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= 043031
(424 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3UC1|A Chain A, Mycobacterium Tuberculosis Gyrase Type Iia Topoisomerase
C-Terminal Domain
Length = 327
Score = 29.6 bits (65), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 25/41 (60%), Gaps = 5/41 (12%)
Query: 336 GQHIRNIIASEGEERIFGHMKIDGWRD-----LFNRFGLVE 371
GQH+ N++A + EERI ++I G+ D L R GLV+
Sbjct: 82 GQHVANLLAFQPEERIAQVIQIRGYTDAPYLVLATRNGLVK 122
>pdb|1X9Y|A Chain A, The Prostaphopain B Structure
pdb|1X9Y|B Chain B, The Prostaphopain B Structure
pdb|1X9Y|C Chain C, The Prostaphopain B Structure
pdb|1X9Y|D Chain D, The Prostaphopain B Structure
Length = 367
Score = 29.3 bits (64), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 38/77 (49%)
Query: 233 NISFLTDIKDFETNEGEVVAVYSPVHLSHMIRKPNCLETFLTELRKINPCVMVVIEVESN 292
NI+ LTD K F E V + L++ I++ +T +L++ + +VE N
Sbjct: 121 NITVLTDEKGFYFEEDGKVRLVKATPLANNIKEKESAKTVSPQLKQELKTTVTPTKVEEN 180
Query: 293 DNLQTFEDRFFGTLFHF 309
+ +Q + ++ TL +F
Sbjct: 181 EAIQEDQVQYENTLKNF 197
>pdb|3EJX|A Chain A, Crystal Structure Of Diaminopimelate Epimerase From
Arabidopsis Thaliana In Complex With Ll-Azidap
pdb|3EJX|B Chain B, Crystal Structure Of Diaminopimelate Epimerase From
Arabidopsis Thaliana In Complex With Ll-Azidap
pdb|3EJX|C Chain C, Crystal Structure Of Diaminopimelate Epimerase From
Arabidopsis Thaliana In Complex With Ll-Azidap
pdb|3EJX|D Chain D, Crystal Structure Of Diaminopimelate Epimerase From
Arabidopsis Thaliana In Complex With Ll-Azidap
pdb|3EJX|E Chain E, Crystal Structure Of Diaminopimelate Epimerase From
Arabidopsis Thaliana In Complex With Ll-Azidap
pdb|3EJX|F Chain F, Crystal Structure Of Diaminopimelate Epimerase From
Arabidopsis Thaliana In Complex With Ll-Azidap
pdb|3EKM|A Chain A, Crystal Structure Of Diaminopimelate Epimerase Form
Arabidopsis Thaliana In Complex With Irreversible
Inhibitor Dl-Azidap
pdb|3EKM|B Chain B, Crystal Structure Of Diaminopimelate Epimerase Form
Arabidopsis Thaliana In Complex With Irreversible
Inhibitor Dl-Azidap
pdb|3EKM|C Chain C, Crystal Structure Of Diaminopimelate Epimerase Form
Arabidopsis Thaliana In Complex With Irreversible
Inhibitor Dl-Azidap
pdb|3EKM|D Chain D, Crystal Structure Of Diaminopimelate Epimerase Form
Arabidopsis Thaliana In Complex With Irreversible
Inhibitor Dl-Azidap
pdb|3EKM|E Chain E, Crystal Structure Of Diaminopimelate Epimerase Form
Arabidopsis Thaliana In Complex With Irreversible
Inhibitor Dl-Azidap
pdb|3EKM|F Chain F, Crystal Structure Of Diaminopimelate Epimerase Form
Arabidopsis Thaliana In Complex With Irreversible
Inhibitor Dl-Azidap
Length = 317
Score = 28.5 bits (62), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 29/110 (26%), Positives = 48/110 (43%), Gaps = 10/110 (9%)
Query: 317 EVCMN--RCHANRMTFEEMYAGQHIRNIIASEG----EERIFGHMKIDGWRDLFNRFGLV 370
E+C N RC A + E G+H I G E + G +K+D + + V
Sbjct: 97 EMCGNGVRCFARFIAELENLQGKHSFTIHTGAGLIVPEIQDDGQVKVDMGTPIL-KAQDV 155
Query: 371 EAELSS---WSLFQAELILRSFACGSSCTIDRNGECLIIGWKGIPHLSLS 417
+LS ++ +AEL++ + +C N C+ G KG P+L +
Sbjct: 156 PTKLSGNKGEAVVEAELVVDGVSWNVTCVSMGNPHCITFGKKGGPNLKVD 205
>pdb|3T1G|A Chain A, Engineering Of Organophosphate Hydrolase By Computational
Design And Directed Evolution
Length = 353
Score = 28.5 bits (62), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 21/38 (55%)
Query: 54 LLSAEKIGSQQFDRASIFLDHVDKYSSTTGNPVQRLVH 91
+++ + IG + + +S+F HV+ Y N + R VH
Sbjct: 178 VVAMDLIGDETIEGSSLFPGHVEAYEGAVKNGIHRTVH 215
>pdb|1HSK|A Chain A, Crystal Structure Of S. Aureus Murb
Length = 326
Score = 28.5 bits (62), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 5/69 (7%)
Query: 40 PEGGIKGVELVHLLLLSAEKIGSQQFD-RASIFLDHVDKYSSTTGNPVQRLVHYFSKALR 98
P G G +L+ L +IG + + + F+ +VD ++T + L+HY K ++
Sbjct: 243 PPGHFAG-KLIQDSNLQGHRIGGVEVSTKHAGFMVNVDNGTATD---YENLIHYVQKTVK 298
Query: 99 ERFNLETGR 107
E+F +E R
Sbjct: 299 EKFGIELNR 307
>pdb|1NSF|A Chain A, D2 Hexamerization Domain Of N-Ethylmaleimide Sensitive
Factor (Nsf)
Length = 273
Score = 28.5 bits (62), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 44/190 (23%), Positives = 79/190 (41%), Gaps = 35/190 (18%)
Query: 61 GSQQFDRASIFLDHVDKYSSTTGNPVQRLVHYFSKALRERFNLETGRITSKGLKSEEVML 120
G+ Q D AS ++ + K+ G+PV R++ +++ N + + S +L
Sbjct: 20 GTNQEDYASYIMNGIIKW----GDPVTRVLDDGELLVQQTKNSDRTPLVS--------VL 67
Query: 121 LLHPEEVMASAKQALIACYQKVPFYQV---------TVFAGIQAVIENVSSAKKIH---- 167
L P +A A IA PF ++ + A QA+ + A K
Sbjct: 68 LEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQLSCV 127
Query: 168 IIDLATRTGSHCP--------AIMQALATRQGCPPELLKITMVVGTTPSKQKFEEIENRL 219
++D R + P + L + PP+ K+ +++GTT K +E+E L
Sbjct: 128 VVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKL-LIIGTTSRKDVLQEME-ML 185
Query: 220 ANFAETINLP 229
F+ TI++P
Sbjct: 186 NAFSTTIHVP 195
>pdb|1D2N|A Chain A, D2 Domain Of N-Ethylmaleimide-Sensitive Fusion Protein
Length = 272
Score = 28.1 bits (61), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 44/190 (23%), Positives = 79/190 (41%), Gaps = 35/190 (18%)
Query: 61 GSQQFDRASIFLDHVDKYSSTTGNPVQRLVHYFSKALRERFNLETGRITSKGLKSEEVML 120
G+ Q D AS ++ + K+ G+PV R++ +++ N + + S +L
Sbjct: 21 GTNQEDYASYIMNGIIKW----GDPVTRVLDDGELLVQQTKNSDRTPLVS--------VL 68
Query: 121 LLHPEEVMASAKQALIACYQKVPFYQV---------TVFAGIQAVIENVSSAKKIH---- 167
L P +A A IA PF ++ + A QA+ + A K
Sbjct: 69 LEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQLSCV 128
Query: 168 IIDLATRTGSHCP--------AIMQALATRQGCPPELLKITMVVGTTPSKQKFEEIENRL 219
++D R + P + L + PP+ K+ +++GTT K +E+E L
Sbjct: 129 VVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKL-LIIGTTSRKDVLQEME-ML 186
Query: 220 ANFAETINLP 229
F+ TI++P
Sbjct: 187 NAFSTTIHVP 196
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
0.325 0.139 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,151,210
Number of Sequences: 62578
Number of extensions: 486049
Number of successful extensions: 1341
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1338
Number of HSP's gapped (non-prelim): 10
length of query: 424
length of database: 14,973,337
effective HSP length: 101
effective length of query: 323
effective length of database: 8,652,959
effective search space: 2794905757
effective search space used: 2794905757
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 bits)