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= 003323
(830 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 = 71.6 bits (174), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 30/59 (50%), Positives = 43/59 (72%)
Query: 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVEE 644
P+ + NI R+WLF+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 = 69.3 bits (168), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 30/56 (53%), Positives = 43/56 (76%), Gaps = 1/56 (1%)
Query: 583 QRG-LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRL 637
+RG LP+ + N++RSWLF+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 = 68.6 bits (166), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 33/59 (55%), Positives = 42/59 (71%)
Query: 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVEE 644
LP+ SV ILR WL+EH + YPS+ +K LL++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 = 66.2 bits (160), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 28/59 (47%), Positives = 41/59 (69%)
Query: 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVEE 644
LP SV ILR W+++H YPS+ +K +L+ +T LS Q+SNWFINAR R+ M+++
Sbjct: 14 LPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQ 72
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 56.2 bits (134), Expect = 8e-08, Method: Composition-based stats.
Identities = 27/72 (37%), Positives = 46/72 (63%), Gaps = 2/72 (2%)
Query: 579 AWRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLW 638
A R +R +++ IL + + H +PYPS+ K LA+++G++ +QVSNWF N R+R
Sbjct: 2 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYK 61
Query: 639 KPMVEEMYQQEA 650
K + + +Q+EA
Sbjct: 62 KNIGK--FQEEA 71
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 55.8 bits (133), Expect = 1e-07, Method: Composition-based stats.
Identities = 27/72 (37%), Positives = 45/72 (62%), Gaps = 2/72 (2%)
Query: 579 AWRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLW 638
A R +R +++ IL + + H +PYPS+ K LA++ G++ +QVSNWF N R+R
Sbjct: 1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 639 KPMVEEMYQQEA 650
K + + +Q+EA
Sbjct: 61 KNIGK--FQEEA 70
>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 = 55.5 bits (132), Expect = 1e-07, Method: Composition-based stats.
Identities = 25/61 (40%), Positives = 38/61 (62%)
Query: 579 AWRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLW 638
A R +R +++ IL + + H +PYPS+ K LAR+ G++ +QVSNWF N R+R
Sbjct: 1 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYK 60
Query: 639 K 639
K
Sbjct: 61 K 61
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 55.1 bits (131), Expect = 1e-07, Method: Composition-based stats.
Identities = 27/72 (37%), Positives = 45/72 (62%), Gaps = 2/72 (2%)
Query: 579 AWRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLW 638
A R +R +++ IL + + H +PYPS+ K LA++ G++ +QVSNWF N R+R
Sbjct: 1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 639 KPMVEEMYQQEA 650
K + + +Q+EA
Sbjct: 61 KNIGK--FQEEA 70
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 50.4 bits (119), Expect = 4e-06, Method: Composition-based stats.
Identities = 22/56 (39%), Positives = 36/56 (64%)
Query: 584 RGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWK 639
R + +++ IL + + H +PYPS+ K LA++ G++ +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 = 47.8 bits (112), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/49 (51%), Positives = 31/49 (63%), Gaps = 3/49 (6%)
Query: 588 ERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVR 636
E+S +LR 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 = 38.1 bits (87), Expect = 0.022, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 575 MEQEAWRPQRG--LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFIN 632
M ++ +P RG + +V IL SW ++ +PY L + T LSR Q+ NW N
Sbjct: 21 MINKSTKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSN 80
Query: 633 AR 634
R
Sbjct: 81 RR 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 = 37.7 bits (86), Expect = 0.028, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 581 RPQRG--LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINAR 634
+P RG + +V IL SW ++ +PY L + T LSR Q+ NW N R
Sbjct: 2 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR 57
>pdb|1LE8|B Chain B, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 83
Score = 36.2 bits (82), Expect = 0.079, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 581 RPQRG--LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVR 636
+P RG + +V IL SW ++ +PY L + T LSR Q+ NW R +
Sbjct: 2 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAK 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 = 35.4 bits (80), Expect = 0.14, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 24/47 (51%)
Query: 588 ERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINAR 634
+ +V IL SW ++ +PY L + T LSR Q+ NW N R
Sbjct: 7 KENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR 53
>pdb|1X19|A Chain A, Crystal Structure Of Bchu Involved In Bacteriochlorophyll
C Biosynthesis
pdb|1X1A|A Chain A, Crystal Structure Of Bchu Complexed With
S-Adenosyl-L-Methionine
pdb|1X1B|A Chain A, Crystal Structure Of Bchu Complexed With
S-Adenosyl-L-Homocysteine
pdb|1X1C|A Chain A, Crystal Structure Of Bchu Complexed With
S-Adenosyl-L-Homocysteine And Zn2+
pdb|1X1D|A Chain A, Crystal Structure Of Bchu Complexed With
S-Adenosyl-L-Homocysteine And Zn-Bacteriopheophorbide D
Length = 359
Score = 33.1 bits (74), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 7/63 (11%)
Query: 519 FRCLKDAIAAQL-KQSCELLGEKDVAGTSGITKGETPRLKLLEQSLRQQRAFHQMGMMEQ 577
F C+K AI L E G KD+A + T PRL++L ++LRQ R + +E
Sbjct: 45 FSCMKAAIELDLFSHMAE--GPKDLATLAADTGSVPPRLEMLLETLRQMRVIN----LED 98
Query: 578 EAW 580
W
Sbjct: 99 GKW 101
>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 = 33.1 bits (74), Expect = 0.69, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 23/37 (62%)
Query: 606 YPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642
+P DA+ + L TGL+R+++ WF + R R + +V
Sbjct: 28 FPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGIV 64
>pdb|2NN6|F Chain F, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 272
Score = 29.3 bits (64), Expect = 9.5, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 6/45 (13%)
Query: 76 DKLRVQGGYEQPPPPLVGIEEE------DQSTELPVYDTAGMLSE 114
D R++G E PP L +EE D + PVY AG+LS+
Sbjct: 4 DHRRIRGPEESQPPQLYAADEEEAPGTRDPTRLRPVYARAGLLSQ 48
>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 = 29.3 bits (64), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 2/65 (3%)
Query: 582 PQRGLPERSVNILRSWLFEHFLHP--YPSDADKHLLARQTGLSRNQVSNWFINARVRLWK 639
P+R P S ++ E H Y + A++ LAR ++ QV WF N R + +
Sbjct: 15 PKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRR 74
Query: 640 PMVEE 644
EE
Sbjct: 75 QTAEE 79
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 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,125,858
Number of Sequences: 62578
Number of extensions: 796848
Number of successful extensions: 1338
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1323
Number of HSP's gapped (non-prelim): 18
length of query: 830
length of database: 14,973,337
effective HSP length: 107
effective length of query: 723
effective length of database: 8,277,491
effective search space: 5984625993
effective search space used: 5984625993
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: 56 (26.2 bits)