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= 035661
(211 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 36.2 bits (82), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 26/52 (50%)
Query: 24 LNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQ 75
QEQ+ LE+ F A ++ +P ++ VW+ N+RA+W+ +
Sbjct: 14 FTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE 65
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 35.8 bits (81), Expect = 0.017, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 26/48 (54%)
Query: 28 QVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQ 75
Q+ LE++F A ++G+ ++ VW+QN+RA+W+ Q
Sbjct: 10 QLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
>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 = 35.8 bits (81), Expect = 0.018, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 26/48 (54%)
Query: 28 QVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQ 75
Q+ LE++F A ++G+ ++ VW+QN+RA+W+ Q
Sbjct: 17 QLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 64
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 35.8 bits (81), Expect = 0.019, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 26/48 (54%)
Query: 28 QVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQ 75
Q+ LE++F A ++G+ ++ VW+QN+RA+W+ Q
Sbjct: 10 QLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 35.4 bits (80), Expect = 0.024, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 24/51 (47%)
Query: 23 RLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
R + +Q LE+ F A L + RQV W+QN+RA+W+
Sbjct: 13 RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 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 = 35.0 bits (79), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 30/72 (41%), Gaps = 5/72 (6%)
Query: 12 HP-----PPNKLNIKKRLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQ 66
HP PP + + + QV LE+ F A L + QV W+Q
Sbjct: 7 HPYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQ 66
Query: 67 NKRARWKTQSLE 78
N+R +W+ Q+ E
Sbjct: 67 NRRTKWRRQTAE 78
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 34.3 bits (77), Expect = 0.053, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 25/50 (50%)
Query: 27 EQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQS 76
EQ+ LER+F A + + +V VW+ N+RARW+ Q+
Sbjct: 12 EQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQA 61
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 34.3 bits (77), Expect = 0.057, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 24/53 (45%)
Query: 24 LNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQS 76
++ QV LER F A L + QV W+QN+R +W+ Q+
Sbjct: 4 FSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQT 56
>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 = 33.5 bits (75), Expect = 0.080, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 24/49 (48%)
Query: 28 QVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQS 76
Q LE+ F A+ L + RQ+ +W+QN+R +WK ++
Sbjct: 7 QTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 55
>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 = 33.5 bits (75), Expect = 0.083, Method: Composition-based stats.
Identities = 14/56 (25%), Positives = 27/56 (48%)
Query: 21 KKRLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQS 76
++ + Q LE+ F A+ L + RQ+ +W+QN+R +WK ++
Sbjct: 6 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61
>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 = 33.5 bits (75), Expect = 0.089, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 20 IKKRLNQEQVRV----LERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQ 75
++KR Q R LE+ F A+ L + RQ+ +W+QN+R +WK +
Sbjct: 1 MRKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 60
Query: 76 S 76
+
Sbjct: 61 N 61
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 33.5 bits (75), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 21/46 (45%)
Query: 28 QVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
Q+ LE+ F A LG+ QV WYQN+R +WK
Sbjct: 28 QLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWK 73
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 33.1 bits (74), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 24/50 (48%)
Query: 24 LNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
EQ+ LE+ F A+ L + QV +W+QN+RA+WK
Sbjct: 14 FTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 63
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 33.1 bits (74), Expect = 0.10, Method: Composition-based stats.
Identities = 14/56 (25%), Positives = 27/56 (48%)
Query: 21 KKRLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQS 76
++ + Q LE+ F A+ L + RQ+ +W+QN+R +WK ++
Sbjct: 7 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 62
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 32.7 bits (73), Expect = 0.16, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 22/49 (44%)
Query: 23 RLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRAR 71
R Q+RVL+ F +N L +P R + VW+QN R +
Sbjct: 13 RFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQK 61
>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 = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 22/44 (50%)
Query: 32 LERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQ 75
LE+ F A+ L + RQ+ +W+QN+R +WK +
Sbjct: 43 LEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 86
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 31.6 bits (70), Expect = 0.33, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 22/46 (47%)
Query: 28 QVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
Q+ L+R F A LG+ QV +W+QNKR++ K
Sbjct: 18 QLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIK 63
>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 = 0.34, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 24/50 (48%)
Query: 24 LNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
+Q QV LER F A+ L + + QV +W+QN+R + K
Sbjct: 9 FSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>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 = 31.2 bits (69), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%)
Query: 27 EQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
EQ+ L+R F +++LG+ Q+ +W+QNKRA+ K
Sbjct: 13 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 59
>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 = 31.2 bits (69), Expect = 0.38, Method: Composition-based stats.
Identities = 14/58 (24%), Positives = 26/58 (44%)
Query: 20 IKKRLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQSL 77
++ LN++Q+ L + G+ R + VW+QNKR + K +S+
Sbjct: 6 VRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI 63
>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 = 0.38, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 25/55 (45%)
Query: 21 KKRLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQ 75
+ ++Q+ LE+ F A QL +P + VW+QN+R + K Q
Sbjct: 5 RTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 31.2 bits (69), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%)
Query: 27 EQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
EQ+ L+R F +++LG+ Q+ +W+QNKRA+ K
Sbjct: 11 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 57
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 30.8 bits (68), Expect = 0.55, Method: Composition-based stats.
Identities = 14/46 (30%), Positives = 22/46 (47%)
Query: 28 QVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
Q+ LER F ++ L + QV +W+QN+RA+ K
Sbjct: 11 QLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 30.8 bits (68), Expect = 0.62, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 24/53 (45%)
Query: 24 LNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQS 76
+Q QV LER F A+ + + QV +W+QN R + K Q+
Sbjct: 9 FSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 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 = 30.4 bits (67), Expect = 0.64, Method: Composition-based stats.
Identities = 13/50 (26%), Positives = 23/50 (46%)
Query: 26 QEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQ 75
+ Q+ LE+ F A L + R + +W+QN+R +WK +
Sbjct: 12 RAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 30.4 bits (67), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 27/58 (46%)
Query: 14 PPNKLNIKKRLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRAR 71
P ++ + EQ+ +L + + A+++G+ R V VW+QN RAR
Sbjct: 14 PQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRAR 71
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 30.4 bits (67), Expect = 0.74, Method: Composition-based stats.
Identities = 13/50 (26%), Positives = 23/50 (46%)
Query: 24 LNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
EQ+ LE F A ++ + +V VW++N+RA+W+
Sbjct: 14 FTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 63
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 30.4 bits (67), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 24/45 (53%)
Query: 27 EQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRAR 71
EQ+ L+R F +++LG+ Q+ +W+QNKRA+
Sbjct: 9 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>pdb|1JGT|A Chain A, Crystal Structure Of Beta-Lactam Synthetase
pdb|1JGT|B Chain B, Crystal Structure Of Beta-Lactam Synthetase
pdb|1M1Z|A Chain A, Beta-Lactam Synthetase Apo Enzyme
pdb|1M1Z|B Chain B, Beta-Lactam Synthetase Apo Enzyme
pdb|1MB9|A Chain A, Beta-Lactam Synthetase Complexed With Atp
pdb|1MB9|B Chain B, Beta-Lactam Synthetase Complexed With Atp
pdb|1MBZ|A Chain A, Beta-Lactam Synthetase With Trapped Intermediate
pdb|1MBZ|B Chain B, Beta-Lactam Synthetase With Trapped Intermediate
pdb|1MC1|A Chain A, Beta-Lactam Synthetase With Product (Dgpc), Amp And Ppi
pdb|1MC1|B Chain B, Beta-Lactam Synthetase With Product (Dgpc), Amp And Ppi
Length = 513
Score = 30.4 bits (67), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 152 EKAGSCSSFSLLHEEYHVHGNDHDHDQGLQIDHELFACLIGNGGHSN 198
E +G+ SSFS L ++ V D H+ Q+ ELF +G G H +
Sbjct: 448 EGSGTTSSFSRLLLDHGV-AEDRVHEAKRQVVRELFDLTVGGGRHPS 493
>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 = 30.0 bits (66), Expect = 0.89, Method: Composition-based stats.
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 59 RQVAVWYQNKRARWKTQSLELDYNTIQ 85
RQ+ +W+QN+R +WK + + IQ
Sbjct: 1 RQIKIWFQNRRMKWKKRVFNDARDIIQ 27
>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 = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 26/50 (52%)
Query: 24 LNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
+ EQ+ L+R F +++LG+ Q+ +W++NKRA+ K
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 59
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 29.6 bits (65), Expect = 1.3, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 21 KKRL--NQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
KKR+ ++ Q+R LER + + + RQ+ +W+QN+R + K
Sbjct: 9 KKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK 63
>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 = 29.3 bits (64), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 25/47 (53%)
Query: 27 EQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
EQ+ L+R F +++LG+ Q+ +W+QN+RA+ K
Sbjct: 11 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIK 57
>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 = 28.9 bits (63), Expect = 1.9, Method: Composition-based stats.
Identities = 14/53 (26%), Positives = 24/53 (45%)
Query: 21 KKRLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
++ + Q LE+ F AN L + RQ+ +W+QN+R + K
Sbjct: 7 RQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSK 59
>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 = 2.1, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 22/50 (44%)
Query: 28 QVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQSL 77
QV LER F A L + QV +W+QN+R + K + L
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQL 64
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 28.9 bits (63), Expect = 2.3, Method: Composition-based stats.
Identities = 8/15 (53%), Positives = 13/15 (86%)
Query: 59 RQVAVWYQNKRARWK 73
RQ+ +W+QN+R +WK
Sbjct: 1 RQIKIWFQNRRMKWK 15
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 28.5 bits (62), Expect = 2.5, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 2/55 (3%)
Query: 21 KKR--LNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
KKR + Q LE+ F A L + RQV +W+QN+R + K
Sbjct: 3 KKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMK 57
>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 = 28.5 bits (62), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 21/44 (47%)
Query: 32 LERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQ 75
LER+F A + + ++ VW+QN+RAR + Q
Sbjct: 33 LERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 76
>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 = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 24/47 (51%)
Query: 27 EQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
EQ+ L+R F +++LG+ Q+ +W+QN RA+ K
Sbjct: 11 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIK 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 = 28.5 bits (62), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 25/50 (50%)
Query: 24 LNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
+ EQ+ L+R F +++LG+ Q+ +W+ NKRA+ K
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIK 55
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 28.5 bits (62), Expect = 3.0, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 21 KKRL--NQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
KKR+ + Q++ LER + + + RQV +W+QN+R + K
Sbjct: 3 KKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 57
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 28.5 bits (62), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 23/50 (46%)
Query: 24 LNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
Q Q+ VLE F A +L + ++ +W+QN+RA+ K
Sbjct: 8 FTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLK 57
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 28.1 bits (61), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 20/42 (47%)
Query: 32 LERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
LE+ F A+ L + RQ+ +W+QN+R + K
Sbjct: 35 LEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLK 76
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 24/48 (50%)
Query: 24 LNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRAR 71
+ EQ+ +R F +++LG+ Q+ +W+QNKRA+
Sbjct: 10 FSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 57
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 27.7 bits (60), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 10/23 (43%), Positives = 18/23 (78%)
Query: 51 ANQLGVPARQVAVWYQNKRARWK 73
+++LG+ Q+ +W+QNKRA+ K
Sbjct: 20 SSELGLNEAQIKIWFQNKRAKIK 42
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 27.7 bits (60), Expect = 4.5, Method: Composition-based stats.
Identities = 14/56 (25%), Positives = 24/56 (42%)
Query: 21 KKRLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQS 76
+ Q+ LE+ F + +L + QV +W++N+R R K QS
Sbjct: 6 RTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQS 61
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 27.7 bits (60), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 19/42 (45%)
Query: 32 LERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
LE+ F A L + RQV +W+QN+R + K
Sbjct: 28 LEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMK 69
>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 = 27.7 bits (60), Expect = 5.4, Method: Composition-based stats.
Identities = 12/55 (21%), Positives = 25/55 (45%)
Query: 21 KKRLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQ 75
+ +Q++ LE +F A + +V VW++N+RA+W+ +
Sbjct: 7 RTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 27.3 bits (59), Expect = 6.6, Method: Composition-based stats.
Identities = 12/55 (21%), Positives = 25/55 (45%)
Query: 21 KKRLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQ 75
+ +Q++ LE +F A + +V VW++N+RA+W+ +
Sbjct: 7 RTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 27.3 bits (59), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 12/54 (22%), Positives = 24/54 (44%)
Query: 20 IKKRLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
++ Q+R ++ F A + G+ R + VW+QN RA+++
Sbjct: 10 MRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFR 63
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 26.9 bits (58), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 23/48 (47%)
Query: 24 LNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRAR 71
+ Q+ VLE F A ++ +P +V VW++N+RA+
Sbjct: 14 FTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAK 61
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 26.9 bits (58), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 8/14 (57%), Positives = 13/14 (92%)
Query: 60 QVAVWYQNKRARWK 73
+V VW+QN+RA+W+
Sbjct: 52 RVQVWFQNRRAKWR 65
>pdb|1QDM|A Chain A, Crystal Structure Of Prophytepsin, A Zymogen Of A Barley
Vacuolar Aspartic Proteinase.
pdb|1QDM|B Chain B, Crystal Structure Of Prophytepsin, A Zymogen Of A Barley
Vacuolar Aspartic Proteinase.
pdb|1QDM|C Chain C, Crystal Structure Of Prophytepsin, A Zymogen Of A Barley
Vacuolar Aspartic Proteinase
Length = 478
Score = 26.9 bits (58), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 62 AVWYQNKRARWKTQSLELDY 81
VW QN+ A+ KTQ L LDY
Sbjct: 359 VVWMQNQLAQNKTQDLILDY 378
>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 = 26.9 bits (58), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 21 KKRLNQEQ-VRV-LERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWK 73
KKR + E +RV LE+SF A+QL + + VW+ N+R + K
Sbjct: 102 KKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEK 156
>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 = 9.6, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 51 ANQLGVPARQVAVWYQNKRARWKTQS 76
ANQLG+ V VW+ N+R + K S
Sbjct: 130 ANQLGLEKDVVRVWFSNRRQKGKRSS 155
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
0.312 0.125 0.367
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,123,038
Number of Sequences: 62578
Number of extensions: 156745
Number of successful extensions: 373
Number of sequences better than 100.0: 62
Number of HSP's better than 100.0 without gapping: 53
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 320
Number of HSP's gapped (non-prelim): 62
length of query: 211
length of database: 14,973,337
effective HSP length: 95
effective length of query: 116
effective length of database: 9,028,427
effective search space: 1047297532
effective search space used: 1047297532
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: 49 (23.5 bits)