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= psy11043
(217 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 271 bits (692), Expect = 3e-73, Method: Compositional matrix adjust.
Identities = 124/191 (64%), Positives = 154/191 (80%), Gaps = 4/191 (2%)
Query: 20 MFALPTLNFTVSQVATVCETLEESGDIERLARFLWSLPVAHPNIGELNKNEAVLRARAIV 79
M LP+ FT QVA VCE L++ G++ERL RFLWSLP L+KNE+VL+A+A+V
Sbjct: 371 MSMLPSFGFTQEQVACVCEVLQQGGNLERLGRFLWSLPACD----HLHKNESVLKAKAVV 426
Query: 80 SFHSGNYREMYSILEHYKFTKDSHGKLQAMWLEAHYQEAEKLRGRPLGPVDKYRVRKKFP 139
+FH GN+RE+Y ILE ++F+ +H KLQ +WL+AHY EAEKLRGRPLG V KYRVR+KFP
Sbjct: 427 AFHRGNFRELYKILESHQFSPHNHPKLQQLWLKAHYVEAEKLRGRPLGAVGKYRVRRKFP 486
Query: 140 LPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRR 199
LPRTIWDGE+ ++CFKE++R +LREWY +PYP+P +KRELA+ATGLT TQV NWFKNRR
Sbjct: 487 LPRTIWDGEETSYCFKEKSRGVLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRR 546
Query: 200 QRDRAAAAKNR 210
QRDRAA AK R
Sbjct: 547 QRDRAAEAKER 557
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 47.8 bits (112), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 35/56 (62%), Gaps = 3/56 (5%)
Query: 149 QKTHCFKERTRSLLREWY---LQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQR 201
+K F ++ +L E++ L +PYP+ K ELA+ +G+T +QV NWF N+R R
Sbjct: 4 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIR 59
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 47.0 bits (110), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 32/51 (62%), Gaps = 3/51 (5%)
Query: 154 FKERTRSLLREWY---LQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQR 201
F ++ +L E++ L +PYP+ K ELA+ G+T +QV NWF N+R R
Sbjct: 8 FNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR 58
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 36/63 (57%), Gaps = 3/63 (4%)
Query: 149 QKTHCFKERTRSLLREWY---LQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAA 205
+K F ++ +L E++ L +PYP+ K ELA+ G+T +QV NWF N+R R +
Sbjct: 3 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN 62
Query: 206 AAK 208
K
Sbjct: 63 IGK 65
>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 = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/52 (44%), Positives = 31/52 (59%), Gaps = 3/52 (5%)
Query: 153 CFKERTRSLLREWYLQD---PYPNPTKKRELAQATGLTPTQVGNWFKNRRQR 201
F + ++ R W Q PYP+ +K++LAQ TGLT QV NWF N R+R
Sbjct: 4 IFPKVATNIXRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRR 55
>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 = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 34/56 (60%), Gaps = 3/56 (5%)
Query: 149 QKTHCFKERTRSLLREWY---LQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQR 201
+K F ++ +L E++ L +PYP+ K ELA+ G+T +QV NWF N+R R
Sbjct: 3 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIR 58
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 43.5 bits (101), Expect = 8e-05, Method: Composition-based stats.
Identities = 23/52 (44%), Positives = 31/52 (59%), Gaps = 2/52 (3%)
Query: 152 HCFKERTRSLLREWY--LQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQR 201
H K+ T L +Y L +PYP+ K ELA+ G+T +QV NWF N+R R
Sbjct: 9 HMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR 60
>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Pknox1
Length = 73
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 146 DGEQKTHCFKERTRSLLREWYLQD---PYPNPTKKRELAQATGLTPTQVGNWFKNRRQR 201
G+ K + +++R W Q PYP +K+++A T LT QV NWF N R+R
Sbjct: 6 SGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRR 64
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 26/42 (61%)
Query: 162 LREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDR 203
LR Y +P P+ K +L + TGL+P + WF+N+R +D+
Sbjct: 18 LRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDK 59
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 27/47 (57%)
Query: 157 RTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDR 203
+ R+ L E + + N +K E+A+ G+TP QV WF N+R R +
Sbjct: 15 QARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 35.8 bits (81), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 27/47 (57%)
Query: 157 RTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDR 203
+ R+ L + + + N +K E+A+ G+TP QV WF N+R R +
Sbjct: 7 QARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>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 = 35.4 bits (80), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 27/44 (61%), Gaps = 3/44 (6%)
Query: 161 LLREWYLQ---DPYPNPTKKRELAQATGLTPTQVGNWFKNRRQR 201
+LR+W + + YP+ +K L+Q T L+ QV NWF N R+R
Sbjct: 19 ILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRR 62
>pdb|1YRN|A Chain A, Crystal Structure Of The Mata1MATALPHA2 HOMEODOMAIN
Heterodimer Bound To Dna
pdb|1F43|A Chain A, Solution Structure Of The Mata1 Homeodomain
Length = 61
Score = 35.4 bits (80), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 27/47 (57%)
Query: 157 RTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDR 203
+ R+ L + + + N +K E+A+ G+TP QV WF N+R R +
Sbjct: 15 QARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1MH3|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form I
pdb|1MH4|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form Ii
Length = 421
Score = 35.0 bits (79), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 27/47 (57%)
Query: 157 RTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDR 203
+ R+ L + + + N +K E+A+ G+TP QV WF N+R R +
Sbjct: 375 QARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>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 = 34.7 bits (78), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 20/31 (64%)
Query: 171 YPNPTKKRELAQATGLTPTQVGNWFKNRRQR 201
YP+ + ELAQ T LT ++ WF+NRR R
Sbjct: 42 YPDIYTREELAQRTNLTEARIQVWFQNRRAR 72
>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 = 34.3 bits (77), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 152 HCFKERTRSLLREWY---LQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRA 204
H F + +L W+ +++PY + L + T L+ Q+ NW NRR++++
Sbjct: 32 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 87
>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 = 34.3 bits (77), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 152 HCFKERTRSLLREWY---LQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRA 204
H F + +L W+ +++PY + L + T L+ Q+ NW NRR++++
Sbjct: 3 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58
>pdb|2DMN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Tgif2lx
Length = 83
Score = 33.9 bits (76), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 3/58 (5%)
Query: 147 GEQKTHCFKERTRSLLREWYLQ---DPYPNPTKKRELAQATGLTPTQVGNWFKNRRQR 201
G+++ + +LR+W + YP+ +K+ L++ T L+ Q+ NWF N R+R
Sbjct: 7 GKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRR 64
>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 = 33.9 bits (76), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 152 HCFKERTRSLLREWY---LQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRA 204
H F + +L W+ +++PY + L + T L+ Q+ NW NRR++++
Sbjct: 7 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 62
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 32.7 bits (73), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 171 YPNPTKKRELAQATGLTPTQVGNWFKNRRQRDR 203
YP+ + ELA GLT ++ WF+NRR + R
Sbjct: 23 YPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 55
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 32.7 bits (73), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 159 RSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAA 206
R L RE Y + + K+R+++ AT L+ Q+ WF+NRR +++ +
Sbjct: 20 RELERE-YAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSG 66
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 32.7 bits (73), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 149 QKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRR 199
Q+TH F + L + ++ YP+ + + E+A T LT +V WFKNRR
Sbjct: 6 QRTH-FTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRR 55
>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 = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 22/34 (64%)
Query: 166 YLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRR 199
+ ++ YP+ + + E+A T LT +V WFKNRR
Sbjct: 22 FQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRR 55
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 32.7 bits (73), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 20/36 (55%)
Query: 171 YPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAA 206
YP+ + ELAQ LT +V WF NRR R R A
Sbjct: 26 YPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQA 61
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 32.3 bits (72), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 171 YPNPTKKRELAQATGLTPTQVGNWFKNRRQRDR 203
YP+ + ELA GLT ++ WF+NRR + R
Sbjct: 23 YPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 55
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 32.0 bits (71), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 30/61 (49%), Gaps = 9/61 (14%)
Query: 141 PRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQ 200
PRTI+ Q R + YL P ++ ELA + GLT TQV WF+N+R
Sbjct: 10 PRTIYSSFQ----LAALQRRFQKTQYLALP-----ERAELAASLGLTQTQVKIWFQNKRS 60
Query: 201 R 201
+
Sbjct: 61 K 61
>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 = 31.6 bits (70), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 171 YPNPTKKRELAQATGLTPTQVGNWFKNRR 199
YP+ + ELA GLT ++ WF+NRR
Sbjct: 30 YPDVFTREELAMKIGLTEARIQVWFQNRR 58
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 31.6 bits (70), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 166 YLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRR 199
+L+ Y ++ LA+A +T QV WF+NRR
Sbjct: 16 FLRQKYLASAERAALAKALRMTDAQVKTWFQNRR 49
>pdb|2LY9|A Chain A, Solution Nmr Structure Of Homeobox 2 Domain From Human
Zhx1 Repressor, Northeast Structural Genomics Consortium
(Nesg) Target Hr7907f
Length = 74
Score = 31.6 bits (70), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 28/52 (53%)
Query: 162 LREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKNRLEV 213
L+ YL++ +P+ ++ L + TGLT ++ WF + R R + + L +
Sbjct: 21 LKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKSNQCLHL 72
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 31.6 bits (70), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 166 YLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAK 208
Y + + K+R ++ T L+ QV WF+NRR +++ K
Sbjct: 26 YATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINK 68
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 31.6 bits (70), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 29/59 (49%)
Query: 148 EQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAA 206
++K + R R L +L+ P P+ + +A GL V WF NRRQ+ + ++
Sbjct: 97 KRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRSS 155
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 31.2 bits (69), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 166 YLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRR 199
+ Q Y + ++ LA LTPTQV WF+N R
Sbjct: 21 FKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHR 54
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 30.8 bits (68), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 166 YLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAK 208
Y + + K+R ++ T L+ QV WF+NRR +++ K
Sbjct: 20 YATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINK 62
>pdb|3NAU|A Chain A, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And Homeoboxes
Protein 2, Homeodomain 2)
pdb|3NAU|B Chain B, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And Homeoboxes
Protein 2, Homeodomain 2)
Length = 66
Score = 30.8 bits (68), Expect = 0.65, Method: Composition-based stats.
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 162 LREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQR 201
L+ +LQ +P+ + L + TGL +++ WF + R R
Sbjct: 19 LKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYR 58
>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 = 30.4 bits (67), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 9/59 (15%)
Query: 141 PRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRR 199
PRT + EQ +E + ++ Y ++++L+ GL Q+ WFKN+R
Sbjct: 6 PRTAFSSEQLARLKRE---------FNENRYLTERRRQQLSSELGLNEAQIKIWFKNKR 55
>pdb|1LE8|B Chain B, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 83
Score = 30.4 bits (67), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 152 HCFKERTRSLLREWY---LQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDR 203
H F + +L W+ +++PY + L + T L+ Q+ NW RR +++
Sbjct: 7 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEK 61
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of Human
Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 30.4 bits (67), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 160 SLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRR 199
S L+ + ++ +P ++ L + TGL+ +V WF +RR
Sbjct: 21 SALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRR 60
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 30.4 bits (67), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 166 YLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRR 199
+ Q Y + ++ E + + LT TQV WF+NRR
Sbjct: 19 FRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRR 52
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 30.4 bits (67), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 29/58 (50%)
Query: 146 DGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDR 203
G++ FK ++ ++ + P+ ++LAQ TGLT + WF+N R + R
Sbjct: 6 SGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFR 63
>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 = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 166 YLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRR 199
+ Q Y + ++ +LA LT TQV WF+NRR
Sbjct: 21 FKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRR 54
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 171 YPNPTKKRELAQATGLTPTQVGNWFKNRR 199
YP+ + +LA T LT +V WF+NRR
Sbjct: 33 YPDVYAREQLAMRTDLTEARVQVWFQNRR 61
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 15/83 (18%)
Query: 127 GPVDKYRVRKKFPLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGL 186
P K R R+ + + E++ HC K Y + T++ ++A A L
Sbjct: 2 APGGKSRRRRTAFTSEQLLELEKEFHCKK---------------YLSLTERSQIAHALKL 46
Query: 187 TPTQVGNWFKNRRQRDRAAAAKN 209
+ QV WF+NRR + + A N
Sbjct: 47 SEVQVKIWFQNRRAKWKRIKAGN 69
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 26/49 (53%)
Query: 162 LREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKNR 210
L + +LQ Y + +L+ L QV WFKNRR+R + + +++
Sbjct: 17 LEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQHK 65
>pdb|1KQF|A Chain A, Formate Dehydrogenase N From E. Coli
pdb|1KQG|A Chain A, Formate Dehydrogenase N From E. Coli
Length = 1015
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 10/81 (12%)
Query: 5 LGENISRLAPVIPCPMFALPTLNFTVSQVATVCETLEESGDIERLARFLWSLPVAHPNIG 64
L E++SR P + + P +F VCE L + +R FL++L +G
Sbjct: 364 LKEHVSRYTPDVVENICGTPKADFL-----KVCEVLASTSAPDRTTTFLYALGWTQHTVG 418
Query: 65 ELNKNEAVLRARAIVSFHSGN 85
N +R A++ GN
Sbjct: 419 AQN-----IRTMAMIQLLLGN 434
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 166 YLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQR 201
+L + Y ++ E+A+ LT QV WF+NRR +
Sbjct: 20 FLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMK 55
>pdb|2CUF|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Hypothetical Protein Flj21616
Length = 95
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/56 (25%), Positives = 27/56 (48%), Gaps = 15/56 (26%)
Query: 160 SLLREWYLQDPYPNPTKKRELAQATG---------------LTPTQVGNWFKNRRQ 200
+++ ++ ++ YP+ K+ E+A A +T +V NWF NRR+
Sbjct: 20 AVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRK 75
>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 = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 166 YLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAA 205
+ Q Y + ++ LA LTPTQV WF+N R + + A
Sbjct: 28 FRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRA 67
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 29/59 (49%)
Query: 148 EQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAA 206
++K + R R L +L+ P P+ + +A GL V WF NRRQ+ + ++
Sbjct: 9 KRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRSS 67
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 28.9 bits (63), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 9/59 (15%)
Query: 141 PRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRR 199
PRT + EQ +E + ++ Y ++++L+ GL Q+ WF+N+R
Sbjct: 2 PRTAFSSEQLARLKRE---------FNENRYLTERRRQQLSSELGLNEAQIKIWFQNKR 51
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 28.9 bits (63), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 9/59 (15%)
Query: 141 PRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRR 199
PRT + EQ +E + ++ Y ++++L+ GL Q+ WF+N+R
Sbjct: 6 PRTAFSSEQLARAKRE---------FNENRYLTERRRQQLSSELGLNEAQIKIWFQNKR 55
>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 = 28.9 bits (63), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 9/59 (15%)
Query: 141 PRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRR 199
PRT + EQ +E + ++ Y ++++L+ GL Q+ WF+N+R
Sbjct: 6 PRTAFSSEQLARLKRE---------FNENRYLTERRRQQLSSELGLNEAQIKIWFQNKR 55
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 169 DPYPNPTKKRELAQATGLTPTQVGNWFKNRR 199
+ Y ++ E+A A LT Q+ WF+NRR
Sbjct: 25 NRYLTRRRRIEIAHALSLTERQIKIWFQNRR 55
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 9/59 (15%)
Query: 141 PRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRR 199
PRT + EQ +E + ++ Y ++++L+ GL Q+ WF+N+R
Sbjct: 4 PRTAFSSEQLARLKRE---------FNENRYLTERRRQQLSSELGLNEAQIKIWFQNKR 53
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 171 YPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAA 206
Y +P +++ LA+ L+ QV WF+NRR + R +
Sbjct: 31 YLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSG 66
>pdb|3NAR|A Chain A, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And Homeoboxes
Protein 1, Homeodomain 4)
pdb|3NAR|B Chain B, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And Homeoboxes
Protein 1, Homeodomain 4)
Length = 96
Score = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 25/39 (64%)
Query: 161 LLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRR 199
+L+ +++ +P+P + +LA+ +GL T + +WF + R
Sbjct: 39 MLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTR 77
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 169 DPYPNPTKKRELAQATGLTPTQVGNWFKNRR 199
+ Y ++ E+A A LT Q+ WF+NRR
Sbjct: 42 NHYLTRRRRIEMAHALSLTERQIKIWFQNRR 72
>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 = 3.3, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 9/59 (15%)
Query: 141 PRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRR 199
PRT + EQ +E + ++ Y ++++L+ GL Q+ WF N+R
Sbjct: 2 PRTAFSSEQLARLKRE---------FNENRYLTERRRQQLSSELGLNEAQIKIWFANKR 51
>pdb|2DMP|A Chain A, Solution Structure Of The Third Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 2
Length = 89
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 154 FKERTRS---LLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQ 200
FKE+T+ +L + +L+ +P + L T L+ ++ +WF RR+
Sbjct: 17 FKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRK 66
>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 = 28.1 bits (61), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 149 QKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQR 201
Q+T + +T L +E++ + Y ++ E+A A LT Q+ WF+NRR +
Sbjct: 31 QRTSYTRYQTLELEKEFHF-NRYLTRRRRIEIAHALSLTERQIKIWFQNRRMK 82
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 161 LLREWYLQDPYPNPTKK--RELAQATGLTPTQVGNWFKNRRQRDRAAA 206
+L + YL D NPT+K +A GL V WF+N R R+R +
Sbjct: 31 ILYQKYLLDS--NPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSG 76
>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 = 28.1 bits (61), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 9/59 (15%)
Query: 141 PRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRR 199
PRT + EQ +E + ++ Y ++++L+ GL Q+ WF+N R
Sbjct: 4 PRTAFSSEQLARLKRE---------FNENRYLTERRRQQLSSELGLNEAQIKIWFQNER 53
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 28.1 bits (61), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 166 YLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQR 201
+L + Y ++ E+A+ LT QV WF+NRR +
Sbjct: 32 FLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMK 67
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 27.7 bits (60), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 27/58 (46%)
Query: 146 DGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDR 203
G ++ F +L + + YP+ + E+A L ++V WFKNRR + R
Sbjct: 6 SGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63
>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 = 27.7 bits (60), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 21/38 (55%)
Query: 166 YLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDR 203
+ Y + ++ LA+ LT TQV WF+NRR + +
Sbjct: 23 FSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTK 60
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 27.7 bits (60), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 166 YLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAA 205
+ Q Y + ++ L LTPTQV WF+N R + + A
Sbjct: 31 FRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRA 70
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 27.7 bits (60), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 27/60 (45%)
Query: 147 GEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAA 206
G + F + L + + YP+ + +LA+ L +V WFKNRR + R +
Sbjct: 7 GRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSG 66
>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 = 27.7 bits (60), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 169 DPYPNPTKKRELAQATGLTPTQVGNWFKNRRQR 201
+ Y ++ E+A A LT Q+ WF+NRR +
Sbjct: 18 NRYLTRRRRIEIAHALSLTERQIKIWFQNRRMK 50
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 27.3 bits (59), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 10/23 (43%), Positives = 17/23 (73%)
Query: 179 ELAQATGLTPTQVGNWFKNRRQR 201
+LA++ GL+ QV W++NRR +
Sbjct: 49 DLAESLGLSQLQVKTWYQNRRMK 71
>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 = 27.3 bits (59), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 169 DPYPNPTKKRELAQATGLTPTQVGNWFKNRR 199
+ Y ++ E+A A LT Q+ WF+NRR
Sbjct: 24 NRYLTRRRRIEIAHALSLTERQIKIWFQNRR 54
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 27.3 bits (59), Expect = 6.2, Method: Composition-based stats.
Identities = 11/46 (23%), Positives = 27/46 (58%)
Query: 161 LLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDRAAA 206
+LR+++ + P+ + +E+A +GL + +WF+N ++R +
Sbjct: 21 VLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSG 66
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 27.3 bits (59), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 169 DPYPNPTKKRELAQATGLTPTQVGNWFKNR 198
+ +P+PT +A GLT Q WFK R
Sbjct: 24 NKHPDPTTLCLIAAEAGLTEEQTQKWFKQR 53
>pdb|2HI3|A Chain A, Solution Structure Of The Homeodomain-Only Protein Hop
Length = 73
Score = 27.3 bits (59), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 171 YPNPTKKRELAQATGLTPTQVGNWFKNR 198
+P+PT +A GLT Q WFK R
Sbjct: 27 HPDPTTLCLIAAEAGLTEEQTQKWFKQR 54
>pdb|3SWJ|A Chain A, Crystal Structure Of Campylobacter Jejuni Chuz
Length = 251
Score = 26.9 bits (58), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 29/98 (29%), Positives = 45/98 (45%), Gaps = 9/98 (9%)
Query: 43 SGDIERLARFLWSL-PVAHPNIGELNKNEAVLRARA-IVSFHSGNYREMYSILEHYKFTK 100
SG + L F+ S VA + LN N V+ + A VS GNY + + EH+ K
Sbjct: 85 SGVEKELNEFMLSFNSVA---LATLNANGEVVCSYAPFVSTQWGNYIYISEVSEHFNNIK 141
Query: 101 DSHGKLQAMWLEAHYQEAEKLRGRPLGPVDKYRVRKKF 138
+ ++ M+LE + A + + L +YRV F
Sbjct: 142 VNPNNIEIMFLEDESKAASVILRKRL----RYRVNASF 175
>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 = 26.9 bits (58), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 169 DPYPNPTKKRELAQATGLTPTQVGNWFKNRR 199
+ Y ++ E+A A LT Q+ WF+NRR
Sbjct: 24 NRYLTRRRRIEIAHALCLTERQIKIWFQNRR 54
>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 = 26.9 bits (58), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 166 YLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQR 201
+L + Y + ++ ELA LT + WF+NRR +
Sbjct: 22 FLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMK 57
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
0.319 0.133 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,468,820
Number of Sequences: 62578
Number of extensions: 261583
Number of successful extensions: 654
Number of sequences better than 100.0: 88
Number of HSP's better than 100.0 without gapping: 79
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 573
Number of HSP's gapped (non-prelim): 88
length of query: 217
length of database: 14,973,337
effective HSP length: 95
effective length of query: 122
effective length of database: 9,028,427
effective search space: 1101468094
effective search space used: 1101468094
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)