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= psy10107
(140 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Pknox1
Length = 73
Score = 53.5 bits (127), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 22/44 (50%), Positives = 32/44 (72%)
Query: 19 LKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRL 62
+++WL +H +PYPT+ EK +A T +TL QV+ WF NARRR+
Sbjct: 22 MRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRI 65
>pdb|2LK2|A Chain A, Solution Nmr Structure Of Homeobox Domain (171-248) Of
Human Homeobox Protein Tgif1, Northeast Structural
Genomics Consortium Target Hr4411b
Length = 89
Score = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 22/44 (50%), Positives = 30/44 (68%)
Query: 19 LKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRL 62
L+ WL EH+ N YP++ EK +L+ T ++ QV WF NARRRL
Sbjct: 20 LRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRL 63
>pdb|3K2A|A Chain A, Crystal Structure Of The Homeobox Domain Of Human
Homeobox Protein Meis2
pdb|3K2A|B Chain B, Crystal Structure Of The Homeobox Domain Of Human
Homeobox Protein Meis2
Length = 67
Score = 50.1 bits (118), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 21/43 (48%), Positives = 31/43 (72%)
Query: 20 KAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRL 62
+AWL +H +PYP++ +K LA T +T+ QV+ WF NARRR+
Sbjct: 14 RAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRI 56
>pdb|2DMN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Tgif2lx
Length = 83
Score = 49.3 bits (116), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 20/44 (45%), Positives = 31/44 (70%)
Query: 19 LKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRL 62
L+ W+ +H+ YP++ EK ML+ T ++L Q+S WF NARRR+
Sbjct: 22 LRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRI 65
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 43.9 bits (102), Expect = 3e-05, Method: Composition-based stats.
Identities = 23/53 (43%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 9 YVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRR 61
Y E + L+ W + NPYP+ EK LA T +T TQVS WF N R+R
Sbjct: 499 YCFKEKSRGVLREW---YAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQR 548
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
TEI L + H NPYP++ K LA + +T++QVS WF N R R KK
Sbjct: 13 ATEI----LNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYKK 62
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 26/46 (56%)
Query: 19 LKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
L + H NPYP++ K LA +T++QVS WF N R R KK
Sbjct: 18 LNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
TEI L + H NPYP++ K LA +T++QVS WF N R R KK
Sbjct: 12 ATEI----LNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 26/46 (56%)
Query: 19 LKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
L + H NPYP++ K LA +T++QVS WF N R R KK
Sbjct: 16 LNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>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 = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 26/46 (56%)
Query: 19 LKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
L + H NPYP++ K LA +T++QVS WF N R R KK
Sbjct: 16 LNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKK 61
>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 = 35.4 bits (80), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 24/44 (54%)
Query: 29 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEP 72
N Y T+ +I +A +T Q+ WF N R + KKENK EP
Sbjct: 24 NRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTKGEP 67
>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 = 35.4 bits (80), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 24/44 (54%)
Query: 29 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEP 72
N Y T+ +I +A +T Q+ WF N R + KKENK EP
Sbjct: 18 NRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTKGEP 61
>pdb|2D5V|A Chain A, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
pdb|2D5V|B Chain B, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
Length = 164
Score = 34.7 bits (78), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 3/55 (5%)
Query: 7 PEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRR 61
P V T++ + TL A E+K+ P+K +I ++ + L+ VS +F NARRR
Sbjct: 100 PRLVFTDVQRRTLHAIFKENKR---PSKELQITISQQLGLELSTVSNFFMNARRR 151
>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 = 34.3 bits (77), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 24/44 (54%)
Query: 29 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEP 72
N Y T+ +I +A +T Q+ WF N R + KKENK EP
Sbjct: 24 NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKTKGEP 67
>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 = 32.3 bits (72), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%)
Query: 19 LKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65
L+A + +NP P E L TKMT ++ +WF+ R+++ E
Sbjct: 19 LRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAE 65
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 32.3 bits (72), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 22/41 (53%)
Query: 25 EHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65
E N Y T+ +I +A +T Q+ WF N R +LKKE
Sbjct: 38 EFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE 78
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 21/38 (55%)
Query: 29 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
N Y T+ +I +A +T Q+ WF N R + KKEN
Sbjct: 25 NRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 62
>pdb|1S7E|A Chain A, Solution Structure Of Hnf-6
Length = 147
Score = 31.2 bits (69), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 3/53 (5%)
Query: 7 PEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANAR 59
P V T++ + TL A E+K+ P+K +I ++ + L+ VS +F NAR
Sbjct: 98 PRLVFTDVQRRTLHAIFKENKR---PSKELQITISQQLGLELSTVSNFFMNAR 147
>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 = 31.2 bits (69), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 29 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67
N Y T+ +I +A +T Q+ WF N R + KKE+K
Sbjct: 50 NRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEHK 88
>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 = 0.23, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 19/33 (57%)
Query: 27 KKNPYPTKGEKIMLAIITKMTLTQVSTWFANAR 59
K+ Y + E+ LA + K+T TQV WF N R
Sbjct: 22 KQQRYLSAPERDQLASVLKLTSTQVKIWFQNRR 54
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 30.8 bits (68), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 29 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67
N Y T+ + +A + +T QV WF N R ++KK NK
Sbjct: 35 NMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINK 73
>pdb|2DMP|A Chain A, Solution Structure Of The Third Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 2
Length = 89
Score = 30.4 bits (67), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 24/36 (66%), Gaps = 1/36 (2%)
Query: 28 KNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63
K+ +PT+ E L + TK++ ++ +WF+ RR+L+
Sbjct: 34 KSSFPTQAELDRLRVETKLSRREIDSWFSE-RRKLR 68
>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 = 30.4 bits (67), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 16/32 (50%)
Query: 28 KNPYPTKGEKIMLAIITKMTLTQVSTWFANAR 59
K Y E+ LA KMT QV TWF N R
Sbjct: 38 KQKYLASAERAALARGLKMTDAQVKTWFQNRR 69
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 30.4 bits (67), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 24/41 (58%)
Query: 27 KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67
K+ Y + E+ LA + +T TQV WF N R ++K++ K
Sbjct: 22 KQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 30.0 bits (66), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 16/32 (50%)
Query: 28 KNPYPTKGEKIMLAIITKMTLTQVSTWFANAR 59
+ Y E+ LA +MT QV TWF N R
Sbjct: 18 RQKYLASAERAALAKALRMTDAQVKTWFQNRR 49
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 30.0 bits (66), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 14 IYKA-TLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
IY + L A +K Y E+ LA +T TQV WF N R ++KK
Sbjct: 13 IYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSG 66
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 30.0 bits (66), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 29 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
N Y T+ + +A + +T QV WF N R ++KK N
Sbjct: 23 NMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKMN 60
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 30.0 bits (66), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 26/49 (53%)
Query: 16 KATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
K LK E+ N + TK ++ ++ T ++ QV+ WF N R + KK
Sbjct: 16 KVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 30.0 bits (66), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 26/49 (53%)
Query: 16 KATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
K LK E+ N + TK ++ ++ T ++ QV+ WF N R + KK
Sbjct: 10 KVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 29.6 bits (65), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 26/49 (53%)
Query: 16 KATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
K L+ E+ N + TK ++ ++ T ++ Q++ WF N R + KK
Sbjct: 16 KGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64
>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 = 29.3 bits (64), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 29 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65
N Y ++ ++ LA++ +T + WF N R + KKE
Sbjct: 25 NKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 29.3 bits (64), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 22/42 (52%)
Query: 27 KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 68
++N YP + +A+ T +T +V WF N R + +K +
Sbjct: 23 QRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEF 64
>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 = 28.9 bits (63), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 22/42 (52%)
Query: 27 KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 68
++N YP + +A+ T +T +V WF N R + +K +
Sbjct: 23 QRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEF 64
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 28.9 bits (63), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 29 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67
N Y ++ ++ +A ++ TQV WF N R + KK +
Sbjct: 56 NKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER 94
>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 = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 22/40 (55%)
Query: 27 KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
++ YP + LA T +T ++ WF N R RL+K++
Sbjct: 38 ERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH 77
>pdb|3FWL|A Chain A, Crystal Structure Of The Full-Length Transglycosylase
Pbp1b From Escherichia Coli
Length = 751
Score = 28.5 bits (62), Expect = 1.2, Method: Composition-based stats.
Identities = 10/35 (28%), Positives = 21/35 (60%)
Query: 40 LAIITKMTLTQVSTWFANARRRLKKENKMTWEPKN 74
L +++ + +++TW A+A L++ N W P+N
Sbjct: 465 LTALSQPKIYRLNTWIADAPIALRQPNGQVWSPQN 499
>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 = 28.5 bits (62), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 27 KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK-ENKMTWE 71
++ Y + E+ LA + ++T TQV WF N R + K+ +N+ +E
Sbjct: 29 RQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGYE 74
>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 = 28.5 bits (62), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 17 ATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
A LK NE N Y T+ + L+ + Q+ WF NAR ++KK
Sbjct: 14 ARLKREFNE---NRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58
>pdb|3VMA|A Chain A, Crystal Structure Of The Full-Length Transglycosylase
Pbp1b From Escherichia Coli
Length = 768
Score = 28.1 bits (61), Expect = 1.5, Method: Composition-based stats.
Identities = 10/35 (28%), Positives = 21/35 (60%)
Query: 40 LAIITKMTLTQVSTWFANARRRLKKENKMTWEPKN 74
L +++ + +++TW A+A L++ N W P+N
Sbjct: 482 LTALSQPKIYRLNTWIADAPIALRQPNGQVWSPQN 516
>pdb|1MNM|C Chain C, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
Crystal Structure
pdb|1MNM|D Chain D, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
Crystal Structure
Length = 87
Score = 28.1 bits (61), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 28/47 (59%), Gaps = 4/47 (8%)
Query: 19 LKAWLNEHKKNPY-PTKG-EKIMLAIITKMTLTQVSTWFANARRRLK 63
L++W ++ +NPY TKG E +M T ++ Q+ W +N RR+ K
Sbjct: 42 LESWFAKNIENPYLDTKGLENLMKN--TSLSRIQIKNWVSNRRRKEK 86
>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 = 28.1 bits (61), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 24/46 (52%)
Query: 29 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEPKN 74
N Y T+ +I +A ++ Q+ WF N R + KK+ + P++
Sbjct: 25 NRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKDRTLDSSPEH 70
>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 = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 17 ATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
A LK NE N Y T+ + L+ + Q+ WFAN R ++KK
Sbjct: 12 ARLKREFNE---NRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 21/42 (50%)
Query: 27 KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 68
+K YP + LA+ T +T +V WF N R + +K +
Sbjct: 29 QKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRERF 70
>pdb|1K61|A Chain A, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|B Chain B, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|C Chain C, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|D Chain D, Matalpha2 Homeodomain Bound To Dna
Length = 60
Score = 27.7 bits (60), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 28/47 (59%), Gaps = 4/47 (8%)
Query: 19 LKAWLNEHKKNPY-PTKG-EKIMLAIITKMTLTQVSTWFANARRRLK 63
L++W ++ +NPY TKG E +M T ++ Q+ W +N RR+ K
Sbjct: 13 LESWFAKNIENPYLDTKGLENLMKN--TSLSRIQIKNWVSNRRRKEK 57
>pdb|2VI6|A Chain A, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|B Chain B, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|C Chain C, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|D Chain D, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|E Chain E, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|F Chain F, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|G Chain G, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|H Chain H, Crystal Structure Of The Nanog Homeodomain
Length = 62
Score = 27.7 bits (60), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 26/53 (49%)
Query: 12 TEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
T +A L A + +K Y + + L+ I ++ QV TWF N R + K+
Sbjct: 8 TVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>pdb|2BF1|A Chain A, Structure Of An Unliganded And Fully-Glycosylated Siv
Gp120 Envelope Glycoprotein
pdb|3FUS|A Chain A, Improved Structure Of The Unliganded Simian
Immunodeficiency Virus Gp120 Core
Length = 316
Score = 27.7 bits (60), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/51 (25%), Positives = 25/51 (49%)
Query: 24 NEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEPKN 74
N+ + + K K++++ T+M TQ STWF R + + W ++
Sbjct: 84 NDTNYSGFMPKCSKVVVSSCTRMMETQTSTWFGFNGTRAENRTYIYWHGRD 134
>pdb|1APL|C Chain C, Crystal Structure Of A Mat-Alpha2 Homeodomain-Operator
Complex Suggests A General Model For Homeodomain-Dna
Interactions
pdb|1APL|D Chain D, Crystal Structure Of A Mat-Alpha2 Homeodomain-Operator
Complex Suggests A General Model For Homeodomain-Dna
Interactions
pdb|1YRN|B Chain B, Crystal Structure Of The Mata1MATALPHA2 HOMEODOMAIN
Heterodimer Bound To Dna
pdb|1AKH|B Chain B, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 83
Score = 27.7 bits (60), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 28/47 (59%), Gaps = 4/47 (8%)
Query: 19 LKAWLNEHKKNPY-PTKG-EKIMLAIITKMTLTQVSTWFANARRRLK 63
L++W ++ +NPY TKG E +M T ++ Q+ W +N RR+ K
Sbjct: 17 LESWFAKNIENPYLDTKGLENLMKN--TSLSRIQIKNWVSNRRRKEK 61
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 26.9 bits (58), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 13/57 (22%), Positives = 27/57 (47%)
Query: 12 TEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 68
T + ++A E ++ YP + LA + ++ WF+N R + ++E K+
Sbjct: 12 TSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL 68
>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 = 26.9 bits (58), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 20/38 (52%)
Query: 29 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
Y + E+ LA K+T TQV WF N R + K++
Sbjct: 26 QKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 63
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 26.9 bits (58), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 27 KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK-ENKMTWE 71
++ Y + E+ L + ++T TQV WF N R + K+ +N+ +E
Sbjct: 32 RQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRAQNEKGYE 77
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 26.6 bits (57), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 27 KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65
++ YP + LA K+T +V WF+N R R +K+
Sbjct: 22 ERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>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 = 26.6 bits (57), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 17 ATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
A LK NE N Y T+ + L+ + Q+ WF N R ++KK
Sbjct: 14 ARLKREFNE---NRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58
>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 = 26.6 bits (57), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
+ T I A K++L +N PT E M+A M + WF+N R++ K+ N
Sbjct: 107 IETNIRVALEKSFL----ENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEKRIN 159
>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 = 26.6 bits (57), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 17 ATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
A LK NE N Y T+ + L+ + QV WF N R ++KK
Sbjct: 17 ARLKREFNE---NRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 26.6 bits (57), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 13/53 (24%), Positives = 22/53 (41%)
Query: 12 TEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
T L+ + N YP E L+ + + + WF NAR++ +K
Sbjct: 12 TRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64
>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 = 26.6 bits (57), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 17 ATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
A LK NE N Y T+ + L+ + Q+ WF N R ++KK
Sbjct: 16 ARLKREFNE---NRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60
>pdb|1O4X|A Chain A, Ternary Complex Of The Dna Binding Domains Of The Oct1 And
Sox2 Transcription Factors With A 19mer Oligonucleotide
From The Hoxb1 Regulatory Element
Length = 167
Score = 26.2 bits (56), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 4/57 (7%)
Query: 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
+ T I A K++L +N PT E M+A M + WF N R++ K+ N
Sbjct: 111 IETNIRVALEKSFL----ENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRIN 163
>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 = 26.2 bits (56), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 4/57 (7%)
Query: 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
+ T I A K++L +N PT E M+A M + WF N R++ K+ N
Sbjct: 110 IETNIRVALEKSFL----ENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRIN 162
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 26.2 bits (56), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 17 ATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
A LK NE N Y T+ + L+ + Q+ WF N R ++KK
Sbjct: 14 ARLKREFNE---NRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58
>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 = 26.2 bits (56), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 4/57 (7%)
Query: 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
+ T I A K++L +N PT E M+A M + WF N R++ K+ N
Sbjct: 103 IETNIRVALEKSFL----ENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRIN 155
>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 = 26.2 bits (56), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 17 ATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
A LK NE N Y T+ + L+ + Q+ WF N R ++KK
Sbjct: 16 ARLKREFNE---NRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 25.8 bits (55), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
+ T I A K++L +N PT E M+A M + WF N R++ K+
Sbjct: 14 IETNIRVALEKSFL----ENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 64
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
0.318 0.131 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,482,389
Number of Sequences: 62578
Number of extensions: 92683
Number of successful extensions: 229
Number of sequences better than 100.0: 68
Number of HSP's better than 100.0 without gapping: 62
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 167
Number of HSP's gapped (non-prelim): 68
length of query: 140
length of database: 14,973,337
effective HSP length: 89
effective length of query: 51
effective length of database: 9,403,895
effective search space: 479598645
effective search space used: 479598645
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 bits)