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= 007660
(594 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 = 68.9 bits (167), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 29/62 (46%), Positives = 43/62 (69%)
Query: 501 LPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEM 560
P+ + ++ RAW+FQ+ HPYP + +K LA +GLT QV+NWFINAR R+ +P I++
Sbjct: 5 FPKVATNIXRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPXIDQS 64
Query: 561 YR 562
R
Sbjct: 65 NR 66
>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Pknox1
Length = 73
Score = 64.7 bits (156), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 28/56 (50%), Positives = 42/56 (75%), Gaps = 1/56 (1%)
Query: 498 QRG-LPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRL 552
+RG LP+ + +V+R+W+FQ+ HPYP + EK +A ++ LT QV+NWFINAR R+
Sbjct: 10 KRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRI 65
>pdb|2DMN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Tgif2lx
Length = 83
Score = 62.8 bits (151), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 26/59 (44%), Positives = 41/59 (69%)
Query: 501 LPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559
LP +SV +LR WM+++ YP + EK +L+ K+ L+ Q+SNWFINAR R+ M+++
Sbjct: 14 LPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQ 72
>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 = 59.3 bits (142), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 26/59 (44%), Positives = 41/59 (69%)
Query: 501 LPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559
LP++SV +LR W++++ + YP + EK LL+ ++ L+ QV NWFINAR RL M+ +
Sbjct: 12 LPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRK 70
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 52.8 bits (125), Expect = 6e-07, Method: Composition-based stats.
Identities = 26/70 (37%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 496 RPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKP 555
R +R +++ +L + + + +PYP + K LA KSG+T +QVSNWF N R+R +K
Sbjct: 4 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIR-YKK 62
Query: 556 MIEEMYREVN 565
I + E N
Sbjct: 63 NIGKFQEEAN 72
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 47/137 (34%), Positives = 63/137 (45%), Gaps = 23/137 (16%)
Query: 429 QVHARFALHTISF--LYKNLRERISS-------QILAMGAHF-DSKSTRGKDTVMVDSF- 477
+ A A H +F LYK L S Q L + AH+ +++ RG+ V +
Sbjct: 421 KAKAVVAFHRGNFRELYKILESHQFSPHNHPKLQQLWLKAHYVEAEKLRGRPLGAVGKYR 480
Query: 478 IKEQWALQQLKKKEHQIWRPQRG---LPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKS 534
++ ++ L + IW + EKS VLR W N PYP EK LA +
Sbjct: 481 VRRKFPLPR------TIWDGEETSYCFKEKSRGVLREWYAHN---PYPSPREKRELAEAT 531
Query: 535 GLTRTQVSNWFINARVR 551
GLT TQVSNWF N R R
Sbjct: 532 GLTTTQVSNWFKNRRQR 548
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 51.2 bits (121), Expect = 2e-06, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 496 RPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKP 555
R +R +++ +L + + + +PYP + K LA K G+T +QVSNWF N R+R +K
Sbjct: 3 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR-YKK 61
Query: 556 MIEEMYREVN 565
I + E N
Sbjct: 62 NIGKFQEEAN 71
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 50.8 bits (120), Expect = 2e-06, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 496 RPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKP 555
R +R +++ +L + + + +PYP + K LA K G+T +QVSNWF N R+R +K
Sbjct: 3 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR-YKK 61
Query: 556 MIEEMYREVN 565
I + E N
Sbjct: 62 NIGKFQEEAN 71
>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 = 49.3 bits (116), Expect = 6e-06, Method: Composition-based stats.
Identities = 22/59 (37%), Positives = 35/59 (59%)
Query: 496 RPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWK 554
R +R +++ +L + + + +PYP + K LA K G+T +QVSNWF N R+R K
Sbjct: 3 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKK 61
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 47.4 bits (111), Expect = 2e-05, Method: Composition-based stats.
Identities = 21/56 (37%), Positives = 34/56 (60%)
Query: 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWK 554
R + +++ +L + + + +PYP + K LA K G+T +QVSNWF N R+R K
Sbjct: 8 RHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>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 = 34.7 bits (78), Expect = 0.15, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 496 RPQRG--LPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINAR 549
+P RG +++V +L +W +N +PY L + L+R 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 = 33.9 bits (76), Expect = 0.26, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 496 RPQRG--LPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINAR 549
+P RG +++V +L +W +N +PY L + L+R Q+ NW N R
Sbjct: 27 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR 82
>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 = 33.5 bits (75), Expect = 0.34, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 33/75 (44%), Gaps = 4/75 (5%)
Query: 497 PQRGLPEKSVSVLRAWMFQNFLHP--YPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWK 554
P+R P S + ++ + H Y AE+ LA +T QV WF N R + +
Sbjct: 15 PKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRR 74
Query: 555 PMIEEMYREVNRRKA 569
EE RE R+ A
Sbjct: 75 QTAEE--REAERQAA 87
>pdb|1LE8|B Chain B, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 83
Score = 33.5 bits (75), Expect = 0.37, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 496 RPQRG--LPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVR 551
+P RG +++V +L +W +N +PY L + L+R Q+ NW R +
Sbjct: 2 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAK 59
>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 = 32.7 bits (73), Expect = 0.62, Method: Composition-based stats.
Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 3/59 (5%)
Query: 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557
R ++ ++ L+A Q+ +P DAE + L +GL R+++ WF + R R + ++
Sbjct: 9 RKKTKEQIAHLKASFLQS---QFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGIV 64
>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 = 32.3 bits (72), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 17/26 (65%)
Query: 526 EKHLLAMKSGLTRTQVSNWFINARVR 551
EK +A K G+T QV WFIN R+R
Sbjct: 394 EKEEVAKKCGITPLQVRVWFINKRMR 419
>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 = 32.0 bits (71), Expect = 1.0, Method: Composition-based stats.
Identities = 14/47 (29%), Positives = 24/47 (51%)
Query: 503 EKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINAR 549
+++V +L +W +N +PY L + L+R Q+ NW N R
Sbjct: 7 KENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR 53
>pdb|3D2O|A Chain A, Crystal Structure Of Manganese-Metallated Gtp
Cyclohydrolase Type Ib
pdb|3D2O|B Chain B, Crystal Structure Of Manganese-Metallated Gtp
Cyclohydrolase Type Ib
Length = 257
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 23/112 (20%), Positives = 49/112 (43%), Gaps = 10/112 (8%)
Query: 85 GRNGMRDFSVGRSGPMDNINFQEQLEDGTPISSTSFATLLAARNGLQENLNNLAISVPSI 144
G + D+ V +G M + + ++ P++S + ++ G +++ +S+ S
Sbjct: 113 GIRSLLDYDVSLTGEMKDGAYGHSMKVMIPVTSLCPCSKEISQYGAHNQRSHVTVSLTSD 172
Query: 145 YPVDVLRNDIANHCSNDLNSSFETSASCGYDEVLGNVNSKWVFDEAHAAPKF 196
V + ++ ET ASC +L + K+V ++A+ PKF
Sbjct: 173 AEVGI----------EEVIDYVETQASCQLYGLLKRPDEKYVTEKAYENPKF 214
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 30.8 bits (68), Expect = 2.2, Method: Composition-based stats.
Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 510 RAWMFQNFLHPYPKDA-EKHLLAMKSGLTRTQVSNWFINARVR 551
RA++ Q F ++ EK +A K G+T QV WFIN R+R
Sbjct: 9 RAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 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 = 30.8 bits (68), Expect = 2.3, Method: Composition-based stats.
Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 510 RAWMFQNFLHPYPKDA-EKHLLAMKSGLTRTQVSNWFINARVR 551
RA++ Q F ++ EK +A K G+T QV WFIN R+R
Sbjct: 17 RAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 59
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 30.8 bits (68), Expect = 2.4, Method: Composition-based stats.
Identities = 14/26 (53%), Positives = 17/26 (65%)
Query: 526 EKHLLAMKSGLTRTQVSNWFINARVR 551
EK +A K G+T QV WFIN R+R
Sbjct: 34 EKEEVAKKCGITPLQVRVWFINKRMR 59
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 30.4 bits (67), Expect = 3.0, Method: Composition-based stats.
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 521 YPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWK 554
YP + LAMK GLT ++ WF N R + W+
Sbjct: 23 YPDVFTREELAMKIGLTEARIQVWFQNRRAK-WR 55
>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 = 30.4 bits (67), Expect = 3.0, Method: Composition-based stats.
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 521 YPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWK 554
YP + LAMK GLT ++ WF N R + W+
Sbjct: 30 YPDVFTREELAMKIGLTEARIQVWFQNRRAK-WR 62
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 30.4 bits (67), Expect = 3.1, Method: Composition-based stats.
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 521 YPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWK 554
YP + LAMK GLT ++ WF N R + W+
Sbjct: 23 YPDVFTREELAMKIGLTEARIQVWFQNRRAK-WR 55
>pdb|3ZYV|A Chain A, Crystal Structure Of The Mouse Liver Aldehyde Oxydase 3
(Maox3)
pdb|3ZYV|B Chain B, Crystal Structure Of The Mouse Liver Aldehyde Oxydase 3
(Maox3)
pdb|3ZYV|C Chain C, Crystal Structure Of The Mouse Liver Aldehyde Oxydase 3
(Maox3)
pdb|3ZYV|D Chain D, Crystal Structure Of The Mouse Liver Aldehyde Oxydase 3
(Maox3)
Length = 1335
Score = 30.4 bits (67), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 106 QEQLEDGTPISSTSFATLLAARNGLQENLNNLAISVPSIYPVDVLRN 152
+E L+D + + L+AA G++E LAIS ++ +DVL+
Sbjct: 487 EEMLDDAGKMICEEVSLLMAAPGGMEEYRKTLAISFLFMFYLDVLKQ 533
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 30.0 bits (66), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 520 PYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559
P KD ++ LA K+GLT+ + WF NAR + + ++ +
Sbjct: 32 PDAKDLKQ--LAQKTGLTKRVLQVWFQNARAKFRRNLLRQ 69
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 28.9 bits (63), Expect = 8.9, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 34/75 (45%), Gaps = 9/75 (12%)
Query: 50 SFSALQGEPISDIHTNLNVTNNSRVFDSDALVTSLGRNG-------MRDFSVGRSGPMDN 102
S++ GE I D TNL VTN R D L T G+ G +RD GR +
Sbjct: 78 SYARPGGESIKD--TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAF 135
Query: 103 INFQEQLEDGTPISS 117
+ + ++ E IS+
Sbjct: 136 VRYNKREEAQEAISA 150
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.131 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,750,735
Number of Sequences: 62578
Number of extensions: 669462
Number of successful extensions: 1483
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1460
Number of HSP's gapped (non-prelim): 29
length of query: 594
length of database: 14,973,337
effective HSP length: 104
effective length of query: 490
effective length of database: 8,465,225
effective search space: 4147960250
effective search space used: 4147960250
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)