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= 015950
(397 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 = 94.7 bits (234), Expect = 7e-20, Method: Compositional matrix adjust.
Identities = 88/334 (26%), Positives = 138/334 (41%), Gaps = 11/334 (3%)
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 EDVARAKGEIFQESKLGDVCVLNADDPLVANLTVPRGVRKVFFGWRRGCDVRLVAAQVAN 288
VA+AKGEIF + + NAD+ N G RKV+ + A +
Sbjct: 196 AGVAKAKGEIFSGLPENGIAIXNADNNDWLNWQSVIGSRKVWRFSPNAANSDFTATNIHV 255
Query: 289 GGLGVQVVLEKEREMVKFVIPSPGLHLXXXXXXXXXXXTLFGVSLAQVGISLSNFSPVQM 348
G + L+ V ++P PG H G +L + L+N V
Sbjct: 256 TSHGTEFTLQTPTGSVDVLLPLPGRHNIANALAAAALSXSVGATLDAIKAGLANLKAVPG 315
Query: 349 RSELLVSRSGIKIVNDAYNANPISTRAAIDLLKD 382
R + +++D+YNAN S AA+ +L +
Sbjct: 316 RLFPIQLAENQLLLDDSYNANVGSXTAAVQVLAE 349
>pdb|2AM1|A Chain A, Sp Protein Ligand 1
pdb|2AM2|A Chain A, Sp Protein Ligand 2
Length = 454
Score = 69.3 bits (168), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 55/227 (24%), Positives = 105/227 (46%), Gaps = 10/227 (4%)
Query: 161 VFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDS 220
+++ GN+NN +G+ +++ + VLE G G+I L+ +ARP+ +V VG++
Sbjct: 128 TYKTQGNYNNEIGLPYTVLHXPEGTEKLVLEXGQDHLGDIHLLSELARPKTAIVTLVGEA 187
Query: 221 HLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLTVPRGVRKVFFGWRRGCDVR 280
HL ++A+ K +I G + + A DP+V + +P + V FG +G ++
Sbjct: 188 HLAFFKDRSEIAKGKXQIADGXASGSLLLAPA-DPIVEDY-LPIDKKVVRFG--QGAELE 243
Query: 281 LVAAQVANGGLGVQV-VLEKEREMVKFVIPSPGLHLXXXXXXXXXXXTLFGVSLAQVGIS 339
+ L + LE+ ++ P G + GVS Q+ ++
Sbjct: 244 ITDLVERKDSLTFKANFLEQALDL-----PVTGKYNATNAXIASYVALQEGVSEEQIRLA 298
Query: 340 LSNFSPVQMRSELLVSRSGIKIVNDAYNANPISTRAAIDLLKDIACN 386
+ + R+E + +G I++D YNANP + + ++ I N
Sbjct: 299 FQHLELTRNRTEWKKAANGADILSDVYNANPTAXKLILETFSAIPAN 345
>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 = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 46/170 (27%), Positives = 67/170 (39%), Gaps = 8/170 (4%)
Query: 208 RPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLTVPRGVR 267
RP I V+ N+ +HL+ GS ED AK I + D VLN + + L
Sbjct: 180 RPHIAVITNLXPTHLDYHGSFEDYVAAKWNIQNQXSSSDFLVLNFNQGISKELAKTTKAT 239
Query: 268 KVFFGWRRGCDVRLVAAQVANGGLGVQVVLEKEREMVKFVIPSPGLHLXXXXXXXXXXXT 327
V F D V + Q+ + E I PG H
Sbjct: 240 IVPFSTTEKVDGAYVQDK--------QLFYKGENIXSVDDIGVPGSHNVENALATIAVAK 291
Query: 328 LFGVSLAQVGISLSNFSPVQMRSELLVSRSGIKIVNDAYNANPISTRAAI 377
L G+S + +LSNF V+ R + L GI ND+ + N ++T+ A+
Sbjct: 292 LAGISNQVIRETLSNFGGVKHRLQSLGKVHGISFYNDSKSTNILATQKAL 341
>pdb|2F00|A Chain A, Escherichia Coli Murc
pdb|2F00|B Chain B, Escherichia Coli Murc
Length = 491
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 39/180 (21%), Positives = 70/180 (38%), Gaps = 12/180 (6%)
Query: 208 RPEIRVVLNVGDSHLESL-GSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLTVPR-G 265
+P + +V N+ H ++ G E++ + V DDP++ L +PR G
Sbjct: 186 QPXVAIVTNIEADHXDTYQGDFENLKQTFINFLHNLPFYGRAVXCVDDPVIREL-LPRVG 244
Query: 266 VRKVFFGWRRGCDVRLVAAQVANGGLGVQVVLEKEREMVKFVIPSPGLHLXXXXXXXXXX 325
+ +G+ DVR+ Q G G +L +++E + + +PG H
Sbjct: 245 RQTTTYGFSEDADVRVEDYQQI-GPQGHFTLLRQDKEPXRVTLNAPGRHNALNAAAAVAV 303
Query: 326 XTLFGVSLAQVGISLSNFSPVQMRSELLVS--------RSGIKIVNDAYNANPISTRAAI 377
T G+ + +L +F R + L +SG + D Y +P A I
Sbjct: 304 ATEEGIDDEAILRALESFQGTGRRFDFLGEFPLEPVNGKSGTAXLVDDYGHHPTEVDATI 363
>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 = 36.2 bits (82), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 57/208 (27%), Positives = 94/208 (45%), Gaps = 21/208 (10%)
Query: 177 SLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLG-SLEDVARAK 235
+L+ +D ++ VLE+ LE + +LNV + H++ L+ AK
Sbjct: 143 ALMLLDDECELYVLEL----SSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAK 198
Query: 236 GEIFQESKLGDVCVLNADDPLVANLTVP-RGV--RKVFFGWRRGCDVRLVAAQVANGGLG 292
I++ +K VCV+NADD L T+P RG R V FG G D L Q G
Sbjct: 199 LRIYENAK---VCVVNADDAL----TMPIRGADERCVSFGVNMG-DYHLNHQQ---GETW 247
Query: 293 VQVVLEKEREMVKFVIPSPGLHLXXXXXXXXXXXTLFGVSLAQVGISLSNFSPVQMRSEL 352
++V EK + + + G H G+ A +L+ F+ + R E+
Sbjct: 248 LRVKGEKVLNVKEMKLS--GQHNYTNALAALALADAAGLPRASSLKALTTFTGLPHRFEV 305
Query: 353 LVSRSGIKIVNDAYNANPISTRAAIDLL 380
++ +G++ +ND+ N ST AA++ L
Sbjct: 306 VLEHNGVRWINDSKATNVGSTEAALNGL 333
>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 = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 56/209 (26%), Positives = 93/209 (44%), Gaps = 21/209 (10%)
Query: 177 SLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLG-SLEDVARAK 235
+L+ +D ++ VLE+ LE + +LNV + H++ L+ A
Sbjct: 143 ALMLLDDECELYVLEL----SSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAX 198
Query: 236 GEIFQESKLGDVCVLNADDPLVANLTVP-RGV--RKVFFGWRRGCDVRLVAAQVANGGLG 292
I++ +K VCV+NADD L T+P RG R V FG G D L Q G
Sbjct: 199 LRIYENAK---VCVVNADDAL----TMPIRGADERCVSFGVNMG-DYHLNHQQ---GETW 247
Query: 293 VQVVLEKEREMVKFVIPSPGLHLXXXXXXXXXXXTLFGVSLAQVGISLSNFSPVQMRSEL 352
++V EK + + + G H G+ A +L+ F+ + R E+
Sbjct: 248 LRVKGEKVLNVKEMKLS--GQHNYTNALAALALADAAGLPRASSLKALTTFTGLPHRFEV 305
Query: 353 LVSRSGIKIVNDAYNANPISTRAAIDLLK 381
++ +G++ +ND+ N ST AA++ L
Sbjct: 306 VLEHNGVRWINDSKATNVGSTEAALNGLH 334
>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 = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 56/209 (26%), Positives = 93/209 (44%), Gaps = 21/209 (10%)
Query: 177 SLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLG-SLEDVARAK 235
+L+ +D ++ VLE+ LE + +LNV + H++ L+ A
Sbjct: 143 ALMLLDDECELYVLEL----SSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAX 198
Query: 236 GEIFQESKLGDVCVLNADDPLVANLTVP-RGV--RKVFFGWRRGCDVRLVAAQVANGGLG 292
I++ +K VCV+NADD L T+P RG R V FG G D L Q G
Sbjct: 199 LRIYENAK---VCVVNADDAL----TMPIRGADERCVSFGVNMG-DYHLNHQQ---GETW 247
Query: 293 VQVVLEKEREMVKFVIPSPGLHLXXXXXXXXXXXTLFGVSLAQVGISLSNFSPVQMRSEL 352
++V EK + + + G H G+ A +L+ F+ + R E+
Sbjct: 248 LRVKGEKVLNVKEMKLS--GQHNYTNALAALALADAAGLPRASSLKALTTFTGLPHRFEV 305
Query: 353 LVSRSGIKIVNDAYNANPISTRAAIDLLK 381
++ +G++ +ND+ N ST AA++ L
Sbjct: 306 VLEHNGVRWINDSKATNVGSTEAALNGLH 334
>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 = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 56/209 (26%), Positives = 93/209 (44%), Gaps = 21/209 (10%)
Query: 177 SLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLG-SLEDVARAK 235
+L+ +D ++ VLE+ LE + +LNV + H++ L+ A
Sbjct: 144 ALMLLDDECELYVLEL----SSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAX 199
Query: 236 GEIFQESKLGDVCVLNADDPLVANLTVP-RGV--RKVFFGWRRGCDVRLVAAQVANGGLG 292
I++ +K VCV+NADD L T+P RG R V FG G D L Q G
Sbjct: 200 LRIYENAK---VCVVNADDAL----TMPIRGADERCVSFGVNMG-DYHLNHQQ---GETW 248
Query: 293 VQVVLEKEREMVKFVIPSPGLHLXXXXXXXXXXXTLFGVSLAQVGISLSNFSPVQMRSEL 352
++V EK + + + G H G+ A +L+ F+ + R E+
Sbjct: 249 LRVKGEKVLNVKEMKLS--GQHNYTNALAALALADAAGLPRASSLKALTTFTGLPHRFEV 306
Query: 353 LVSRSGIKIVNDAYNANPISTRAAIDLLK 381
++ +G++ +ND+ N ST AA++ L
Sbjct: 307 VLEHNGVRWINDSKATNVGSTEAALNGLH 335
>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 = 1.7, 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 = 1.8, 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|2D1Y|A Chain A, Crystal Structure Of Tt0321 From Thermus Thermophilus Hb8
pdb|2D1Y|B Chain B, Crystal Structure Of Tt0321 From Thermus Thermophilus Hb8
pdb|2D1Y|C Chain C, Crystal Structure Of Tt0321 From Thermus Thermophilus Hb8
pdb|2D1Y|D Chain D, Crystal Structure Of Tt0321 From Thermus Thermophilus Hb8
Length = 256
Score = 29.6 bits (65), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 17/33 (51%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 277 CDVRLVAAQVAN--GGLGVQVVLEKEREMVKFV 307
CD+R +VA GG QV LE ERE V+FV
Sbjct: 36 CDLRPEGKEVAEAIGGAFFQVDLEDERERVRFV 68
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 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,821,079
Number of Sequences: 62578
Number of extensions: 415182
Number of successful extensions: 849
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 832
Number of HSP's gapped (non-prelim): 23
length of query: 397
length of database: 14,973,337
effective HSP length: 101
effective length of query: 296
effective length of database: 8,652,959
effective search space: 2561275864
effective search space used: 2561275864
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)