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= 006230
(655 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 = 69.7 bits (169), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 29/59 (49%), Positives = 43/59 (72%)
Query: 407 LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEE 465
P+ + ++ RAWLF+H HPYPS+ K LA+ TGL+ QV+NWFINAR R+ +P +++
Sbjct: 5 FPKVATNIXRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPXIDQ 63
>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Pknox1
Length = 73
Score = 66.6 bits (161), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 29/56 (51%), Positives = 43/56 (76%), Gaps = 1/56 (1%)
Query: 404 QRG-LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRL 458
+RG LP+ + +V+R+WLF+H HPYP++ +K +A QT L+ QV+NWFINAR R+
Sbjct: 10 KRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRI 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 = 66.2 bits (160), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 31/59 (52%), Positives = 42/59 (71%)
Query: 407 LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEE 465
LP+ SV +LR WL+EH + YPS+ +K +L++QT LS QV NWFINAR RL M+ +
Sbjct: 12 LPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRK 70
>pdb|2DMN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Tgif2lx
Length = 83
Score = 64.3 bits (155), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 27/59 (45%), Positives = 41/59 (69%)
Query: 407 LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEE 465
LP SV +LR W+++H YPS+ +K +L+ +T LS Q+SNWFINAR R+ M+++
Sbjct: 14 LPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQ 72
>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 = 52.8 bits (125), Expect = 6e-07, Method: Composition-based stats.
Identities = 24/59 (40%), Positives = 37/59 (62%)
Query: 402 RPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 460
R +R +++ +L + + H +PYPS+ K LAR+ G++ SQVSNWF N R+R K
Sbjct: 3 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKK 61
>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 = 23/59 (38%), Positives = 38/59 (64%)
Query: 402 RPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 460
R +R +++ +L + + H +PYPS+ K LA+++G++ SQVSNWF N R+R K
Sbjct: 4 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYKK 62
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 52.4 bits (124), Expect = 9e-07, Method: Composition-based stats.
Identities = 23/59 (38%), Positives = 37/59 (62%)
Query: 402 RPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 460
R +R +++ +L + + H +PYPS+ K LA++ G++ SQVSNWF N R+R K
Sbjct: 3 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 52.0 bits (123), Expect = 1e-06, Method: Composition-based stats.
Identities = 23/59 (38%), Positives = 37/59 (62%)
Query: 402 RPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 460
R +R +++ +L + + H +PYPS+ K LA++ G++ SQVSNWF N R+R K
Sbjct: 3 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 49.3 bits (116), Expect = 8e-06, Method: Composition-based stats.
Identities = 22/56 (39%), Positives = 36/56 (64%)
Query: 405 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 460
R + +++ +L + + H +PYPS+ K LA++ G++ SQVSNWF 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 = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/49 (53%), Positives = 32/49 (65%), Gaps = 3/49 (6%)
Query: 409 ERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVR 457
E+S VLR W + H +PYPS +K LA TGL+ +QVSNWF N R R
Sbjct: 503 EKSRGVLREW-YAH--NPYPSPREKRELAEATGLTTTQVSNWFKNRRQR 548
>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 = 36.2 bits (82), Expect = 0.056, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 391 QQMSMMESHPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNW 450
Q M + P+R R + +V +L +W ++ +PY L + T LSR Q+ NW
Sbjct: 19 QDMINKSTKPYRGHR-FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNW 77
Query: 451 FINAR 455
N R
Sbjct: 78 VSNRR 82
>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 = 35.4 bits (80), Expect = 0.089, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 398 SHPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINAR 455
+ P+R R + +V +L +W ++ +PY L + T LSR Q+ NW N R
Sbjct: 1 TKPYRGHR-FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR 57
>pdb|1LE8|B Chain B, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 83
Score = 34.3 bits (77), Expect = 0.22, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 1/60 (1%)
Query: 398 SHPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVR 457
+ P+R R + +V +L +W ++ +PY L + T LSR Q+ NW R +
Sbjct: 1 TKPYRGHR-FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAK 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 = 32.3 bits (72), Expect = 0.91, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 24/47 (51%)
Query: 409 ERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINAR 455
+ +V +L +W ++ +PY L + T LSR Q+ NW N R
Sbjct: 7 KENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR 53
>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 = 32.0 bits (71), Expect = 1.3, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 427 YPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 463
+P D + + L TGL+RS++ WF + R R + +V
Sbjct: 28 FPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGIV 64
>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 = 30.8 bits (68), Expect = 2.2, Method: Composition-based stats.
Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 6/83 (7%)
Query: 393 MSMMESHPWR----PQRGLPERSVSVLRAWLFEHFLHP--YPSDVDKHILARQTGLSRSQ 446
M+ HP++ P+R P S + ++ E H Y + ++ LAR ++ +Q
Sbjct: 1 MARRIGHPYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQ 60
Query: 447 VSNWFINARVRLWKPMVEEMYLE 469
V WF N R + + EE E
Sbjct: 61 VKTWFQNRRTKWRRQTAEEREAE 83
>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 = 30.0 bits (66), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 427 YPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 460
YP + LA++T L+ +++ WF N R RL K
Sbjct: 42 YPDIYTREELAQRTNLTEARIQVWFQNRRARLRK 75
>pdb|3OB8|A Chain A, Structure Of The Beta-Galactosidase From Kluyveromyces
Lactis In Complex With Galactose
pdb|3OB8|B Chain B, Structure Of The Beta-Galactosidase From Kluyveromyces
Lactis In Complex With Galactose
pdb|3OB8|D Chain D, Structure Of The Beta-Galactosidase From Kluyveromyces
Lactis In Complex With Galactose
pdb|3OB8|C Chain C, Structure Of The Beta-Galactosidase From Kluyveromyces
Lactis In Complex With Galactose
pdb|3OBA|A Chain A, Structure Of The Beta-Galactosidase From Kluyveromyces
Lactis
pdb|3OBA|C Chain C, Structure Of The Beta-Galactosidase From Kluyveromyces
Lactis
pdb|3OBA|D Chain D, Structure Of The Beta-Galactosidase From Kluyveromyces
Lactis
pdb|3OBA|B Chain B, Structure Of The Beta-Galactosidase From Kluyveromyces
Lactis
Length = 1032
Score = 29.6 bits (65), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 239 KEFCSLGTKQNDATKLKSN-KAKQQWDDEN 267
KEF S TK+N+ T K N KA + W EN
Sbjct: 281 KEFISFSTKKNEETAFKINVKAPEHWTAEN 310
>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 = 29.6 bits (65), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 23/35 (65%), Gaps = 3/35 (8%)
Query: 426 PYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 460
P P + DK LA+++GL+R+ + +WF + R WK
Sbjct: 50 PSPEEYDK--LAKESGLARTDIVSWFGDTRY-AWK 81
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 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,852,979
Number of Sequences: 62578
Number of extensions: 661529
Number of successful extensions: 1326
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1308
Number of HSP's gapped (non-prelim): 22
length of query: 655
length of database: 14,973,337
effective HSP length: 105
effective length of query: 550
effective length of database: 8,402,647
effective search space: 4621455850
effective search space used: 4621455850
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: 55 (25.8 bits)