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= 000448
(1497 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 51.2 bits (121), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/57 (45%), Positives = 38/57 (66%), Gaps = 6/57 (10%)
Query: 34 PKRQMK------TPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
PKR+ + T FQLE LEKA++ YP TR EL+ K+GL++ ++Q+WF +RR
Sbjct: 2 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRR 58
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 51.2 bits (121), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 23/45 (51%), Positives = 33/45 (73%)
Query: 40 TPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
T FQLE LEKA++ YP TR EL+ K+GL++ ++Q+WF +RR
Sbjct: 7 TSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRR 51
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 50.4 bits (119), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/45 (51%), Positives = 33/45 (73%)
Query: 40 TPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
T FQLE LEKA++ YP TR EL+ K+GL++ ++Q+WF +RR
Sbjct: 7 TSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRR 51
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 43.1 bits (100), Expect = 0.001, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 34/55 (61%)
Query: 31 QGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
+G+ KR T QL+ LE+ YA+ + ++ R +S LS+RQ+ +WF +RR+
Sbjct: 6 EGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRV 60
>pdb|1FJL|A Chain A, Homeodomain From The Drosophila Paired Protein Bound To
A Dna Oligonucleotide
pdb|1FJL|B Chain B, Homeodomain From The Drosophila Paired Protein Bound To
A Dna Oligonucleotide
pdb|1FJL|C Chain C, Homeodomain From The Drosophila Paired Protein Bound To
A Dna Oligonucleotide
Length = 81
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 36/55 (65%), Gaps = 3/55 (5%)
Query: 33 KPKRQMKTPF---QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
+ +R+ +T F QL+ LE+A+ YP TR EL+++ L++ ++Q+WF +RR
Sbjct: 16 RKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRR 70
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 35/60 (58%), Gaps = 3/60 (5%)
Query: 29 GQQGKPKRQMKTPF---QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
G G R+ + P+ QL LE+ YA+ + ++ R ++S LS+RQ+ +WF +RR+
Sbjct: 1 GSSGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRV 60
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 42.4 bits (98), Expect = 0.002, Method: Composition-based stats.
Identities = 20/54 (37%), Positives = 33/54 (61%)
Query: 32 GKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
G+ KR T QL+ LE+ YA+ + ++ R +S LS+RQ+ +WF +RR+
Sbjct: 1 GRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRV 54
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 34/58 (58%)
Query: 27 NEGQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
+ G G+ R + + FQL L++ + Y + RAEL+ LGL+ Q+++WF ++R
Sbjct: 2 SSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKR 59
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 42.0 bits (97), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 35/53 (66%), Gaps = 3/53 (5%)
Query: 35 KRQMKTPF---QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
+R+ +T F QLE LE+A+ YP TR EL+++ L++ ++Q+WF +RR
Sbjct: 2 QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRR 54
>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 = 0.003, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 35/59 (59%)
Query: 27 NEGQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
+ ++G+ R + T QL LEK + + Y S R +L+E LGLS Q++ W+ +RR+
Sbjct: 12 TKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRM 70
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 42.0 bits (97), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 32/56 (57%)
Query: 29 GQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
G G+ R + T QLE LE + YP TR +L+ K+ L + ++++WF +RR
Sbjct: 4 GSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRR 59
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 41.6 bits (96), Expect = 0.003, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 31/50 (62%)
Query: 36 RQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
RQ T +Q LEK + + Y + R E++ L L++RQ+++WF +RR+
Sbjct: 24 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRM 73
>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 = 40.4 bits (93), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 31/54 (57%)
Query: 32 GKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
K RQ T +Q LEK + Y + R +++ L LS+RQ+++WF +RR+
Sbjct: 3 SKRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRM 56
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 40.4 bits (93), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 32/56 (57%)
Query: 29 GQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
G G+ +R T QL+ LE +A YP R E++ K+ L + ++Q+WF +RR
Sbjct: 4 GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRR 59
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 40.4 bits (93), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 33/52 (63%), Gaps = 3/52 (5%)
Query: 36 RQMKTPF---QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
R+ +TPF QL LE+ + + Y S + RAE S L L++ Q+++WF +RR
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRR 52
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 40.0 bits (92), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 26 SNEGQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
SN+G++ + R T +QLE LEK + YP R +L+ + L++ ++Q+WF +RR
Sbjct: 4 SNKGKK-RRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRR 61
>pdb|2R5Y|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd
Site
pdb|2R5Z|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A DNA SEQUENCE
Derived From The Fkh Gene
Length = 88
Score = 39.7 bits (91), Expect = 0.012, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 33/59 (55%)
Query: 27 NEGQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
N + K +R T +Q LEK + Y + R E++ L L++RQ+++WF +RR+
Sbjct: 23 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRM 81
>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 = 39.7 bits (91), Expect = 0.013, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 31/53 (58%)
Query: 33 KPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
K RQ T +Q LEK + Y + R E++ L L++RQ+++WF +RR+
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRM 55
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 39.7 bits (91), Expect = 0.013, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 31/53 (58%)
Query: 33 KPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
K RQ T +Q LEK + Y + R E++ L L++RQ+++WF +RR+
Sbjct: 4 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRM 56
>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 = 39.3 bits (90), Expect = 0.016, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 31/53 (58%)
Query: 33 KPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
K RQ T +Q LEK + Y + R E++ L L++RQ+++WF +RR+
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 55
>pdb|2CQX|A Chain A, Solution Structure Of Rsgi Ruh-034, A Homeodomain From
Mouse Cdna
Length = 72
Score = 39.3 bits (90), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/41 (48%), Positives = 26/41 (63%), Gaps = 1/41 (2%)
Query: 45 ETLEKAYASET-YPSESTRAELSEKLGLSDRQLQMWFCHRR 84
+TLEK + S T YP E LS++L S R++Q WF HRR
Sbjct: 21 DTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRR 61
>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 = 0.025, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 30/56 (53%)
Query: 29 GQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
G G+ R T Q+E LEK + YP R L+ K+ L + ++Q+WF +RR
Sbjct: 4 GSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRR 59
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 38.5 bits (88), Expect = 0.032, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 31/53 (58%)
Query: 33 KPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
+ KR T +Q LEK + Y + R E++ L L++RQ+++WF +RR+
Sbjct: 2 RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRM 54
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 38.1 bits (87), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 3/59 (5%)
Query: 29 GQQGKPKRQMKTPF---QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
G G ++M+T F QL T++ +A P +L++K GL+ R LQ+WF + R
Sbjct: 1 GSSGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNAR 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 = 37.7 bits (86), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 29/54 (53%)
Query: 32 GKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
K R T QL LEK + Y S R EL+ L L++R +++WF +RR+
Sbjct: 3 NKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRM 56
>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 = 37.4 bits (85), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 31/53 (58%), Gaps = 3/53 (5%)
Query: 36 RQMKTPF---QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
R+ +T F QL LEK + E Y S R EL+ +L L + +++WF +RR+
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRM 54
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 37.0 bits (84), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 28/53 (52%)
Query: 32 GKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
G+ R T Q+E LE + YP +L++KL L ++Q+WF +RR
Sbjct: 1 GRRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRR 53
>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 = 0.085, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 28/42 (66%)
Query: 43 QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
QL L++ + Y +E R +LS +LGL++ Q+++WF ++R
Sbjct: 10 QLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKR 51
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 36.6 bits (83), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 34/56 (60%), Gaps = 3/56 (5%)
Query: 32 GKPKRQMKTPF---QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
G R+ +T F QL LEK + + Y S + R++++ L LS+ Q+++WF +RR
Sbjct: 4 GGKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRR 59
>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 = 36.6 bits (83), Expect = 0.12, Method: Composition-based stats.
Identities = 16/46 (34%), Positives = 28/46 (60%)
Query: 40 TPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
T +Q LEK + Y + R E++ L L++RQ+++WF +RR+
Sbjct: 4 TRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRM 49
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 35.8 bits (81), Expect = 0.17, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 30/53 (56%)
Query: 33 KPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
+ KR T Q LEK + Y + R E++ L L++RQ+++WF +RR+
Sbjct: 14 RKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRM 66
>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 = 35.8 bits (81), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 28/42 (66%)
Query: 43 QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
QL L++ + Y +E R +LS +LGL++ Q+++WF ++R
Sbjct: 14 QLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKR 55
>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 = 35.8 bits (81), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 28/42 (66%)
Query: 43 QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
QL L++ + Y +E R +LS +LGL++ Q+++WF ++R
Sbjct: 14 QLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKR 55
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 35.8 bits (81), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 28/42 (66%)
Query: 43 QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
QL L++ + Y +E R +LS +LGL++ Q+++WF ++R
Sbjct: 10 QLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKR 51
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 35.8 bits (81), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 28/42 (66%)
Query: 43 QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
QL L++ + Y +E R +LS +LGL++ Q+++WF ++R
Sbjct: 12 QLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKR 53
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 35.4 bits (80), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%)
Query: 28 EGQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
E Q+ K R TP QLE L + Y ++ P+ ++ ++GL R +Q+WF + R
Sbjct: 13 EPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTR 69
>pdb|2L7F|P Chain P, Solution Structure Of The Pitx2 Homeodomain
pdb|2LKX|A Chain A, Nmr Structure Of The Homeodomain Of Pitx2 In Complex
With A Taatcc Dna Binding Site
Length = 68
Score = 35.4 bits (80), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 32/53 (60%), Gaps = 3/53 (5%)
Query: 35 KRQMKTPF---QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
+R+ +T F QL+ LE + YP STR E++ L++ ++++WF +RR
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRR 55
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 35.4 bits (80), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 27/43 (62%)
Query: 43 QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
QL LEK + Y S + R E++ L L++ Q+++WF +RR+
Sbjct: 45 QLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRM 87
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 35.4 bits (80), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 25/38 (65%)
Query: 47 LEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
LEK + ++ Y S R L++ L LS+RQ++ WF +RR
Sbjct: 22 LEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRR 59
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 35.4 bits (80), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 22/39 (56%)
Query: 46 TLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
L + YA YPS + EL+E GL+ Q+ WF +RR
Sbjct: 508 VLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRR 546
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 35.4 bits (80), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 32/53 (60%), Gaps = 3/53 (5%)
Query: 35 KRQMKTPF---QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
+R+ +T F QL+ LE + YP STR E++ L++ ++++WF +RR
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRR 55
>pdb|1BW5|A Chain A, The Nmr Solution Structure Of The Homeodomain Of The Rat
Insulin Gene Enhancer Protein Isl-1, 50 Structures
Length = 66
Score = 35.0 bits (79), Expect = 0.35, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 24/42 (57%)
Query: 43 QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
QL TL YA+ P + +L E GLS R +++WF ++R
Sbjct: 14 QLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKR 55
>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 = 34.7 bits (78), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 27/45 (60%)
Query: 40 TPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
T Q+ LEK + + Y + + RA L+ L ++D Q++ WF +RR
Sbjct: 25 TRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRR 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 = 34.7 bits (78), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 27/42 (64%)
Query: 43 QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
QL L++ + Y +E R +LS +LGL++ Q+++WF + R
Sbjct: 12 QLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNER 53
>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 = 34.3 bits (77), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 28/42 (66%)
Query: 43 QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
Q+ LE+ ++ + Y S RA L++ L L++ Q+++WF +RR
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRR 56
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 34.3 bits (77), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 30/49 (61%), Gaps = 3/49 (6%)
Query: 39 KTPFQLETLEKA---YASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
+T F E L +A + Y +E R +LS +LGL++ Q+++WF ++R
Sbjct: 7 RTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKR 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 = 34.3 bits (77), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 27/42 (64%)
Query: 43 QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
QL L++ + Y +E R +LS +LGL++ Q+++WF + R
Sbjct: 12 QLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNAR 53
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 33.5 bits (75), Expect = 0.82, Method: Composition-based stats.
Identities = 13/36 (36%), Positives = 24/36 (66%)
Query: 50 AYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
++ S YPSE + EL++K G++ Q+ WF ++R+
Sbjct: 24 SHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRI 59
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 33.5 bits (75), Expect = 0.89, Method: Composition-based stats.
Identities = 13/36 (36%), Positives = 24/36 (66%)
Query: 50 AYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
++ S YPSE + EL++K G++ Q+ WF ++R+
Sbjct: 22 SHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRI 57
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 33.5 bits (75), Expect = 0.90, Method: Composition-based stats.
Identities = 13/36 (36%), Positives = 24/36 (66%)
Query: 50 AYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
++ S YPSE + EL++K G++ Q+ WF ++R+
Sbjct: 22 SHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRI 57
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of
Human Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 32.7 bits (73), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 27/49 (55%)
Query: 36 RQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
+ K+ QL L+ ++ +P +S L++ GLS R+++ WF RR
Sbjct: 12 KNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRR 60
>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 = 1.4, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 33/56 (58%), Gaps = 3/56 (5%)
Query: 32 GKPKRQMKTPF---QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
G +++ +T F QL L++ + Y +E R +LS +LGL++ Q++ WF + R
Sbjct: 1 GSDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMR 56
>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 = 32.7 bits (73), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 23/36 (63%)
Query: 50 AYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
++ S YPSE + EL+ K G++ Q+ WF ++R+
Sbjct: 22 SHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRI 57
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 32.7 bits (73), Expect = 1.5, Method: Composition-based stats.
Identities = 13/36 (36%), Positives = 24/36 (66%)
Query: 50 AYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
++ S YPSE + EL++K G++ Q+ WF ++R+
Sbjct: 23 SHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRI 58
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 32.7 bits (73), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 35 KRQMKTPFQL---ETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
KR+ +T + + LE+ + + PS ++E+L L +++WFC+RR
Sbjct: 87 KRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRR 139
>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 = 32.3 bits (72), Expect = 2.1, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 3/54 (5%)
Query: 35 KRQMKTPF---QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRL 85
K++M+T F QL L+ + + Y S ELS L LS +Q++ WF ++R+
Sbjct: 3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRM 56
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 32.0 bits (71), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 25/37 (67%)
Query: 48 EKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
++ + Y +E R +LS +LGL++ Q+++WF ++R
Sbjct: 2 KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKR 38
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 32.0 bits (71), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 27/42 (64%)
Query: 43 QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
Q+ LE+ + + Y + + RA L++ L ++D Q++ WF +RR
Sbjct: 8 QVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRR 49
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 31.6 bits (70), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 36 RQMKTPF---QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
R+ +T F Q+ LE+ + Y + A+LS KL L Q+++WF +RR
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRR 54
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 31.2 bits (69), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 23/45 (51%)
Query: 40 TPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
T +QL L+ + + YP + +LS L L R + +WF + R
Sbjct: 15 TDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNAR 59
>pdb|2DMP|A Chain A, Solution Structure Of The Third Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 2
Length = 89
Score = 31.2 bits (69), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 26/46 (56%)
Query: 39 KTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
KT Q++ LE ++ ++P+++ L + LS R++ WF RR
Sbjct: 20 KTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERR 65
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 30.8 bits (68), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 25/52 (48%)
Query: 29 GQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWF 80
G GK R T QL L + + PSE E+++K GL + ++ WF
Sbjct: 4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWF 55
>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 = 30.4 bits (67), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 25/42 (59%)
Query: 43 QLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRR 84
Q+ LE+ + + Y S R +L+ L L+ Q+++WF +RR
Sbjct: 13 QVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRR 54
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
0.315 0.131 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 38,824,765
Number of Sequences: 62578
Number of extensions: 1527646
Number of successful extensions: 3528
Number of sequences better than 100.0: 72
Number of HSP's better than 100.0 without gapping: 66
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 3462
Number of HSP's gapped (non-prelim): 72
length of query: 1497
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1386
effective length of database: 8,027,179
effective search space: 11125670094
effective search space used: 11125670094
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.9 bits)