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= 012938
(453 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 74.3 bits (181), Expect = 1e-13, Method: Composition-based stats.
Identities = 31/62 (50%), Positives = 44/62 (70%)
Query: 362 LPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEM 421
P+ + I R+WLF+H HPYP++ +K+ LA TGLT QV+NWFINAR R+ +P I++
Sbjct: 5 FPKVATNIXRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPXIDQS 64
Query: 422 YR 423
R
Sbjct: 65 NR 66
>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Pknox1
Length = 73
Score = 70.9 bits (172), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 29/52 (55%), Positives = 40/52 (76%)
Query: 362 LPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRL 413
LP+ + ++RSWLF+H HPYP + EK+ +A+QT LT QV+NWFINAR R+
Sbjct: 14 LPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRI 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 = 68.6 bits (166), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 34/70 (48%), Positives = 47/70 (67%), Gaps = 4/70 (5%)
Query: 362 LPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEM 421
LP+ SV ILR WL+EH + YP++ EK LL+ QT L+ QV NWFINAR RL + +M
Sbjct: 12 LPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRL----LPDM 67
Query: 422 YREEFADSSE 431
R++ D ++
Sbjct: 68 LRKDGKDPNQ 77
>pdb|2DMN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Tgif2lx
Length = 83
Score = 66.6 bits (161), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 28/59 (47%), Positives = 42/59 (71%)
Query: 362 LPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEE 420
LP SV ILR W+++H YP++ EKQ+L+ +T L+ Q+SNWFINAR R+ M+++
Sbjct: 14 LPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQ 72
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 51.6 bits (122), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 35/56 (62%)
Query: 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWK 415
R + + + IL + + H +PYP++ K+ LA + G+T +QVSNWF N R+R K
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 = 51.6 bits (122), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 27/49 (55%), Positives = 32/49 (65%), Gaps = 3/49 (6%)
Query: 364 ETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVR 412
E S G+LR W + H +PYP+ EK+ LA TGLT QVSNWF N R R
Sbjct: 503 EKSRGVLREW-YAH--NPYPSPREKRELAEATGLTTTQVSNWFKNRRQR 548
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 51.6 bits (122), Expect = 9e-07, Method: Composition-based stats.
Identities = 27/87 (31%), Positives = 46/87 (52%), Gaps = 9/87 (10%)
Query: 357 RPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKP 416
R R + + IL + + H +PYP++ K+ LA ++G+T +QVSNWF N R+R
Sbjct: 4 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIR---- 59
Query: 417 MIEEMYREEFADSSEDSNPSFAGSSAT 443
Y++ E++N A ++ T
Sbjct: 60 -----YKKNIGKFQEEANIYAAKTAVT 81
>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 = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 35/59 (59%)
Query: 357 RPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWK 415
R R + + IL + + H +PYP++ K+ LA + G+T +QVSNWF N R+R K
Sbjct: 3 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKK 61
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 51.2 bits (121), Expect = 1e-06, Method: Composition-based stats.
Identities = 27/87 (31%), Positives = 45/87 (51%), Gaps = 9/87 (10%)
Query: 357 RPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKP 416
R R + + IL + + H +PYP++ K+ LA + G+T +QVSNWF N R+R
Sbjct: 3 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR---- 58
Query: 417 MIEEMYREEFADSSEDSNPSFAGSSAT 443
Y++ E++N A ++ T
Sbjct: 59 -----YKKNIGKFQEEANIYAAKTAVT 80
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 50.4 bits (119), Expect = 2e-06, Method: Composition-based stats.
Identities = 23/59 (38%), Positives = 35/59 (59%)
Query: 357 RPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWK 415
R R + + IL + + H +PYP++ K+ LA + G+T +QVSNWF N R+R K
Sbjct: 3 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>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 = 34.3 bits (77), Expect = 0.14, Method: Composition-based stats.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 357 RPIRG--LPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINAR 410
+P RG + +V IL SW ++ +PY + + L T L++ Q+ NW N R
Sbjct: 2 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR 57
>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 = 0.16, Method: Composition-based stats.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 357 RPIRG--LPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINAR 410
+P RG + +V IL SW ++ +PY + + L T L++ Q+ NW N R
Sbjct: 27 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR 82
>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 = 33.1 bits (74), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 384 NDSEKQLLASQTGLTKNQVSNWFINARVR 412
N EK+ +A + G+T QV WFIN R+R
Sbjct: 391 NSKEKEEVAKKCGITPLQVRVWFINKRMR 419
>pdb|1LE8|B Chain B, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 83
Score = 33.1 bits (74), Expect = 0.36, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 357 RPIRG--LPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVR 412
+P RG + +V IL SW ++ +PY + + L T L++ Q+ NW R +
Sbjct: 2 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAK 59
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 32.0 bits (71), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 23/38 (60%)
Query: 383 PNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEE 420
P+ + + LA +TGLTK + WF NAR + + ++ +
Sbjct: 32 PDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQ 69
>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 = 32.0 bits (71), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 21/34 (61%)
Query: 382 YPNDSEKQLLASQTGLTKNQVSNWFINARVRLWK 415
YP+ ++ LA +T LT+ ++ WF N R RL K
Sbjct: 42 YPDIYTREELAQRTNLTEARIQVWFQNRRARLRK 75
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 32.0 bits (71), Expect = 0.82, Method: Composition-based stats.
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 384 NDSEKQLLASQTGLTKNQVSNWFINARVR 412
N EK+ +A + G+T QV WFIN R+R
Sbjct: 31 NSKEKEEVAKKCGITPLQVRVWFINKRMR 59
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 32.0 bits (71), Expect = 0.82, Method: Composition-based stats.
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 384 NDSEKQLLASQTGLTKNQVSNWFINARVR 412
N EK+ +A + G+T QV WFIN R+R
Sbjct: 23 NSKEKEEVAKKCGITPLQVRVWFINKRMR 51
>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 = 32.0 bits (71), Expect = 0.83, Method: Composition-based stats.
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 384 NDSEKQLLASQTGLTKNQVSNWFINARVR 412
N EK+ +A + G+T QV WFIN R+R
Sbjct: 31 NSKEKEEVAKKCGITPLQVRVWFINKRMR 59
>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 = 31.6 bits (70), Expect = 0.86, Method: Composition-based stats.
Identities = 15/45 (33%), Positives = 24/45 (53%)
Query: 366 SVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINAR 410
+V IL SW ++ +PY + + L T L++ Q+ NW N R
Sbjct: 9 NVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR 53
>pdb|3L7V|A Chain A, Crystal Structure Of A Hypothetical Protein Smu.1377c From
Streptococcus Mutans Ua159
Length = 295
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 27/54 (50%)
Query: 18 FIISDSITAQNLANQHFDTYGSALRGNNILPHSFGVLPSIQSLGERISRSMDLV 71
F+I + + +A + ++ G + ++ P G ++ +GERI +DLV
Sbjct: 161 FVIKFGVAGEQIAKEXWEKEGRXVYASSANPSGKGNRGKVEGIGERIESXVDLV 214
>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 = 30.4 bits (67), Expect = 2.2, Method: Composition-based stats.
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 382 YPNDSEKQLLASQTGLTKNQVSNWFINAR 410
+P+DSE L TGLTK ++ WF + R
Sbjct: 30 FPHDSEIIRLMKITGLTKGEIKKWFSDTR 58
>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 = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 382 YPNDSEKQLLASQTGLTKNQVSNWFINARVRLWK 415
Y + +Q L+S+ GL + Q+ WF NAR ++ K
Sbjct: 25 YLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58
>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 = 29.6 bits (65), Expect = 3.2, Method: Composition-based stats.
Identities = 11/37 (29%), Positives = 22/37 (59%)
Query: 382 YPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418
+P+D+E L TGL ++++ WF + R R + ++
Sbjct: 28 FPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGIV 64
>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 = 29.3 bits (64), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 380 HPYPNDSEKQLLASQTGLTKNQVSNWFINARVRL 413
+P P D E L S+T +T+ ++ +WF R ++
Sbjct: 29 NPLPLDEELDRLRSETKMTRREIDSWFSERRKKV 62
>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 = 28.5 bits (62), Expect = 7.9, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 7/45 (15%)
Query: 382 YPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEMYREEF 426
YP+ S ++ +A T LT+ +V WF N R + W+ REEF
Sbjct: 27 YPDMSTREEIAVWTNLTEARVRVWFKNRRAK-WRK------REEF 64
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 28.5 bits (62), Expect = 8.8, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 7/45 (15%)
Query: 382 YPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEMYREEF 426
YP+ S ++ +A T LT+ +V WF N R + W+ REEF
Sbjct: 27 YPDMSTREEIAVWTNLTEARVRVWFKNRRAK-WRK------REEF 64
>pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|M Chain M, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|D Chain D, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
pdb|1YNJ|D Chain D, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNJ|J Chain J, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNN|D Chain D, Taq Rna Polymerase-rifampicin Complex
pdb|1YNN|J Chain J, Taq Rna Polymerase-rifampicin Complex
Length = 1524
Score = 28.1 bits (61), Expect = 9.6, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 4/74 (5%)
Query: 210 YHGSRRGGLR--LSSELKAEMCNTGTLSAEKQELHLRIAKLISLLE--EVESKYEIYYNQ 265
Y R LR LS+ ++ E G + AE E +L A+ ++E ++ + IY Q
Sbjct: 215 YLRKERAALRIPLSAWVEKEAYRPGEVLAELSEPYLFRAEESGVVELKDLAEGHLIYLRQ 274
Query: 266 MEEVVSSYEVIAGL 279
EEVV+ Y + AG+
Sbjct: 275 EEEVVARYFLPAGM 288
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.315 0.130 0.372
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,091,298
Number of Sequences: 62578
Number of extensions: 513145
Number of successful extensions: 1242
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1217
Number of HSP's gapped (non-prelim): 29
length of query: 453
length of database: 14,973,337
effective HSP length: 102
effective length of query: 351
effective length of database: 8,590,381
effective search space: 3015223731
effective search space used: 3015223731
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)