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= 003058
(852 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3RIP|A Chain A, Crystal Structure Of Human Gamma-Tubulin Complex Protein 4
(Gcp4)
Length = 677
Score = 57.4 bits (137), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 86/217 (39%), Gaps = 15/217 (6%)
Query: 639 VYIKKQVDHIGKLILSNLMNDWRLMDE-------LAVLRAIYLLGSGDLLQHFLTVIFNK 691
V ++ VD I + +L W+LM E L +++ YLLG G+L Q F+ +
Sbjct: 323 VDFEQVVDRIRSTVAEHL---WKLMVEESDLLGQLKIIKDFYLLGRGELFQAFIDTAQHM 379
Query: 692 LDKGENWDDDFELNTLLQESIRNSADGKLLSAPDALEVLITESHGSNSDEQPSMANLAST 751
L + ++N Q+S P + E HG + S
Sbjct: 380 LKTPPTAVTEHDVNVAFQQSAHKVLLDDDNLLPLLHLTI--EYHGKEHKDATQAREGPS- 436
Query: 752 PRKSHPHSFGIDGLDLLKFTYKVSWPLELIANMEAIKKYNQVMGFLLKVKRAKFALDKAR 811
R++ P G L +YKV WPL ++ ++KYN V +LL V+R + L
Sbjct: 437 -RETSPREAPASGWAALGLSYKVQWPLHILFTPAVLEKYNVVFKYLLSVRRVQAELQHCW 495
Query: 812 RWMWKGRSLATNSHSHKRHWLVEQKLLHFVDAFHQYV 848
+ + L +N + W + + VD Y+
Sbjct: 496 ALQMQRKHLKSNQTDAIK-WRLRNHMAFLVDNLQYYL 531
>pdb|3CUX|A Chain A, Atomic Resolution Structures Of Escherichia Coli And
Bacillis Anthracis Malate Synthase A: Comparison With
Isoform G And Implications For Structure Based Drug
Design
Length = 528
Score = 32.3 bits (72), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 7/59 (11%)
Query: 307 QNGLRESIS-----LSSSVKGLQACPLF--IKDIAKSIISAGKSLQLIRHVSSKSNDDR 358
+ GLR +IS ++S + G A P++ ++D A + IS + Q IRH K ND R
Sbjct: 410 EEGLRMNISVGIQYIASWLSGRGAAPIYNLMEDAATAEISRAQVWQWIRHEGGKLNDGR 468
>pdb|1FZT|A Chain A, Solution Structure And Dynamics Of An Open B-Sheet,
Glycolytic Enzyme-Monomeric 23.7 Kda Phosphoglycerate
Mutase From Schizosaccharomyces Pombe
Length = 211
Score = 30.8 bits (68), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 39/91 (42%), Gaps = 7/91 (7%)
Query: 519 WNALNLSRNYYLPPLNDEVLRKAVLGAESGNISELKGTNYAFGFQFGES-EHLRSQCDTK 577
WN LNL + P L++ +++A LG E LK Y F F + + + C
Sbjct: 20 WNKLNLFTGWKDPALSETGIKEAKLGGE-----RLKSRGYKFDIAFTSALQRAQKTCQII 74
Query: 578 LLEVLFP-FPTILPSFRDELHISELLPFQKN 607
L EV P TI +E + +L K+
Sbjct: 75 LEEVGEPNLETIKSEKLNERYYGDLQGLNKD 105
>pdb|4FWI|B Chain B, Crystal Structure Of The Nucleotide-binding Domain Of A
Dipeptide Abc Transporter
Length = 334
Score = 29.6 bits (65), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 208 DEVCLVQGGEVEEYQMLLHIFVGSLLPYIEGL 239
D+V ++ GG + EY IF L PY GL
Sbjct: 223 DKVAVIYGGNLVEYNSTFQIFKNPLHPYTRGL 254
>pdb|3ID7|A Chain A, Crystal Structure Of Renal Dipeptidase From Streptomyces
Coelicolor A3(2)
pdb|3K5X|A Chain A, Crystal Structure Of Dipeptidase From Streptomics
Coelicolor Complexed With Phosphinate Pseudodipeptide
L-Ala-D-Asp At 1.4a Resolution.
pdb|3ITC|A Chain A, Crystal Structure Of Sco3058 With Bound Citrate And
Glycerol
pdb|3ISI|X Chain X, Crystal Structure Of Sco3058 With Bound Inhibitor
L-Ala-L-Asp Phosphinodipeptide
pdb|3S2J|A Chain A, Crystal Structure Of Dipeptidase From Streptomyces
Coelicolor Complexed With Phosphinate Pseudodipeptide
L-Leu-D-Ala
pdb|3S2L|A Chain A, Crystal Structure Of Dipeptidase From Streptomyces
Coelicolor Complexed With Phosphinate Pseudodipeptide
L-Leu-D-Glu
pdb|3S2M|A Chain A, Crystal Structure Of Dipeptidase From Streptomyces
Coelicolor Complexed With Phosphinate Pseudodipeptide
L-Phe-D-Asp
pdb|3S2N|A Chain A, Crystal Structure Of Dipeptidase From Streptomyces
Coelicolor Complexed With Phosphinate Pseudodipeptide
L-Tyr-D-Asp
Length = 400
Score = 29.6 bits (65), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 20/93 (21%), Positives = 39/93 (41%), Gaps = 2/93 (2%)
Query: 408 WQDDSCESEFIPSLPSYMNDQMTRNGNTETLAV-LTHSEKTWFKFLLDTLLQKGVIDQKS 466
W D + + + L ++ ++ R N E + V L+H T + LDT + S
Sbjct: 156 WADSATDEPGVGGLSAF-GREVVREMNREGMLVDLSHVAATTMRDALDTSTAPVIFSHSS 214
Query: 467 GNKVASNVPNMKEENMGKIIENNLFTQKTFCPE 499
V + N+ ++ + ++ N TF P+
Sbjct: 215 SRAVCDHPRNIPDDVLERLSANGGMAMVTFVPK 247
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
0.320 0.135 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,903,782
Number of Sequences: 62578
Number of extensions: 959101
Number of successful extensions: 1990
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1985
Number of HSP's gapped (non-prelim): 10
length of query: 852
length of database: 14,973,337
effective HSP length: 107
effective length of query: 745
effective length of database: 8,277,491
effective search space: 6166730795
effective search space used: 6166730795
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)