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= 006550
(641 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Pknox1
Length = 73
Score = 71.6 bits (174), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 32/56 (57%), Positives = 42/56 (75%), Gaps = 1/56 (1%)
Query: 422 QRG-LPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRL 476
+RG LP+ A V+R+WLF+H HPYPT+ EK +A QT L+ QV+NWFINAR R+
Sbjct: 10 KRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRI 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 = 71.2 bits (173), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 29/59 (49%), Positives = 43/59 (72%)
Query: 425 LPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVEE 483
P+ A + RAWLF+H HPYP++ +K LA+ TGL+ QV+NWFINAR R+ +P +++
Sbjct: 5 FPKVATNIXRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPXIDQ 63
>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 = 66.6 bits (161), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 30/59 (50%), Positives = 42/59 (71%)
Query: 425 LPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVEE 483
LP+ +V +LR WL+EH + YP++ EK +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 = 65.9 bits (159), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 27/59 (45%), Positives = 42/59 (71%)
Query: 425 LPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVEE 483
LP +V +LR W+++H YP++ EK ML+++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 = 54.7 bits (130), Expect = 2e-07, Method: Composition-based stats.
Identities = 24/59 (40%), Positives = 38/59 (64%)
Query: 420 RPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWK 478
R +R ++A +L + + H +PYP++ K LAK++G++ SQVSNWF N R+R K
Sbjct: 4 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYKK 62
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 53.9 bits (128), Expect = 3e-07, Method: Composition-based stats.
Identities = 24/59 (40%), Positives = 37/59 (62%)
Query: 420 RPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWK 478
R +R ++A +L + + H +PYP++ K LAK+ G++ SQVSNWF N R+R K
Sbjct: 3 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 53.9 bits (128), Expect = 3e-07, Method: Composition-based stats.
Identities = 24/59 (40%), Positives = 37/59 (62%)
Query: 420 RPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWK 478
R +R ++A +L + + H +PYP++ K LAK+ G++ SQVSNWF N R+R K
Sbjct: 3 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>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 = 52.4 bits (124), Expect = 7e-07, Method: Composition-based stats.
Identities = 23/59 (38%), Positives = 37/59 (62%)
Query: 420 RPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWK 478
R +R ++A +L + + H +PYP++ K LA++ G++ SQVSNWF N R+R K
Sbjct: 3 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKK 61
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 50.8 bits (120), Expect = 2e-06, Method: Composition-based stats.
Identities = 23/56 (41%), Positives = 36/56 (64%)
Query: 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWK 478
R + ++A +L + + H +PYP++ K LAK+ 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 = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/49 (51%), Positives = 33/49 (67%), Gaps = 3/49 (6%)
Query: 427 ERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVR 475
E++ VLR W + H +PYP+ EK 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 = 35.8 bits (81), Expect = 0.083, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 405 VLNSGFIERQSQPVWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLM-LAKQTGLSRS 463
V+ I + ++P +R R E V +L +W ++ +PY DT+ L L K T LSR
Sbjct: 16 VVTQDMINKSTKP-YRGHRFTKEN-VRILESWFAKNIENPY-LDTKGLENLMKNTSLSRI 72
Query: 464 QVSNWFINAR 473
Q+ NW N R
Sbjct: 73 QIKNWVSNRR 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 = 0.090, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 420 RPQRG--LPERAVTVLRAWLFEHFLHPYPTDTEKLM-LAKQTGLSRSQVSNWFINAR 473
+P RG + V +L +W ++ +PY DT+ L L K T LSR Q+ NW N R
Sbjct: 2 KPYRGHRFTKENVRILESWFAKNIENPY-LDTKGLENLMKNTSLSRIQIKNWVSNRR 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 = 21/59 (35%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
Query: 420 RPQRG--LPERAVTVLRAWLFEHFLHPYPTDTEKLM-LAKQTGLSRSQVSNWFINARVR 475
+P RG + V +L +W ++ +PY DT+ L L K T LSR Q+ NW R +
Sbjct: 2 KPYRGHRFTKENVRILESWFAKNIENPY-LDTKGLENLMKNTSLSRIQIKNWVAARRAK 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 = 33.9 bits (76), Expect = 0.32, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 445 YPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMV 481
+P D E L + TGL+RS++ WF + R R + +V
Sbjct: 28 FPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGIV 64
>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 = 33.5 bits (75), Expect = 0.35, Method: Composition-based stats.
Identities = 19/45 (42%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 430 VTVLRAWLFEHFLHPYPTDTEKLM-LAKQTGLSRSQVSNWFINAR 473
V +L +W ++ +PY DT+ L L K T LSR Q+ NW N R
Sbjct: 10 VRILESWFAKNIENPY-LDTKGLENLMKNTSLSRIQIKNWVSNRR 53
>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 = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 25/50 (50%)
Query: 427 ERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRL 476
ERA LRA +P P D E L +T ++R ++ +WF R ++
Sbjct: 13 ERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKV 62
>pdb|2D5V|A Chain A, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
pdb|2D5V|B Chain B, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
Length = 164
Score = 30.4 bits (67), Expect = 3.2, Method: Composition-based stats.
Identities = 13/30 (43%), Positives = 21/30 (70%)
Query: 446 PTDTEKLMLAKQTGLSRSQVSNWFINARVR 475
P+ ++ +++Q GL S VSN+F+NAR R
Sbjct: 122 PSKELQITISQQLGLELSTVSNFFMNARRR 151
>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 = 3.3, Method: Composition-based stats.
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 445 YPTDTEKLMLAKQTGLSRSQVSNWFINAR 473
+P D+E + L K TGL++ ++ WF + R
Sbjct: 30 FPHDSEIIRLMKITGLTKGEIKKWFSDTR 58
>pdb|3B5Y|A Chain A, Crystal Structure Of Msba From Salmonella Typhimurium With
Amppnp
pdb|3B5Y|B Chain B, Crystal Structure Of Msba From Salmonella Typhimurium With
Amppnp
pdb|3B5Y|C Chain C, Crystal Structure Of Msba From Salmonella Typhimurium With
Amppnp
pdb|3B5Y|D Chain D, Crystal Structure Of Msba From Salmonella Typhimurium With
Amppnp
pdb|3B5Z|A Chain A, Crystal Structure Of Msba From Salmonella Typhimurium With
Adp Vanadate
pdb|3B5Z|B Chain B, Crystal Structure Of Msba From Salmonella Typhimurium With
Adp Vanadate
pdb|3B5Z|C Chain C, Crystal Structure Of Msba From Salmonella Typhimurium With
Adp Vanadate
pdb|3B5Z|D Chain D, Crystal Structure Of Msba From Salmonella Typhimurium With
Adp Vanadate
pdb|3B60|A Chain A, Crystal Structure Of Msba From Salmonella Typhimurium With
Amppnp, Higher Resolution Form
pdb|3B60|B Chain B, Crystal Structure Of Msba From Salmonella Typhimurium With
Amppnp, Higher Resolution Form
pdb|3B60|C Chain C, Crystal Structure Of Msba From Salmonella Typhimurium With
Amppnp, Higher Resolution Form
pdb|3B60|D Chain D, Crystal Structure Of Msba From Salmonella Typhimurium With
Amppnp, Higher Resolution Form
Length = 582
Score = 30.0 bits (66), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 347 APFANLALKAMSKHFRSL-KNAITDQLQFTNKAQIQANRGKDEASTFG 393
AP ++A++ +SK FRS+ KN Q T A+ Q +G E FG
Sbjct: 175 APIVSIAIRVVSKRFRSISKNMQNTMGQVTTSAE-QMLKGHKEVLIFG 221
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 30.0 bits (66), Expect = 3.9, Method: Composition-based stats.
Identities = 18/43 (41%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 434 RAWLFEHFLHPYPTDT-EKLMLAKQTGLSRSQVSNWFINARVR 475
RA+L E F ++ EK +AK+ G++ QV WFIN R+R
Sbjct: 17 RAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 59
>pdb|2HOS|A Chain A, Phage-selected Homeodomain Bound To Unmodified Dna
pdb|2HOS|B Chain B, Phage-selected Homeodomain Bound To Unmodified Dna
pdb|2HOT|A Chain A, Phage Selected Homeodomain Bound To Modified Dna
pdb|2HOT|B Chain B, Phage Selected Homeodomain Bound To Modified Dna
Length = 63
Score = 28.9 bits (63), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 445 YPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWK 478
Y T+ + L+ + GL+ +QV WF N R ++ K
Sbjct: 28 YLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61
>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 = 28.9 bits (63), Expect = 9.9, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 445 YPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWK 478
Y T+ + L+ + GL+ +Q+ WF NAR ++ K
Sbjct: 25 YLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58
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
0.316 0.132 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,875,025
Number of Sequences: 62578
Number of extensions: 635744
Number of successful extensions: 3768
Number of sequences better than 100.0: 46
Number of HSP's better than 100.0 without gapping: 31
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 3730
Number of HSP's gapped (non-prelim): 51
length of query: 641
length of database: 14,973,337
effective HSP length: 105
effective length of query: 536
effective length of database: 8,402,647
effective search space: 4503818792
effective search space used: 4503818792
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)