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= 029280
(196 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/51 (47%), Positives = 35/51 (68%), Gaps = 1/51 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
FS EQ+ L+ F +E+ L R++ Q+++ELGL Q+ IWFQNKRA+ K
Sbjct: 10 FSSEQLARLKREF-NENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 59
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/51 (47%), Positives = 35/51 (68%), Gaps = 1/51 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
FS EQ+ L+ F +E+ L R++ Q+++ELGL Q+ IWFQNKRA+ K
Sbjct: 8 FSSEQLARLKREF-NENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 57
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 43.5 bits (101), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 23/49 (46%), Positives = 34/49 (69%), Gaps = 1/49 (2%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRAR 77
FS EQ+ L+ F +E+ L R++ Q+++ELGL Q+ IWFQNKRA+
Sbjct: 6 FSSEQLARLKREF-NENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/51 (45%), Positives = 35/51 (68%), Gaps = 1/51 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
FS EQ+ L+ F +E+ L R++ Q+++ELGL Q+ IWF+NKRA+ K
Sbjct: 10 FSSEQLARLKREF-NENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/51 (45%), Positives = 35/51 (68%), Gaps = 1/51 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
FS EQ+ L+ F +E+ L R++ Q+++ELGL Q+ IWFQN+RA+ K
Sbjct: 8 FSSEQLARLKREF-NENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIK 57
>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 = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/51 (45%), Positives = 34/51 (66%), Gaps = 1/51 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
FS EQ+ L+ F +E+ L R++ Q+++ELGL Q+ IWFQN RA+ K
Sbjct: 8 FSSEQLARLKREF-NENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIK 57
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/51 (45%), Positives = 34/51 (66%), Gaps = 1/51 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
FS EQ+ L+ F +E+ L R++ Q+++ELGL Q+ IWF NKRA+ K
Sbjct: 6 FSSEQLARLKREF-NENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIK 55
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 33/49 (67%), Gaps = 1/49 (2%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRAR 77
FS EQ+ + F +E+ L R++ Q+++ELGL Q+ IWFQNKRA+
Sbjct: 10 FSSEQLARAKREF-NENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 57
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 33/51 (64%), Gaps = 1/51 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
FS++Q LE FE++ L P ++ ++A L L RQV WFQN+RA+W+
Sbjct: 14 FSNDQTIELEKKFETQKY-LSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 63
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 18/37 (48%), Positives = 27/37 (72%)
Query: 43 SESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
+E+ L R++ Q+++ELGL Q+ IWFQNKRA+ K
Sbjct: 6 NENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 42
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 36/51 (70%), Gaps = 1/51 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
F+DEQ+ LE++F+ E+ + + Q+A ++ L+ +V +WF+N+RA+W+
Sbjct: 14 FTDEQLEALENLFQ-ETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 63
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 23/32 (71%)
Query: 48 LEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
L R+++++A L L RQ+ IWFQN+R +WK
Sbjct: 28 LTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 59
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
F+ EQ+ LE F + L ++ Q+A L L QV IWFQN+RA+WK
Sbjct: 14 FTSEQLLELEKEFHCKKY-LSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 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 = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 23/32 (71%)
Query: 48 LEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
L R+++++A L L RQ+ IWFQN+R +WK
Sbjct: 21 LTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 52
>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 = 0.002, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 23/32 (71%)
Query: 48 LEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
L R+++++A L L RQ+ IWFQN+R +WK
Sbjct: 27 LTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 58
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 23/33 (69%)
Query: 48 LEPRKKMQVATELGLQPRQVAIWFQNKRARWKS 80
L R+++++A L L RQ+ IWFQN+R +WK
Sbjct: 27 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 59
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 23/32 (71%)
Query: 48 LEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
L R+++++A L L RQ+ IWFQN+R +WK
Sbjct: 53 LTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 84
>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 = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 33/51 (64%), Gaps = 1/51 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
FS EQ+ L+ F +E+ L R++ Q+++ELGL QV WF+N RA+ K
Sbjct: 11 FSSEQLARLKREF-NENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 60
>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 = 35.8 bits (81), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 36 LLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
LE +F + + L ++K +VA + G+ P QV +WF NKR R K
Sbjct: 379 FLEQVFRRKQS-LNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 35.4 bits (80), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 37 LESIFESESTKLEPRKKM--QVATELGLQPRQVAIWFQNKRAR 77
LE +++ P +KM +A E+GL+ R V +WFQN RAR
Sbjct: 29 LEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRAR 71
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 35.4 bits (80), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
F++ Q+ LE FE + P ++ +A LGL QV W+QN+R +WK
Sbjct: 24 FTELQLMGLEKRFEKQKYLSTP-DRIDLAESLGLSQLQVKTWYQNRRMKWK 73
>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 = 35.4 bits (80), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 36 LLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
LE +F + + L ++K +VA + G+ P QV +WF NKR R K
Sbjct: 19 FLEQVFRRKQS-LNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 35.4 bits (80), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 36 LLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
LE +F + + L ++K +VA + G+ P QV +WF NKR R K
Sbjct: 11 FLEQVFRRKQS-LNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 35.4 bits (80), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 36 LLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
LE +F + + L ++K +VA + G+ P QV +WF NKR R K
Sbjct: 19 FLEEVFRRKQS-LNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 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 = 35.0 bits (79), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 22/31 (70%)
Query: 52 KKMQVATELGLQPRQVAIWFQNKRARWKSKQ 82
+++++A L L R + IWFQN+R +WK ++
Sbjct: 32 RRVELAVMLNLTERHIKIWFQNRRMKWKKEE 62
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 34.3 bits (77), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 22/32 (68%)
Query: 48 LEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
L R+++++A L L RQ+ IWFQN+R + K
Sbjct: 45 LTRRRRIEMAHALSLTERQIKIWFQNRRMKLK 76
>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 = 34.3 bits (77), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 51 RKKMQVATELGLQPRQVAIWFQNKRARWK 79
R+++ +A L L RQ+ IWFQN+R + K
Sbjct: 31 RRRIDIANALSLSERQIKIWFQNRRMKSK 59
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 33.9 bits (76), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 24/38 (63%), Gaps = 2/38 (5%)
Query: 52 KKMQVATELGLQPRQVAIWFQNKRARWKSKQIEHDYAQ 89
++ +VA L L RQV IWFQN+R K K+I D A+
Sbjct: 42 RRYEVARLLNLTERQVKIWFQNRRM--KMKKINKDRAK 77
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 33.9 bits (76), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
+S Q+ L+ F+ P ++ ++A LGL QV IWFQNKR++ K
Sbjct: 14 YSSFQLAALQRRFQKTQYLALP-ERAELAASLGLTQTQVKIWFQNKRSKIK 63
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 33.1 bits (74), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 33/54 (61%), Gaps = 1/54 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQ 82
F+ Q+ LE F S + + + ++A ++GL ++ +WFQN+RA+W+ ++
Sbjct: 6 FTSFQLEELEKAF-SRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 33.1 bits (74), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
F Q+R ++S F + + Q+A + GL R + +WFQN RA+++
Sbjct: 14 FKHHQLRTMKSYFAINHNP-DAKDLKQLAQKTGLTKRVLQVWFQNARAKFR 63
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 33.1 bits (74), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
FS Q+ LE F+ + P ++ +A+ + L P QV IWFQN R + K
Sbjct: 9 FSQAQVYELERRFKQQKYLSAPERE-HLASMIHLTPTQVKIWFQNHRYKMK 58
>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 = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 9/59 (15%)
Query: 29 FSDEQIRLLESIFESESTKLEPRK----KMQVATELGLQPRQVAIWFQNKRARWKSKQI 83
+++Q+ L + + + PR K Q+ GL PR + +WFQNKR + K + I
Sbjct: 10 LNEKQLHTLRTCYAAN-----PRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI 63
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 32.7 bits (73), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 10/28 (35%), Positives = 22/28 (78%)
Query: 55 QVATELGLQPRQVAIWFQNKRARWKSKQ 82
++A ++GL ++ +WFQN+RA+W+ ++
Sbjct: 31 ELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>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 = 32.7 bits (73), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEHDY 87
F+ Q LE F + P ++ +A+ + L P QV IWFQN R + K Q E Y
Sbjct: 16 FTKAQTYELERRFRQQRYLSAPERE-HLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGY 73
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQ 82
F+ Q+ LE +F+ ++ + + Q+A L +V +WFQN+RA+W+ ++
Sbjct: 16 FTSYQLEELEKVFQ-KTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRE 68
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 32.3 bits (72), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRAR 77
F+D Q+R+L+ F++ + + + Q++ L L R + +WFQN R +
Sbjct: 14 FTDYQLRVLQDFFDANAYPKDDEFE-QLSNLLNLPTRVIVVWFQNARQK 61
>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 = 32.3 bits (72), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 10/28 (35%), Positives = 22/28 (78%)
Query: 55 QVATELGLQPRQVAIWFQNKRARWKSKQ 82
++A ++GL ++ +WFQN+RA+W+ ++
Sbjct: 38 ELAMKIGLTEARIQVWFQNRRAKWRKQE 65
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 32.0 bits (71), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 31/53 (58%), Gaps = 5/53 (9%)
Query: 29 FSDEQIRLLESIFESES--TKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
+S Q+R LE + + TK + R+K+ AT L RQ+ IWFQN+R + K
Sbjct: 14 YSKGQLRELEREYAANKFITK-DKRRKISAATSL--SERQITIWFQNRRVKEK 63
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 32.0 bits (71), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 9/63 (14%)
Query: 29 FSDEQIRLLESIFESESTK----LEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIE 84
F+ QI +LE++F LE +A +L L+ ++ IWFQN+RA+ K E
Sbjct: 8 FTQNQIEVLENVFRVNCYPGIDILE-----DLAQKLNLELDRIQIWFQNRRAKLKRSHRE 62
Query: 85 HDY 87
+
Sbjct: 63 SQF 65
>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 = 31.6 bits (70), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 31/53 (58%), Gaps = 3/53 (5%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSK 81
FS Q+ LE F+ + P ++ Q+A+ L L QV IWFQN+ R+KSK
Sbjct: 9 FSQAQVYELERRFKQQRYLSAP-ERDQLASVLKLTSTQVKIWFQNR--RYKSK 58
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 31.6 bits (70), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 25/51 (49%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
+++Q+ +LE F + +P +A E GL Q WF+ + A W+
Sbjct: 8 MTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 58
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 31.6 bits (70), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIE 84
F+ Q+ LE F L +++++A L L QV IWFQN+R + K ++ E
Sbjct: 41 FTTRQLTELEKEFHFNKY-LSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE 95
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 31.2 bits (69), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEHDY 87
F+ Q LE F + P ++ + + + L P QV IWFQN R + K Q E Y
Sbjct: 19 FTKAQTYELERRFRQQRYLSAPERE-HLTSLIRLTPTQVKIWFQNHRYKTKRAQNEKGY 76
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 31.2 bits (69), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 35/55 (63%), Gaps = 3/55 (5%)
Query: 29 FSDEQIRLLESIFE-SESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQ 82
F+ +Q++ LE+ F+ + + R+++ V T L +V +WF+N+RA+W+ ++
Sbjct: 10 FTSQQLQELEATFQRNHYPDMSTREEIAVWT--NLTEARVRVWFKNRRAKWRKRE 62
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 31.2 bits (69), Expect = 0.36, Method: Composition-based stats.
Identities = 14/28 (50%), Positives = 19/28 (67%)
Query: 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79
++ +VA L L RQV IWFQN+R + K
Sbjct: 30 RRYEVARVLNLTERQVKIWFQNRRMKMK 57
>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 = 31.2 bits (69), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKR 75
F+ +Q+ LE F E+ PR+ ++A +L L + +WFQN+R
Sbjct: 8 FTRDQLGRLEKEFYKENYVSRPRR-CELAAQLNLPESTIKVWFQNRR 53
>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 = 30.8 bits (68), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 53 KMQVATELGLQPRQVAIWFQNKRARWKSKQI 83
+ +A L L QV IWFQN+R + K KQ+
Sbjct: 34 RAHLAKNLKLTETQVKIWFQNRRYKTKRKQL 64
>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 = 30.8 bits (68), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 35/55 (63%), Gaps = 3/55 (5%)
Query: 29 FSDEQIRLLESIFE-SESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQ 82
F+ +Q++ LE+ F+ + + R+++ V T L +V +WF+N+RA+W+ ++
Sbjct: 10 FTSQQLQELEATFQRNRYPDMSTREEIAVWT--NLTEARVRVWFKNRRAKWRKRE 62
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 30.8 bits (68), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 31/52 (59%), Gaps = 3/52 (5%)
Query: 29 FSDEQIRLLESIFE-SESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
F+ EQI LE FE + + R+++ A ++ L ++ +WF N+RA+W+
Sbjct: 14 FTQEQIEALEKEFERTHYPDVFARERL--AAKIDLPEARIQVWFSNRRAKWR 63
>pdb|2HI3|A Chain A, Solution Structure Of The Homeodomain-Only Protein Hop
Length = 73
Score = 30.8 bits (68), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 25/50 (50%)
Query: 30 SDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
+++Q+ +LE F + +P +A E GL Q WF+ + A W+
Sbjct: 10 TEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 59
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 30.8 bits (68), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 50 PRKKMQVATELGLQPRQVAIWFQNKRAR 77
PR+K ++A GL QV+ WF+N+R R
Sbjct: 521 PREKRELAEATGLTTTQVSNWFKNRRQR 548
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 30.8 bits (68), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 29 FSDEQIRLLESIFESESTKLEPRK--KMQVATELGLQPRQVAIWFQNKRARWK 79
F+ + +L F S + P + K ++A + G+ QV+ WF NKR R+K
Sbjct: 8 FNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 30.4 bits (67), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 29 FSDEQIRLLESIFESESTKLEPRK--KMQVATELGLQPRQVAIWFQNKRARWK 79
F+ + +L F S + P + K ++A + G+ QV+ WF NKR R+K
Sbjct: 8 FNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 30.4 bits (67), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79
K+ +++ L RQV IWFQN+R + K
Sbjct: 36 KRRRISATTNLSERQVTIWFQNRRVKEK 63
>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 = 30.4 bits (67), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 29 FSDEQIRLLESIFESESTKLEPRK--KMQVATELGLQPRQVAIWFQNKRARWK 79
FS + +L F S + P + K ++A + G+ QV+ WF NKR R+K
Sbjct: 8 FSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYK 60
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 30.0 bits (66), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 52 KKMQVATELGLQPRQVAIWFQNKRARWK 79
K+ +++ L RQV IWFQN+R + K
Sbjct: 30 KRRRISATTNLSERQVTIWFQNRRVKEK 57
>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 = 0.76, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEH 85
F+ QI LE F PR ++ +L L QV IWF+N+R R K + +H
Sbjct: 9 FTSSQIAELEQHFLQGRYLTAPRL-ADLSAKLALGTAQVKIWFKNRRRRHKIQSDQH 64
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 30.0 bits (66), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSK 81
F+ EQ+ LE FE + + + ++A L +V +WF N+RARW+ +
Sbjct: 9 FTAEQLEELERAFER-THYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 29.3 bits (64), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 53 KMQVATELGLQPRQVAIWFQNKRARWK 79
K ++A + G+ QV+ WF NKR R+K
Sbjct: 36 KEELAKKCGITVSQVSNWFGNKRIRYK 62
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 29.3 bits (64), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
F+ Q+ LE F + L ++ + ++ L L QV IWFQN+RA+ K
Sbjct: 7 FTTAQLLALERKFRQKQY-LSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
>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 = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 65 RQVAIWFQNKRARWKSK 81
RQ+ IWFQN+R +WK +
Sbjct: 1 RQIKIWFQNRRMKWKKR 17
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 28.9 bits (63), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 33/51 (64%), Gaps = 1/51 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
F+ Q+ +LE++F +++ + + +VA ++ L +V +WF+N+RA+ +
Sbjct: 14 FTRAQLDVLEALF-AKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63
>pdb|2DA4|A Chain A, Solution Structure Of The Homeobox Domain Of The
Hypothetical Protein, Dkfzp686k21156
Length = 80
Score = 28.9 bits (63), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 3/59 (5%)
Query: 29 FSDEQIRLLESIFESESTKLE--PRKKMQ-VATELGLQPRQVAIWFQNKRARWKSKQIE 84
FSD + L+ +++ T L R+K++ VATEL + V W N+R +++ IE
Sbjct: 15 FSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMGIE 73
>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 = 28.9 bits (63), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEHDYA 88
F+ Q+ LE F + L ++ +A L + QV WFQN+R +W+ + E A
Sbjct: 24 FTRIQVAELEKRFHKQKY-LASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEEREA 82
Query: 89 QLRA 92
+ +A
Sbjct: 83 ERQA 86
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 29 FSDEQIRLLESIFESESTKLEPRK--KMQVATELGLQPRQVAIWFQNKRARWK 79
F+ + +L F S + P + K ++A + G+ QV+ WF NKR R+K
Sbjct: 9 FNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYK 61
>pdb|3NAR|A Chain A, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And
Homeoboxes Protein 1, Homeodomain 4)
pdb|3NAR|B Chain B, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And
Homeoboxes Protein 1, Homeodomain 4)
Length = 96
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 30 SDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWKSKQIEHDYAQ 89
+ EQ+ +L+S F + P + ++A E GL + WF + R WK+ ++ Y
Sbjct: 33 TPEQLHMLKSAF-VRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNLKWYYYY 91
Query: 90 LRAN 93
AN
Sbjct: 92 QSAN 95
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 28.5 bits (62), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
FS Q+ LE F + L ++ +A L + QV WFQN+R +W+
Sbjct: 4 FSRSQVLELERRFLRQKY-LASAERAALAKALRMTDAQVKTWFQNRRTKWR 53
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 22/36 (61%)
Query: 44 ESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
E +K ++ M++A EL L+ V +WF N+R R K
Sbjct: 108 EHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREK 143
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 28.1 bits (61), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 65 RQVAIWFQNKRARWKS 80
RQ+ IWFQN+R +WK
Sbjct: 1 RQIKIWFQNRRMKWKK 16
>pdb|2D5V|A Chain A, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
pdb|2D5V|B Chain B, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
Length = 164
Score = 27.7 bits (60), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 5/51 (9%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVAT--ELGLQPRQVAIWFQNKRAR 77
F+D Q R L +IF+ P K++Q+ +LGL+ V+ +F N R R
Sbjct: 104 FTDVQRRTLHAIFKENK---RPSKELQITISQQLGLELSTVSNFFMNARRR 151
>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 = 27.7 bits (60), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
FS Q+ L+ F+ + L ++ ++++ L L +QV WFQN+R + K
Sbjct: 10 FSQAQLCALKDRFQKQKY-LSLQQMQELSSILNLSYKQVKTWFQNQRMKCK 59
>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 = 26.9 bits (58), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 29 FSDEQIRLLESIFE-SESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
FS Q+ LE FE ++ + R+++ A L ++ +WFQN+RAR +
Sbjct: 25 FSASQLDELERAFERTQYPDIYTREEL--AQRTNLTEARIQVWFQNRRARLR 74
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 26.9 bits (58), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 37 LESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
LE++F +S K ++ +A +LGL+ V +WF N+R + K
Sbjct: 111 LETMF-LKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGK 152
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 26.6 bits (57), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 29 FSDEQIRLLESIFESESTKLEPRKKMQVATELGLQPRQVAIWFQNKRARWK 79
FS Q+ +L F+ + L ++ +++ L L +QV WFQN+R + K
Sbjct: 29 FSSTQLCVLNDRFQRQKY-LSLQQMQELSNILNLSYKQVKTWFQNQRMKSK 78
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 0.130 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,817,919
Number of Sequences: 62578
Number of extensions: 90644
Number of successful extensions: 314
Number of sequences better than 100.0: 78
Number of HSP's better than 100.0 without gapping: 73
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 240
Number of HSP's gapped (non-prelim): 78
length of query: 196
length of database: 14,973,337
effective HSP length: 94
effective length of query: 102
effective length of database: 9,091,005
effective search space: 927282510
effective search space used: 927282510
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 49 (23.5 bits)