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= 008290
(571 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MKT|A Chain A, Structure Of A Cation-Bound Multidrug And Toxin Compound
Extrusion (Mate) Transporter
pdb|3MKT|B Chain B, Structure Of A Cation-Bound Multidrug And Toxin Compound
Extrusion (Mate) Transporter
pdb|3MKU|A Chain A, Structure Of A Cation-Bound Multidrug And Toxin Compound
Extrusion (Mate) Transporter
pdb|3MKU|B Chain B, Structure Of A Cation-Bound Multidrug And Toxin Compound
Extrusion (Mate) Transporter
Length = 460
Score = 34.7 bits (78), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 85/407 (20%), Positives = 164/407 (40%), Gaps = 49/407 (12%)
Query: 113 DLIMLSLPAIAGQAIEPMAQLMETAYIGRLGPLELASAGVSTSIFNILSKVFNIPLLSVA 172
+LI L+ P + + ++T G + +++A+ ++ SI+ + S +F + LL
Sbjct: 13 NLIKLATPVLIASVAQTGMGFVDTIMAGGVSAIDMAAVSIAASIW-LPSILFGVGLLMAL 71
Query: 173 TSFVAEXXXXXXXXXXXXXXXCPNVSYNGCDESTDRKLLPSVSTALVLALTIGILEALAM 232
VA+ NG K+ V L+LAL + + +A+
Sbjct: 72 VPVVAQL--------------------NGAGR--QHKIPFEVHQGLILALLVSV-PIIAV 108
Query: 233 YFGSGLFLDIMGISSASSMRIPAQRFLSLRAIGAPAVVLSLAIQGIFRGFKDTRTPVFCL 292
F + + M + A + + + A+ PA +L A++ G T+ P +
Sbjct: 109 LFQTQFIIRFMDVEEAMATKTVGYMHAVIFAV--PAYLLFQALRSFTDGMSLTK-PAMVI 165
Query: 293 GLGNFSAVFMFPMLMYYF--------KLGVTGAAISTVGSQYMVTLLMIWYL-NKRTILS 343
G F + + L + F +LG G ++T +++ LL+++Y+ + +
Sbjct: 166 G---FIGLLLNIPLNWIFVYGKFGAPELGGVGCGVATAIVYWIMLLLLLFYIVTSKRLAH 222
Query: 344 IPNMKNLHF---GDYLRSGGYLLGRTLAAVM--TITLSTSIA---ARQGALAMAAHQICL 395
+ + H + +R + LG +AA + +TL +A A G+ +AAHQ+ L
Sbjct: 223 VKVFETFHKPQPKELIRL--FRLGFPVAAALFFEVTLFAVVALLVAPLGSTVVAAHQVAL 280
Query: 396 QVWLSVSMLADAQAASGQALIASSFAKGDYNTVKEITHFALKTGLFTGVTLAVILGASFN 455
V M + A+ + + D + L TGL T A++
Sbjct: 281 NFSSLVFMFPMSIGAAVSIRVGHKLGEQDTKGAAIAANVGLMTGLATACITALLTVLFRE 340
Query: 456 YLATLFTSDTQVLGIVRSGLLFVSASQPVTAVAYIFDGLHYGVSDFS 502
+A L+T + V+ + LLF + Q + AV + G G D +
Sbjct: 341 QIALLYTENQVVVALAMQLLLFAAIYQCMDAVQVVAAGSLRGYKDMT 387
>pdb|3ZQD|A Chain A, B. Subtilis L,D-Transpeptidase
pdb|4A52|A Chain A, Nmr Structure Of The Imipenem-Acylated L,D-Transpeptidase
From Bacillus Subtilis
Length = 175
Score = 32.3 bits (72), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 25/96 (26%), Positives = 42/96 (43%), Gaps = 19/96 (19%)
Query: 25 NKMGKAFPIY--SMVIAPPNCSFGVINRAKNGFNPAIMCCGSVSDQHASDYITINPSGVG 82
N++ K +PI ++ P F +INR +N P S+S QH + T NP+ +G
Sbjct: 76 NRVMKTYPIAVGKILTQTPTGEFYIINRQRNPGGPFGAYWLSLSKQHYGIHGTNNPASIG 135
Query: 83 ERLASDGGELSNESRKSAATSQSCVQNVQLDLIMLS 118
+ A S+ C++ D+I L+
Sbjct: 136 K-----------------AVSKGCIRMHNKDVIELA 154
>pdb|2YL9|A Chain A, Inhibition Of The Pneumococcal Virulence Factor Strh And
Molecular Insights Into N-Glycan Recognition And
Hydrolysis
pdb|2YL9|B Chain B, Inhibition Of The Pneumococcal Virulence Factor Strh And
Molecular Insights Into N-Glycan Recognition And
Hydrolysis
pdb|2YL9|C Chain C, Inhibition Of The Pneumococcal Virulence Factor Strh And
Molecular Insights Into N-Glycan Recognition And
Hydrolysis
pdb|2YL9|D Chain D, Inhibition Of The Pneumococcal Virulence Factor Strh And
Molecular Insights Into N-Glycan Recognition And
Hydrolysis
Length = 457
Score = 30.4 bits (67), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 20/38 (52%)
Query: 529 SAVWWGLTLFMSLRVAAGYFRLLSKNGPWWFLQKHMPK 566
S WWG L +A+ ++ L+ NG W+++ P+
Sbjct: 268 SKGWWGYNLASPQYLASKGYKFLNTNGDWYYILGQKPE 305
>pdb|2YL5|A Chain A, Inhibition Of The Pneumococcal Virulence Factor Strh And
Molecular Insights Into N-Glycan Recognition And
Hydrolysis
pdb|2YL5|B Chain B, Inhibition Of The Pneumococcal Virulence Factor Strh And
Molecular Insights Into N-Glycan Recognition And
Hydrolysis
pdb|2YL5|C Chain C, Inhibition Of The Pneumococcal Virulence Factor Strh And
Molecular Insights Into N-Glycan Recognition And
Hydrolysis
pdb|2YL5|D Chain D, Inhibition Of The Pneumococcal Virulence Factor Strh And
Molecular Insights Into N-Glycan Recognition And
Hydrolysis
Length = 442
Score = 30.4 bits (67), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 20/38 (52%)
Query: 529 SAVWWGLTLFMSLRVAAGYFRLLSKNGPWWFLQKHMPK 566
S WWG L +A+ ++ L+ NG W+++ P+
Sbjct: 251 SKGWWGYNLASPQYLASKGYKFLNTNGDWYYILGQKPE 288
>pdb|2YLA|A Chain A, Inhibition Of The Pneumococcal Virulence Factor Strh And
Molecular Insights Into N-Glycan Recognition And
Hydrolysis
pdb|2YLA|B Chain B, Inhibition Of The Pneumococcal Virulence Factor Strh And
Molecular Insights Into N-Glycan Recognition And
Hydrolysis
pdb|2YLA|C Chain C, Inhibition Of The Pneumococcal Virulence Factor Strh And
Molecular Insights Into N-Glycan Recognition And
Hydrolysis
pdb|2YLA|D Chain D, Inhibition Of The Pneumococcal Virulence Factor Strh And
Molecular Insights Into N-Glycan Recognition And
Hydrolysis
Length = 442
Score = 30.4 bits (67), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 20/38 (52%)
Query: 529 SAVWWGLTLFMSLRVAAGYFRLLSKNGPWWFLQKHMPK 566
S WWG L +A+ ++ L+ NG W+++ P+
Sbjct: 251 SKGWWGYNLASPQYLASKGYKFLNTNGDWYYILGQKPE 288
>pdb|4HUK|A Chain A, Mate Transporter Norm-ng In Complex With Tpp And Monobody
pdb|4HUL|A Chain A, Mate Transporter Norm-ng In Complex With Cs+ And Monobody
pdb|4HUM|A Chain A, Mate Transporter Norm-ng In Complex With Ethidium And
Monobody
pdb|4HUN|A Chain A, Mate Transporter Norm-ng In Complex With R6g And Monobody
Length = 459
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 3/76 (3%)
Query: 280 RGFKDTRTPVFCLGLGNFSAVFMFP--MLMYYFKLGVTGAAISTVGSQYMVTLLMIWYLN 337
RG+K T+ P+F + F + P +L Y F +G+ G + + S + + ++W L
Sbjct: 384 RGYKVTKVPMF-IHAAAFWGCGLLPGYLLAYRFDMGIYGFWTALIASLTIAAVALVWCLE 442
Query: 338 KRTILSIPNMKNLHFG 353
K ++ + + K + G
Sbjct: 443 KYSMELVKSHKAVSSG 458
Score = 30.0 bits (66), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 23/96 (23%), Positives = 46/96 (47%)
Query: 388 MAAHQICLQVWLSVSMLADAQAASGQALIASSFAKGDYNTVKEITHFALKTGLFTGVTLA 447
+AA Q+ + + + M+ + ++G I S + +++ + I+ +L +G V
Sbjct: 276 VAAQQVGISLSGILYMIPQSVGSAGTVRIGFSLGRREFSRARYISGVSLVSGWVLAVITV 335
Query: 448 VILGASFNYLATLFTSDTQVLGIVRSGLLFVSASQP 483
+ L + LA+++ D VL I + LLF QP
Sbjct: 336 LSLVLFRSPLASMYNDDPAVLSIASTVLLFAGLFQP 371
>pdb|1FBL|A Chain A, Structure Of Full-Length Porcine Synovial Collagenase
(Mmp1) Reveals A C-Terminal Domain Containing A
Calcium-Linked, Four-Bladed Beta- Propeller
Length = 370
Score = 29.6 bits (65), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 392 QICLQVWLSVSMLADAQAASGQALIASSFAKGDY 425
+ Q+W +VS L + + GQA I SF +GD+
Sbjct: 36 EKAFQLWSNVSPLTFTKVSEGQADIMISFVRGDH 69
>pdb|3PK0|A Chain A, Crystal Structure Of Short-Chain DehydrogenaseREDUCTASE
SDR FROM Mycobacterium Smegmatis
pdb|3PK0|B Chain B, Crystal Structure Of Short-Chain DehydrogenaseREDUCTASE
SDR FROM Mycobacterium Smegmatis
pdb|3PK0|C Chain C, Crystal Structure Of Short-Chain DehydrogenaseREDUCTASE
SDR FROM Mycobacterium Smegmatis
pdb|3PK0|D Chain D, Crystal Structure Of Short-Chain DehydrogenaseREDUCTASE
SDR FROM Mycobacterium Smegmatis
Length = 262
Score = 28.9 bits (63), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 42/90 (46%), Gaps = 12/90 (13%)
Query: 382 RQGALAMAAHQICLQVWLSVSMLADAQAASGQALIAS---SFAKGDYNTVKEITHFAL-- 436
R A+ +A H+I + + +++ + +G+ IAS S G T ++I H A
Sbjct: 173 RTAAIELAPHKITVNAIMPGNIMTEGLLENGEEYIASMARSIPAGALGTPEDIGHLAAFL 232
Query: 437 ---KTGLFTGVTLAV----ILGASFNYLAT 459
+ G TG +AV +L S + +AT
Sbjct: 233 ATKEAGYITGQAIAVDGGQVLPESLDAIAT 262
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
0.324 0.136 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,945,211
Number of Sequences: 62578
Number of extensions: 507040
Number of successful extensions: 1336
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1328
Number of HSP's gapped (non-prelim): 9
length of query: 571
length of database: 14,973,337
effective HSP length: 104
effective length of query: 467
effective length of database: 8,465,225
effective search space: 3953260075
effective search space used: 3953260075
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: 54 (25.4 bits)