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= 019637
(338 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/51 (50%), Positives = 32/51 (62%)
Query: 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
R S DQ LEK FE + L P + +LA+ L L RQV WFQNRRA+W+
Sbjct: 13 RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 63
>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 = 46.2 bits (108), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 60 KKRRLSVD--QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116
K++R S Q LEK F L R++++A L L RQ+ +WFQNRR +WK +
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH 87
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/46 (45%), Positives = 28/46 (60%)
Query: 68 QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
Q+ LEK FE + L ++ LA+ LGL QV W+QNRR +WK
Sbjct: 28 QLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWK 73
>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 = 45.4 bits (106), Expect = 4e-05, Method: Composition-based stats.
Identities = 20/48 (41%), Positives = 28/48 (58%)
Query: 68 QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115
Q LEK F L R++++A L L RQ+ +WFQNRR +WK +
Sbjct: 7 QTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 54
>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 = 45.4 bits (106), Expect = 5e-05, Method: Composition-based stats.
Identities = 20/48 (41%), Positives = 28/48 (58%)
Query: 68 QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115
Q LEK F L R++++A L L RQ+ +WFQNRR +WK +
Sbjct: 13 QTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 60
>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 = 45.1 bits (105), Expect = 5e-05, Method: Composition-based stats.
Identities = 20/48 (41%), Positives = 28/48 (58%)
Query: 68 QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115
Q LEK F L R++++A L L RQ+ +WFQNRR +WK +
Sbjct: 13 QTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 60
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 44.7 bits (104), Expect = 7e-05, Method: Composition-based stats.
Identities = 20/48 (41%), Positives = 28/48 (58%)
Query: 68 QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115
Q LEK F L R++++A L L RQ+ +WFQNRR +WK +
Sbjct: 14 QTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/56 (39%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 60 KKRR--LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
++RR + +Q+ LEK F + L + ++A L L QV +WFQNRRA+WK
Sbjct: 8 RRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 63
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 19/48 (39%), Positives = 28/48 (58%)
Query: 68 QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115
Q LEK F + L R++++A L L RQ+ +WFQNRR + K +
Sbjct: 31 QTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE 78
>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 = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 30/55 (54%)
Query: 68 QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYG 122
QV LE+ F + L + LA+ L L QV +WFQNRR + K KQL + G
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSELG 69
>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 = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 27/46 (58%)
Query: 68 QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
Q+ LEK F + R+V+LA L L R + +WFQNRR +WK
Sbjct: 14 QLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWK 59
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 42.0 bits (97), Expect = 5e-04, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 31/58 (53%)
Query: 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLE 118
+ + Q+ LEK F L R+V++A L L QV +WFQNRR + K ++ E
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE 95
>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 = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 27/51 (52%)
Query: 68 QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLE 118
QV LEK F + L + LA+ L + QV WFQNRR +W+ + E
Sbjct: 28 QVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAE 78
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 25/46 (54%)
Query: 68 QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
Q LEK F + R++ +A L L RQ+ +WFQNRR + K
Sbjct: 14 QTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSK 59
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 32/49 (65%)
Query: 68 QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116
Q++ LEK F + + + +LA ++GL ++ VWFQNRRA+W+ ++
Sbjct: 10 QLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 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 = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 30/50 (60%)
Query: 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
S +Q+ L++ F L R+ +L+ ELGL Q+ +WFQN+RA+ K
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 59
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 18/46 (39%), Positives = 28/46 (60%)
Query: 68 QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
Q+ AL++ F+ L + +LA LGL QV +WFQN+R++ K
Sbjct: 18 QLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIK 63
>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 = 0.003, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 30/50 (60%)
Query: 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
S +Q+ L++ F L R+ +L+ ELGL Q+ +WFQN+RA+ K
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 57
>pdb|1JGG|A Chain A, Even-Skipped Homeodomain Complexed To At-Rich Dna
pdb|1JGG|B Chain B, Even-Skipped Homeodomain Complexed To At-Rich Dna
Length = 60
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 27/46 (58%)
Query: 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109
+ DQ+ LEK F EN + R+ +LA +L L + VWFQNRR
Sbjct: 8 FTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRR 53
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 29/48 (60%)
Query: 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111
S +Q+ L++ F L R+ +L+ ELGL Q+ +WFQN+RA+
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 20/46 (43%), Positives = 27/46 (58%)
Query: 68 QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
Q LEK F L +R+ ++A+ L L RQV +WFQNRR + K
Sbjct: 12 QTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMK 57
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 27/52 (51%)
Query: 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115
S QV LE+ F + L + LA+ L + QV WFQNRR +W+ +
Sbjct: 4 FSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>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 = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 29/50 (58%)
Query: 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
S +Q+ L++ F L R+ +L+ ELGL Q+ +WFQN RA+ K
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIK 57
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 38.1 bits (87), Expect = 0.007, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 38/67 (56%), Gaps = 2/67 (2%)
Query: 58 SEKKRRLSVD--QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115
S K+ R S Q++ ++ F + + + + +LAQ+ GL R + VWFQN RA+++
Sbjct: 6 SGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRN 65
Query: 116 QLERDYG 122
L ++ G
Sbjct: 66 LLRQENG 72
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 32/50 (64%)
Query: 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
+ +Q++ALEK FE + + + +LA ++ L ++ VWF NRRA+W+
Sbjct: 14 FTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWR 63
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 31/53 (58%), Gaps = 2/53 (3%)
Query: 68 QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERD 120
Q LEK F L +R+ ++A+ L L RQV +WFQNRR K K++ +D
Sbjct: 24 QTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRM--KMKKINKD 74
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 30/46 (65%)
Query: 68 QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
Q++ LEK F + + + +LA ++GL ++ VWFQNRRA+W+
Sbjct: 10 QLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 55
>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 = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 29/50 (58%)
Query: 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
S +Q+ L++ F L R+ +L+ ELGL Q+ +WFQN RA+ K
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIK 57
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 37.7 bits (86), Expect = 0.009, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 31/52 (59%)
Query: 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115
+ +Q++ LE+ FE + + + +LAQ L +V VWF NRRARW+ +
Sbjct: 9 FTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 58 SEKKRRL--SVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
S +K+R+ S Q++ LE+ + + +++ K++ L RQ+ +WFQNRR + K
Sbjct: 6 SGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK 63
>pdb|2HDD|A Chain A, Engrailed Homeodomain Q50k Variant Dna Complex
pdb|2HDD|B Chain B, Engrailed Homeodomain Q50k Variant Dna Complex
Length = 61
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 30/50 (60%)
Query: 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
S +Q+ L++ F L R+ +L+ ELGL Q+ +WF+N+RA+ K
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 59
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 58 SEKKRRLSVDQVKALEKNFEVENKL-EPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
SE ++ DQV+ LE NF NK +P +A E GL Q WF+ R A W+
Sbjct: 2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 58
>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 = 37.0 bits (84), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 29/50 (58%)
Query: 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
S +Q+ L++ F L R+ +L+ ELGL Q+ +WF N+RA+ K
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIK 55
>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 = 37.0 bits (84), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 30/46 (65%)
Query: 68 QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
Q++ LEK F + + + +LA ++GL ++ VWFQNRRA+W+
Sbjct: 17 QLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 62
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 37.0 bits (84), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111
S +Q+ ++ F L R+ +L+ ELGL Q+ +WFQN+RA+
Sbjct: 10 FSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 57
>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 = 37.0 bits (84), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 2/65 (3%)
Query: 59 EKKRRL--SVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116
++KRR+ + Q LE+ F + L + LA + L P QV +WFQN R + K Q
Sbjct: 9 KRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ 68
Query: 117 LERDY 121
E+ Y
Sbjct: 69 NEKGY 73
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 36.6 bits (83), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 27/50 (54%)
Query: 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
+ Q+ ALE+ F + L + + + L L QV +WFQNRRA+ K
Sbjct: 7 FTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 35.8 bits (81), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 35/57 (61%), Gaps = 2/57 (3%)
Query: 59 EKKRR--LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
++KRR +S+ ALE++F +K + +++A+EL L+ V VWF NRR R K
Sbjct: 87 KRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREK 143
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 35.8 bits (81), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 2/65 (3%)
Query: 59 EKKRRL--SVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116
++KRR+ + Q LE+ F + L + L + L P QV +WFQN R + K Q
Sbjct: 12 KRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRAQ 71
Query: 117 LERDY 121
E+ Y
Sbjct: 72 NEKGY 76
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 35.8 bits (81), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 60 KKRRL--SVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
+KRR+ S QV LE+ F+ + L + LA + L P QV +WFQN R + K
Sbjct: 3 RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMK 58
>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 = 35.4 bits (80), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 27/50 (54%)
Query: 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
S Q+ LE+ FE + + +LAQ L ++ VWFQNRRAR +
Sbjct: 25 FSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLR 74
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 35.4 bits (80), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 32/47 (68%)
Query: 67 DQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
+Q++ALE F+ + + +LA+++ L+ +V VWF+NRRA+W+
Sbjct: 17 EQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 63
>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 = 35.4 bits (80), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 28/50 (56%)
Query: 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
S +Q+ L++ F L R+ +L+ ELGL QV WF+N RA+ K
Sbjct: 11 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 60
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 35.0 bits (79), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 26/44 (59%)
Query: 68 QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111
Q+K LE+ + + +++ +++ L RQV +WFQNRR +
Sbjct: 18 QLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVK 61
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 35.0 bits (79), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 17/30 (56%), Positives = 21/30 (70%), Gaps = 2/30 (6%)
Query: 84 PERKV--KLAQELGLQPRQVAVWFQNRRAR 111
P RK+ +A E+GL+ R V VWFQN RAR
Sbjct: 42 PTRKMLDHIAHEVGLKKRVVQVWFQNTRAR 71
>pdb|2HI3|A Chain A, Solution Structure Of The Homeodomain-Only Protein Hop
Length = 73
Score = 35.0 bits (79), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 67 DQVKALEKNFEVENK-LEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
DQV+ LE NF NK +P +A E GL Q WF+ R A W+
Sbjct: 12 DQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 59
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 35.0 bits (79), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 22/32 (68%)
Query: 82 LEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
L R+ +L+ ELGL Q+ +WFQN+RA+ K
Sbjct: 11 LTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 42
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 34.7 bits (78), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 35/61 (57%), Gaps = 4/61 (6%)
Query: 60 KKRR----LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115
KKRR + Q++ LEK F+ + + + +LA L +V VWFQNRRA+W+ +
Sbjct: 8 KKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKR 67
Query: 116 Q 116
+
Sbjct: 68 E 68
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 34.7 bits (78), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 26/44 (59%)
Query: 68 QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111
Q+K LE+ + + +++ +++ L RQV +WFQNRR +
Sbjct: 12 QLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVK 55
>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 = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 25/40 (62%)
Query: 72 LEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111
LE+ F + L + K ++A++ G+ P QV VWF N+R R
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 419
>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 = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 25/46 (54%)
Query: 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109
S QV LE+ F+ + L + +LA L L QV +WFQNRR
Sbjct: 9 FSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRR 54
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 26/48 (54%)
Query: 68 QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115
Q+ LE++F L R L+ +L L QV +WF+NRR R K +
Sbjct: 13 QIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQ 60
>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 = 33.1 bits (74), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 27/61 (44%)
Query: 67 DQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYGVLKA 126
+Q+ L+ F PE KLA+E GL + WF + R WK L+ Y A
Sbjct: 35 EQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNLKWYYYYQSA 94
Query: 127 N 127
N
Sbjct: 95 N 95
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 33.1 bits (74), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 30/55 (54%)
Query: 67 DQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDY 121
+Q++ LE F V + LAQ+L L+ ++ +WFQNRRA+ K E +
Sbjct: 11 NQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRESQF 65
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 33.1 bits (74), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 25/40 (62%)
Query: 72 LEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111
LE+ F + L + K ++A++ G+ P QV VWF N+R R
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 51
>pdb|1BW5|A Chain A, The Nmr Solution Structure Of The Homeodomain Of The Rat
Insulin Gene Enhancer Protein Isl-1, 50 Structures
Length = 66
Score = 33.1 bits (74), Expect = 0.25, Method: Composition-based stats.
Identities = 16/54 (29%), Positives = 28/54 (51%)
Query: 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117
L+ Q+ L + + + K +L + GL PR + VWFQN+R + K + +
Sbjct: 10 LNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI 63
>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 = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 26/42 (61%)
Query: 72 LEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
LE+ F + L + K ++A++ G+ P QV VWF N+R R K
Sbjct: 20 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 32.3 bits (72), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 26/42 (61%)
Query: 72 LEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
LE+ F + L + K ++A++ G+ P QV VWF N+R R K
Sbjct: 20 LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 31.2 bits (69), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 18/28 (64%)
Query: 84 PERKVKLAQELGLQPRQVAVWFQNRRAR 111
P K +LA+ GL QV+ WF+NRR R
Sbjct: 521 PREKRELAEATGLTTTQVSNWFKNRRQR 548
>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 = 31.2 bits (69), Expect = 0.82, Method: Composition-based stats.
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 99 RQVAVWFQNRRARWKTK 115
RQ+ +WFQNRR +WK +
Sbjct: 1 RQIKIWFQNRRMKWKKR 17
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 56 HVSEKKRRLSVDQ--VKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109
H+ +K+R S++ ALEK+F K E +A +L ++ + VWF NRR
Sbjct: 4 HMRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRR 59
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 36/61 (59%), Gaps = 2/61 (3%)
Query: 58 SEKKRR--LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115
S++++R + Q++ LE F+ + + + ++A L +V VWF+NRRA+W+ +
Sbjct: 2 SQRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61
Query: 116 Q 116
+
Sbjct: 62 E 62
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 30.0 bits (66), Expect = 2.0, Method: Composition-based stats.
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 99 RQVAVWFQNRRARWK 113
RQ+ +WFQNRR +WK
Sbjct: 1 RQIKIWFQNRRMKWK 15
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 27/45 (60%)
Query: 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQN 107
R++ DQ++ L + F++ N E+ ++A + GL + + WF+N
Sbjct: 13 RITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRN 57
>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 = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 29/53 (54%)
Query: 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116
+ Q++ LE F+ + + ++A L +V VWF+NRRA+W+ ++
Sbjct: 10 FTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 85 ERKVKLAQELGLQPRQVAVWFQNRRARWK 113
E K +LA++ G+ QV+ WF N+R R+K
Sbjct: 32 EAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 60 KKRRLSVDQ--VKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
+K+R S++ ALEK+F K E +A++L ++ + VWF NRR + K
Sbjct: 102 RKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEK 157
>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 = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 32/52 (61%), Gaps = 2/52 (3%)
Query: 60 KKRRLSVD-QVK-ALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109
+K+R S++ V+ ALEK+F K E + +A++L ++ + VWF NRR
Sbjct: 2 RKKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRR 53
>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 = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRA---RW 112
S Q+ AL+ F+ + L ++ +L+ L L +QV WFQN+R RW
Sbjct: 10 FSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW 61
>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 = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 60 KKRRLSVDQ--VKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
+K+R S++ ALEK+F K E +A +L ++ + VWF 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 = 3.0, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 85 ERKVKLAQELGLQPRQVAVWFQNRRARWK 113
E K +LA++ G+ QV+ WF N+R R+K
Sbjct: 32 EAKEELARKCGITVSQVSNWFGNKRIRYK 60
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 29.3 bits (64), Expect = 3.7, Method: Composition-based stats.
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 85 ERKVKLAQELGLQPRQVAVWFQNRRARWK 113
E K +LA++ G+ QV+ WF N+R R+K
Sbjct: 32 EAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 28.9 bits (63), Expect = 4.1, Method: Composition-based stats.
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 85 ERKVKLAQELGLQPRQVAVWFQNRRARWK 113
E K +LA++ G+ QV+ WF N+R R+K
Sbjct: 34 EAKEELAKKCGITVSQVSNWFGNKRIRYK 62
>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 = 28.9 bits (63), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 60 KKRRLSVDQ--VKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
+K+R S++ ALEK+F K E +A +L ++ + VWF NRR + K
Sbjct: 105 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 160
>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 = 28.5 bits (62), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 60 KKRRLSVDQ--VKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
+K+R S++ ALEK+F K E +A +L ++ + VWF 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 = 6.0, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 60 KKRRLSVDQ--VKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
+K+R S++ ALEK+F K E +A +L ++ + VWF NRR + K
Sbjct: 97 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 152
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 28.5 bits (62), Expect = 6.0, Method: Composition-based stats.
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 85 ERKVKLAQELGLQPRQVAVWFQNRRARWK 113
E K +LA++ G+ QV+ WF N+R R+K
Sbjct: 33 EAKEELAKKSGITVSQVSNWFGNKRIRYK 61
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 28.5 bits (62), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 58 SEKKRRLSVD-QVK-ALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113
+ K++R S++ +V+ +LE F K ++ +A +LGL+ V VWF NRR + K
Sbjct: 95 ARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGK 152
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 28.1 bits (61), Expect = 7.6, Method: Composition-based stats.
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 100 QVAVWFQNRRARWK 113
Q+ +WFQNRR +WK
Sbjct: 2 QIKIWFQNRRMKWK 15
>pdb|2PRO|A Chain A, Pro Region Of Alpha-Lytic Protease
pdb|2PRO|B Chain B, Pro Region Of Alpha-Lytic Protease
pdb|2PRO|C Chain C, Pro Region Of Alpha-Lytic Protease
pdb|3PRO|C Chain C, Alpha-Lytic Protease Complexed With C-Terminal Truncated
Pro Region
pdb|3PRO|D Chain D, Alpha-Lytic Protease Complexed With C-Terminal Truncated
Pro Region
pdb|4PRO|C Chain C, Alpha-lytic Protease Complexed With Pro Region
pdb|4PRO|D Chain D, Alpha-lytic Protease Complexed With Pro Region
Length = 166
Score = 28.1 bits (61), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 12/44 (27%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 80 NKLEPERKVKLAQELGLQPRQVAVWFQNRR-ARWKTKQLERDYG 122
++++P+ K + ++LG+ P Q+ + Q + AR + +ER++G
Sbjct: 2 DQVDPQLKFAMQRDLGIFPTQLPQYLQTEKLARTQAAAIEREFG 45
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 0.130 0.375
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,213,214
Number of Sequences: 62578
Number of extensions: 270836
Number of successful extensions: 682
Number of sequences better than 100.0: 94
Number of HSP's better than 100.0 without gapping: 87
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 593
Number of HSP's gapped (non-prelim): 95
length of query: 338
length of database: 14,973,337
effective HSP length: 99
effective length of query: 239
effective length of database: 8,778,115
effective search space: 2097969485
effective search space used: 2097969485
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: 52 (24.6 bits)