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= 022702
(293 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 48.9 bits (115), Expect = 3e-06, Method: Composition-based stats.
Identities = 26/62 (41%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 78 GEKKRR---LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKT 134
GE KR+ Q LEK F L R++++A AL L RQ+ IWFQNRR +WK
Sbjct: 26 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 85
Query: 135 KQ 136
+
Sbjct: 86 EH 87
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/51 (47%), Positives = 31/51 (60%)
Query: 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
R + +Q LEK FE L P + +LA+ L L RQV WFQNRRA+W+
Sbjct: 13 RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 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 = 48.5 bits (114), Expect = 4e-06, Method: Composition-based stats.
Identities = 23/52 (44%), Positives = 30/52 (57%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEK 139
Q LEK F L R++++A AL L RQ+ IWFQNRR +WK + K
Sbjct: 7 QTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTK 58
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 26/63 (41%), Positives = 34/63 (53%)
Query: 71 SDDGSQAGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRA 130
S G ++ ++ EQ+ LEK F L + Q+A AL L QV IWFQNRRA
Sbjct: 1 SAPGGKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRA 60
Query: 131 RWK 133
+WK
Sbjct: 61 KWK 63
>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 = 48.1 bits (113), Expect = 6e-06, Method: Composition-based stats.
Identities = 23/52 (44%), Positives = 30/52 (57%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEK 139
Q LEK F L R++++A AL L RQ+ IWFQNRR +WK + K
Sbjct: 13 QTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKTK 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 = 48.1 bits (113), Expect = 6e-06, Method: Composition-based stats.
Identities = 23/52 (44%), Positives = 30/52 (57%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEK 139
Q LEK F L R++++A AL L RQ+ IWFQNRR +WK + K
Sbjct: 13 QTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTK 64
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 47.4 bits (111), Expect = 9e-06, Method: Composition-based stats.
Identities = 22/48 (45%), Positives = 29/48 (60%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTK 135
Q LEK F L R++++A AL L RQ+ IWFQNRR +WK +
Sbjct: 14 QTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 44.3 bits (103), Expect = 9e-05, Method: Composition-based stats.
Identities = 21/48 (43%), Positives = 29/48 (60%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTK 135
Q LEK F + L R++++A AL L RQ+ IWFQNRR + K +
Sbjct: 31 QTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE 78
>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 = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 20/49 (40%), Positives = 29/49 (59%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQ 136
Q+ LEK F + R+++LA L L R + IWFQNRR +WK ++
Sbjct: 14 QLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE 62
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/42 (45%), Positives = 24/42 (57%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRR 129
Q LEK F + R++ +A AL L RQ+ IWFQNRR
Sbjct: 14 QTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRR 55
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 22/46 (47%), Positives = 27/46 (58%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
Q LEK F L +R+ ++AR L L RQV IWFQNRR + K
Sbjct: 12 QTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMK 57
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 25/53 (47%), Positives = 31/53 (58%), Gaps = 2/53 (3%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKD 140
Q LEK F L +R+ ++AR L L RQV IWFQNRR K K++ KD
Sbjct: 24 QTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRM--KMKKINKD 74
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 75 SQAGEKKRRLNME-QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
++ G + R + E Q+ LEK FE L ++ LA +LGL QV W+QNRR +WK
Sbjct: 14 AKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWK 73
>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 = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 71 SDDGSQAGEKKRRLNMEQVKT--LEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNR 128
+ DG ++KRR+ + +T LE+ F L + LA + L P QV IWFQN
Sbjct: 1 ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNH 60
Query: 129 RARWKTKQLEKDYD 142
R + K Q EK Y+
Sbjct: 61 RYKTKRAQNEKGYE 74
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 2/72 (2%)
Query: 73 DGSQAGEKKRRLNMEQVKT--LEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRA 130
DG ++KRR+ + +T LE+ F L + L + L P QV IWFQN R
Sbjct: 6 DGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRY 65
Query: 131 RWKTKQLEKDYD 142
+ K Q EK Y+
Sbjct: 66 KTKRAQNEKGYE 77
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 29/51 (56%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLE 138
Q+ LEK F L R++++A L L QV IWFQNRR + K ++ E
Sbjct: 45 QLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE 95
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 28/47 (59%)
Query: 87 EQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
EQ+ L++ F L R+ QL+ LGL Q+ IWFQN+RA+ K
Sbjct: 13 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 59
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 28/47 (59%)
Query: 87 EQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
EQ+ L++ F L R+ QL+ LGL Q+ IWFQN+RA+ K
Sbjct: 11 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 57
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/50 (46%), Positives = 27/50 (54%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQL 137
QV LE+ F L + LA+ L L QV IWFQNRR + K KQL
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQL 64
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 26/51 (50%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLE 138
QV LEK F L + LAR L + QV WFQNRR +W+ + E
Sbjct: 28 QVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAE 78
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 27/45 (60%)
Query: 87 EQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRAR 131
EQ+ L++ F L R+ QL+ LGL Q+ IWFQN+RA+
Sbjct: 9 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>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 = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 27/47 (57%)
Query: 87 EQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
EQ+ L++ F L R+ QL+ LGL Q+ IWFQN RA+ K
Sbjct: 11 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIK 57
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 30/47 (63%)
Query: 87 EQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
EQ++ LE F+ + + QLAR + L+ +V +WF+NRRA+W+
Sbjct: 17 EQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 63
>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 = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 27/47 (57%)
Query: 87 EQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
EQ+ L++ F L R+ QL+ LGL Q+ IWFQN RA+ K
Sbjct: 11 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIK 57
>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 = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 28/47 (59%)
Query: 87 EQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
EQ+ L++ F L R+ QL+ LGL Q+ IWF+N+RA+ K
Sbjct: 13 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 59
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 31/49 (63%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQ 136
Q++ LEK F + + + +LA +GL ++ +WFQNRRA+W+ ++
Sbjct: 10 QLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 28/46 (60%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
Q+ L++ F+ L + +LA +LGL QV IWFQN+R++ K
Sbjct: 18 QLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIK 63
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 34/63 (53%)
Query: 74 GSQAGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
GS + EQ++ LEK FE + + + +LA + L ++ +WF NRRA+W+
Sbjct: 4 GSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWR 63
Query: 134 TKQ 136
++
Sbjct: 64 REE 66
>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 = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 27/47 (57%)
Query: 87 EQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
EQ+ L++ F L R+ QL+ LGL Q+ IWF N+RA+ K
Sbjct: 9 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIK 55
>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 = 0.009, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 29/54 (53%)
Query: 84 LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQL 137
LN +Q+ TL + + + K QL GL PR + +WFQN+R + K + +
Sbjct: 10 LNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI 63
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 25/46 (54%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
QV LE+ F L + LA+AL + QV WFQNRR +W+
Sbjct: 8 QVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWR 53
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 77 AGEKKRR-LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRAR 131
+G KKR + Q++ LE+ + + +++ +++ A L RQ+ IWFQNRR +
Sbjct: 6 SGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVK 61
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 26/45 (57%)
Query: 87 EQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRAR 131
EQ+ ++ F L R+ QL+ LGL Q+ IWFQN+RA+
Sbjct: 13 EQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 57
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 29/46 (63%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
Q++ LEK F + + + +LA +GL ++ +WFQNRRA+W+
Sbjct: 10 QLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 55
>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 = 37.0 bits (84), Expect = 0.012, Method: Composition-based stats.
Identities = 16/35 (45%), Positives = 22/35 (62%), Gaps = 4/35 (11%)
Query: 119 RQVAIWFQNRRARWKTKQLEKDYDLLK----RQYE 149
RQ+ IWFQNRR +WK + D+++ RQYE
Sbjct: 1 RQIKIWFQNRRMKWKKRVFNDARDIIQRMHLRQYE 35
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 25/46 (54%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
Q+ LE++F G L R L+ L L QV IWF+NRR R K
Sbjct: 13 QIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 36.6 bits (83), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 28/64 (43%), Positives = 37/64 (57%), Gaps = 6/64 (9%)
Query: 80 KKRRL--NMEQVKTLEKNFELGNKLE-PERKMQLARALGLQPRQVAIWFQNRRARWKTKQ 136
+KRR+ + QV LE+ F+ L PER+ LA + L P QV IWFQN R+K K+
Sbjct: 3 RKRRVLFSQAQVYELERRFKQQKYLSAPERE-HLASMIHLTPTQVKIWFQNH--RYKMKR 59
Query: 137 LEKD 140
KD
Sbjct: 60 QAKD 63
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 36.2 bits (82), Expect = 0.020, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 35/60 (58%), Gaps = 2/60 (3%)
Query: 78 GEKKRR--LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTK 135
G+++ R EQ++ LE+ FE + + + +LA+ L +V +WF NRRARW+ +
Sbjct: 1 GQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>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 = 36.2 bits (82), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 29/46 (63%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
Q++ LEK F + + + +LA +GL ++ +WFQNRRA+W+
Sbjct: 17 QLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 62
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 36.2 bits (82), Expect = 0.022, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 78 GEKKR-RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
G KKR Q+K LE+ + + +++ +++ L RQV IWFQNRR + K
Sbjct: 7 GRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 63
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 36.2 bits (82), Expect = 0.022, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 78 GEKKR-RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
G KKR Q+K LE+ + + +++ +++ L RQV IWFQNRR + K
Sbjct: 1 GRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 57
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 35.8 bits (81), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 29/47 (61%), Gaps = 4/47 (8%)
Query: 87 EQVKTLEKNFELGNKLEPERKM--QLARALGLQPRQVAIWFQNRRAR 131
EQ++ L + + L + P RKM +A +GL+ R V +WFQN RAR
Sbjct: 27 EQLEILYQKYLLDS--NPTRKMLDHIAHEVGLKKRVVQVWFQNTRAR 71
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 35.8 bits (81), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 35/67 (52%)
Query: 74 GSQAGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
GS + Q++T++ F + + + + QLA+ GL R + +WFQN RA+++
Sbjct: 4 GSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFR 63
Query: 134 TKQLEKD 140
L ++
Sbjct: 64 RNLLRQE 70
>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 = 35.8 bits (81), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 20/42 (47%), Positives = 23/42 (54%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRR 129
QV LE+ F+ L + QLA L L QV IWFQNRR
Sbjct: 13 QVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRR 54
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 35.4 bits (80), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 75 SQAGEKKRR---LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRAR 131
S G+K+R Q++ LEK F+ + + + QLA L +V +WFQNRRA+
Sbjct: 4 SNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAK 63
Query: 132 WKTKQ 136
W+ ++
Sbjct: 64 WRKRE 68
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 35.4 bits (80), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 16/32 (50%), Positives = 21/32 (65%)
Query: 102 LEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
L R+ QL+ LGL Q+ IWFQN+RA+ K
Sbjct: 11 LTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 42
>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 = 34.7 bits (78), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 26/47 (55%)
Query: 87 EQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
EQ+ L++ F L R+ QL+ LGL QV WF+N RA+ K
Sbjct: 14 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 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 = 34.7 bits (78), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 8/74 (10%)
Query: 68 DDFSDDGSQAG----EKKRR----LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPR 119
+D SD S+ G K+RR + Q+ LE+ FE + + +LA+ L
Sbjct: 1 EDISDCESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEA 60
Query: 120 QVAIWFQNRRARWK 133
++ +WFQNRRAR +
Sbjct: 61 RIQVWFQNRRARLR 74
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 33.9 bits (76), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 25/46 (54%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
Q+ LE+ F L + + + +L L QV IWFQNRRA+ K
Sbjct: 11 QLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
>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 = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 92 LEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRAR 131
LE+ F L + K ++A+ G+ P QV +WF N+R R
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 419
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 33.5 bits (75), Expect = 0.16, Method: Composition-based stats.
Identities = 30/94 (31%), Positives = 45/94 (47%), Gaps = 11/94 (11%)
Query: 77 AGEKKRRLNMEQVKTLEKNF--ELGNKLEPER-KMQLARALGLQPRQVAIWFQNRRARWK 133
A K+R N + + L + F L N E K +LA+ G+ QV+ WF N+R R+K
Sbjct: 1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 134 TKQLEKDYDLLKRQYEA-VKADREALQAQNQKLH 166
++ K Q EA + A + A+ A N H
Sbjct: 61 K-------NIGKFQEEANIYAAKTAVTATNVSAH 87
>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 = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 92 LEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRAR 131
LE+ F L + K ++A+ G+ P QV +WF N+R R
Sbjct: 20 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 59
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 92 LEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRAR 131
LE+ F L + K ++A+ G+ P QV +WF N+R R
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 51
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 15/28 (53%), Positives = 18/28 (64%)
Query: 104 PERKMQLARALGLQPRQVAIWFQNRRAR 131
P K +LA A GL QV+ WF+NRR R
Sbjct: 521 PREKRELAEATGLTTTQVSNWFKNRRQR 548
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 33.1 bits (74), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 92 LEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRAR 131
LE+ F L + K ++A+ G+ P QV +WF N+R R
Sbjct: 20 LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 59
>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 = 32.7 bits (73), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 24/43 (55%)
Query: 87 EQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRR 129
+Q+ LEK F N + R+ +LA L L + +WFQNRR
Sbjct: 11 DQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRR 53
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 32.0 bits (71), Expect = 0.39, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 77 AGEKKRRLNMEQVKTLEKNF--ELGNKLEPER-KMQLARALGLQPRQVAIWFQNRRARWK 133
A K+R N + + L + F L N E K +LA+ G+ QV+ WF N+R R+K
Sbjct: 1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 31.6 bits (70), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 74 GSQAGEKKRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWK 133
GSQ ++ +Q++ LE F+ + + + ++A L +V +WF+NRRA+W+
Sbjct: 1 GSQRRQRTH-FTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWR 59
Query: 134 TKQ 136
++
Sbjct: 60 KRE 62
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 31.6 bits (70), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 62 EEANGEDDFSDDGSQAGEKKRR----LNMEQVKTLEKNFELGNKLEPERKMQLARALGLQ 117
EEA ++ A E+KR+ +++ LE++F +K + M++A L L+
Sbjct: 68 EEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLE 127
Query: 118 PRQVAIWFQNRRARWK 133
V +WF NRR R K
Sbjct: 128 KEVVRVWFCNRRQREK 143
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 31.6 bits (70), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 28/54 (51%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKDY 141
Q++ LE F + + LA+ L L+ ++ IWFQNRRA+ K E +
Sbjct: 12 QIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRESQF 65
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 31.6 bits (70), Expect = 0.62, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 77 AGEKKRRLNMEQVKTLEKNF--ELGNKLEPER-KMQLARALGLQPRQVAIWFQNRRARWK 133
A K+R N + + L + F L N E K +LA+ G+ QV+ WF N+R R+K
Sbjct: 2 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYK 61
>pdb|2HI3|A Chain A, Solution Structure Of The Homeodomain-Only Protein Hop
Length = 73
Score = 31.2 bits (69), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 87 EQVKTLEKNFELGNKL-EPERKMQLARALGLQPRQVAIWFQNRRARWK 133
+QV+ LE NF NK +P +A GL Q WF+ R A W+
Sbjct: 12 DQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 59
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 31.2 bits (69), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 84 LNMEQVKTLEKNFELGNKL-EPERKMQLARALGLQPRQVAIWFQNRRARWK 133
+ +QV+ LE NF NK +P +A GL Q WF+ R A W+
Sbjct: 8 MTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 58
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 30.8 bits (68), Expect = 0.89, Method: Composition-based stats.
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 119 RQVAIWFQNRRARWK 133
RQ+ IWFQNRR +WK
Sbjct: 1 RQIKIWFQNRRMKWK 15
>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 = 0.96, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 29/50 (58%)
Query: 87 EQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQ 136
+Q++ LE F+ + + ++A L +V +WF+NRRA+W+ ++
Sbjct: 13 QQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
>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 = 1.2, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 77 AGEKKRRLNMEQVKTLEKNF--ELGNKLEPER-KMQLARALGLQPRQVAIWFQNRRARWK 133
A K+R + + + L + F L N E K +LAR G+ QV+ WF N+R R+K
Sbjct: 1 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYK 60
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 29.6 bits (65), Expect = 1.8, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 82 RRLNMEQVKTLEKNF--ELGNKLEPER-KMQLARALGLQPRQVAIWFQNRRARWK 133
R +N + + L + F L N E K +LA+ G+ QV+ WF N+R R+K
Sbjct: 8 RHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 62
>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 = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 24/55 (43%)
Query: 87 EQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRARWKTKQLEKDY 141
EQ+ L+ F PE +LA+ GL + WF + R WK L+ Y
Sbjct: 35 EQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNLKWYY 89
>pdb|1OBH|A Chain A, Leucyl-Trna Synthetase From Thermus Thermophilus Complexed
With A Pre-Transfer Editing Substrate Analogue In Both
Synthetic Active Site And Editing Site
pdb|2BTE|A Chain A, Thermus Thermophilus Leucyl-Trna Synthetase Complexed With
With A Trnaleu Transcript In The Post-Editing
Conformation And A Post-Transfer Editing Substrate
Analogue
pdb|2BTE|D Chain D, Thermus Thermophilus Leucyl-Trna Synthetase Complexed With
With A Trnaleu Transcript In The Post-Editing
Conformation And A Post-Transfer Editing Substrate
Analogue
pdb|2BYT|A Chain A, Thermus Thermophilus Leucyl-Trna Synthetase Complexed With
A Trnaleu Transcript In The Post-Editing Conformation
pdb|2BYT|D Chain D, Thermus Thermophilus Leucyl-Trna Synthetase Complexed With
A Trnaleu Transcript In The Post-Editing Conformation
pdb|1H3N|A Chain A, Leucyl-Trna Synthetase From Thermus Thermophilus Complexed
With A Sulphamoyl Analogue Of Leucyl-Adenylate
pdb|1OBC|A Chain A, Leucyl-Trna Synthetase From Thermus Thermophilus Complexed
With A Post-Transfer Editing Substrate Analogue
pdb|2V0G|A Chain A, Leucyl-Trna Synthetase From Thermus Thermophilus Complexed
With A Trna(Leu) Transcript With 5-Fluoro-1,3-Dihydro-1-
Hydroxy-2,1-Benzoxaborole (An2690) Forming An Adduct To
The Ribose Of Adenosine-76 In The Enzyme Editing Site.
pdb|2V0G|D Chain D, Leucyl-Trna Synthetase From Thermus Thermophilus Complexed
With A Trna(Leu) Transcript With 5-Fluoro-1,3-Dihydro-1-
Hydroxy-2,1-Benzoxaborole (An2690) Forming An Adduct To
The Ribose Of Adenosine-76 In The Enzyme Editing Site
Length = 878
Score = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 132 WKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSREVTESIN--LNKETE 188
W + ++ + L R Y V DREAL + AE + K RE+ ++ L K TE
Sbjct: 676 WTEEGVQGAWRFLNRIYRRVAEDREALLETSGVFQAEALEGKDRELYGKLHETLKKVTE 734
>pdb|2V0C|A Chain A, Leucyl-Trna Synthetase From Thermus Thermophilus Complexed
With A Sulphamoyl Analogue Of Leucyl-Adenylate In The
Synthetic Site And An Adduct Of Amp With 5-Fluoro-1,3-
Dihydro-1-Hydroxy-2,1-Benzoxaborole (An2690) In The
Editing Site
Length = 878
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 132 WKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKSREVTESIN--LNKETE 188
W + ++ + L R Y V DREAL + AE + K RE+ ++ L K TE
Sbjct: 676 WTEEGVQGAWRFLNRIYRRVAEDREALLETSGVFQAEALEGKDRELYGKLHETLKKVTE 734
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 28.9 bits (63), Expect = 3.1, Method: Composition-based stats.
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 120 QVAIWFQNRRARWK 133
Q+ IWFQNRR +WK
Sbjct: 2 QIKIWFQNRRMKWK 15
>pdb|3CUX|A Chain A, Atomic Resolution Structures Of Escherichia Coli And
Bacillis Anthracis Malate Synthase A: Comparison With
Isoform G And Implications For Structure Based Drug
Design
Length = 528
Score = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 29/149 (19%), Positives = 55/149 (36%), Gaps = 13/149 (8%)
Query: 128 RRARWKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALK-------SREVTES 180
R A W +L KD + + + + + A N H + + +
Sbjct: 70 READWTIAKLPKDLEDRRVEITGPVDRKMVINALNSGAHLFMADFEDSNSPTWENAIEGQ 129
Query: 181 INLNKETEGSCSNRSENSSDIKLDISRTPAIDSPMSTHPTSRNL-FPTKSTSSVRPTVAA 239
INL +G+ S+++EN + +L+ I P H +++ K+ S
Sbjct: 130 INLRDAVKGTISHKNENGKEYRLNSKTAVLIVRPRGWHLEEKHMQVDGKNMSGSLVDFGL 189
Query: 240 QLFHNSSS-----SRPDLQCQKIEQNMQG 263
FHN+ + S P K+E ++
Sbjct: 190 YFFHNAKALLEKGSGPYFYLPKMESYLEA 218
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 28.5 bits (62), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 24/49 (48%)
Query: 83 RLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRAR 131
R Q++ L+ F+ + + QL+ L L R + +WFQN R +
Sbjct: 13 RFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQK 61
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 28.1 bits (61), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRR---ARW 132
Q+ L F+ L ++ +L+ L L +QV WFQN+R RW
Sbjct: 33 QLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRW 80
>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 = 8.6, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 3/49 (6%)
Query: 88 QVKTLEKNFELGNKLEPERKMQLARALGLQPRQVAIWFQNRRA---RWK 133
Q+ L+ F+ L ++ +L+ L L +QV WFQN+R RW+
Sbjct: 14 QLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRWQ 62
>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 428
Score = 27.7 bits (60), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 28/43 (65%)
Query: 132 WKTKQLEKDYDLLKRQYEAVKADREALQAQNQKLHAEIMALKS 174
+K K+LEK+Y+LL Q + +K ++ L+ + ++ E+ ++S
Sbjct: 49 FKLKKLEKEYELLTLQEDYIKDEQRHLKRELKRAQEEVKRIQS 91
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 0.126 0.367
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,262,309
Number of Sequences: 62578
Number of extensions: 316140
Number of successful extensions: 623
Number of sequences better than 100.0: 100
Number of HSP's better than 100.0 without gapping: 82
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 537
Number of HSP's gapped (non-prelim): 103
length of query: 293
length of database: 14,973,337
effective HSP length: 98
effective length of query: 195
effective length of database: 8,840,693
effective search space: 1723935135
effective search space used: 1723935135
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: 51 (24.3 bits)