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= 025268
(255 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 = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/51 (45%), Positives = 30/51 (58%)
Query: 51 RLTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
R + DQ LEK FE L P + +LA+ L L RQ+ WFQNRRA+ +
Sbjct: 13 RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 63
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 43 SQATEKKR-RLTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
+++T KKR T Q LEK F + L DR+ ++A L L RQ+ +WFQNRR ++K
Sbjct: 10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMK 69
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 28/49 (57%)
Query: 53 TVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
T Q LEK F + L R++++A L L RQI +WFQNRR + K
Sbjct: 11 TRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 59
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/66 (42%), Positives = 37/66 (56%), Gaps = 5/66 (7%)
Query: 40 EEASQATEKKRRLTVD---QVKALEKNFEVDNKLE-PDRKVKLAEELGLQPRQIAVWFQN 95
E ++A + +R TV Q+ LEK FE L PDR + LAE LGL Q+ W+QN
Sbjct: 9 EPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDR-IDLAESLGLSQLQVKTWYQN 67
Query: 96 RRARLK 101
RR + K
Sbjct: 68 RRMKWK 73
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKELERDYG 110
T Q+ LEK F + L R+V++A L L Q+ +WFQNR R+K K+ ER+ G
Sbjct: 41 FTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNR--RMKQKKREREGG 97
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 28/49 (57%)
Query: 53 TVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
T Q LEK F + L R++++A L L RQI +WFQNRR + K
Sbjct: 4 TRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 52
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 21/48 (43%), Positives = 30/48 (62%)
Query: 56 QVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSK 103
Q LEK F ++ L R++++A L L RQI +WFQNRR +LK +
Sbjct: 31 QTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE 78
>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 = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 28/49 (57%)
Query: 53 TVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
T Q LEK F + L R++++A L L RQI +WFQNRR + K
Sbjct: 36 TRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 84
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 28/49 (57%)
Query: 53 TVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
T Q LEK F + L R++++A L L RQI +WFQNRR + K
Sbjct: 10 TRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 58
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 46 TEKKR-RLTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKS 102
T KKR T Q LEK F + L DR+ ++A L L RQ+ +WFQNRR ++K
Sbjct: 1 TRKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 32/50 (64%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
+ +Q+ L++ F + L R+ +L+ ELGL QI +WFQN+RA++K
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 57
>pdb|1FTZ|A Chain A, Nuclear Magnetic Resonance Solution Structure Of The Fushi
Tarazu Homeodomain From Drosophila And Comparison With
The Antennapedia Homeodomain
Length = 70
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 56 QVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKE 104
Q LEK F + + R++ +A L L RQI +WFQNR R+KSK+
Sbjct: 14 QTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNR--RMKSKK 60
>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 = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 32/50 (64%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
+ +Q+ L++ F + L R+ +L+ ELGL QI +WFQN+RA++K
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 59
>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 = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 30/52 (57%)
Query: 53 TVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKE 104
T Q+ LEK F + + R+V+LA L L R I +WFQNRR + K +E
Sbjct: 11 TRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE 62
>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 = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 29/55 (52%)
Query: 56 QVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKELERDYG 110
QV LE+ F L + LA+ L L Q+ +WFQNRR + K K+L + G
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSELG 69
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 31/50 (62%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
+ +Q+ L++ F + L R+ +L+ ELGL QI +WFQN RA++K
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIK 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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/46 (45%), Positives = 27/46 (58%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRR 97
T DQ+ LEK F +N + R+ +LA +L L I VWFQNRR
Sbjct: 8 FTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRR 53
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 31/50 (62%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
+ +Q+ L++ F + L R+ +L+ ELGL QI +WFQN RA++K
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIK 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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 32/50 (64%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
+ +Q+ L++ F + L R+ +L+ ELGL QI +WF+N+RA++K
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 59
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 31/49 (63%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARL 100
+ +Q+ L++ F + L R+ +L+ ELGL QI +WFQN+RA++
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKI 54
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 37 DCREEASQATEKKRR-----LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAV 91
DC E A ++K+R + Q+ LE+ FE + + +LA+ L +I V
Sbjct: 5 DCESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQV 64
Query: 92 WFQNRRARLK 101
WFQNRRARL+
Sbjct: 65 WFQNRRARLR 74
>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 = 0.002, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 29/46 (63%)
Query: 56 QVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
Q+ AL++ F+ L + +LA LGL Q+ +WFQN+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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 31/50 (62%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
+ +Q+ L++ F + L R+ +L+ ELGL QI +WF N+RA++K
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIK 55
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 33/58 (56%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKELERDY 109
T +Q++ LE F V+ D LA++L L+ +I +WFQNRRA+LK E +
Sbjct: 8 FTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRESQF 65
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 38.5 bits (88), Expect = 0.004, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 38/62 (61%), Gaps = 2/62 (3%)
Query: 42 ASQATEKKRRL--TVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRAR 99
+S ++ +K+R+ + Q++ LE+ + + + D++ K++ L RQI +WFQNRR +
Sbjct: 2 SSGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVK 61
Query: 100 LK 101
K
Sbjct: 62 EK 63
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 31/50 (62%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
+ +Q+ ++ F + L R+ +L+ ELGL QI +WFQN+RA+++
Sbjct: 10 FSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIR 59
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 42 ASQATEKKRR--LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRAR 99
A ++RR T +Q+ LEK F L + ++A L L Q+ +WFQNRRA+
Sbjct: 2 APGGKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAK 61
Query: 100 LK 101
K
Sbjct: 62 WK 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 = 38.1 bits (87), Expect = 0.005, Method: Composition-based stats.
Identities = 20/48 (41%), Positives = 28/48 (58%)
Query: 56 QVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSK 103
Q LEK F + L R++++A L L RQI +WFQNRR + K +
Sbjct: 13 QTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 60
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 27/41 (65%)
Query: 61 EKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
++ F + L R+ +L+ ELGL QI +WFQN+RA++K
Sbjct: 2 KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 42
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 27/44 (61%)
Query: 56 QVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRAR 99
Q+K LE+ + + + D++ +++ L RQ+ +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 = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 33/50 (66%), Gaps = 4/50 (8%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKV--KLAEELGLQPRQIAVWFQNRRAR 99
+T +Q++ L + + +D+ P RK+ +A E+GL+ R + VWFQN RAR
Sbjct: 24 ITPEQLEILYQKYLLDS--NPTRKMLDHIAHEVGLKKRVVQVWFQNTRAR 71
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 27/44 (61%)
Query: 56 QVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRAR 99
Q+K LE+ + + + D++ +++ L RQ+ +WFQNRR +
Sbjct: 12 QLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVK 55
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 26/50 (52%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
T Q+ ALE+ F L + + + L L Q+ +WFQNRRA+ K
Sbjct: 7 FTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 37.0 bits (84), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 33/53 (62%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKE 104
T +Q++ALEK FE + + + +LA ++ L +I VWF NRRA+ + +E
Sbjct: 14 FTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREE 66
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 48 KKRRLTVDQ--VKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
+KRR+ Q V LE+ F+ L + LA + L P Q+ +WFQN R ++K
Sbjct: 3 RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMK 58
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 33/57 (57%), Gaps = 2/57 (3%)
Query: 47 EKKRRLTVDQVK--ALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
++KRR T+ ALE++F +K +++AEEL L+ + VWF NRR R K
Sbjct: 87 KRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREK 143
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 32/53 (60%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKE 104
T Q++ LEK F + + + +LA ++GL +I VWFQNRRA+ + +E
Sbjct: 6 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 36.6 bits (83), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 32/53 (60%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKE 104
T Q++ LEK F + + + +LA ++GL +I VWFQNRRA+ + +E
Sbjct: 6 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>pdb|1NK2|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES
pdb|1NK3|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, MINIMIZED AVERAGE
Structure
pdb|1VND|A Chain A, VndNK-2 Protein (Homeodomain), Nmr
Length = 77
Score = 36.6 bits (83), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 2/65 (3%)
Query: 47 EKKRRL--TVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKE 104
++KRR+ T Q LE+ F L + LA + L P Q+ +WFQN R + K +
Sbjct: 9 KRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ 68
Query: 105 LERDY 109
E+ Y
Sbjct: 69 NEKGY 73
>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 = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 30/50 (60%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
+ +Q+ L++ F + L R+ +L+ ELGL Q+ WF+N RA++K
Sbjct: 11 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 60
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 35.8 bits (81), Expect = 0.023, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 42 ASQATEKKRRLTVD--QVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRAR 99
+S ++ K+ R + Q++ ++ F +++ + +LA++ GL R + VWFQN RA+
Sbjct: 2 SSGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAK 61
Query: 100 LKSKELERDYG 110
+ L ++ G
Sbjct: 62 FRRNLLRQENG 72
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 35.8 bits (81), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 26/50 (52%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
T Q+ LE++F L R L+ +L L Q+ +WF+NRR R K
Sbjct: 9 FTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58
>pdb|3A01|B Chain B, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
pdb|3A01|F Chain F, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
Length = 67
Score = 35.4 bits (80), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 32/53 (60%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKE 104
T Q++ LEK F + + + +LA ++GL +I VWFQNRRA+ + +E
Sbjct: 13 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 65
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 35.4 bits (80), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 47 EKKRRL--TVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKE 104
++KRR+ T Q LE+ F L + L + L P Q+ +WFQN R + K +
Sbjct: 12 KRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRAQ 71
Query: 105 LERDY 109
E+ Y
Sbjct: 72 NEKGY 76
>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 = 34.7 bits (78), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 17/37 (45%), Positives = 22/37 (59%), Gaps = 2/37 (5%)
Query: 71 EPDRKVK--LAEELGLQPRQIAVWFQNRRARLKSKEL 105
PD +K L E GL PR I VWFQN+R + K + +
Sbjct: 27 RPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI 63
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 33.9 bits (76), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 45 ATEKKRRLTVDQVKALEKNF-EVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSK 103
+E +T DQV+ LE NF +V+ +P +A E GL Q WF+ R A +
Sbjct: 1 GSEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60
Query: 104 E 104
E
Sbjct: 61 E 61
>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 = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 25/55 (45%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKELE 106
T QV LEK F L + LA L + Q+ WFQNRR + + + E
Sbjct: 24 FTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAE 78
>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 = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 25/46 (54%)
Query: 56 QVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
QV LE+ F+ L + +LA L L Q+ +WFQNRR + K
Sbjct: 13 QVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 29/50 (58%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
T +Q++ LE+ FE + + + +LA+ L ++ VWF NRRAR +
Sbjct: 9 FTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWR 58
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 32.3 bits (72), Expect = 0.23, Method: Composition-based stats.
Identities = 15/54 (27%), Positives = 31/54 (57%)
Query: 42 ASQATEKKRRLTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQN 95
S + R+T DQ++ L + F+++N ++ ++A++ GL + I WF+N
Sbjct: 4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRN 57
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 32.3 bits (72), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 34/61 (55%), Gaps = 4/61 (6%)
Query: 48 KKRR----LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSK 103
KKRR T Q++ LEK F+ + + + +LA L ++ VWFQNRRA+ + +
Sbjct: 8 KKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKR 67
Query: 104 E 104
E
Sbjct: 68 E 68
>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 = 16/42 (38%), Positives = 24/42 (57%)
Query: 60 LEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
LE+ F L K ++A++ G+ P Q+ VWF N+R R K
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 36/63 (57%), Gaps = 3/63 (4%)
Query: 42 ASQATEKKRRLTV---DQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRA 98
S + +R T+ +Q++ALE F+ + + +LA ++ L+ ++ VWF+NRRA
Sbjct: 1 GSSGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRA 60
Query: 99 RLK 101
+ +
Sbjct: 61 KWR 63
>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 = 32.0 bits (71), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 33/73 (45%)
Query: 43 SQATEKKRRLTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKS 102
S +T K + T +Q+ L+ F P+ KLA+E GL I WF + R K+
Sbjct: 23 SGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKN 82
Query: 103 KELERDYGLLKAN 115
L+ Y AN
Sbjct: 83 GNLKWYYYYQSAN 95
>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 = 32.0 bits (71), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 24/42 (57%)
Query: 60 LEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
LE+ F L K ++A++ G+ P Q+ VWF N+R R K
Sbjct: 20 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>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 = 32.0 bits (71), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 24/42 (57%)
Query: 60 LEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
LE+ F L K ++A++ G+ P Q+ VWF N+R R K
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>pdb|2HI3|A Chain A, Solution Structure Of The Homeodomain-Only Protein Hop
Length = 73
Score = 32.0 bits (71), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 53 TVDQVKALEKNF-EVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKE 104
T DQV+ LE NF +V+ +P +A E GL Q WF+ R A + E
Sbjct: 10 TEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 62
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 31.6 bits (70), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 21/33 (63%)
Query: 72 PDRKVKLAEELGLQPRQIAVWFQNRRARLKSKE 104
P K +LAE GL Q++ WF+NRR R ++ E
Sbjct: 521 PREKRELAEATGLTTTQVSNWFKNRRQRDRAAE 553
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 31.6 bits (70), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 24/42 (57%)
Query: 60 LEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
LE+ F L K ++A++ G+ P Q+ VWF N+R R K
Sbjct: 20 LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 31.2 bits (69), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 23/47 (48%)
Query: 55 DQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
QV LE+ F L + LA+ L + Q+ WFQNRR + +
Sbjct: 7 SQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWR 53
>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 = 16/39 (41%), Positives = 24/39 (61%)
Query: 59 ALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRR 97
ALEK+F + K + + +AE+L ++ I VWF NRR
Sbjct: 15 ALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRR 53
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 30/53 (56%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKE 104
T Q++ LE F+ ++ + + ++A L ++ VWF+NRRA+ + +E
Sbjct: 10 FTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%)
Query: 59 ALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRR 97
ALEK+F + K + +AE+L ++ I VWF NRR
Sbjct: 115 ALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRR 153
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 27/51 (52%)
Query: 51 RLTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
R T Q++ L+ F+ + + D +L+ L L R I VWFQN R + +
Sbjct: 13 RFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKAR 63
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 33 LEEEDCREEASQATEKKRRLTVDQVK-ALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAV 91
L+E E QA ++KR ++V+ +LE F K + +A +LGL+ + V
Sbjct: 83 LQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRV 142
Query: 92 WFQNRRARLK 101
WF NRR + K
Sbjct: 143 WFSNRRQKGK 152
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 42 ASQATEKKRRLTVD-QVK-ALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRR 97
A+Q ++K+R +++ VK ALE +F K LA+ L L+ + VWF NRR
Sbjct: 94 AAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRR 151
>pdb|2VI6|A Chain A, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|B Chain B, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|C Chain C, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|D Chain D, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|E Chain E, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|F Chain F, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|G Chain G, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|H Chain H, Crystal Structure Of The Nanog Homeodomain
Length = 62
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 45 ATEKKRRLTVDQVK--ALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
T++K R Q + AL+ F+ L + +L+ L L +Q+ WFQN+R + K
Sbjct: 1 GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCK 59
>pdb|2EQB|B Chain B, Crystal Structure Of The Rab Gtpase Sec4p, The Sec2p Gef
Domain, And Phosphate Complex
pdb|2EQB|C Chain C, Crystal Structure Of The Rab Gtpase Sec4p, The Sec2p Gef
Domain, And Phosphate Complex
Length = 97
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 28/47 (59%)
Query: 110 GLLKANYDALRLDYNNLQQENEALTAELRELKAKLCQENEETSHAVE 156
G L +NY+ L+ DYN L++E E++ L+ + +ENE + A E
Sbjct: 1 GPLGSNYNQLKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEE 47
>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 = 15/39 (38%), Positives = 23/39 (58%)
Query: 59 ALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRR 97
ALEK+F + K + +A++L ++ I VWF NRR
Sbjct: 114 ALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRR 152
>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 = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 29/53 (54%)
Query: 52 LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKE 104
T Q++ LE F+ + + + ++A L ++ VWF+NRRA+ + +E
Sbjct: 10 FTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 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 = 3.0, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%)
Query: 40 EEASQATEKKRRLTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRAR 99
E S+ +K+ + + ALEK+F + K + +A++L ++ I VWF NRR +
Sbjct: 99 EGLSERRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQK 158
Query: 100 LK 101
K
Sbjct: 159 EK 160
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 23/39 (58%)
Query: 59 ALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRR 97
ALEK+F + K + +A++L ++ I VWF NRR
Sbjct: 21 ALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRR 59
>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 = 3.5, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 31/58 (53%)
Query: 40 EEASQATEKKRRLTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRR 97
E S+ +K+ + + ALEK+F + K + +A++L ++ I VWF NRR
Sbjct: 91 EGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRR 148
>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 = 3.5, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 31/58 (53%)
Query: 40 EEASQATEKKRRLTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRR 97
E S+ +K+ + + ALEK+F + K + +A++L ++ I VWF NRR
Sbjct: 98 EGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRR 155
>pdb|2XAF|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With
Para-Bromo- (+)-Cis-2-Phenylcyclopropyl-1-Amine
pdb|2XAG|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With
Para-Bromo- (-)-Trans-2-Phenylcyclopropyl-1-Amine
pdb|2XAH|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With (+)-
Trans-2-Phenylcyclopropyl-1-Amine
pdb|2XAJ|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With
(-)-Trans- 2-Phenylcyclopropyl-1-Amine
pdb|2XAQ|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With A
Tranylcypromine Derivative (Mc2584, 13b)
pdb|2XAS|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With A
Tranylcypromine Derivative (Mc2580, 14e)
Length = 482
Score = 28.5 bits (62), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 22 YGREFQAMMDCLEEEDCREEASQATEKKRRLTVDQV 57
YGR+FQA+ D + + + + +RR +D+V
Sbjct: 398 YGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEV 433
>pdb|4ETU|A Chain A, Crystal Structure Of Rabbit Ryanodine Receptor 1 Mutant
R2939s
Length = 210
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 29/88 (32%), Positives = 36/88 (40%), Gaps = 4/88 (4%)
Query: 36 EDCREEASQATEKKRRLTVDQVKALEKNFEVDNKLEPD-RKVKLAEELGLQPRQIAVWFQ 94
E RE + TEKK+ + Q E N PD V L+ EL Q+A +
Sbjct: 94 EKAREGEEERTEKKKTRKISQTAQTYDPREGYNPQPPDLSGVTLSRELQAMAEQLAENYH 153
Query: 95 NRRARLKSKELERDYG---LLKANYDAL 119
N R K +ELE G L YD L
Sbjct: 154 NTWGRKKKQELEAKGGGTHPLLVPYDTL 181
>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 = 4.8, Method: Compositional matrix adjust.
Identities = 12/44 (27%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 68 NKLEPDRKVKLAEELGLQPRQIAVWFQNRR-ARLKSKELERDYG 110
++++P K + +LG+ P Q+ + Q + AR ++ +ER++G
Sbjct: 2 DQVDPQLKFAMQRDLGIFPTQLPQYLQTEKLARTQAAAIEREFG 45
>pdb|3RQR|A Chain A, Crystal Structure Of The Ryr Domain Of The Rabbit
Ryanodine Receptor
Length = 227
Score = 28.1 bits (61), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 29/88 (32%), Positives = 36/88 (40%), Gaps = 4/88 (4%)
Query: 36 EDCREEASQATEKKRRLTVDQVKALEKNFEVDNKLEPD-RKVKLAEELGLQPRQIAVWFQ 94
E RE + TEKK+ + Q E N PD V L+ EL Q+A +
Sbjct: 111 EKAREGEEERTEKKKTRKISQTAQTYDPREGYNPQPPDLSGVTLSRELQAMAEQLAENYH 170
Query: 95 NRRARLKSKELERDYG---LLKANYDAL 119
N R K +ELE G L YD L
Sbjct: 171 NTWGRKKKQELEAKGGGTHPLLVPYDTL 198
>pdb|4ERT|A Chain A, Crystal Structure Of Rabbit Ryanodine Receptor 1
(2734-2940)
Length = 210
Score = 28.1 bits (61), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 29/88 (32%), Positives = 36/88 (40%), Gaps = 4/88 (4%)
Query: 36 EDCREEASQATEKKRRLTVDQVKALEKNFEVDNKLEPD-RKVKLAEELGLQPRQIAVWFQ 94
E RE + TEKK+ + Q E N PD V L+ EL Q+A +
Sbjct: 94 EKAREGEEERTEKKKTRKISQTAQTYDPREGYNPQPPDLSGVTLSRELQAMAEQLAENYH 153
Query: 95 NRRARLKSKELERDYG---LLKANYDAL 119
N R K +ELE G L YD L
Sbjct: 154 NTWGRKKKQELEAKGGGTHPLLVPYDTL 181
>pdb|3OA7|A Chain A, Structure Of The C-Terminal Domain Of Cnm67, A Core
Component Of The Spindle Pole Body Of Saccharomyces
Cerevisiae
Length = 206
Score = 28.1 bits (61), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 112 LKANYDALRLDYNNLQQENEALTAELRELKAKLCQENEETSHAVEAEAPVSEQSKNHVSS 171
L+ NY + +YN+L + + L+ EL L+++ TS + + + QS+ +S+
Sbjct: 35 LRVNYGSFVSEYNDLTKSHNTLSKELDNLRSRFGNLEGNTSERITIKNIL--QSRPDISA 92
Query: 172 ENAN 175
E N
Sbjct: 93 EECN 96
>pdb|4ESU|A Chain A, Crystal Structure Of Rabbit Ryanodine Receptor 1 Mutant
S2776m
Length = 210
Score = 27.7 bits (60), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 29/88 (32%), Positives = 36/88 (40%), Gaps = 4/88 (4%)
Query: 36 EDCREEASQATEKKRRLTVDQVKALEKNFEVDNKLEPD-RKVKLAEELGLQPRQIAVWFQ 94
E RE + TEKK+ + Q E N PD V L+ EL Q+A +
Sbjct: 94 EKAREGEEERTEKKKTRKISQTAQTYDPREGYNPQPPDLSGVTLSRELQAMAEQLAENYH 153
Query: 95 NRRARLKSKELERDYG---LLKANYDAL 119
N R K +ELE G L YD L
Sbjct: 154 NTWGRKKKQELEAKGGGTHPLLVPYDTL 181
>pdb|4ETT|A Chain A, Crystal Structure Of Rabbit Ryanodine Receptor 1 Mutant
E2764k
Length = 210
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 29/88 (32%), Positives = 36/88 (40%), Gaps = 4/88 (4%)
Query: 36 EDCREEASQATEKKRRLTVDQVKALEKNFEVDNKLEPD-RKVKLAEELGLQPRQIAVWFQ 94
E RE + TEKK+ + Q E N PD V L+ EL Q+A +
Sbjct: 94 EKAREGEEERTEKKKTRKISQTAQTYDPREGYNPQPPDLSGVTLSRELQAMAEQLAENYH 153
Query: 95 NRRARLKSKELERDYG---LLKANYDAL 119
N R K +ELE G L YD L
Sbjct: 154 NTWGRKKKQELEAKGGGTHPLLVPYDTL 181
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 78 LAEELGLQPRQIAVWFQNRRARLK 101
LA++ G+ Q++ WF N+R R K
Sbjct: 37 LAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|3K7D|A Chain A, C-Terminal (Adenylylation) Domain Of E.Coli Glutamine
Synthetase Adenylyltransferase
pdb|3K7D|B Chain B, C-Terminal (Adenylylation) Domain Of E.Coli Glutamine
Synthetase Adenylyltransferase
Length = 498
Score = 27.7 bits (60), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 44/86 (51%), Gaps = 8/86 (9%)
Query: 64 FEVDNKLEPDRKVKL---AEELGLQPRQIAVWFQNRRARLKSKELERDYG--LLKANYDA 118
+EVD +L P + + E ++ W +A ++++ + YG L A++DA
Sbjct: 301 YEVDARLRPSGAAGMLVTSAEAFADYQKNEAWTWEHQALVRARVV---YGDPQLTAHFDA 357
Query: 119 LRLDYNNLQQENEALTAELRELKAKL 144
+R + L +E + L E+RE++ K+
Sbjct: 358 VRREIMTLPREGKTLQTEVREMREKM 383
>pdb|2DA5|A Chain A, Solution Structure Of The Second Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 3 (Triple Homeobox 1
Protein)
Length = 75
Score = 27.7 bits (60), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 2/67 (2%)
Query: 42 ASQATEKKRRLTVDQVKALEKNFEVDNKLEPDRKV-KLAEELGLQPRQIAVWFQNRRARL 100
S K + +Q++ALE +F N L D ++ +L E + R+I WF RR ++
Sbjct: 4 GSSGPTKYKERAPEQLRALESSF-AQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKV 62
Query: 101 KSKELER 107
++E ++
Sbjct: 63 NAEETKK 69
>pdb|2V1D|B Chain B, Structural Basis Of Lsd1-Corest Selectivity In Histone H3
Recognition
pdb|2Y48|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With A N-
Terminal Snail Peptide
Length = 178
Score = 27.3 bits (59), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 22 YGREFQAMMDCLEEEDCREEASQATEKKRRLTVDQV 57
YGR+FQA+ D + + + + +RR +D+V
Sbjct: 94 YGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEV 129
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 27.3 bits (59), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 78 LAEELGLQPRQIAVWFQNRRARLK 101
LA++ G+ Q++ WF N+R R K
Sbjct: 37 LAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 27.3 bits (59), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 40 EEASQATEKKRRLTVDQVK-ALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRA 98
E QA ++KR ++V+ +LE F K + +A +LGL+ + VWF NRR
Sbjct: 2 ETLVQARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQ 61
Query: 99 RLK 101
+ K
Sbjct: 62 KGK 64
>pdb|3D1N|I Chain I, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|J Chain J, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|K Chain K, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|L Chain L, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|M Chain M, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|N Chain N, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|O Chain O, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|P Chain P, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
Length = 151
Score = 27.3 bits (59), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 41 EASQATEKKRRLTVDQVKALEKNFEVDNKLEPDRKV-KLAEELGLQPRQIAVWFQNRRAR 99
E S+ +++ T ++AL FE N L +++ + A+EL + VWF NRR
Sbjct: 89 EPSKKRKRRTSFTPQAIEALNAYFE-KNPLPTGQEITEXAKELNYDREVVRVWFSNRRQT 147
Query: 100 LKS 102
LK+
Sbjct: 148 LKN 150
>pdb|2IW5|B Chain B, Structural Basis For Corest-dependent Demethylation Of
Nucleosomes By The Human Lsd1 Histone Demethylase
pdb|2UXN|B Chain B, Structural Basis Of Histone Demethylation By Lsd1 Revealed
By Suicide Inactivation
pdb|2UXX|B Chain B, Human Lsd1 Histone Demethylase-Corest In Complex With An
Fad-Tranylcypromine Adduct
Length = 235
Score = 27.3 bits (59), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 22 YGREFQAMMDCLEEEDCREEASQATEKKRRLTVDQV 57
YGR+FQA+ D + + + + +RR +D+V
Sbjct: 151 YGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEV 186
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.312 0.127 0.358
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,462,781
Number of Sequences: 62578
Number of extensions: 221279
Number of successful extensions: 586
Number of sequences better than 100.0: 121
Number of HSP's better than 100.0 without gapping: 90
Number of HSP's successfully gapped in prelim test: 31
Number of HSP's that attempted gapping in prelim test: 494
Number of HSP's gapped (non-prelim): 124
length of query: 255
length of database: 14,973,337
effective HSP length: 97
effective length of query: 158
effective length of database: 8,903,271
effective search space: 1406716818
effective search space used: 1406716818
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: 50 (23.9 bits)