARLKREFNENR--YLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 30.8 bits (68), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 15/28 (53%), Positives = 20/28 (71%)
Query: 38 REALAKDTGLSVRVVQVWFQNQRAKMKK 65
R+ LAK LS R V+ WFQN+RAK ++
Sbjct: 37 RKRLAKMLQLSERQVKTWFQNRRAKWRR 64
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 30.8 bits (68), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
+ + +E LAK G++V V WF N+R + KK
Sbjct: 32 SEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 30.8 bits (68), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
T R ++ T LS R + +WFQN+R K KK
Sbjct: 33 TKDKRRKISAATSLSERQITIWFQNRRVKEKK 64
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 30.8 bits (68), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 22/34 (64%)
Query: 32 HKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
+ + + +E LAK +G++V V WF N+R + KK
Sbjct: 29 YPSEEAKEELAKKSGITVSQVSNWFGNKRIRYKK 62
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 30.4 bits (67), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 32 HKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
+ + + +E LAK G++V V WF N+R + KK
Sbjct: 28 YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 30.0 bits (66), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 18/28 (64%)
Query: 38 REALAKDTGLSVRVVQVWFQNQRAKMKK 65
RE LA L+ V++WFQN R KMK+
Sbjct: 32 REHLASMIHLTPTQVKIWFQNHRYKMKR 59
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 30.0 bits (66), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 23/39 (58%)
Query: 29 CPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67
C + + R +A LS V++WFQN+RAK K+I+
Sbjct: 28 CKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKRIK 66
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 30.0 bits (66), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 37 VREALAKDTGLSVRVVQVWFQNQRAKMKK 65
RE LA+ L+ VQVWF N+RA+ +K
Sbjct: 31 TREELAQRAKLTEARVQVWFSNRRARWRK 59
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 30.0 bits (66), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
T + R +A L+ R +++WFQN+R K+KK
Sbjct: 46 TRRRRIEMAHALSLTERQIKIWFQNRRMKLKK 77
>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 = 0.61, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 13 RLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
R L+++ + FN + + AL+ LS R +++WFQN+R K KK
Sbjct: 12 RYQTLELEKEFHFNRYITRRRRIDIANALS----LSERQIKIWFQNRRMKSKK 60
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 29.6 bits (65), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
+ +E LAK G++V V WF N+R + KK
Sbjct: 32 EAKEELAKKCGITVSQVSNWFGNKRIRYKK 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 = 29.6 bits (65), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 20/30 (66%)
Query: 38 REALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67
R LAK+ L+ V++WFQN+R K K+ Q
Sbjct: 34 RAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 63
>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 = 29.6 bits (65), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 13 RLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
R L+++ + FN + ++ AL+ L+ R +++WFQN+R K KK
Sbjct: 5 RYQTLELEKEFHFNRYLTRRRRIEIAHALS----LTERQIKIWFQNRRMKWKK 53
>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 = 29.6 bits (65), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 32 HKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
+ + + +E LA+ G++V V WF N+R + KK
Sbjct: 28 YPSEEAKEELARKCGITVSQVSNWFGNKRIRYKK 61
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 29.3 bits (64), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 37 VREALAKDTGLSVRVVQVWFQNQRAKMKK 65
RE LA+ L V+VWF+N+RAK ++
Sbjct: 36 TREQLARKVHLREEKVEVWFKNRRAKWRR 64
>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 = 29.3 bits (64), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 13 RLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
R L+++ + FN + ++ AL+ L+ R +++WFQN+R K KK
Sbjct: 11 RYQTLELEKEFHFNRYLTRRRRIEIAHALS----LTERQIKIWFQNRRMKWKK 59
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 29.3 bits (64), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 13 RLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
R L+++ + FN + ++ AL+ L+ R +++WFQN+R K KK
Sbjct: 12 RYQTLELEKEFHFNRYLTRRRRIEIAHALS----LTERQIKIWFQNRRMKWKK 60
>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 = 29.3 bits (64), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 18/30 (60%)
Query: 38 REALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67
RE LA L+ V++WFQN R K K+ Q
Sbjct: 39 REHLASLIRLTPTQVKIWFQNHRYKTKRAQ 68
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 29.3 bits (64), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQ--RKAKQQEGDKS 78
RE LA L +QVWF N+RAK ++ + R ++Q G S
Sbjct: 36 ARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQRRQSGPSS 79
>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 = 29.3 bits (64), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 13 RLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
R L+++ + FN + ++ AL+ L+ R +++WFQN+R K KK
Sbjct: 37 RYQTLELEKEFHFNRYLTRRRRIEIAHALS----LTERQIKIWFQNRRMKWKK 85
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 20/29 (68%)
Query: 37 VREALAKDTGLSVRVVQVWFQNQRAKMKK 65
RE +A T L+ V+VWF+N+RAK +K
Sbjct: 32 TREEIAVWTNLTEARVRVWFKNRRAKWRK 60
>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 = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 20/29 (68%)
Query: 37 VREALAKDTGLSVRVVQVWFQNQRAKMKK 65
RE +A T L+ V+VWF+N+RAK +K
Sbjct: 32 TREEIAVWTNLTEARVRVWFKNRRAKWRK 60
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 39 EALAKDTGLSVRVVQVWFQNQRAKMKK 65
E L+ L RV+ VWFQN R K +K
Sbjct: 38 EQLSNLLNLPTRVIVVWFQNARQKARK 64
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of
Human Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 28.5 bits (62), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 39 EALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67
E L K TGLS R V+ WF ++R + ++
Sbjct: 39 EHLTKVTGLSTREVRKWFSDRRYHCRNLK 67
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 28.1 bits (61), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 6/53 (11%)
Query: 16 NLKVKLKTSF--NSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66
N++V L+ SF N T + E L + V++VWF N+R K K+I
Sbjct: 111 NIRVALEKSFMENQKPTSEDITLIAEQL----NMEKEVIRVWFSNRRQKEKRI 159
>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 = 28.1 bits (61), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 13 RLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
R L+++ + FN + ++ AL L+ R +++WFQN+R K KK
Sbjct: 11 RYQTLELEKEFHFNRYLTRRRRIEIAHALC----LTERQIKIWFQNRRMKWKK 59
>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 = 28.1 bits (61), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 6/53 (11%)
Query: 16 NLKVKLKTSF--NSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66
N++V L+ SF N + T + + L + V++VWF N+R K K+I
Sbjct: 110 NIRVALEKSFLENQKPTSEEITMIADQL----NMEKEVIRVWFSNRRQKEKRI 158
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 28.1 bits (61), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 20/32 (62%)
Query: 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
+T R LA+ GLS V+ W+QN+R K KK
Sbjct: 43 STPDRIDLAESLGLSQLQVKTWYQNRRMKWKK 74
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 27.7 bits (60), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 38 REALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67
RE L L+ V++WFQN R K K+ Q
Sbjct: 42 REHLTSLIRLTPTQVKIWFQNHRYKTKRAQ 71
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 27.7 bits (60), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 39 EALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68
+ L+ LS + V+ WFQNQR K K+ Q+
Sbjct: 53 QELSNILNLSYKQVKTWFQNQRMKSKRWQK 82
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 27.7 bits (60), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 37 VREALAKDTGLSVRVVQVWFQNQRAKMK 64
+RE +A L VQVWF+N+RAK +
Sbjct: 36 MREEVALKINLPESRVQVWFKNRRAKCR 63
>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 = 3.5, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 38 REALAKDTGLSVRVVQVWFQNQRAKMKK 65
R LA L+ R +++WFQN+R K KK
Sbjct: 33 RVELAVMLNLTERHIKIWFQNRRMKWKK 60
>pdb|3K2A|A Chain A, Crystal Structure Of The Homeobox Domain Of Human
Homeobox Protein Meis2
pdb|3K2A|B Chain B, Crystal Structure Of The Homeobox Domain Of Human
Homeobox Protein Meis2
Length = 67
Score = 27.3 bits (59), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 41 LAKDTGLSVRVVQVWFQNQRAKM 63
LA+DTGL++ V WF N R ++
Sbjct: 34 LAQDTGLTILQVNNWFINARRRI 56
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 27.3 bits (59), Expect = 3.9, Method: Composition-based stats.
Identities = 11/35 (31%), Positives = 21/35 (60%)
Query: 38 REALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQ 72
+ LA+ TGL+ V WF+N+R + + + K ++
Sbjct: 524 KRELAEATGLTTTQVSNWFKNRRQRDRAAEAKERE 558
>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 = 27.3 bits (59), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 21/36 (58%)
Query: 32 HKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67
+ + Q + L+ LS + V+ WFQNQR K K+ Q
Sbjct: 27 YLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRWQ 62
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 27.3 bits (59), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 38 REALAKDTGLSVRVVQVWFQNQRAKMKKI 66
R + L+ V++WFQN+RAK K++
Sbjct: 30 RAEFSSSLSLTETQVKIWFQNRRAKAKRL 58
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 26.9 bits (58), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 29 CPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
CP Q+ +A GL VV+VWF N+R K K+
Sbjct: 30 CPKPSLQQI-THIANQLGLEKDVVRVWFCNRRQKGKR 65
>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 = 26.6 bits (57), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 6/53 (11%)
Query: 16 NLKVKLKTSF--NSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66
N++V L+ SF N + T + + L + V++VWF N+R K K+I
Sbjct: 114 NIRVALEKSFLENQKPTSEEITMIADQL----NMEKEVIRVWFCNRRQKEKRI 162
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 26.6 bits (57), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 38 REALAKDTGLSVRVVQVWFQNQRAKMKKIQRKA 70
R +A L+ V++WFQN+R K KK +R+
Sbjct: 64 RVEIAATLELNETQVKIWFQNRRMKQKKREREG 96
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 26.6 bits (57), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 41 LAKDTGLSVRVVQVWFQNQRAKMKK 65
+A GL VV+VWF N+R K K+
Sbjct: 129 IANQLGLEKDVVRVWFSNRRQKGKR 153
>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 = 26.2 bits (56), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 28/45 (62%), Gaps = 3/45 (6%)
Query: 38 REALAKDTGLSVRVVQVWFQNQRAKMKKI---QRKAKQQEGDKSL 79
R ALA+ ++ V+ WFQN+R K ++ +R+A++Q ++ +
Sbjct: 47 RAALARGLKMTDAQVKTWFQNRRTKWRRQTAEEREAERQAANRLM 91
>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 = 26.2 bits (56), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 6/53 (11%)
Query: 16 NLKVKLKTSF--NSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66
N++V L+ SF N + T + + L + V++VWF N+R K K+I
Sbjct: 113 NIRVALEKSFLENQKPTSEEITMIADQL----NMEKEVIRVWFCNRRQKEKRI 161
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 26.2 bits (56), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 10/27 (37%), Positives = 19/27 (70%)
Query: 41 LAKDTGLSVRVVQVWFQNQRAKMKKIQ 67
+A++ L VV+VWF N+R + K+++
Sbjct: 120 MAEELNLEKEVVRVWFCNRRQREKRVK 146
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 26.2 bits (56), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 29 CPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKA 70
CP ++ LA L VV+VWF N+R K K++ A
Sbjct: 121 CPKPSAHEI-TGLADSLQLEKEVVRVWFCNRRQKEKRMTPAA 161
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 26.2 bits (56), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 38 REALAKDTGLSVRVVQVWFQNQRAKMKK 65
R ALAK ++ V+ WFQN+R K ++
Sbjct: 27 RAALAKALRMTDAQVKTWFQNRRTKWRR 54
>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 = 25.8 bits (55), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 6/53 (11%)
Query: 16 NLKVKLKTSF--NSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66
N++V L+ SF N + T + + L + V++VWF N+R K K+I
Sbjct: 106 NIRVALEKSFLENQKPTSEEITMIADQL----NMEKEVIRVWFCNRRQKEKRI 154
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
0.315 0.129 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,817,616
Number of Sequences: 62578
Number of extensions: 128673
Number of successful extensions: 349
Number of sequences better than 100.0: 85
Number of HSP's better than 100.0 without gapping: 78
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 270
Number of HSP's gapped (non-prelim): 86
length of query: 159
length of database: 14,973,337
effective HSP length: 91
effective length of query: 68
effective length of database: 9,278,739
effective search space: 630954252
effective search space used: 630954252
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 bits)