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= 004454
(753 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 45.8 bits (107), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 34/50 (68%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
T+ QLE LEK ++ YP R EL+ ++GL++ ++Q+WF +RR K RK
Sbjct: 7 TSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56
>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 = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 34/50 (68%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
T+ QLE LEK ++ YP R EL+ ++GL++ ++Q+WF +RR K RK
Sbjct: 14 TSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 63
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 35/54 (64%)
Query: 25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
R T+ QLE LEK ++ YP R EL+ ++GL++ ++Q+WF +RR K RK
Sbjct: 3 RTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 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 = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 33/50 (66%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
T QL LEK + E+Y S R EL+AQL L + +++WF +RR+KD++
Sbjct: 9 TRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 58
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 32/50 (64%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
T QL LEK + Y S A R E++A L L++ Q+++WF +RR+K +K
Sbjct: 42 TTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 33/48 (68%)
Query: 32 QLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
QL LE+ YA + ++ R ++SA LS+RQ+ +WF +RR+K++K+
Sbjct: 18 QLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKS 65
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 42.4 bits (98), Expect = 0.001, Method: Composition-based stats.
Identities = 20/50 (40%), Positives = 33/50 (66%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
T QL+ LE+ YA + ++ R +SA LS+RQ+ +WF +RR+K++K
Sbjct: 15 TKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64
>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 = 0.001, Method: Composition-based stats.
Identities = 20/50 (40%), Positives = 33/50 (66%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
T QL+ LE+ YA + ++ R +SA LS+RQ+ +WF +RR+K++K
Sbjct: 9 TKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58
>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 = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 31/50 (62%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
T +QL LEK + Y S R EL+ L L++R +++WF +RR+K +K
Sbjct: 11 TRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 34/55 (61%)
Query: 25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
R T QLEIL + Y ++S P+ + ++ ++GL R +Q+WF + R ++RK+
Sbjct: 21 RTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKS 75
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 33/53 (62%)
Query: 25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDR 77
R T +QL++LE +A YP +R E++ ++ L + ++Q+WF +RR K R
Sbjct: 11 RTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 33/50 (66%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
T +QL LE+ + + Y S A RAE S+ L L++ Q+++WF +RR K ++
Sbjct: 8 TTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>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 = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 34/54 (62%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTA 82
+ASQL+ LE+ + YP R EL+ + L++ ++Q+WF +RR + RK T+
Sbjct: 26 SASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHTS 79
>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 = 40.0 bits (92), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 34/62 (54%)
Query: 25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKR 84
R+ T Q LEK + Y + R +++ L LS+RQ+++WF +RR+K +K T
Sbjct: 7 RQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKDRTLDS 66
Query: 85 QP 86
P
Sbjct: 67 SP 68
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 40.0 bits (92), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 31/50 (62%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
TA QLE LE+ + YP R EL+ + L++ ++Q+WF +RR + RK
Sbjct: 10 TAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRK 59
>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 = 0.006, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 35/62 (56%)
Query: 25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKR 84
R+ T Q LEK + Y + R E++ L L++RQ+++WF +RR+K +K K
Sbjct: 6 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTKG 65
Query: 85 QP 86
+P
Sbjct: 66 EP 67
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 32/51 (62%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
T +Q+E+LE + V YP + +L+ +L L ++Q+WF +RR K +++
Sbjct: 9 TQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRS 59
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKRQ 85
T Q+E LEK + YP R L+A++ L + ++Q+WF +RR K R+ + Q
Sbjct: 15 TQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQ 71
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 39.7 bits (91), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 31/50 (62%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
T+ QLE LEK + YP R +L+ + L++ ++Q+WF +RR K RK
Sbjct: 17 TSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRK 66
>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 = 39.7 bits (91), Expect = 0.007, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 35/62 (56%)
Query: 25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKR 84
R+ T Q LEK + Y + R E++ L L++RQ+++WF +RR+K +K K
Sbjct: 6 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKTKG 65
Query: 85 QP 86
+P
Sbjct: 66 EP 67
>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 = 0.008, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 35/51 (68%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
++ QL L++ + Y +E R +LS++LGL++ Q+++WF ++R K +K+
Sbjct: 7 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKKS 57
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 38.9 bits (89), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 31/50 (62%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
T+ QL+ LE T+ YP + R E++ L++ ++++WF +RR K RK
Sbjct: 11 TSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
>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 = 38.9 bits (89), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 31/50 (62%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
T+ QL+ LE T+ YP + R E++ L++ ++++WF +RR K RK
Sbjct: 11 TSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
>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 = 38.9 bits (89), Expect = 0.012, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 31/51 (60%)
Query: 36 LEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKRQP 86
LEK + Y + R E++ L L++RQ+++WF +RR+K +K K +P
Sbjct: 11 LEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTKGEP 61
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 38.9 bits (89), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 29/51 (56%)
Query: 35 ILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKRQ 85
+L + YA YPS + EL+ GL+ Q+ WF +RR +DR A +R+
Sbjct: 508 VLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEAKERE 558
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 35/55 (63%)
Query: 25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
R + ++ QL L++ + Y + RAEL+A LGL+ Q+++WF ++R K +K+
Sbjct: 11 RTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKS 65
>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 = 38.5 bits (88), Expect = 0.015, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 28/54 (51%)
Query: 25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
R + QL L YA P ++ +L GLS R +++WF ++R KD+K
Sbjct: 7 RTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKK 60
>pdb|2HDD|A Chain A, Engrailed Homeodomain Q50k Variant Dna Complex
pdb|2HDD|B Chain B, Engrailed Homeodomain Q50k Variant Dna Complex
Length = 61
Score = 38.5 bits (88), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 35/51 (68%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
++ QL L++ + Y +E R +LS++LGL++ Q+++WF ++R K +K+
Sbjct: 11 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKKS 61
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 38.5 bits (88), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 35/51 (68%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
++ QL L++ + Y +E R +LS++LGL++ Q+++WF ++R K +K+
Sbjct: 9 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 59
>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 = 38.1 bits (87), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 35/51 (68%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
++ QL L++ + Y +E R +LS++LGL++ Q+++WF ++R K +K+
Sbjct: 11 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 61
>pdb|2DMP|A Chain A, Solution Structure Of The Third Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 2
Length = 89
Score = 38.1 bits (87), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 28/48 (58%)
Query: 26 KMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRR 73
K KT Q++ILE ++ S+P++A L + LS R++ WF RR
Sbjct: 18 KEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERR 65
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 38.1 bits (87), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%)
Query: 25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTA 82
R+ T Q LEK + Y + R E++ L L++RQ+++WF +RR+K +K A
Sbjct: 24 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEIQA 81
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 37.7 bits (86), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 32/55 (58%)
Query: 25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
R + T QLE LE + YP R +L+ ++ L + ++++WF +RR K R++
Sbjct: 11 RTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRS 65
>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 = 37.4 bits (85), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 28/43 (65%)
Query: 36 LEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
LEK + Y + R E++ L L++RQ+++WF +RR+K +K
Sbjct: 43 LEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 85
>pdb|1P7J|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52e
Length = 59
Score = 37.4 bits (85), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 34/51 (66%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
++ QL L++ + Y +E R +LS++LGL++ Q+++WF + R K +K+
Sbjct: 9 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKKS 59
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 37.4 bits (85), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 33/55 (60%)
Query: 25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
R + T QL LEK + + Y S R +L+ LGLS Q++ W+ +RR+K +K+
Sbjct: 21 RTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKS 75
>pdb|2CQX|A Chain A, Solution Structure Of Rsgi Ruh-034, A Homeodomain From
Mouse Cdna
Length = 72
Score = 37.0 bits (84), Expect = 0.036, Method: Composition-based stats.
Identities = 20/47 (42%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 34 EILEKTY-AVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
+ LEK + +V YP E LS QL S R++Q WF HRR +D+ +
Sbjct: 21 DTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPS 67
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 36.6 bits (83), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 27/44 (61%)
Query: 36 LEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
LEK + + Y S R L+ L LS+RQ++ WF +RR K R++
Sbjct: 22 LEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRS 65
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 36.6 bits (83), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 32/47 (68%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLK 75
++ QL L++ + Y +E R +LS++LGL++ Q+++WF ++R K
Sbjct: 7 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 36.6 bits (83), Expect = 0.049, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 32/54 (59%)
Query: 25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
R+ T Q LEK + Y + R E++ L L++RQ+++WF +RR+K +K
Sbjct: 7 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 60
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 36.6 bits (83), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 34/51 (66%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
++ QL ++ + Y +E R +LS++LGL++ Q+++WF ++R K R++
Sbjct: 11 SSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRRS 61
>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 = 36.6 bits (83), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 34/51 (66%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
++ QL L++ + Y +E R +LS++LGL++ Q+++WF + R K +K+
Sbjct: 9 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKKS 59
>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 = 35.8 bits (81), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 33/57 (57%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKRQ 85
T Q+ LEK + + Y + A RA L+ L ++D Q++ WF +RR K R+ +R+
Sbjct: 25 TRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEERE 81
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 35.8 bits (81), Expect = 0.098, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 30/50 (60%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
T Q LEK + Y + R E++ L L++RQ+++WF +RR+K +K
Sbjct: 9 TKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58
>pdb|2BXR|A Chain A, Human Monoamine Oxidase A In Complex With Clorgyline,
Crystal Form A
pdb|2BXR|B Chain B, Human Monoamine Oxidase A In Complex With Clorgyline,
Crystal Form A
pdb|2BXS|A Chain A, Human Monoamine Oxidase A In Complex With Clorgyline,
Crystal Form B
pdb|2BXS|B Chain B, Human Monoamine Oxidase A In Complex With Clorgyline,
Crystal Form B
Length = 527
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 34/132 (25%), Positives = 57/132 (43%), Gaps = 13/132 (9%)
Query: 178 MGHQKHSVRPLEAKEYERLDVKPFKDMFTIHPQGATRTVHEYKFLPEQPTVRSETHEKAA 237
MG + + P EA+ ++ D K++ I T+T + +L V SE HE +A
Sbjct: 134 MGKEIPTDAPWEAQHADKWDKMTMKEL--IDKICWTKTARRFAYLFVNINVTSEPHEVSA 191
Query: 238 SSYPYGSPADGSTARNSSLRAG---HPFMHGSEQISSGYGFPGQLPNLNLLSHQGRHSHL 294
+ + G T R S+ G F+ GS Q+S ++LL Q + +H
Sbjct: 192 LWFLWYVKQCGGTTRIFSVTNGGQERKFVGGSGQVSERI--------MDLLGDQVKLNHP 243
Query: 295 LPSVSGEYENIL 306
+ V +NI+
Sbjct: 244 VTHVDQSSDNII 255
>pdb|2Z5Y|A Chain A, Crystal Structure Of Human Monoamine Oxidase A (G110a)
With Harmine
Length = 513
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 34/132 (25%), Positives = 57/132 (43%), Gaps = 13/132 (9%)
Query: 178 MGHQKHSVRPLEAKEYERLDVKPFKDMFTIHPQGATRTVHEYKFLPEQPTVRSETHEKAA 237
MG + + P EA+ ++ D K++ I T+T + +L V SE HE +A
Sbjct: 123 MGKEIPTDAPWEAQHADKWDKMTMKEL--IDKICWTKTARRFAYLFVNINVTSEPHEVSA 180
Query: 238 SSYPYGSPADGSTARNSSLRAG---HPFMHGSEQISSGYGFPGQLPNLNLLSHQGRHSHL 294
+ + G T R S+ G F+ GS Q+S ++LL Q + +H
Sbjct: 181 LWFLWYVKQCGGTTRIFSVTNGGQERKFVGGSGQVSERI--------MDLLGDQVKLNHP 232
Query: 295 LPSVSGEYENIL 306
+ V +NI+
Sbjct: 233 VTHVDQSSDNII 244
>pdb|1O5W|A Chain A, The Structure Basis Of Specific Recognitions For
Substrates And Inhibitors Of Rat Monoamine Oxidase A
pdb|1O5W|B Chain B, The Structure Basis Of Specific Recognitions For
Substrates And Inhibitors Of Rat Monoamine Oxidase A
pdb|1O5W|C Chain C, The Structure Basis Of Specific Recognitions For
Substrates And Inhibitors Of Rat Monoamine Oxidase A
pdb|1O5W|D Chain D, The Structure Basis Of Specific Recognitions For
Substrates And Inhibitors Of Rat Monoamine Oxidase A
Length = 534
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 29/96 (30%), Positives = 43/96 (44%), Gaps = 5/96 (5%)
Query: 178 MGHQKHSVRPLEAKEYERLDVKPFKDMFTIHPQGATRTVHEYKFLPEQPTVRSETHEKAA 237
MG + P +A+ + D KD+ I T+T E+ +L V SE HE +A
Sbjct: 142 MGKEIPVDAPWQARHAQEWDKMTMKDL--IDKICWTKTAREFAYLFVNINVTSEPHEVSA 199
Query: 238 SSYPYGSPADGSTARNSSLRAG---HPFMHGSEQIS 270
+ + G TAR S+ G F+ GS Q+S
Sbjct: 200 LWFLWYVRQCGGTARIFSVTNGGQERKFVGGSGQVS 235
>pdb|2Z5X|A Chain A, Crystal Structure Of Human Monoamine Oxidase A With
Harmine
Length = 513
Score = 35.4 bits (80), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 34/132 (25%), Positives = 57/132 (43%), Gaps = 13/132 (9%)
Query: 178 MGHQKHSVRPLEAKEYERLDVKPFKDMFTIHPQGATRTVHEYKFLPEQPTVRSETHEKAA 237
MG + + P EA+ ++ D K++ I T+T + +L V SE HE +A
Sbjct: 123 MGKEIPTDAPWEAQHADKWDKMTMKEL--IDKICWTKTARRFAYLFVNINVTSEPHEVSA 180
Query: 238 SSYPYGSPADGSTARNSSLRAG---HPFMHGSEQISSGYGFPGQLPNLNLLSHQGRHSHL 294
+ + G T R S+ G F+ GS Q+S ++LL Q + +H
Sbjct: 181 LWFLWYVKQCGGTTRIFSVTNGGQERKFVGGSGQVSERI--------MDLLGDQVKLNHP 232
Query: 295 LPSVSGEYENIL 306
+ V +NI+
Sbjct: 233 VTHVDQSSDNII 244
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 35.4 bits (80), Expect = 0.12, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 30/50 (60%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
T Q LEK + Y + R E++ L L++RQ+++WF +RR+K +K
Sbjct: 21 TKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70
>pdb|2HOS|A Chain A, Phage-selected Homeodomain Bound To Unmodified Dna
pdb|2HOS|B Chain B, Phage-selected Homeodomain Bound To Unmodified Dna
pdb|2HOT|A Chain A, Phage Selected Homeodomain Bound To Modified Dna
pdb|2HOT|B Chain B, Phage Selected Homeodomain Bound To Modified Dna
Length = 63
Score = 35.0 bits (79), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 33/52 (63%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAP 80
++ QL L++ + Y +E R +LS++LGL++ Q++ WF + R K +K+
Sbjct: 12 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKKST 63
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 35.0 bits (79), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 27/35 (77%)
Query: 45 YPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
Y +E R +LS++LGL++ Q+++WF ++R K +K+
Sbjct: 10 YLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 44
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 34.7 bits (78), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 32/50 (64%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
T+ QL LEK + + Y S R++++ L LS+ Q+++WF +RR K ++
Sbjct: 15 TSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKR 64
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 34.3 bits (77), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 30/48 (62%)
Query: 31 SQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
SQ+ LE+ + + Y + A RA L+ L ++D Q++ WF +RR K R+
Sbjct: 7 SQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRR 54
>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 = 0.26, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 31/48 (64%)
Query: 31 SQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
+Q+ LE+ ++ + Y S RA L+ L L++ Q+++WF +RR K ++
Sbjct: 14 TQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of
Human Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 33.9 bits (76), Expect = 0.36, Method: Composition-based stats.
Identities = 16/62 (25%), Positives = 30/62 (48%)
Query: 25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAKR 84
+ K+ QL L+ ++ +P ++ L+ GLS R+++ WF RR R ++
Sbjct: 12 KNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGSRS 71
Query: 85 QP 86
P
Sbjct: 72 GP 73
>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 = 33.5 bits (75), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 25 RKMKTASQLEI---LEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
RK +T+ + I LEK++ P+ ++ QL + +++WFC+RR K+++
Sbjct: 105 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 161
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 33.1 bits (74), Expect = 0.54, Method: Composition-based stats.
Identities = 17/54 (31%), Positives = 32/54 (59%)
Query: 25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
R + +++QL +L + + Y S ELS L LS +Q++ WF ++R+K ++
Sbjct: 26 RTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKR 79
>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 = 33.1 bits (74), Expect = 0.54, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 25 RKMKTASQLEI---LEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
RK +T+ + I LEK++ P+ ++ QL + +++WFC+RR K+++
Sbjct: 97 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 153
>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 = 33.1 bits (74), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 25 RKMKTASQLEI---LEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
RK +T+ + I LEK++ P+ ++ QL + +++WFC+RR K+++
Sbjct: 104 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 160
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 33.1 bits (74), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 25 RKMKTA---SQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
++M+T+ QL ++ +A+ P +L+ + GL+ R LQ+WF + R K R+
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRR 64
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 32.7 bits (73), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 23/34 (67%)
Query: 45 YPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
YPSE + EL+ + G++ Q+ WF ++R++ +K
Sbjct: 29 YPSEEAKEELAKKSGITVSQVSNWFGNKRIRYKK 62
>pdb|2VI6|A Chain A, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|B Chain B, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|C Chain C, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|D Chain D, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|E Chain E, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|F Chain F, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|G Chain G, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|H Chain H, Crystal Structure Of The Nanog Homeodomain
Length = 62
Score = 32.7 bits (73), Expect = 0.76, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 34/57 (59%), Gaps = 3/57 (5%)
Query: 25 RKMKTA---SQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
+KM+T +QL L+ + + Y S ELS+ L LS +Q++ WF ++R+K ++
Sbjct: 4 QKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 32.7 bits (73), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 28/45 (62%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRR 73
T+SQ+ LE+ + Y + A+LSA+L L Q+++WF +RR
Sbjct: 10 TSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRR 54
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 29/51 (56%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
T QL +L + + + + PSE E++ + GL + ++ WF + K+R++
Sbjct: 15 TDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQS 65
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 27/51 (52%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
T QL +L+ + +YP + +LS L L R + +WF + R K RK+
Sbjct: 15 TDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKS 65
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 25 RKMKTASQLEI---LEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
RK +T+ + I LEK++ P+ ++ QL + +++WFC+RR K+++
Sbjct: 8 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 64
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 32.0 bits (71), Expect = 1.3, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 23/34 (67%)
Query: 45 YPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
YPSE + EL+ + G++ Q+ WF ++R++ +K
Sbjct: 30 YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 32.0 bits (71), Expect = 1.3, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 23/34 (67%)
Query: 45 YPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
YPSE + EL+ + G++ Q+ WF ++R++ +K
Sbjct: 28 YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>pdb|1X2M|A Chain A, Solution Structure Of The Homeobox Domain Of Mouse Lag1
Longevity Assurance Homolog 6
Length = 64
Score = 32.0 bits (71), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 29 TASQLEILEKTY-AVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDR 77
TA ILEK + A+ +P E LS QL R +Q WF RR +++
Sbjct: 8 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 57
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 31.6 bits (70), Expect = 1.6, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 23/34 (67%)
Query: 45 YPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
YPSE + EL+ + G++ Q+ WF ++R++ +K
Sbjct: 28 YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>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 = 31.6 bits (70), Expect = 1.8, Method: Composition-based stats.
Identities = 15/57 (26%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 25 RKMKTASQLEI---LEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
RK +T+ + + LEK++ P+ ++ QL + +++WFC+RR K+++
Sbjct: 2 RKKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEKR 58
>pdb|2HI3|A Chain A, Solution Structure Of The Homeodomain-Only Protein Hop
Length = 73
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 29 TASQLEILEKTY-AVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
T Q+EILE + V +P ++A+ GL++ Q Q WF R + R++
Sbjct: 10 TEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 61
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 31.2 bits (69), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 29 TASQLEILEKTY-AVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
T Q+EILE + V +P ++A+ GL++ Q Q WF R + R++
Sbjct: 9 TEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60
>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 = 31.2 bits (69), Expect = 2.5, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 23/34 (67%)
Query: 45 YPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRK 78
YPSE + EL+ + G++ Q+ WF ++R++ +K
Sbjct: 28 YPSEEAKEELARKCGITVSQVSNWFGNKRIRYKK 61
>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 = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 32/53 (60%)
Query: 25 RKMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDR 77
R + + +Q+ LE+ + + Y S R +L++ L L+ Q+++WF +RR K +
Sbjct: 6 RVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>pdb|2ECB|A Chain A, The Solution Structure Of The Third Homeobox Domain Of
Human Zinc Fingers And Homeoboxes Protein
Length = 89
Score = 30.8 bits (68), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%)
Query: 26 KMKTASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRR 73
K KTA QL +L+ ++ S ++ L AQ L+ R++ WF ++
Sbjct: 16 KEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKK 63
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 30.8 bits (68), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 30/55 (54%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK 83
T +Q LE+ + + Y S R L++ + L+ Q+++WF + R K ++A K
Sbjct: 20 TKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRAQNEK 74
>pdb|1X7P|A Chain A, Crystal Structure Of The Spou Methyltransferase Avirb From
Streptomyces Viridochromogenes In Complex With The
Cofactor Adomet
pdb|1X7P|B Chain B, Crystal Structure Of The Spou Methyltransferase Avirb From
Streptomyces Viridochromogenes In Complex With The
Cofactor Adomet
Length = 287
Score = 30.4 bits (67), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 33/105 (31%), Positives = 47/105 (44%), Gaps = 16/105 (15%)
Query: 90 QSLVPAGEKELAGSELVRGGMAVQRYYAVPMAPMLPFPLPQRNIVEMRVIAFVESQLGE- 148
++L+ G++EL S+ R + R + MAP L L ++N V+A VE +
Sbjct: 60 RTLLYDGQREL--SKWARELLRTVRTEQIAMAPDLLMELGEKNEAPPEVVAVVEMPADDL 117
Query: 149 ---PLREDGPILGVEFDSLPPDAFGRPIGPAAMGHQKHSVRPLEA 190
P+RED LGV FD RP P +G S L A
Sbjct: 118 DRIPVRED--FLGVLFD--------RPTSPGNIGSIIRSADALGA 152
>pdb|4AYT|A Chain A, Structure Of The Human Mitochondrial Abc Transporter,
Abcb10
pdb|4AYX|A Chain A, Structure Of The Human Mitochondrial Abc Transporter,
Abcb10 (Rod Form B)
pdb|3ZDQ|A Chain A, Structure Of The Human Mitochondrial Abc Transporter,
Abcb10 (nucleotide-free Form)
Length = 595
Score = 30.0 bits (66), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 285 LSHQGRHSHLLPSVSGEYENILRKNSFISAAMDAH 319
++ G+H LL +G Y ++ K SFISAA + +
Sbjct: 559 ITEYGKHEELLSKPNGIYRKLMNKQSFISAAENLY 593
>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 = 30.0 bits (66), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 30/55 (54%)
Query: 29 TASQLEILEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAPTAK 83
T +Q LE+ + + Y S R L++ + L+ Q+++WF + R K ++A K
Sbjct: 17 TKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEK 71
>pdb|1DGJ|A Chain A, Crystal Structure Of The Aldehyde Oxidoreductase From
Desulfovibrio Desulfuricans Atcc 27774
Length = 907
Score = 30.0 bits (66), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 10/83 (12%)
Query: 45 YPSEALRAELSAQLGLSDRQLQMWFCHRR---LKDRKAPTAKRQPKDFQSLVPAGE---- 97
+PSE L EL+ +LG+ +L+ C+R + P P+ F + P E
Sbjct: 544 FPSEVLMDELAEKLGMDPFELRALNCYREGDTTSSGQIPEVMSLPEMFDKMRPYYEESKK 603
Query: 98 --KELAGSELVRG-GMAVQRYYA 117
KE + +E+ RG G+A+ Y A
Sbjct: 604 RVKERSTAEIKRGVGVALGVYGA 626
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 29.6 bits (65), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 25/45 (55%)
Query: 36 LEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKAP 80
LE+ + S PS ++ +L L +++WFC+RR ++++
Sbjct: 102 LERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRVK 146
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 29.6 bits (65), Expect = 7.3, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 24/44 (54%)
Query: 36 LEKTYAVESYPSEALRAELSAQLGLSDRQLQMWFCHRRLKDRKA 79
LE + PS ++ QLGL +++WFC+RR K +++
Sbjct: 23 LETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS 66
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
0.317 0.134 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,071,659
Number of Sequences: 62578
Number of extensions: 853743
Number of successful extensions: 1890
Number of sequences better than 100.0: 91
Number of HSP's better than 100.0 without gapping: 78
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 1809
Number of HSP's gapped (non-prelim): 94
length of query: 753
length of database: 14,973,337
effective HSP length: 106
effective length of query: 647
effective length of database: 8,340,069
effective search space: 5396024643
effective search space used: 5396024643
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)