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= 022062
(303 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1GG4|A Chain A, Crystal Structure Of Escherichia Coli Udpmurnac-Tripeptide
D-Alanyl-D-Alanine-Adding Enzyme (Murf) At 2.3 Angstrom
Resolution
pdb|1GG4|B Chain B, Crystal Structure Of Escherichia Coli Udpmurnac-Tripeptide
D-Alanyl-D-Alanine-Adding Enzyme (Murf) At 2.3 Angstrom
Resolution
Length = 452
Score = 75.9 bits (185), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 67/226 (29%), Positives = 99/226 (43%), Gaps = 14/226 (6%)
Query: 49 ICTDTRILAPNKNQWFFAITGQHFDAHEFISPELYGKGCVGVIGNQVCNNWDKGFVQVEG 108
+ TDTR L P F A+ G+ FDAH+F G ++ + + + V+
Sbjct: 27 VTTDTRKLTPGC--LFVALKGERFDAHDFADQAKAGGAGALLVSRPLDIDLPQLIVK--- 81
Query: 109 NGNVNTLNSLVNMACYARNSRFXXXXXXXXXXXXXXXXXXMIALALESLGVNVFQSYGNW 168
+T + +A + R + A L G N + GN
Sbjct: 82 ----DTRLAFGELAAWVRQ-QVPARVVALTGSSGKTSVKEXTAAILSQCG-NTLYTAGNL 135
Query: 169 NNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLGSL 228
NN +GV +L+ + D AV+E+G + +GEI + RPE +V N+ +HLE GSL
Sbjct: 136 NNDIGVPXTLLRLTPEYDYAVIELGANHQGEIAWTVSLTRPEAALVNNLAAAHLEGFGSL 195
Query: 229 EDVARAKGEIFQESKLGDVCVLNADDPLVANLTVPRGVRKVFFGWR 274
VA+AKGEIF + + NAD+ N G RKV WR
Sbjct: 196 AGVAKAKGEIFSGLPENGIAIXNADNNDWLNWQSVIGSRKV---WR 238
>pdb|2AM1|A Chain A, Sp Protein Ligand 1
pdb|2AM2|A Chain A, Sp Protein Ligand 2
Length = 454
Score = 54.3 bits (129), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 35/129 (27%), Positives = 66/129 (51%), Gaps = 4/129 (3%)
Query: 154 LESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRV 213
L S +++ GN+NN +G+ +++ + VLE G G+I L+ +ARP+ +
Sbjct: 121 LLSTRYKTYKTQGNYNNEIGLPYTVLHXPEGTEKLVLEXGQDHLGDIHLLSELARPKTAI 180
Query: 214 VLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLTVPRGVRKVFFGW 273
V VG++HL ++A+ K +I G + + A DP+V + +P + V FG
Sbjct: 181 VTLVGEAHLAFFKDRSEIAKGKXQIADGXASGSLLLAPA-DPIVEDY-LPIDKKVVRFG- 237
Query: 274 RRGCDVRLV 282
+G ++ +
Sbjct: 238 -QGAELEIT 245
>pdb|3LK7|A Chain A, The Crystal Structure Of Udp-N-Acetylmuramoylalanine-D-
Glutamate (Murd) Ligase From Streptococcus Agalactiae To
1.5a
Length = 451
Score = 35.0 bits (79), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 23/44 (52%)
Query: 208 RPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLN 251
RP I V+ N+ +HL+ GS ED AK I + D VLN
Sbjct: 180 RPHIAVITNLXPTHLDYHGSFEDYVAAKWNIQNQXSSSDFLVLN 223
>pdb|1E0D|A Chain A, Udp-N-Acetylmuramoyl-L-Alanine:d-Glutamate Ligase
pdb|1EEH|A Chain A, Udp-N-Acetylmuramoyl-L-Alanine:d-Glutamate Ligase
Length = 437
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 33/104 (31%), Positives = 50/104 (48%), Gaps = 15/104 (14%)
Query: 177 SLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLG-SLEDVARAK 235
+L+ +D ++ VLE+ LE + +LNV + H++ L+ AK
Sbjct: 143 ALMLLDDECELYVLEL----SSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAK 198
Query: 236 GEIFQESKLGDVCVLNADDPLVANLTVP-RGV--RKVFFGWRRG 276
I++ +K VCV+NADD LT+P RG R V FG G
Sbjct: 199 LRIYENAK---VCVVNADDA----LTMPIRGADERCVSFGVNMG 235
>pdb|1O5Z|A Chain A, Crystal Structure Of Folylpolyglutamate Synthase (Tm0166)
From Thermotoga Maritima At 2.10 A Resolution
Length = 442
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 4/61 (6%)
Query: 182 DRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLG-SLEDVARAKGEIFQ 240
++ VDIAVLE+G+ G+ L+ + P ++ V H ++LG ++E +A K I +
Sbjct: 146 EKNVDIAVLEVGLGGR---LDATNVVFPLCSTIVTVDRDHEKTLGYTIEQIAWEKSGIIK 202
Query: 241 E 241
E
Sbjct: 203 E 203
>pdb|2RCA|B Chain B, Crystal Structure Of The Nr3b Ligand Binding Core Complex
With Glycine At 1.58 Angstrom Resolution
pdb|2RCB|A Chain A, Crystal Structure Of The Nr3b Ligand Binding Core Complex
With D- Serine At 1.62 Angstrom Resolution
pdb|2RCB|B Chain B, Crystal Structure Of The Nr3b Ligand Binding Core Complex
With D- Serine At 1.62 Angstrom Resolution
pdb|2RCA|A Chain A, Crystal Structure Of The Nr3b Ligand Binding Core Complex
With Glycine At 1.58 Angstrom Resolution
Length = 292
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 34/67 (50%)
Query: 207 ARPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLTVPRGV 266
ARP++RVV V + + S ED G++ + D L+A + N +VPR +
Sbjct: 3 ARPKLRVVTLVEHPFVFTRESDEDGQCPAGQLCLDPGTNDSARLDALFAALVNGSVPRTL 62
Query: 267 RKVFFGW 273
R+ +G+
Sbjct: 63 RRCCYGY 69
>pdb|2WJP|A Chain A, Crystal Structure Of Murd Ligase In Complex With D-Glu
Containing Rhodanine Inhibitor
pdb|2X5O|A Chain A, Discovery Of Novel 5-Benzylidenerhodanine- And
5-Benzylidene- Thiazolidine-2,4-Dione Inhibitors Of Murd
Ligase
pdb|2XPC|A Chain A, Second-Generation Sulfonamide Inhibitors Of Murd: Activity
Optimisation With Conformationally Rigid Analogues Of D-
Glutamic Acid
Length = 439
Score = 28.5 bits (62), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 32/104 (30%), Positives = 49/104 (47%), Gaps = 15/104 (14%)
Query: 177 SLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLG-SLEDVARAK 235
+L+ +D ++ VLE+ LE + +LNV + H++ L+ A
Sbjct: 143 ALMLLDDECELYVLEL----SSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAX 198
Query: 236 GEIFQESKLGDVCVLNADDPLVANLTVP-RGV--RKVFFGWRRG 276
I++ +K VCV+NADD LT+P RG R V FG G
Sbjct: 199 LRIYENAK---VCVVNADDA----LTMPIRGADERCVSFGVNMG 235
>pdb|2UAG|A Chain A, Udp-N-Acetylmuramoyl-L-Alanine:d-Glutamate Ligase
pdb|3UAG|A Chain A, Udp-N-Acetylmuramoyl-L-Alanine:d-Glutamate Ligase
pdb|4UAG|A Chain A, Udp-N-Acetylmuramoyl-L-Alanine:d-Glutamate Ligase
pdb|1UAG|A Chain A, Udp-N-Acetylmuramoyl-L-Alanine:d-Glutamate Ligase
Length = 437
Score = 28.5 bits (62), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 32/104 (30%), Positives = 49/104 (47%), Gaps = 15/104 (14%)
Query: 177 SLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLG-SLEDVARAK 235
+L+ +D ++ VLE+ LE + +LNV + H++ L+ A
Sbjct: 143 ALMLLDDECELYVLEL----SSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAX 198
Query: 236 GEIFQESKLGDVCVLNADDPLVANLTVP-RGV--RKVFFGWRRG 276
I++ +K VCV+NADD LT+P RG R V FG G
Sbjct: 199 LRIYENAK---VCVVNADDA----LTMPIRGADERCVSFGVNMG 235
>pdb|2JFF|A Chain A, Crystal Structure Of Murd Ligase In Complex With D-Glu
Containing Sulfonamide Inhibitor
pdb|2JFG|A Chain A, Crystal Structure Of Murd Ligase In Complex With Uma And
Adp
pdb|2JFH|A Chain A, Crystal Structure Of Murd Ligase In Complex With L-Glu
Containing Sulfonamide Inhibitor
pdb|2UUO|A Chain A, Crystal Structure Of Murd Ligase In Complex With D-Glu
Containing Sulfonamide Inhibitor
pdb|2UUP|A Chain A, Crystal Structure Of Murd Ligase In Complex With D-Glu
Containing Sulfonamide Inhibitor
pdb|2VTD|A Chain A, Crystal Structure Of Murd Ligase In Complex With D-Glu
Containing Sulfonamide Inhibitor
pdb|2VTE|A Chain A, Crystal Structure Of Murd Ligase In Complex With D-Glu
Containing Sulfonamide Inhibitor
pdb|2Y68|A Chain A, Structure-Based Design Of A New Series Of D-Glutamic Acid-
Based Inhibitors Of Bacterial Murd Ligase
pdb|2Y66|A Chain A, New 5-Benzylidenethiazolidine-4-One Inhibitors Of
Bacterial Murd Ligase: Design, Synthesis, Crystal
Structures, And Biological Evaluation
pdb|2Y67|A Chain A, New 5-Benzylidenethiazolidine-4-One Inhibitors Of
Bacterial Murd Ligase: Design, Synthesis, Crystal
Structures, And Biological Evaluation
pdb|2Y1O|A Chain A, Dual-target Inhibitor Of Murd And Mure Ligases: Design,
Synthesis And Binding Mode Studies
Length = 445
Score = 28.5 bits (62), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 32/104 (30%), Positives = 49/104 (47%), Gaps = 15/104 (14%)
Query: 177 SLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLG-SLEDVARAK 235
+L+ +D ++ VLE+ LE + +LNV + H++ L+ A
Sbjct: 144 ALMLLDDECELYVLEL----SSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAX 199
Query: 236 GEIFQESKLGDVCVLNADDPLVANLTVP-RGV--RKVFFGWRRG 276
I++ +K VCV+NADD LT+P RG R V FG G
Sbjct: 200 LRIYENAK---VCVVNADDA----LTMPIRGADERCVSFGVNMG 236
>pdb|1YPX|A Chain A, Crystal Structure Of The Putative Vitamin-B12 Independent
Methionine Synthase From Listeria Monocytogenes,
Northeast Structural Genomics Target Lmr13
Length = 375
Score = 27.7 bits (60), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 4/71 (5%)
Query: 174 VALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLGSLEDVAR 233
VA +L G +D LE G+ L + RP++++VL + S G LED A
Sbjct: 256 VAETLFG-KLNIDGFFLEYDNERSGDFAPLKYVTRPDLKIVLGLITS---KTGELEDEAA 311
Query: 234 AKGEIFQESKL 244
K I + S++
Sbjct: 312 IKARIEEASEI 322
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
0.321 0.137 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,528,058
Number of Sequences: 62578
Number of extensions: 338041
Number of successful extensions: 714
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 708
Number of HSP's gapped (non-prelim): 22
length of query: 303
length of database: 14,973,337
effective HSP length: 98
effective length of query: 205
effective length of database: 8,840,693
effective search space: 1812342065
effective search space used: 1812342065
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: 51 (24.3 bits)