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= 041808
(197 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4HUC|A Chain A, Crystal Structure Of Ldtmt2, A L,D-Transpeptidase From
Mycobacterium Tuberculosis: Domain B And C
pdb|4HUC|B Chain B, Crystal Structure Of Ldtmt2, A L,D-Transpeptidase From
Mycobacterium Tuberculosis: Domain B And C
Length = 262
Score = 29.3 bits (64), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 34/76 (44%)
Query: 85 LFGQDAAATDTVPSFDLDKNKDREIRGQSVNINGRSWKSLRSSISKNGTALLKVDFATKF 144
+FG+D T ++ D + +V +NG KS+ +S+ K+ T +
Sbjct: 91 MFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGS 150
Query: 145 RYKTIGIKSKHHGAKL 160
RYK I + S +G +
Sbjct: 151 RYKHIIMDSSTYGVPV 166
>pdb|4GSQ|A Chain A, Structural Basis For The Inhibition Of Mycobacterium
Tuberculosis L,d- Transpeptidase By Meropenem, A Drug
Effective Against Extensively Drug-resistant Strains
pdb|4GSR|A Chain A, Structural Basis For The Inhibition Of Mycobacterium
Tuberculosis L,d- Transpeptidase By Meropenem, A Drug
Effective Against Extensively Drug-resistant Strains
pdb|4GSU|A Chain A, Structural Basis For The Inhibition Of Mycobacterium
Tuberculosis L,d- Transpeptidase By Meropenem, A Drug
Effective Against Extensively Drug-resistant Strains
pdb|4GSU|B Chain B, Structural Basis For The Inhibition Of Mycobacterium
Tuberculosis L,d- Transpeptidase By Meropenem, A Drug
Effective Against Extensively Drug-resistant Strains
Length = 287
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 34/76 (44%)
Query: 85 LFGQDAAATDTVPSFDLDKNKDREIRGQSVNINGRSWKSLRSSISKNGTALLKVDFATKF 144
+FG+D T ++ D + +V +NG KS+ +S+ K+ T +
Sbjct: 108 MFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGS 167
Query: 145 RYKTIGIKSKHHGAKL 160
RYK I + S +G +
Sbjct: 168 RYKHIIMDSSTYGVPV 183
>pdb|3TUR|A Chain A, Crystal Structure Of M. Tuberculosis Ld-Transpeptidase
Type 2 Complexed With A Peptidoglycan Fragment
pdb|3TUR|B Chain B, Crystal Structure Of M. Tuberculosis Ld-Transpeptidase
Type 2 Complexed With A Peptidoglycan Fragment
pdb|3U1Q|A Chain A, Crystal Structure Of M. Tuberculosis Ld-Transpeptidase
Type 2 With 2- Mercaptoethanol
pdb|3U1Q|B Chain B, Crystal Structure Of M. Tuberculosis Ld-Transpeptidase
Type 2 With 2- Mercaptoethanol
Length = 287
Score = 28.9 bits (63), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 34/76 (44%)
Query: 85 LFGQDAAATDTVPSFDLDKNKDREIRGQSVNINGRSWKSLRSSISKNGTALLKVDFATKF 144
+FG+D T ++ D + +V +NG KS+ +S+ K+ T +
Sbjct: 116 MFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGS 175
Query: 145 RYKTIGIKSKHHGAKL 160
RYK I + S +G +
Sbjct: 176 RYKHIIMDSSTYGVPV 191
>pdb|3U1P|A Chain A, Crystal Structure Of M. Tuberculosis Ld-Transpeptidase
Type 2 With Modified Catalytic Cysteine (C354)
pdb|3U1P|B Chain B, Crystal Structure Of M. Tuberculosis Ld-Transpeptidase
Type 2 With Modified Catalytic Cysteine (C354)
pdb|3VAE|A Chain A, Crystal Structure Of M. Tuberculosis Ld-Transpeptidase
Type 2 With Modified Catalytic Cysteine (C354)
pdb|3VAE|B Chain B, Crystal Structure Of M. Tuberculosis Ld-Transpeptidase
Type 2 With Modified Catalytic Cysteine (C354)
Length = 287
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 34/76 (44%)
Query: 85 LFGQDAAATDTVPSFDLDKNKDREIRGQSVNINGRSWKSLRSSISKNGTALLKVDFATKF 144
+FG+D T ++ D + +V +NG KS+ +S+ K+ T +
Sbjct: 116 MFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGS 175
Query: 145 RYKTIGIKSKHHGAKL 160
RYK I + S +G +
Sbjct: 176 RYKHIIMDSSTYGVPV 191
>pdb|3TX4|A Chain A, Crystal Structure Of Mutant (C354a) M. Tuberculosis
Ld-Transpeptidase Type 2
pdb|3TX4|B Chain B, Crystal Structure Of Mutant (C354a) M. Tuberculosis
Ld-Transpeptidase Type 2
Length = 287
Score = 28.9 bits (63), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 34/76 (44%)
Query: 85 LFGQDAAATDTVPSFDLDKNKDREIRGQSVNINGRSWKSLRSSISKNGTALLKVDFATKF 144
+FG+D T ++ D + +V +NG KS+ +S+ K+ T +
Sbjct: 116 MFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGS 175
Query: 145 RYKTIGIKSKHHGAKL 160
RYK I + S +G +
Sbjct: 176 RYKHIIMDSSTYGVPV 191
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 0.133 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,620,860
Number of Sequences: 62578
Number of extensions: 158018
Number of successful extensions: 336
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 331
Number of HSP's gapped (non-prelim): 5
length of query: 197
length of database: 14,973,337
effective HSP length: 94
effective length of query: 103
effective length of database: 9,091,005
effective search space: 936373515
effective search space used: 936373515
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: 49 (23.5 bits)