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= psy5913
(341 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 = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 23/50 (46%), Positives = 35/50 (70%)
Query: 13 RETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRL 62
+ T+ +++WL +H +PYPT+ EK +A T +TL QV+ WF NARRR+
Sbjct: 16 KHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRI 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 = 54.3 bits (129), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 23/50 (46%), Positives = 33/50 (66%)
Query: 13 RETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRL 62
+E+ L+ WL EH+ N YP++ EK +L+ T ++ QV WF NARRRL
Sbjct: 14 KESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRL 63
>pdb|2DMN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Tgif2lx
Length = 83
Score = 53.9 bits (128), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 36/56 (64%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRL 62
R+ N E+ L+ W+ +H+ YP++ EK ML+ T ++L Q+S WF NARRR+
Sbjct: 10 RKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRI 65
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 50.4 bits (119), Expect = 1e-06, Method: Composition-based stats.
Identities = 23/58 (39%), Positives = 34/58 (58%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
+R+N ++ T L + H NPYP++ K LA + +T++QVS WF N R R KK
Sbjct: 5 KRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYKK 62
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 49.7 bits (117), Expect = 2e-06, Method: Composition-based stats.
Identities = 23/58 (39%), Positives = 33/58 (56%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
+R+N ++ T L + H NPYP++ K LA +T++QVS WF N R R KK
Sbjct: 4 KRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>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 = 49.7 bits (117), Expect = 2e-06, Method: Composition-based stats.
Identities = 22/47 (46%), Positives = 33/47 (70%)
Query: 16 TSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRL 62
T+ +AWL +H +PYP++ +K LA T +T+ QV+ WF NARRR+
Sbjct: 10 TNIXRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRI 56
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 49.3 bits (116), Expect = 3e-06, Method: Composition-based stats.
Identities = 23/58 (39%), Positives = 33/58 (56%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
+R+N ++ T L + H NPYP++ K LA +T++QVS WF N R R KK
Sbjct: 4 KRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 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 = 47.8 bits (112), Expect = 9e-06, Method: Composition-based stats.
Identities = 22/58 (37%), Positives = 34/58 (58%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
+R+N +++ + L + H NPYP++ K LA +T++QVS WF N R R KK
Sbjct: 4 KRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKK 61
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 21/56 (37%), Positives = 31/56 (55%)
Query: 9 KNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
++ ++ T L + H NPYP++ K LA +T++QVS WF N R R KK
Sbjct: 8 RHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>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 = 0.004, Method: Compositional matrix adjust.
Identities = 21/44 (47%), Positives = 26/44 (59%), Gaps = 3/44 (6%)
Query: 18 TLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRR 61
L+ W + NPYP+ EK LA T +T TQVS WF N R+R
Sbjct: 508 VLREW---YAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQR 548
>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 = 37.7 bits (86), Expect = 0.009, Method: Composition-based stats.
Identities = 24/65 (36%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 8 RKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67
R+ TR T L+ E N Y T+ +I +A +T Q+ WF N R + KKENK
Sbjct: 6 RQTYTRYQTLELE---KEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 62
Query: 68 MTWEP 72
EP
Sbjct: 63 TKGEP 67
>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 = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 24/65 (36%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 8 RKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67
R+ TR T L+ E N Y T+ +I +A +T Q+ WF N R + KKENK
Sbjct: 6 RQTYTRYQTLELE---KEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 62
Query: 68 MTWEP 72
EP
Sbjct: 63 TKGEP 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 = 36.6 bits (83), Expect = 0.019, Method: Composition-based stats.
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|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 = 35.8 bits (81), Expect = 0.031, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 32/63 (50%)
Query: 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
G++R+ T T+ L+ ++N YP + +A+ T +T +V WF N R + +K
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Query: 65 ENK 67
+
Sbjct: 61 REE 63
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 35.8 bits (81), Expect = 0.034, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 28/62 (45%)
Query: 4 NGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63
NG RR+ T E N Y T+ +I +A +T Q+ WF N R +LK
Sbjct: 17 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLK 76
Query: 64 KE 65
KE
Sbjct: 77 KE 78
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 35.8 bits (81), Expect = 0.039, Method: Composition-based stats.
Identities = 20/67 (29%), Positives = 32/67 (47%)
Query: 1 MDINGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARR 60
M G +R+N T T+ L+ +K YP + LA+ T +T +V WF N R
Sbjct: 3 MSNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRA 62
Query: 61 RLKKENK 67
+ +K +
Sbjct: 63 KWRKRER 69
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 35.4 bits (80), Expect = 0.045, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 32/63 (50%)
Query: 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
G++R+ T T+ L+ ++N YP + +A+ T +T +V WF N R + +K
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Query: 65 ENK 67
+
Sbjct: 61 REE 63
>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 = 34.7 bits (78), Expect = 0.088, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 30/61 (49%)
Query: 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
G+ ++ T T + L E N Y ++ ++ LA++ +T + WF N R + KK
Sbjct: 1 GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60
Query: 65 E 65
E
Sbjct: 61 E 61
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 8 RKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
R+ TR T L+ E N Y T+ +I +A +T Q+ WF N R + KKEN
Sbjct: 7 RQTYTRYQTLELE---KEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 62
>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 = 33.1 bits (74), Expect = 0.21, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 12 TRETTSTLKAWLNEHKKNPY-PTKG-EKIMLAIITKMTLTQVSTWFANARRRLK 63
T+E L++W ++ +NPY TKG E +M T ++ Q+ W +N RR+ K
Sbjct: 35 TKENVRILESWFAKNIENPYLDTKGLENLMKN--TSLSRIQIKNWVSNRRRKEK 86
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 33.1 bits (74), Expect = 0.24, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 28/57 (49%)
Query: 8 RKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
RK T LK E+ N + TK ++ ++ T ++ QV+ WF N R + KK
Sbjct: 2 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58
>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 = 32.7 bits (73), Expect = 0.28, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 12 TRETTSTLKAWLNEHKKNPY-PTKG-EKIMLAIITKMTLTQVSTWFANARRRLK 63
T+E L++W ++ +NPY TKG E +M T ++ Q+ W +N RR+ K
Sbjct: 6 TKENVRILESWFAKNIENPYLDTKGLENLMKN--TSLSRIQIKNWVSNRRRKEK 57
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 32.7 bits (73), Expect = 0.30, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 28/57 (49%)
Query: 8 RKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
RK T LK E+ N + TK ++ ++ T ++ QV+ WF N R + KK
Sbjct: 8 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 32.0 bits (71), Expect = 0.45, Method: Composition-based stats.
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|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 32.0 bits (71), Expect = 0.46, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 30/61 (49%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
RRK + + + K+ Y + E+ LA + +T TQV WF N R ++K++
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61
Query: 67 K 67
K
Sbjct: 62 K 62
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 31.6 bits (70), Expect = 0.58, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 27/57 (47%)
Query: 8 RKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
RK T ++ L A +K Y E+ LA +T TQV WF N R ++KK
Sbjct: 8 RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64
>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 = 31.6 bits (70), Expect = 0.70, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 30/60 (50%)
Query: 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
G ++K T + + L A + +K Y + + L+ I ++ QV TWF N R + K+
Sbjct: 1 GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>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 = 31.2 bits (69), Expect = 0.77, 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|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 31.2 bits (69), Expect = 0.82, Method: Composition-based stats.
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|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 = 0.85, 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|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 31.2 bits (69), Expect = 0.87, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 28 KNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65
+ Y E+ LA +MT QV TWF N R + +++
Sbjct: 18 RQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>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 = 31.2 bits (69), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 12 TRETTSTLKAWLNEHKKNPY-PTKG-EKIMLAIITKMTLTQVSTWFANARRRLK 63
T+E L++W ++ +NPY TKG E +M T ++ Q+ W +N RR+ K
Sbjct: 10 TKENVRILESWFAKNIENPYLDTKGLENLMKN--TSLSRIQIKNWVSNRRRKEK 61
>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 = 31.2 bits (69), Expect = 0.90, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 30/60 (50%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
+R++ T + S L ++ YP + LA T +T ++ WF N R RL+K++
Sbjct: 18 QRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH 77
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 30.8 bits (68), Expect = 1.0, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 28/57 (49%)
Query: 8 RKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
RK T TT+ L A + ++ Y + E+ + +T TQV WF N R + K+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>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 = 1.1, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 21/37 (56%)
Query: 27 KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63
K+ Y + E+ LA + K+T TQV WF N R + K
Sbjct: 22 KQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%)
Query: 15 TTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67
TT L E N Y ++ ++ +A ++ TQV WF N R + KK +
Sbjct: 42 TTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER 94
>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 = 30.0 bits (66), Expect = 1.8, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 26/59 (44%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65
R+K T T + K Y E+ LA KMT QV TWF N R + +++
Sbjct: 17 RKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQ 75
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 30.0 bits (66), Expect = 2.0, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 29/60 (48%)
Query: 6 ARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65
+R++ T T L+ ++ YP + LA K+T +V WF+N R R +K+
Sbjct: 1 GQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 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 = 29.6 bits (65), Expect = 2.8, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 25/58 (43%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
RRK T T+ A +N PT E M+A M + WF N R++ K+
Sbjct: 7 RRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 64
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 29/60 (48%)
Query: 9 KNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 68
+N T T ++A E ++ YP + LA + ++ WF+N R + ++E K+
Sbjct: 9 RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL 68
>pdb|1HDP|A Chain A, Solution Structure Of A Pou-Specific Homeodomain: 3d-Nmr
Studies Of Human B-Cell Transcription Factor Oct-2
Length = 63
Score = 29.3 bits (64), Expect = 3.4, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 26/60 (43%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
RRK T T+ A N PT E +++A M + WF N R++ K+ N
Sbjct: 1 RRKKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEKRIN 60
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 28.9 bits (63), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 25/46 (54%)
Query: 19 LKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
L+ E+ N + TK ++ ++ T ++ Q++ WF N R + KK
Sbjct: 19 LRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64
>pdb|1O4X|A Chain A, Ternary Complex Of The Dna Binding Domains Of The Oct1 And
Sox2 Transcription Factors With A 19mer Oligonucleotide
From The Hoxb1 Regulatory Element
Length = 167
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 26/60 (43%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
RRK T T+ A +N PT E M+A M + WF N R++ K+ N
Sbjct: 104 RRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRIN 163
>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 = 28.5 bits (62), Expect = 5.4, Method: Composition-based stats.
Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 2/40 (5%)
Query: 26 HKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65
H+K Y + E+ LA K+T TQV WF N R + K++
Sbjct: 25 HQK--YLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRK 62
>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 = 28.5 bits (62), Expect = 6.0, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 3/57 (5%)
Query: 8 RKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
R + E + LK NE N Y T+ + L+ + Q+ WFAN R ++KK
Sbjct: 3 RTAFSSEQLARLKREFNE---NRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56
>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 = 6.1, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 3/57 (5%)
Query: 8 RKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
R + E + LK NE N Y T+ + L+ + Q+ WF NAR ++KK
Sbjct: 5 RTAFSSEQLARLKREFNE---NRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58
>pdb|1CQT|A Chain A, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
pdb|1CQT|B Chain B, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
Length = 163
Score = 28.1 bits (61), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 26/60 (43%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
RRK T T+ A +N PT E M+A M + WF N R++ K+ N
Sbjct: 103 RRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRIN 162
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 28.1 bits (61), Expect = 8.2, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 24/53 (45%)
Query: 12 TRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
TR T L+ + N YP E L+ + + + WF NAR++ +K
Sbjct: 12 TRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64
>pdb|3HJE|A Chain A, Crystal Structure Of Sulfolobus Tokodaii Hypothetical
Maltooligosyl Trehalose Synthase
Length = 704
Score = 27.7 bits (60), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 26/39 (66%), Gaps = 1/39 (2%)
Query: 233 HHLPHPNSYRHDLYRLYGSHLGAHPG-STEFLEQYQRHI 270
H++ +PN ++D YRLY + +G+ G + E+ E+ + H+
Sbjct: 470 HNILNPNIDKNDEYRLYQTIVGSFDGFNNEYKERLKAHM 508
>pdb|2DMP|A Chain A, Solution Structure Of The Third Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 2
Length = 89
Score = 27.7 bits (60), Expect = 8.7, Method: Composition-based stats.
Identities = 14/50 (28%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 14 ETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63
+T +K + K+ +PT+ E L + TK++ ++ +WF+ RR+L+
Sbjct: 20 KTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSE-RRKLR 68
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
0.314 0.131 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,872,083
Number of Sequences: 62578
Number of extensions: 419721
Number of successful extensions: 606
Number of sequences better than 100.0: 64
Number of HSP's better than 100.0 without gapping: 55
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 548
Number of HSP's gapped (non-prelim): 64
length of query: 341
length of database: 14,973,337
effective HSP length: 100
effective length of query: 241
effective length of database: 8,715,537
effective search space: 2100444417
effective search space used: 2100444417
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 52 (24.6 bits)