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= 021862
(306 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 86.7 bits (213), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 75/278 (26%), Positives = 140/278 (50%), Gaps = 25/278 (8%)
Query: 28 VMSELDFAAQVIPRSIKILAVTGTNGKSTVVTFVGQMLNHLGIEAFVGGNLGNPLSEAAF 87
V++E++ A V +++ +TG+NGK+T T + ++LN G + GN+G P SE
Sbjct: 99 VLTEVELAYLV--SESQLIGITGSNGKTTTTTXIAEVLNAGGQRGLLAGNIGFPASE--- 153
Query: 88 HCIALPSSKPKFQVAVVEVSSYQMEIPNKYFCPTVSVVLNLTPDHLERHKTMKNYALTKC 147
+ + K V E+SS+Q+ K F P ++V+ NL P HL+ H + ++Y K
Sbjct: 154 -VVQAANDKDTL---VXELSSFQL-XGVKEFRPHIAVITNLXPTHLDYHGSFEDYVAAKW 208
Query: 148 HLFSHMVNTKLGLLPFGNQHLNEAIKGHRFNLAWIGAFPGV-KID---TEAKTASFEVPA 203
++ + ++ +L F NQ +++ + + A I F K+D + K ++
Sbjct: 209 NIQNQXSSSDFLVLNF-NQGISKELA--KTTKATIVPFSTTEKVDGAYVQDKQLFYKGEN 265
Query: 204 VGVVSQLQLHNMKVMGRHNYHNAAVAALSVLGLDIGVDVEALNSTIEILRTPPHRMQIVH 263
+ V ++ V G HN N A+A ++V L G+ + + T+ HR+Q +
Sbjct: 266 IXSVD-----DIGVPGSHNVEN-ALATIAVAKL-AGISNQVIRETLSNFGGVKHRLQSLG 318
Query: 264 RDIQGVTWVDDSKATNLEATCTGLMDLKGHKCVILLGG 301
+ + G+++ +DSK+TN+ AT L K +++ GG
Sbjct: 319 K-VHGISFYNDSKSTNILATQKALSGFDNTKVILIAGG 355
>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 = 84.0 bits (206), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 83/284 (29%), Positives = 129/284 (45%), Gaps = 65/284 (22%)
Query: 45 ILAVTGTNGKSTVVTFVGQMLNHLGIEAFVGGNLGNPLSEAAFHCIALPSSKPKFQVAVV 104
I+A+TG+NGKSTV T VG+M G+ VGGN+G P AL + ++ V+
Sbjct: 106 IVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLP---------ALMLLDDECELYVL 156
Query: 105 EVSSYQMEIPNKYFCPTVSVVLNLTPDHLERHK-TMKNYALTKCHLFSH----MVNTKLG 159
E+SS+Q+E + + +LN+T DH++R+ ++ Y K ++ + +VN
Sbjct: 157 ELSSFQLETTSS-LQAVAATILNVTEDHMDRYPFGLQQYRAAKLRIYENAKVCVVNADDA 215
Query: 160 L-LP--------------FGNQHLNEAIKGHRFNLAWIGAFPGVKIDTEAKTASFEVPAV 204
L +P G+ HLN H+ W+ G K+
Sbjct: 216 LTMPIRGADERCVSFGVNMGDYHLN-----HQQGETWL-RVKGEKV-------------- 255
Query: 205 GVVSQLQLHNMKVMGRHNYHNAAVAALSVLGLDIGVDVEALNSTIEILRT---PPHRMQI 261
L + MK+ G+HNY NA A S+++ L T PHR ++
Sbjct: 256 -----LNVKEMKLSGQHNYTNALAALALAD-----AAGLPRASSLKALTTFTGLPHRFEV 305
Query: 262 VHRDIQGVTWVDDSKATNLEATCTGLMDLKGHKCV-ILLGGQAK 304
V + GV W++DSKATN+ +T L L + +LLGG K
Sbjct: 306 V-LEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGK 348
>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 = 81.6 bits (200), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 82/284 (28%), Positives = 128/284 (45%), Gaps = 65/284 (22%)
Query: 45 ILAVTGTNGKSTVVTFVGQMLNHLGIEAFVGGNLGNPLSEAAFHCIALPSSKPKFQVAVV 104
I+A+TG+NGKSTV T VG+M G+ VGGN+G P AL + ++ V+
Sbjct: 107 IVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLP---------ALMLLDDECELYVL 157
Query: 105 EVSSYQMEIPNKYFCPTVSVVLNLTPDHLERHK-TMKNYALTKCHLFSH----MVNTKLG 159
E+SS+Q+E + + +LN+T DH++R+ ++ Y ++ + +VN
Sbjct: 158 ELSSFQLETTSS-LQAVAATILNVTEDHMDRYPFGLQQYRAAXLRIYENAKVCVVNADDA 216
Query: 160 L-LP--------------FGNQHLNEAIKGHRFNLAWIGAFPGVKIDTEAKTASFEVPAV 204
L +P G+ HLN H+ W+ G K+
Sbjct: 217 LTMPIRGADERCVSFGVNMGDYHLN-----HQQGETWL-RVKGEKV-------------- 256
Query: 205 GVVSQLQLHNMKVMGRHNYHNAAVAALSVLGLDIGVDVEALNSTIEILRT---PPHRMQI 261
L + MK+ G+HNY NA A S+++ L T PHR ++
Sbjct: 257 -----LNVKEMKLSGQHNYTNALAALALAD-----AAGLPRASSLKALTTFTGLPHRFEV 306
Query: 262 VHRDIQGVTWVDDSKATNLEATCTGLMDLKGHKCV-ILLGGQAK 304
V + GV W++DSKATN+ +T L L + +LLGG K
Sbjct: 307 V-LEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGK 349
>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 = 81.6 bits (200), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 82/284 (28%), Positives = 128/284 (45%), Gaps = 65/284 (22%)
Query: 45 ILAVTGTNGKSTVVTFVGQMLNHLGIEAFVGGNLGNPLSEAAFHCIALPSSKPKFQVAVV 104
I+A+TG+NGKSTV T VG+M G+ VGGN+G P AL + ++ V+
Sbjct: 106 IVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLP---------ALMLLDDECELYVL 156
Query: 105 EVSSYQMEIPNKYFCPTVSVVLNLTPDHLERHK-TMKNYALTKCHLFSH----MVNTKLG 159
E+SS+Q+E + + +LN+T DH++R+ ++ Y ++ + +VN
Sbjct: 157 ELSSFQLETTSS-LQAVAATILNVTEDHMDRYPFGLQQYRAAXLRIYENAKVCVVNADDA 215
Query: 160 L-LP--------------FGNQHLNEAIKGHRFNLAWIGAFPGVKIDTEAKTASFEVPAV 204
L +P G+ HLN H+ W+ G K+
Sbjct: 216 LTMPIRGADERCVSFGVNMGDYHLN-----HQQGETWL-RVKGEKV-------------- 255
Query: 205 GVVSQLQLHNMKVMGRHNYHNAAVAALSVLGLDIGVDVEALNSTIEILRT---PPHRMQI 261
L + MK+ G+HNY NA A S+++ L T PHR ++
Sbjct: 256 -----LNVKEMKLSGQHNYTNALAALALAD-----AAGLPRASSLKALTTFTGLPHRFEV 305
Query: 262 VHRDIQGVTWVDDSKATNLEATCTGLMDLKGHKCV-ILLGGQAK 304
V + GV W++DSKATN+ +T L L + +LLGG K
Sbjct: 306 V-LEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGK 348
>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 = 81.6 bits (200), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 82/284 (28%), Positives = 128/284 (45%), Gaps = 65/284 (22%)
Query: 45 ILAVTGTNGKSTVVTFVGQMLNHLGIEAFVGGNLGNPLSEAAFHCIALPSSKPKFQVAVV 104
I+A+TG+NGKSTV T VG+M G+ VGGN+G P AL + ++ V+
Sbjct: 106 IVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLP---------ALMLLDDECELYVL 156
Query: 105 EVSSYQMEIPNKYFCPTVSVVLNLTPDHLERHK-TMKNYALTKCHLFSH----MVNTKLG 159
E+SS+Q+E + + +LN+T DH++R+ ++ Y ++ + +VN
Sbjct: 157 ELSSFQLETTSS-LQAVAATILNVTEDHMDRYPFGLQQYRAAXLRIYENAKVCVVNADDA 215
Query: 160 L-LP--------------FGNQHLNEAIKGHRFNLAWIGAFPGVKIDTEAKTASFEVPAV 204
L +P G+ HLN H+ W+ G K+
Sbjct: 216 LTMPIRGADERCVSFGVNMGDYHLN-----HQQGETWL-RVKGEKV-------------- 255
Query: 205 GVVSQLQLHNMKVMGRHNYHNAAVAALSVLGLDIGVDVEALNSTIEILRT---PPHRMQI 261
L + MK+ G+HNY NA A S+++ L T PHR ++
Sbjct: 256 -----LNVKEMKLSGQHNYTNALAALALAD-----AAGLPRASSLKALTTFTGLPHRFEV 305
Query: 262 VHRDIQGVTWVDDSKATNLEATCTGLMDLKGHKCV-ILLGGQAK 304
V + GV W++DSKATN+ +T L L + +LLGG K
Sbjct: 306 V-LEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGK 348
>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 = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 67/289 (23%), Positives = 125/289 (43%), Gaps = 44/289 (15%)
Query: 44 KILAVTGTNGKSTVVTFVGQMLNHLGIEAFVGGNLGNPLSEAAFHCIALPSS----KPKF 99
+++A+TG++GK++V +L+ G + GNL N I +P + P++
Sbjct: 101 RVVALTGSSGKTSVKEXTAAILSQCGNTLYTAGNLNND--------IGVPXTLLRLTPEY 152
Query: 100 QVAVVEV-SSYQMEIP--NKYFCPTVSVVLNLTPDHLERHKTMKNYALTKCHLFSHMVNT 156
AV+E+ +++Q EI P ++V NL HLE ++ A K +FS +
Sbjct: 153 DYAVIELGANHQGEIAWTVSLTRPEAALVNNLAAAHLEGFGSLAGVAKAKGEIFSGLPEN 212
Query: 157 KLGLLPFGNQH-LN-EAIKGHRFNLAWIGAFPGVKIDTEAKTASFEVPAVGVVSQLQLHN 214
+ + N LN +++ G R W F +++ + V + G LQ
Sbjct: 213 GIAIXNADNNDWLNWQSVIGSR--KVW--RFSPNAANSDFTATNIHVTSHGTEFTLQTPT 268
Query: 215 MKVM------GRHNYHNAAVAALSVLGLDIGVDVEALNSTIEILRTPPHRM---QIVHRD 265
V GRHN NA AA +G ++A+ + + L+ P R+ Q+
Sbjct: 269 GSVDVLLPLPGRHNIANALAAAALS--XSVGATLDAIKAGLANLKAVPGRLFPIQLAENQ 326
Query: 266 IQGVTWVDDSKATNLEATCTG---LMDLKGHKCVIL-----LGGQAKEC 306
+ +DDS N+ + L + G++ +++ LG +++ C
Sbjct: 327 L----LLDDSYNANVGSXTAAVQVLAEXPGYRVLVVGDXAELGAESEAC 371
>pdb|3EAG|A Chain A, The Crystal Structure Of
Udp-n-acetylmuramate:l-alanyl-gamma-d-
Glutamyl-meso-diaminopimelate Ligase (mpl) From
Neisseria Meningitides
pdb|3EAG|B Chain B, The Crystal Structure Of
Udp-n-acetylmuramate:l-alanyl-gamma-d-
Glutamyl-meso-diaminopimelate Ligase (mpl) From
Neisseria Meningitides
Length = 326
Score = 36.2 bits (82), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 54/221 (24%), Positives = 90/221 (40%), Gaps = 16/221 (7%)
Query: 45 ILAVTGTNGKSTVVTFVGQMLNHLGIE-AFVGGNLGNPLSEAAFHCIALPSSKPKFQVA- 102
+L V GT+GK+T + + +L + G+ F+ G + +A P P Q
Sbjct: 110 VLGVAGTHGKTTTASXLAWVLEYAGLAPGFLIGGVPENFGVSA-RLPQTPRQDPNSQSPF 168
Query: 103 -VVEVSSYQMEIPNK-----YFCPTVSVVLNLTPDHLERHKTMKNYALTKCHLFSHMVNT 156
V+E Y +K ++ P +V+ NL DH + + T+ H V +
Sbjct: 169 FVIEADEYDTAFFDKRSKFVHYRPRTAVLNNLEFDHADIFADLGAIQ-TQFHYLVRTVPS 227
Query: 157 KLGLLPFGNQH-LNEAI-KGHRFNLAWIGAFPGVKIDTEAKTASFEVPAVGVVSQLQLHN 214
+ ++ G Q L + + KG + G G + SF+V G +
Sbjct: 228 EGLIVCNGRQQSLQDTLDKGCWTPVEKFGTEHGWQAGEANADGSFDVLLDGKTAGRV--K 285
Query: 215 MKVMGRHNYHN--AAVAALSVLGLDIGVDVEALNSTIEILR 253
+ GRHN N A +AA +G+DI EAL + + R
Sbjct: 286 WDLXGRHNRXNALAVIAAARHVGVDIQTACEALGAFKNVKR 326
>pdb|3HN7|A Chain A, Crystal Structure Of A Murein Peptide Ligase Mpl
(Psyc_0032) From Psychrobacter Arcticus 273-4 At 1.65 A
Resolution
Length = 524
Score = 34.7 bits (78), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 32/131 (24%), Positives = 59/131 (45%), Gaps = 18/131 (13%)
Query: 22 LQSGKRVMSELDFAAQVIPRSIKILAVTGTNGKSTVVTFVGQMLNHLGIEA--FVGG--- 76
L +G R S F ++ + +S ++AV GT+GK+T T + +L++ GI+A +GG
Sbjct: 101 LDTGLRYTSGPQFLSEQVLQSRHVIAVAGTHGKTTTTTXLAWILHYAGIDAGFLIGGVPL 160
Query: 77 ------NLGNPLSEAAFHCIALPSSKPKFQVA--VVEVSSYQMEIPNK-----YFCPTVS 123
NL + +++ S V+E Y +K ++ P +
Sbjct: 161 VNTTDTNLQQVFAHSSYLGTEKDDSDNSVNTGYFVIEADEYDSAFFDKRSKFVHYRPRTA 220
Query: 124 VVLNLTPDHLE 134
++ NL DH +
Sbjct: 221 ILNNLEFDHAD 231
>pdb|1GQQ|A Chain A, Murc - Crystal Structure Of The Apo-Enzyme From
Haemophilus Influenzae
pdb|1GQQ|B Chain B, Murc - Crystal Structure Of The Apo-Enzyme From
Haemophilus Influenzae
pdb|1GQY|A Chain A, Murc- Crystal Structure Of The Enzyme From Haemophilus
Influenzae Complexed With Amppcp
pdb|1GQY|B Chain B, Murc- Crystal Structure Of The Enzyme From Haemophilus
Influenzae Complexed With Amppcp
Length = 475
Score = 32.0 bits (71), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 43/93 (46%), Gaps = 11/93 (11%)
Query: 46 LAVTGTNGKSTVVTFVGQMLNHLGIE-AFVGGNLGNPLSEAAFHCIALPSSKPKFQVAVV 104
+AV GT+GK+T + + ++ FV G L + A H A ++ +A
Sbjct: 121 IAVAGTHGKTTTTAMISMIYTQAKLDPTFVNGGLVKSAGKNA-HLGA-----SRYLIAEA 174
Query: 105 EVSSYQMEIPNKYFCPTVSVVLNLTPDHLERHK 137
+ S + P VSVV N+ PDH++ ++
Sbjct: 175 DESDASF----LHLQPMVSVVTNMEPDHMDTYE 203
>pdb|4HV4|A Chain A, 2.25 Angstrom Resolution Crystal Structure Of
Udp-N-Acetylmuramate--L- Alanine Ligase (Murc) From
Yersinia Pestis Co92 In Complex With Amp
pdb|4HV4|B Chain B, 2.25 Angstrom Resolution Crystal Structure Of
Udp-N-Acetylmuramate--L- Alanine Ligase (Murc) From
Yersinia Pestis Co92 In Complex With Amp
Length = 494
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 45/93 (48%), Gaps = 11/93 (11%)
Query: 46 LAVTGTNGKSTVVTFVGQMLNHLGIE-AFVGGNLGNPLSEAAFHCIALPSSKPKFQVAVV 104
+AV GT+GK+T + + G++ FV G L + A H L SS ++ +A
Sbjct: 125 IAVAGTHGKTTTTAMLSSIYAEAGLDPTFVNGGL---VKAAGTHA-RLGSS--RYLIAEA 178
Query: 105 EVSSYQMEIPNKYFCPTVSVVLNLTPDHLERHK 137
+ S + P V++V N+ DH++ ++
Sbjct: 179 DESDASF----LHLQPMVAIVTNIEADHMDTYQ 207
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
0.322 0.136 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,828,480
Number of Sequences: 62578
Number of extensions: 339317
Number of successful extensions: 871
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 842
Number of HSP's gapped (non-prelim): 20
length of query: 306
length of database: 14,973,337
effective HSP length: 98
effective length of query: 208
effective length of database: 8,840,693
effective search space: 1838864144
effective search space used: 1838864144
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: 51 (24.3 bits)