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= 041877
(254 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 = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 34/70 (48%)
Query: 21 VHGDEDLSDDGSQVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAI 80
VH + + ++ Q LEK F L R++++A AL L RQI I
Sbjct: 15 VHLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKI 74
Query: 81 WFQNRRARWK 90
WFQNRR +WK
Sbjct: 75 WFQNRRMKWK 84
>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 = 47.4 bits (111), Expect = 7e-06, Method: Composition-based stats.
Identities = 24/52 (46%), Positives = 30/52 (57%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQLEK 96
Q LEK F L R++++A AL L RQI IWFQNRR +WK + K
Sbjct: 7 QTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTK 58
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 47.4 bits (111), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/51 (45%), Positives = 31/51 (60%)
Query: 40 RLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
R + +Q LEK FE L P + +LA+ L L RQ+ WFQNRRA+W+
Sbjct: 13 RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 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 = 46.6 bits (109), Expect = 1e-05, Method: Composition-based stats.
Identities = 24/52 (46%), Positives = 30/52 (57%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQLEK 96
Q LEK F L R++++A AL L RQI 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 = 46.6 bits (109), Expect = 1e-05, Method: Composition-based stats.
Identities = 24/52 (46%), Positives = 30/52 (57%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQLEK 96
Q LEK F L R++++A AL L RQI 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 = 45.8 bits (107), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/48 (47%), Positives = 29/48 (60%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTK 92
Q LEK F L R++++A AL L RQI IWFQNRR +WK +
Sbjct: 14 QTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 33/63 (52%)
Query: 28 SDDGSQVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRA 87
S G + ++ EQ+ LEK F L + Q+A AL L Q+ IWFQNRRA
Sbjct: 1 SAPGGKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRA 60
Query: 88 RWK 90
+WK
Sbjct: 61 KWK 63
>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 = 43.9 bits (102), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 20/42 (47%), Positives = 24/42 (57%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRR 86
Q LEK F + R++ +A AL L RQI IWFQNRR
Sbjct: 14 QTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRR 55
>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 = 43.1 bits (100), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/49 (42%), Positives = 29/49 (59%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93
Q+ LEK F + R+++LA L L R I IWFQNRR +WK ++
Sbjct: 14 QLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE 62
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 43.1 bits (100), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/48 (45%), Positives = 29/48 (60%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTK 92
Q LEK F + L R++++A AL L RQI IWFQNRR + K +
Sbjct: 31 QTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE 78
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 27/46 (58%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
Q+ LEK FE L ++ LA +LGL Q+ W+QNRR +WK
Sbjct: 28 QLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWK 73
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 42.0 bits (97), Expect = 4e-04, Method: Composition-based stats.
Identities = 21/46 (45%), Positives = 27/46 (58%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
Q LEK F L +R+ ++AR L L RQ+ IWFQNRR + K
Sbjct: 12 QTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMK 57
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 41.2 bits (95), Expect = 6e-04, Method: Composition-based stats.
Identities = 24/53 (45%), Positives = 31/53 (58%), Gaps = 2/53 (3%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQLEKD 97
Q LEK F L +R+ ++AR L L RQ+ IWFQNRR K K++ KD
Sbjct: 24 QTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRM--KMKKINKD 74
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 28 SDDGSQVGEKKKRLNLE--QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNR 85
+ DG ++K+R+ Q LE+ F L + LA + L P Q+ IWFQN
Sbjct: 1 ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNH 60
Query: 86 RARWKTKQLEKDYE 99
R + K Q EK YE
Sbjct: 61 RYKTKRAQNEKGYE 74
>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna
Complex At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|1HDD|D Chain D, Crystal Structure Of An Engrailed Homeodomain-Dna
Complex At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|2JWT|A Chain A, Solution Structure Of Engrailed Homeodomain Wt
Length = 61
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 28/47 (59%)
Query: 44 EQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
EQ+ L++ F L R+ QL+ LGL QI IWFQN+RA+ K
Sbjct: 13 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 59
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 30/46 (65%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
Q++ LEK+F + + + +LA +GL +I +WFQNRRA+W+
Sbjct: 10 QLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 55
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 39.3 bits (90), Expect = 0.002, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 32/49 (65%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93
Q++ LEK+F + + + +LA +GL +I +WFQNRRA+W+ ++
Sbjct: 10 QLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 28/47 (59%)
Query: 44 EQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
EQ+ L++ F L R+ QL+ LGL QI IWFQN+RA+ K
Sbjct: 11 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 57
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 29/51 (56%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQLE 95
Q+ LEK F L R++++A L L Q+ IWFQNRR + K ++ E
Sbjct: 45 QLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE 95
>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 = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 28/53 (52%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQLEKD 97
QV LE+ F L + LA+ L L Q+ IWFQNRR + K KQL +
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSE 67
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 31/47 (65%)
Query: 44 EQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
EQ++ALE F+ + + QLAR + L+ ++ +WF+NRRA+W+
Sbjct: 17 EQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 63
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%)
Query: 31 GSQVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
GS + EQ++ALEK FE + + + +LA + L +I +WF NRRA+W+
Sbjct: 4 GSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWR 63
Query: 91 TKQ 93
++
Sbjct: 64 REE 66
>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 = 38.1 bits (87), Expect = 0.004, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 32/49 (65%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93
Q++ LEK+F + + + +LA +GL +I +WFQNRRA+W+ ++
Sbjct: 17 QLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 65
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/45 (44%), Positives = 27/45 (60%)
Query: 44 EQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRAR 88
EQ+ L++ F L R+ QL+ LGL QI IWFQN+RA+
Sbjct: 9 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 34/73 (46%), Gaps = 2/73 (2%)
Query: 29 DDGSQVGEKKKRLNLE--QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRR 86
DG ++K+R+ Q LE+ F L + L + L P Q+ IWFQN R
Sbjct: 5 SDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHR 64
Query: 87 ARWKTKQLEKDYE 99
+ K Q EK YE
Sbjct: 65 YKTKRAQNEKGYE 77
>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 = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 27/47 (57%)
Query: 44 EQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
EQ+ L++ F L R+ QL+ LGL QI IWFQN RA+ K
Sbjct: 11 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIK 57
>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 = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 26/51 (50%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQLE 95
QV LEK F L + LAR L + Q+ WFQNRR +W+ + E
Sbjct: 28 QVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAE 78
>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 = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 34 VGEKKKR--LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
+ EK+ R + EQ+ L++ F L R+ QL+ LGL QI IWF+N+RA+ K
Sbjct: 1 MAEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 59
>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 = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 27/47 (57%)
Query: 44 EQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
EQ+ L++ F L R+ QL+ LGL QI IWFQN RA+ K
Sbjct: 11 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIK 57
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 37.0 bits (84), Expect = 0.010, Method: Composition-based stats.
Identities = 18/46 (39%), Positives = 29/46 (63%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
Q+ AL++ F+ L + +LA +LGL Q+ IWFQN+R++ K
Sbjct: 18 QLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIK 63
>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 = 36.6 bits (83), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 27/47 (57%)
Query: 44 EQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
EQ+ L++ F L R+ QL+ LGL QI IWF N+RA+ K
Sbjct: 9 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIK 55
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 36.2 bits (82), Expect = 0.016, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 36/60 (60%), Gaps = 2/60 (3%)
Query: 35 GEKKKRLNL--EQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTK 92
G+++ R EQ++ LE++FE + + + +LA+ L ++ +WF NRRARW+ +
Sbjct: 1 GQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 26/45 (57%)
Query: 44 EQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRAR 88
EQ+ ++ F L R+ QL+ LGL QI IWFQN+RA+
Sbjct: 13 EQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 57
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 36.2 bits (82), Expect = 0.019, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 34/60 (56%)
Query: 31 GSQVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
GS +K+ + Q++ LE+ + + +++ +++ A L RQI IWFQNRR + K
Sbjct: 4 GSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK 63
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 35.8 bits (81), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 25/46 (54%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
QV LE+ F L + LA+AL + Q+ WFQNRR +W+
Sbjct: 8 QVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWR 53
>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 = 35.8 bits (81), Expect = 0.021, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 28/54 (51%)
Query: 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQL 94
LN +Q+ L + + + K QL GL PR I +WFQN+R + K + +
Sbjct: 10 LNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI 63
>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 = 17/49 (34%), Positives = 30/49 (61%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93
Q++ LEK F+ + + + QLA L ++ +WFQNRRA+W+ ++
Sbjct: 20 QLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRE 68
>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 = 35.0 bits (79), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 35 GEKKKRLNLEQ--VKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRR 86
G +K R+ Q V LE+ F+ L + QLA L L Q+ IWFQNRR
Sbjct: 1 GRRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRR 54
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 35.0 bits (79), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 35 GEKKKRLNL--EQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
G ++ R Q+ LE+ F G L R L+ L L Q+ IWF+NRR R K
Sbjct: 1 GPRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58
>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 = 35.0 bits (79), Expect = 0.041, Method: Composition-based stats.
Identities = 19/50 (38%), Positives = 28/50 (56%)
Query: 44 EQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93
+Q+ LEK F N + R+ +LA L L I +WFQNRR + K ++
Sbjct: 11 DQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQR 60
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 34.7 bits (78), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 23/40 (57%)
Query: 51 KSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
+ F L R+ QL+ LGL QI IWFQN+RA+ K
Sbjct: 3 REFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 42
>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 = 0.057, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 8/77 (10%)
Query: 25 EDLSDDGSQVGEKKKR--------LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPR 76
ED+SD S+ G KR + Q+ LE++FE + + +LA+ L
Sbjct: 1 EDISDCESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEA 60
Query: 77 QIAIWFQNRRARWKTKQ 93
+I +WFQNRRAR + +
Sbjct: 61 RIQVWFQNRRARLRKQH 77
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 34.3 bits (77), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 24/54 (44%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 45 QVKALEKSFELGNKLE-PERKLQLARALGLQPRQIAIWFQNRRARWKTKQLEKD 97
QV LE+ F+ L PER+ LA + L P Q+ IWFQN R+K K+ KD
Sbjct: 13 QVYELERRFKQQKYLSAPERE-HLASMIHLTPTQVKIWFQNH--RYKMKRQAKD 63
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 34.3 bits (77), Expect = 0.069, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 27/46 (58%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
Q+K LE+ + + +++ +++ L RQ+ IWFQNRR + K
Sbjct: 12 QLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 57
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 34.3 bits (77), Expect = 0.077, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 27/46 (58%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
Q+K LE+ + + +++ +++ L RQ+ IWFQNRR + K
Sbjct: 18 QLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 63
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 33.9 bits (76), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 26/46 (56%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
Q+ ALE+ F L + + + +L L Q+ IWFQNRRA+ K
Sbjct: 11 QLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 31/53 (58%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQLEKD 97
Q++ ++ F + + + + QLA+ GL R + +WFQN RA+++ L ++
Sbjct: 18 QLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQE 70
>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 = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 26/47 (55%)
Query: 44 EQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
EQ+ L++ F L R+ QL+ LGL Q+ WF+N RA+ K
Sbjct: 14 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 60
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 31 GSQVGEKKKRLNLEQ--VKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRR 86
GS + +KKR ++E ALEKSF K E +A L ++ I +WF NRR
Sbjct: 2 GSHMRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRR 59
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 32.7 bits (73), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 18/28 (64%)
Query: 61 PERKLQLARALGLQPRQIAIWFQNRRAR 88
P K +LA A GL Q++ WF+NRR R
Sbjct: 521 PREKRELAEATGLTTTQVSNWFKNRRQR 548
>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 = 32.7 bits (73), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 49 LEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRAR 88
LE+ F L + K ++A+ G+ P Q+ +WF N+R R
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 419
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 30/50 (60%), Gaps = 4/50 (8%)
Query: 41 LNLEQVKALEKSFELGNKLEPERKL--QLARALGLQPRQIAIWFQNRRAR 88
+ EQ++ L + + L + P RK+ +A +GL+ R + +WFQN RAR
Sbjct: 24 ITPEQLEILYQKYLLDSN--PTRKMLDHIAHEVGLKKRVVQVWFQNTRAR 71
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 32.3 bits (72), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 49 LEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRAR 88
LE+ F L + K ++A+ G+ P Q+ +WF N+R R
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 51
>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 = 32.3 bits (72), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 24/42 (57%)
Query: 49 LEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
LE+ F L + K ++A+ G+ P Q+ +WF N+R R K
Sbjct: 20 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 32.0 bits (71), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 24/42 (57%)
Query: 49 LEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
LE+ F L + K ++A+ G+ P Q+ +WF N+R R K
Sbjct: 20 LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>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 = 32.0 bits (71), Expect = 0.35, Method: Composition-based stats.
Identities = 12/28 (42%), Positives = 19/28 (67%)
Query: 76 RQIAIWFQNRRARWKTKQLEKDYEVLKK 103
RQI IWFQNRR +WK + +++++
Sbjct: 1 RQIKIWFQNRRMKWKKRVFNDARDIIQR 28
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 31.6 bits (70), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 31/50 (62%)
Query: 44 EQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93
+Q++ LE +F+ + + + ++A L ++ +WF+NRRA+W+ ++
Sbjct: 13 QQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
>pdb|1OX4|A Chain A, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
pdb|1OX6|A Chain A, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
pdb|1OX6|B Chain B, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
Length = 555
Score = 31.6 bits (70), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 5/69 (7%)
Query: 35 GEKKKRLNLEQVKALEKSFELGNKLEPERKLQ-LARALGLQPRQIAI----WFQNRRARW 89
G K + + V A EK +ELGN+ + ++ +++A G Q I++ + N +A
Sbjct: 360 GADKVSIGTDAVYAAEKYYELGNRGDGTSPIETISKAYGAQAVVISVDPKRVYVNSQADT 419
Query: 90 KTKQLEKDY 98
K K E +Y
Sbjct: 420 KNKVFETEY 428
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 31.6 bits (70), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 28/54 (51%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQLEKDY 98
Q++ LE F + + LA+ L L+ +I IWFQNRRA+ K E +
Sbjct: 12 QIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRESQF 65
>pdb|1JVN|A Chain A, Crystal Structure Of Imidazole Glycerol Phosphate
Synthase: A Tunnel Through A (BetaALPHA)8 BARREL JOINS
TWO ACTIVE SITES
pdb|1JVN|B Chain B, Crystal Structure Of Imidazole Glycerol Phosphate
Synthase: A Tunnel Through A (BetaALPHA)8 BARREL JOINS
TWO ACTIVE SITES
pdb|1OX4|B Chain B, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
pdb|1OX5|A Chain A, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
pdb|1OX5|B Chain B, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
Length = 555
Score = 31.6 bits (70), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 5/69 (7%)
Query: 35 GEKKKRLNLEQVKALEKSFELGNKLEPERKLQ-LARALGLQPRQIAI----WFQNRRARW 89
G K + + V A EK +ELGN+ + ++ +++A G Q I++ + N +A
Sbjct: 360 GADKVSIGTDAVYAAEKYYELGNRGDGTSPIETISKAYGAQAVVISVDPKRVYVNSQADT 419
Query: 90 KTKQLEKDY 98
K K E +Y
Sbjct: 420 KNKVFETEY 428
>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 = 31.2 bits (69), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 30/50 (60%)
Query: 44 EQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93
+Q++ LE +F+ + + ++A L ++ +WF+NRRA+W+ ++
Sbjct: 13 QQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
>pdb|1HDP|A Chain A, Solution Structure Of A Pou-Specific Homeodomain: 3d-Nmr
Studies Of Human B-Cell Transcription Factor Oct-2
Length = 63
Score = 30.8 bits (68), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 30/52 (57%), Gaps = 2/52 (3%)
Query: 37 KKKRLNLE-QVK-ALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRR 86
+KKR ++E V+ ALEKSF K E L +A L ++ I +WF NRR
Sbjct: 2 RKKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRR 53
>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 = 30.4 bits (67), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 25/55 (45%)
Query: 44 EQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQLEKDY 98
EQ+ L+ +F PE +LA+ GL I WF + R WK L+ Y
Sbjct: 35 EQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNLKWYY 89
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 62 ERKLQLARALGLQPRQIAIWFQNRRARWK 90
E K +LA+ G+ Q++ WF N+R R+K
Sbjct: 32 EAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|4H9M|A Chain A, The First Jack Bean Urease (Canavalia Ensiformis) Complex
Obtained At 1.52 Resolution
Length = 840
Score = 29.6 bits (65), Expect = 1.5, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 6/49 (12%)
Query: 182 KQLFPTSTRPAAGSMTQLLQGSSIPDHLQCLKIDHHQMVQV-QDESFCH 229
K + P+ST P T+ L ++I +HL L + HH ++ +D +F H
Sbjct: 564 KNVLPSSTNP-----TRPLTSNTIDEHLDMLMVXHHLDREIPEDLAFAH 607
>pdb|4GY7|A Chain A, Crystallographic Structure Analysis Of Urease From Jack
Bean (Canavalia Ensiformis) At 1.49 A Resolution
Length = 840
Score = 29.6 bits (65), Expect = 1.5, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 6/49 (12%)
Query: 182 KQLFPTSTRPAAGSMTQLLQGSSIPDHLQCLKIDHHQMVQV-QDESFCH 229
K + P+ST P T+ L ++I +HL L + HH ++ +D +F H
Sbjct: 564 KNVLPSSTNP-----TRPLTSNTIDEHLDMLMVXHHLDREIPEDLAFAH 607
>pdb|3LA4|A Chain A, Crystal Structure Of The First Plant Urease From Jack Bean
(Canavalia Ensiformis)
Length = 840
Score = 29.6 bits (65), Expect = 1.5, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 6/49 (12%)
Query: 182 KQLFPTSTRPAAGSMTQLLQGSSIPDHLQCLKIDHHQMVQV-QDESFCH 229
K + P+ST P T+ L ++I +HL L + HH ++ +D +F H
Sbjct: 564 KNVLPSSTNP-----TRPLTSNTIDEHLDMLMVXHHLDREIPEDLAFAH 607
>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 = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 37 KKKRLNLE-QVK-ALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
+KKR ++E ++ ALEKSF K E +A L ++ I +WF NRR + K
Sbjct: 101 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEK 156
>pdb|1B8I|B Chain B, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
pdb|2R5Y|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd
Site
pdb|2R5Z|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A DNA SEQUENCE
Derived From The Fkh Gene
Length = 63
Score = 29.3 bits (64), Expect = 2.3, Method: Composition-based stats.
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 62 ERKLQLARALGLQPRQIAIWFQNRRARWK 90
E K +LAR G+ Q++ WF N+R R+K
Sbjct: 32 EAKEELARKCGITVSQVSNWFGNKRIRYK 60
>pdb|1O4X|A Chain A, Ternary Complex Of The Dna Binding Domains Of The Oct1 And
Sox2 Transcription Factors With A 19mer Oligonucleotide
From The Hoxb1 Regulatory Element
Length = 167
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 37 KKKRLNLEQ--VKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
+KKR ++E ALEKSF K E +A L ++ I +WF NRR + K
Sbjct: 105 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 160
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 37 KKKRLNLE-QVK-ALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
+KKR ++E ++ ALEKSF K E +A L ++ I +WF NRR + K
Sbjct: 102 RKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEK 157
>pdb|1CQT|A Chain A, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
pdb|1CQT|B Chain B, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
Length = 163
Score = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 37 KKKRLNLEQ--VKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
+KKR ++E ALEKSF K E +A L ++ I +WF NRR + K
Sbjct: 104 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 159
>pdb|1OCT|C Chain C, Crystal Structure Of The Oct-1 Pou Domain Bound To An
Octamer Site: Dna Recognition With Tethered Dna-Binding
Modules
Length = 156
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 37 KKKRLNLEQ--VKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRR 86
+KKR ++E ALEKSF K E +A L ++ I +WF NRR
Sbjct: 97 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRR 148
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 28.5 bits (62), Expect = 3.6, Method: Composition-based stats.
Identities = 12/15 (80%), Positives = 13/15 (86%)
Query: 76 RQIAIWFQNRRARWK 90
RQI IWFQNRR +WK
Sbjct: 1 RQIKIWFQNRRMKWK 15
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 28.5 bits (62), Expect = 3.7, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 37 KKKRLNLEQVKALEKSF--ELGNKLEPER-KLQLARALGLQPRQIAIWFQNRRARWK 90
K++ N + + L + F L N E K +LA+ G+ Q++ WF N+R R+K
Sbjct: 4 KRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 28.5 bits (62), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 36 EKKKRLNLEQVKALEKSFELGNK-LEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
E + +QV+ LE +F NK +P +A GL Q WF+ R A W+
Sbjct: 3 EGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 58
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 28.5 bits (62), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 11/14 (78%), Positives = 12/14 (85%)
Query: 77 QIAIWFQNRRARWK 90
QI IWFQNRR +WK
Sbjct: 2 QIKIWFQNRRMKWK 15
>pdb|2HI3|A Chain A, Solution Structure Of The Homeodomain-Only Protein Hop
Length = 73
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 44 EQVKALEKSFELGNK-LEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
+QV+ LE +F NK +P +A GL Q WF+ R A W+
Sbjct: 12 DQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 59
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 28.1 bits (61), Expect = 4.7, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 24/49 (48%)
Query: 40 RLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRAR 88
R Q++ L+ F+ + + QL+ L L R I +WFQN R +
Sbjct: 13 RFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQK 61
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 28.1 bits (61), Expect = 5.0, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 37 KKKRLNLEQVKALEKSF--ELGNKLEPER-KLQLARALGLQPRQIAIWFQNRRARWK 90
K++ N + + L + F L N E K +LA+ G+ Q++ WF N+R R+K
Sbjct: 5 KRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYK 61
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 27.7 bits (60), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 48 ALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90
ALE+ F +K + +++A L L+ + +WF NRR R K
Sbjct: 101 ALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREK 143
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 27.7 bits (60), Expect = 6.2, Method: Composition-based stats.
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 62 ERKLQLARALGLQPRQIAIWFQNRRARWK 90
E K +LA+ G+ Q++ WF N+R R+K
Sbjct: 34 EAKEELAKKCGITVSQVSNWFGNKRIRYK 62
>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 = 6.3, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRA---RW 89
Q+ AL+ F+ L ++ +L+ L L +Q+ WFQN+R RW
Sbjct: 14 QLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW 61
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of
Human Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 27.3 bits (59), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 44 EQVKALEKSFELGNKLEPERKLQ-LARALGLQPRQIAIWFQNRR 86
EQ+ AL+ SF N+ + +++ L + GL R++ WF +RR
Sbjct: 18 EQLSALKGSF-CRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRR 60
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
0.314 0.127 0.370
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,891,501
Number of Sequences: 62578
Number of extensions: 244295
Number of successful extensions: 755
Number of sequences better than 100.0: 108
Number of HSP's better than 100.0 without gapping: 89
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 661
Number of HSP's gapped (non-prelim): 113
length of query: 254
length of database: 14,973,337
effective HSP length: 97
effective length of query: 157
effective length of database: 8,903,271
effective search space: 1397813547
effective search space used: 1397813547
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 bits)