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= 009293
(538 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 191 bits (485), Expect = 8e-49, Method: Compositional matrix adjust.
Identities = 138/465 (29%), Positives = 224/465 (48%), Gaps = 68/465 (14%)
Query: 68 IVDFKNRKGWIHFVGIXXXXXXXXXXXXXXQGFEVSGSDLVWSSYMEGLLEAGANLHIGH 127
I+ R IHF+GI +G+++SGSD+ + L +AGA ++IGH
Sbjct: 11 IIPEMRRVQQIHFIGIGGAGMSGIAEILLNEGYQISGSDIADGVVTQRLAQAGAKIYIGH 70
Query: 128 SVSNIQGNDGSRFPNAVVASSAIPQDNVEILHAKSVGVPIYKRDYWLAKLTEKYNLIAVS 187
+ +I+G + VV SSAI DN E++ +K +P+ +R LA++ + IAV+
Sbjct: 71 AEEHIEG------ASVVVVSSAIKDDNPELVTSKQKRIPVIQRAQMLAEIMRFRHGIAVA 124
Query: 188 GSHGKSTTASMLAYVLKAMGDDLTAIVGAHVPQFPDGSIFYGGGKN--------FVLEAD 239
G+HGK+TT +M++ + D P F +G + GKN + EAD
Sbjct: 125 GTHGKTTTTAMISMIYTQAKLD---------PTFVNGGLVKSAGKNAHLGASRYLIAEAD 175
Query: 240 EYDGCFLGLSPSVAVVTNLDWEHVDIFE-DEDAVKSIFRRFLKQIRVGGHLVICGDSQCA 298
E D FL L P V+VVTN++ +H+D +E D + +K+ + +FL + G V+C D
Sbjct: 176 ESDASFLHLQPMVSVVTNMEPDHMDTYEGDFEKMKATYVKFLHNLPFYGLAVMCADDPVL 235
Query: 299 RSLLDQIKQDTGLKYSGGVVSNQSSDLWGQGHDYKIITYGFSSFNDWYAESVCPNVQGGS 358
L+ ++ + ++ITYGFS D+ E G
Sbjct: 236 MELVPKVGR-------------------------QVITYGFSEQADYRIEDYEQTGFQGH 270
Query: 359 DYILCERGRPLAQISLQIPGVHNVLNSLAVIATVLTLIGDKRQSHESIACLKLPLSKFMG 418
++C + + L +PG HN LN+ A +A K + + A L+ L+ F G
Sbjct: 271 YTVICPNNERI-NVLLNVPGKHNALNATAALAVA------KEEGIANEAILE-ALADFQG 322
Query: 419 VSRRFDLIGTIY----GCHIYDDFAHHPTEVRAVLQAARQRFPNKALIAVFQPHTYSRLV 474
RRFD +G + DD+ HHPTEV ++AAR+ + +K ++ +FQPH YSR
Sbjct: 323 AGRRFDQLGEFIRPNGKVRLVDDYGHHPTEVGVTIKAAREGWGDKRIVMIFQPHRYSRTR 382
Query: 475 VLKDDFANALSEADQVVVSAVLVFWLIIFAVSSFWLIMAINSVIC 519
L DDF LS+ D +++ L ++A ++ A + +C
Sbjct: 383 DLFDDFVQVLSQVDALIM-------LDVYAAGEAPIVGADSKSLC 420
>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 = 190 bits (483), Expect = 2e-48, Method: Compositional matrix adjust.
Identities = 147/463 (31%), Positives = 217/463 (46%), Gaps = 57/463 (12%)
Query: 67 CIVDFKNRKGWIHFVGIXXXXXXXXXXXXXXQGFEVSGSDLVWSSYMEGLLEAGANLHIG 126
IV R IHFVGI +G+++SGSDL +S + L GA ++
Sbjct: 14 TIVPEMRRVRHIHFVGIGGAGMGGIAEVLANEGYQISGSDLAPNSVTQHLTALGAQIYFH 73
Query: 127 HSVSNIQGNDGSRFPNAVVASSAIPQDNVEILHAKSVGVPIYKRDYWLAKLTEKYNLIAV 186
H N+ D S VV S+AI DN EI+ A+ +P+ +R LA+L + IAV
Sbjct: 74 HRPENVL--DAS----VVVVSTAISADNPEIVAAREARIPVIRRAEMLAELMRYRHGIAV 127
Query: 187 SGSHGKSTTASMLAYVLKAMGDDLTAIVGAHVPQFPDGSIFYGGGKNFVLEADEYDGCFL 246
+G+HGK+TT +ML+ + G D T + G V + G + + EADE D FL
Sbjct: 128 AGTHGKTTTTAMLSSIYAEAGLDPTFVNGGLV-KAAGTHARLGSSRYLIAEADESDASFL 186
Query: 247 GLSPSVAVVTNLDWEHVDIFE-DEDAVKSIFRRFLKQIRVGGHLVICGDSQCARSLLDQI 305
L P VA+VTN++ +H+D ++ D + +K F FL + G V+C D R LL ++
Sbjct: 187 HLQPMVAIVTNIEADHMDTYQGDFENLKQTFINFLHNLPFYGRAVMCIDDPVVRELLPRV 246
Query: 306 KQDTGLKYSGGVVSNQSSDLWGQGHDYKIITYGFSSFNDWYAESVCPNVQGGSDYILCER 365
+ I TYGFS D S G + L +
Sbjct: 247 GR-------------------------HITTYGFSDDADVQIASYRQEGPQGH-FTLRRQ 280
Query: 366 GRPLAQISLQIPGVHNVLNSLAVIATVLTLIGDKRQSHESIACLKLPLSKFMGVSRRFDL 425
+PL +++L PG HN LN+ A +A + E L+ L F G RRFD
Sbjct: 281 DKPLIEVTLNAPGRHNALNAAAAVAVA------TEEGIEDEDILRA-LVGFQGTGRRFDF 333
Query: 426 IGTIY---------GCHIYDDFAHHPTEVRAVLQAARQRFPNKALIAVFQPHTYSRLVVL 476
+G + DD+ HHPTEV A ++AAR +P+K ++ +FQPH Y+R L
Sbjct: 334 LGNFPLAPVNGKEGSAMLVDDYGHHPTEVDATIKAARAGWPDKRIVMLFQPHRYTRTRDL 393
Query: 477 KDDFANALSEADQVVVSAVLVFWLIIFAVSSFWLIMAINSVIC 519
DDFAN LS+ D ++ L ++A + A + +C
Sbjct: 394 YDDFANVLSQVD-------VLLMLDVYAAGEPPIPGADSRALC 429
>pdb|1P31|A Chain A, Crystal Structure Of Udp-N-Acetylmuramic Acid:l-Alanine
Ligase (Murc) From Haemophilus Influenzae
pdb|1P31|B Chain B, Crystal Structure Of Udp-N-Acetylmuramic Acid:l-Alanine
Ligase (Murc) From Haemophilus Influenzae
pdb|1P3D|A Chain A, Crystal Structure Of Udp-N-Acetylmuramic Acid:l-Alanine
Ligase (Murc) In Complex With Uma And Anp.
pdb|1P3D|B Chain B, Crystal Structure Of Udp-N-Acetylmuramic Acid:l-Alanine
Ligase (Murc) In Complex With Uma And Anp
Length = 475
Score = 172 bits (436), Expect = 4e-43, Method: Compositional matrix adjust.
Identities = 138/465 (29%), Positives = 219/465 (47%), Gaps = 68/465 (14%)
Query: 68 IVDFKNRKGWIHFVGIXXXXXXXXXXXXXXQGFEVSGSDLVWSSYMEGLLEAGANLHIGH 127
I+ R IHF+GI +G+++SGSD+ + L +AGA ++IGH
Sbjct: 11 IIPEXRRVQQIHFIGIGGAGXSGIAEILLNEGYQISGSDIADGVVTQRLAQAGAKIYIGH 70
Query: 128 SVSNIQGNDGSRFPNAVVASSAIPQDNVEILHAKSVGVPIYKRDYWLAKLTEKYNLIAVS 187
+ +I+G + VV SSAI DN E++ +K +P+ +R LA++ + IAV+
Sbjct: 71 AEEHIEG------ASVVVVSSAIKDDNPELVTSKQKRIPVIQRAQXLAEIXRFRHGIAVA 124
Query: 188 GSHGKSTTASMLAYVLKAMGDDLTAIVGAHVPQFPDGSIFYGGGKN--------FVLEAD 239
G+HGK+TT + ++ + D P F +G + GKN + EAD
Sbjct: 125 GTHGKTTTTAXISXIYTQAKLD---------PTFVNGGLVKSAGKNAHLGASRYLIAEAD 175
Query: 240 EYDGCFLGLSPSVAVVTNLDWEHVDIFE-DEDAVKSIFRRFLKQIRVGGHLVICGDSQCA 298
E D FL L P V+VVTN + +H D +E D + K+ + +FL + G V C D
Sbjct: 176 ESDASFLHLQPXVSVVTNXEPDHXDTYEGDFEKXKATYVKFLHNLPFYGLAVXCADDPVL 235
Query: 299 RSLLDQIKQDTGLKYSGGVVSNQSSDLWGQGHDYKIITYGFSSFNDWYAESVCPNVQGGS 358
L+ ++ + ++ITYGFS D+ E G
Sbjct: 236 XELVPKVGR-------------------------QVITYGFSEQADYRIEDYEQTGFQGH 270
Query: 359 DYILCERGRPLAQISLQIPGVHNVLNSLAVIATVLTLIGDKRQSHESIACLKLPLSKFMG 418
++C + + L +PG HN LN+ A +A K + + A L+ L+ F G
Sbjct: 271 YTVICPNNERI-NVLLNVPGKHNALNATAALAVA------KEEGIANEAILE-ALADFQG 322
Query: 419 VSRRFDLIGTIY----GCHIYDDFAHHPTEVRAVLQAARQRFPNKALIAVFQPHTYSRLV 474
RRFD +G + DD+ HHPTEV ++AAR+ + +K ++ +FQPH YSR
Sbjct: 323 AGRRFDQLGEFIRPNGKVRLVDDYGHHPTEVGVTIKAAREGWGDKRIVXIFQPHRYSRTR 382
Query: 475 VLKDDFANALSEADQVVVSAVLVFWLIIFAVSSFWLIMAINSVIC 519
L DDF LS+ D ++ L ++A ++ A + +C
Sbjct: 383 DLFDDFVQVLSQVDALIX-------LDVYAAGEAPIVGADSKSLC 420
>pdb|2F00|A Chain A, Escherichia Coli Murc
pdb|2F00|B Chain B, Escherichia Coli Murc
Length = 491
Score = 169 bits (428), Expect = 3e-42, Method: Compositional matrix adjust.
Identities = 138/435 (31%), Positives = 206/435 (47%), Gaps = 50/435 (11%)
Query: 67 CIVDFKNRKGWIHFVGIXXXXXXXXXXXXXXQGFEVSGSDLVWSSYMEGLLEAGANLHIG 126
IV R IHFVGI +G+++SGSDL + + L GA ++
Sbjct: 11 SIVPEXRRVRHIHFVGIGGAGXGGIAEVLANEGYQISGSDLAPNPVTQQLXNLGATIYFN 70
Query: 127 HSVSNIQGNDGSRFPNAVVASSAIPQDNVEILHAKSVGVPIYKRDYWLAKLTEKYNLIAV 186
H N+ R + VV SSAI DN EI+ A +P+ +R LA+L + IA+
Sbjct: 71 HRPENV------RDASVVVVSSAISADNPEIVAAHEARIPVIRRAEXLAELXRFRHGIAI 124
Query: 187 SGSHGKSTTASMLAYVLKAMGDDLTAIVGAHVPQFPDGSIFYGGGKNFVLEADEYDGCFL 246
+G+HGK+TT + ++ + G D T + G V + G G+ + EADE D FL
Sbjct: 125 AGTHGKTTTTAXVSSIYAEAGLDPTFVNGGLV-KAAGVHARLGHGRYLIAEADESDASFL 183
Query: 247 GLSPSVAVVTNLDWEHVDIFE-DEDAVKSIFRRFLKQIRVGGHLVICGDSQCARSLLDQI 305
L P VA+VTN++ +H D ++ D + +K F FL + G V C D R LL ++
Sbjct: 184 HLQPXVAIVTNIEADHXDTYQGDFENLKQTFINFLHNLPFYGRAVXCVDDPVIRELLPRV 243
Query: 306 KQDTGLKYSGGVVSNQSSDLWGQGHDYKIITYGFSSFNDWYAESVCPNVQGGSDYILCER 365
+ T TYGFS D E + + L +
Sbjct: 244 GRQT-------------------------TTYGFSEDADVRVEDYQ-QIGPQGHFTLLRQ 277
Query: 366 GRPLAQISLQIPGVHNVLNSLAVIATVLTLIGDKRQSHESIACLKLPLSKFMGVSRRFDL 425
+ +++L PG HN LN+ A +A + + A L+ L F G RRFD
Sbjct: 278 DKEPXRVTLNAPGRHNALNAAAAVAVA------TEEGIDDEAILRA-LESFQGTGRRFDF 330
Query: 426 IG-----TIYG----CHIYDDFAHHPTEVRAVLQAARQRFPNKALIAVFQPHTYSRLVVL 476
+G + G + DD+ HHPTEV A ++AAR +P+K L+ +FQPH ++R L
Sbjct: 331 LGEFPLEPVNGKSGTAXLVDDYGHHPTEVDATIKAARAGWPDKNLVXLFQPHRFTRTRDL 390
Query: 477 KDDFANALSEADQVV 491
DDFAN L++ D ++
Sbjct: 391 YDDFANVLTQVDTLL 405
>pdb|1J6U|A Chain A, Crystal Structure Of Udp-N-Acetylmuramate-Alanine Ligase
Murc (Tm0231) From Thermotoga Maritima At 2.3 A
Resolution
Length = 469
Score = 127 bits (318), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 129/425 (30%), Positives = 190/425 (44%), Gaps = 63/425 (14%)
Query: 80 FVGIXXXXXXXXXXXXXXQGFEVSGSDLVWSSYMEGLLEAGANLHIGHSVSNIQGNDGSR 139
FVGI G +V GS++ + L + G + + HS N
Sbjct: 17 FVGIGGIGXSAVALHEFSNGNDVYGSNIEETERTAYLRKLGIPIFVPHSADNWYD----- 71
Query: 140 FPNAVVASSAIPQDNVEILHAKSVGVPIYKRDYWLAKL--TEKYNLIAVSGSHGKSTTAS 197
P+ V+ + A+ DN EI+ A+ VPI R ++ EK AV+G+ GK+TT +
Sbjct: 72 -PDLVIKTPAVRDDNPEIVRARXERVPIENRLHYFRDTLKREKKEEFAVTGTDGKTTTTA 130
Query: 198 MLAYVLKAMGDDLTAIVGAHVPQFPDGSIFYGGGKNFVLEADEYDGCFLGLSPSVAVVTN 257
+A+VLK + T +G G+ G G V E DE + F SP+ ++TN
Sbjct: 131 XVAHVLKHLRKSPTVFLGGIXDSLEHGNYEKGNGP-VVYELDESEEFFSEFSPNYLIITN 189
Query: 258 LDWEHVDIFEDEDAVKSIFRRFLKQIRVGGHLVICGDSQCA-RSLLDQIKQDTGLKYSGG 316
G HL G+S RS ++I ++T L
Sbjct: 190 AR--------------------------GDHLENYGNSLTRYRSAFEKISRNTDL----- 218
Query: 317 VVSNQSSDLWGQGHDY----KIITYGFSSFNDWYAESVCPNVQGGSDYILCERGRPLAQI 372
VV+ +L D K TY + AE + G Y+ ++
Sbjct: 219 VVTFAEDELTSHLGDVTFGVKKGTYTLEXRSASRAEQKAXVEKNGKRYL---------EL 269
Query: 373 SLQIPGVHNVLNSLAVIATVLTLIGDKRQSHESIACLKLPLSKFMGVSRRFDLIGTIYGC 432
L++PG HNVLN+LAVIA +L D +A + L +F GV RRF +
Sbjct: 270 KLKVPGFHNVLNALAVIALFDSLGYD-------LAPVLEALEEFRGVHRRFSIAFHDPET 322
Query: 433 HIY--DDFAHHPTEVRAVLQAARQRFPNKALIAVFQPHTYSRLVVLKDDFANALSEADQV 490
+IY DD+AH P E+R +LQ A++ F N+ ++ +FQPH YSRL +FA AL AD+V
Sbjct: 323 NIYVIDDYAHTPDEIRNLLQTAKEVFENEKIVVIFQPHRYSRLEREDGNFAKALQLADEV 382
Query: 491 VVSAV 495
VV+ V
Sbjct: 383 VVTEV 387
>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 = 120 bits (302), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 115/450 (25%), Positives = 206/450 (45%), Gaps = 60/450 (13%)
Query: 78 IHFVGIXXXXXXXXXXXXXXQGFEVSGSDL-VWSSYMEGLLEAGANLHIGHSVSNIQGND 136
IH +GI G V+GSD ++ L +AG + G+ ++++Q
Sbjct: 22 IHILGICGTFXGSLALLARALGHTVTGSDANIYPPXSTQLEQAGVTIEEGYLIAHLQ--- 78
Query: 137 GSRFPNAVVASSAIPQDNVEILHAKSVGVPIYKRDYWLA-KLTEKYNLIAVSGSHGKSTT 195
P+ VV +A + I + G+ +L+ ++ + ++IAV+G+HGK+TT
Sbjct: 79 --PAPDLVVVGNAXKRGXDVIEYXLDTGLRYTSGPQFLSEQVLQSRHVIAVAGTHGKTTT 136
Query: 196 ASMLAYVLKAMGDDLTAIVGA---------HVPQFPDGSIFYGGGKN----------FVL 236
+ LA++L G D ++G ++ Q S + G K+ FV+
Sbjct: 137 TTXLAWILHYAGIDAGFLIGGVPLVNTTDTNLQQVFAHSSYLGTEKDDSDNSVNTGYFVI 196
Query: 237 EADEYDGCFLG-------LSPSVAVVTNLDWEHVDIFEDEDAVKSIFRRFLKQIRVGGHL 289
EADEYD F P A++ NL+++H DIF D DA+++ F ++ I G +
Sbjct: 197 EADEYDSAFFDKRSKFVHYRPRTAILNNLEFDHADIFADLDAIQTQFHHXVRXIPSTGKI 256
Query: 290 V-----ICGDSQCARSLLDQIKQDTGLKYSGGVVSNQSSDLWGQGHDYKIITYGFSSFND 344
+ I + A+ + I + + + + V + S L + + +D
Sbjct: 257 IXPAATISLEDTLAKGVWTPIWRTSVIDSTISSVRREDSPLENSQAE---------NSSD 307
Query: 345 WYAESVCPNVQGGSDYILC--ERGRPLAQISLQIPGVHNVLNSLAVIATVLTLIGDKRQS 402
W AE + + GS + + + A ++ G+HNV N+L IA IG ++
Sbjct: 308 WQAELISAD---GSQFTVSFNDNKEATALVNWSXSGLHNVNNALVAIAAAYN-IGVSVKT 363
Query: 403 HESIACLKLPLSKFMGVSRRFDLIGTIYGCHIYDDFAHHPTEVRAVLQAARQRFPNKALI 462
AC L S F G+ RR +LIG + ++DDFAHHPT + L A+++ ++ L
Sbjct: 364 ----ACAAL--SAFAGIKRRXELIGDVNDILVFDDFAHHPTAITTTLDGAKKKLADRRLW 417
Query: 463 AVFQPHTYS-RLVVLKDDFANALSEADQVV 491
A+ +P + + + + +D A + + AD +
Sbjct: 418 AIIEPRSNTXKXGIHQDSLAQSATLADHTL 447
>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 = 84.3 bits (207), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 88/336 (26%), Positives = 142/336 (42%), Gaps = 65/336 (19%)
Query: 99 GFEVSGSDLVWSSYMEGLLEA-GANLHIGHSVSNIQGNDGSRFPNAVVASSAIPQDNVEI 157
GFEVSG D LEA G +++ G + + F V + + ++
Sbjct: 28 GFEVSGCDAKXYPPXSTQLEALGIDVYEGFDAAQL-----DEFKADVYVIGNVAKRGXDV 82
Query: 158 LHA-KSVGVPIYKRDYWLAK-LTEKYNLIAVSGSHGKSTTASMLAYVLKAMGDDLTAIVG 215
+ A ++G+P WL++ + + ++ V+G+HGK+TTAS LA+VL+ G ++G
Sbjct: 83 VEAILNLGLPYISGPQWLSENVLHHHWVLGVAGTHGKTTTASXLAWVLEYAGLAPGFLIG 142
Query: 216 ---------AHVPQFP-----DGSIFYGGGKNFVLEADEYDGCFLG-------LSPSVAV 254
A +PQ P S F FV+EADEYD F P AV
Sbjct: 143 GVPENFGVSARLPQTPRQDPNSQSPF------FVIEADEYDTAFFDKRSKFVHYRPRTAV 196
Query: 255 VTNLDWEHVDIFEDEDAVKSIFRRFLKQIRVGGHLVICGDSQCARSLLDQIKQDTGLKYS 314
+ NL+++H DIF D A+++ F ++ + G +V G Q + LD+
Sbjct: 197 LNNLEFDHADIFADLGAIQTQFHYLVRTVPSEGLIVCNGRQQSLQDTLDK---------- 246
Query: 315 GGVVSNQSSDLWGQGHDYKIITYGFSSFNDWYAESVCPNVQGGSDYILCERGRPLAQISL 374
W F + + W A N G D +L G+ ++
Sbjct: 247 ---------GCW-------TPVEKFGTEHGWQAGEA--NADGSFDVLL--DGKTAGRVKW 286
Query: 375 QIPGVHNVLNSLAVIATVLTLIGDKRQSHESIACLK 410
+ G HN N+LAVIA + D + + E++ K
Sbjct: 287 DLXGRHNRXNALAVIAAARHVGVDIQTACEALGAFK 322
>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 = 57.8 bits (138), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 85/333 (25%), Positives = 126/333 (37%), Gaps = 70/333 (21%)
Query: 145 VASSAIPQDNVEILHAKSVGVPIYKRDYWLAKLTEKYNLIAVSGSHGKSTTASMLAYVLK 204
+ + IP +N + A +P+ + LA L + LI ++GS+GK+TT + +A VL
Sbjct: 77 IKNPGIPYNNPXVKKALEKQIPVLT-EVELAYLVSESQLIGITGSNGKTTTTTXIAEVLN 135
Query: 205 AMGDD--LTAIVGAHVPQFPDGSIFYGGGKNFVLEADEYDGCFLGLS---PSVAVVTNLD 259
A G L +G FP + L + G+ P +AV+TNL
Sbjct: 136 AGGQRGLLAGNIG-----FPASEVVQAANDKDTLVXELSSFQLXGVKEFRPHIAVITNLX 190
Query: 260 WEHVDI---FEDEDAVKSIFRRFLKQIRVGGHLVICGDSQCARSLLDQIKQ-----DTGL 311
H+D FED A K Q LV+ + ++ L K T
Sbjct: 191 PTHLDYHGSFEDYVAAK---WNIQNQXSSSDFLVLNFNQGISKELAKTTKATIVPFSTTE 247
Query: 312 KYSGGVVSNQSSDLWGQGHDYKIITYGFSSFNDWYAESVCPNVQGGSDYILCERGRPLAQ 371
K G V Q L+ +G + S +D
Sbjct: 248 KVDGAYV--QDKQLFYKGEN-------IXSVDD--------------------------- 271
Query: 372 ISLQIPGVHNVLNSLAVIATVLTLIGDKRQSHESIACLKLPLSKFMGVSRRFDLIGTIYG 431
+ +PG HNV N+LA IA V L G Q ++ LS F GV R +G ++G
Sbjct: 272 --IGVPGSHNVENALATIA-VAKLAGISNQ------VIRETLSNFGGVKHRLQSLGKVHG 322
Query: 432 CHIYDDFAHHPTEVRAVLQAARQRFPNKALIAV 464
Y+D T + A Q A F N +I +
Sbjct: 323 ISFYND--SKSTNILAT-QKALSGFDNTKVILI 352
>pdb|3MVN|A Chain A, Crystal Structure Of A Domain From A Putative
Udp-N-Acetylmu
Alanyl-Gamma-D-Glutamayl-Medo-Diaminopimelate Ligase
From H Ducreyi 35000hp
Length = 163
Score = 55.5 bits (132), Expect = 8e-08, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 421 RRFDLIGTIYGCHIYDDFAHHPTEVRAVLQAARQRFPNKALIAVFQPHTYS-RLVVLKDD 479
RR ++ G + +YDDFAHHPT + A + A R + + ++AV +P + + + V K +
Sbjct: 26 RRLEVKGVVNNITVYDDFAHHPTAITATIDALRAKVGQQRILAVLEPRSNTXKXGVHKHE 85
Query: 480 FANALSEADQVVV 492
A +L +AD V +
Sbjct: 86 LATSLQDADSVFI 98
>pdb|2WTZ|A Chain A, Mure Ligase Of Mycobacterium Tuberculosis
pdb|2WTZ|B Chain B, Mure Ligase Of Mycobacterium Tuberculosis
pdb|2WTZ|C Chain C, Mure Ligase Of Mycobacterium Tuberculosis
pdb|2WTZ|D Chain D, Mure Ligase Of Mycobacterium Tuberculosis
pdb|2XJA|A Chain A, Structure Of Mure From M.Tuberculosis With Dipeptide And
Adp
pdb|2XJA|B Chain B, Structure Of Mure From M.Tuberculosis With Dipeptide And
Adp
pdb|2XJA|C Chain C, Structure Of Mure From M.Tuberculosis With Dipeptide And
Adp
pdb|2XJA|D Chain D, Structure Of Mure From M.Tuberculosis With Dipeptide And
Adp
Length = 535
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 31/121 (25%), Positives = 51/121 (42%), Gaps = 10/121 (8%)
Query: 345 WYAESVCPNVQGGSDYILCERGRPLAQISLQIPGVHNVLNSLAVIATVLTLIGDKRQSHE 404
W A V P GG + + I +++PG +NV N L +A + T+ Q+
Sbjct: 308 WRATDVAPTDAGGQQFTAIDPAGVGHHIGIRLPGRYNVANCLVALAILDTVGVSPEQAVP 367
Query: 405 SIACLKLPLSKFMGVSRRFDLIGTIYGCHIYDDFAHHPTEVRAVLQAARQRFPNKALIAV 464
+ +++P R + I G D+AH P +R+VL P++ L V
Sbjct: 368 GLREIRVP--------GRLEQIDRGQGFLALVDYAHKPEALRSVLTTLAH--PDRRLAVV 417
Query: 465 F 465
F
Sbjct: 418 F 418
>pdb|1KCA|A Chain A, Crystal Structure Of The Lambda Repressor C-Terminal
Domain Octamer
pdb|1KCA|B Chain B, Crystal Structure Of The Lambda Repressor C-Terminal
Domain Octamer
pdb|1KCA|C Chain C, Crystal Structure Of The Lambda Repressor C-Terminal
Domain Octamer
pdb|1KCA|D Chain D, Crystal Structure Of The Lambda Repressor C-Terminal
Domain Octamer
pdb|1KCA|E Chain E, Crystal Structure Of The Lambda Repressor C-Terminal
Domain Octamer
pdb|1KCA|F Chain F, Crystal Structure Of The Lambda Repressor C-Terminal
Domain Octamer
pdb|1KCA|G Chain G, Crystal Structure Of The Lambda Repressor C-Terminal
Domain Octamer
pdb|1KCA|H Chain H, Crystal Structure Of The Lambda Repressor C-Terminal
Domain Octamer
Length = 109
Score = 31.2 bits (69), Expect = 1.3, Method: Composition-based stats.
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 188 GSHGKSTTASMLAYVLKAMGDDLTAIVGAHVPQFPDGSI 226
GSH + AS A+ L+ G+ +TA G+ P FPDG +
Sbjct: 1 GSHMTTKKASDSAFWLEVEGNSMTAPTGSK-PSFPDGML 38
>pdb|2AM1|A Chain A, Sp Protein Ligand 1
pdb|2AM2|A Chain A, Sp Protein Ligand 2
Length = 454
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 23/32 (71%), Gaps = 2/32 (6%)
Query: 172 YWLAKLTEKYNLIAVSGSHGKSTTASMLAYVL 203
Y+L K T ++ AV+GS+GK+TT LA++L
Sbjct: 93 YYLEKTT--VDVFAVTGSNGKTTTKDXLAHLL 122
>pdb|3BIC|A Chain A, Crystal Structure Of Human Methylmalonyl-Coa Mutase
pdb|3BIC|B Chain B, Crystal Structure Of Human Methylmalonyl-Coa Mutase
pdb|2XIJ|A Chain A, Crystal Structure Of Human Methylmalonyl-Coa Mutase In
Complex With Adenosylcobalamin
pdb|2XIQ|A Chain A, Crystal Structure Of Human Methylmalonyl-Coa Mutase In
Complex With Adenosylcobalamin And Malonyl-Coa
pdb|2XIQ|B Chain B, Crystal Structure Of Human Methylmalonyl-Coa Mutase In
Complex With Adenosylcobalamin And Malonyl-Coa
Length = 762
Score = 29.6 bits (65), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 173 WLAKLTEKYNLIAVSGSHGKSTTASMLAYVLKAMGDDL----TAI-VGAHVPQF-PDGSI 226
+ AK K+N I++SG H + A + + + D L T + G + +F P S
Sbjct: 238 YTAKHMPKFNSISISGYHMQEAGADAILELAYTLADGLEYSRTGLQAGLTIDEFAPRLSF 297
Query: 227 FYGGGKNFVLE 237
F+G G NF +E
Sbjct: 298 FWGIGMNFYME 308
>pdb|2GCB|A Chain A, G51sS52T DOUBLE MUTANT OF L. CASEI FPGS
Length = 428
Score = 29.3 bits (64), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 23/34 (67%)
Query: 174 LAKLTEKYNLIAVSGSHGKSTTASMLAYVLKAMG 207
L ++ I V+G++GKST A+ +A+VL+A G
Sbjct: 32 LGNPQQQGRYIHVTGTNGKSTAANAIAHVLEASG 65
>pdb|4A62|A Chain A, Parm From R1 Plasmid In Complex With Peptide From C-
Terminus Of Parr
pdb|4A62|B Chain B, Parm From R1 Plasmid In Complex With Peptide From C-
Terminus Of Parr
Length = 320
Score = 28.9 bits (63), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 7/45 (15%)
Query: 221 FPDGSIFYGGGKNFVLEADEYDGCFLGLSPSVAVVTNLDWEHVDI 265
F D +F N+ L ++Y F +SP V TN+ W++ D+
Sbjct: 40 FGDKKVF-----NYTLNGEQY--SFDPISPDAVVTTNIAWQYSDV 77
>pdb|4A61|A Chain A, Parm From Plasmid R1 In Complex With Amppnp
Length = 326
Score = 28.9 bits (63), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 7/45 (15%)
Query: 221 FPDGSIFYGGGKNFVLEADEYDGCFLGLSPSVAVVTNLDWEHVDI 265
F D +F N+ L ++Y F +SP V TN+ W++ D+
Sbjct: 46 FGDKKVF-----NYTLNGEQY--SFDPISPDAVVTTNIAWQYSDV 83
>pdb|1MWK|A Chain A, Parm From Plasmid R1 Apo Form
pdb|1MWK|B Chain B, Parm From Plasmid R1 Apo Form
pdb|1MWM|A Chain A, Parm From Plasmid R1 Adp Form
pdb|1MWM|B Chain B, Parm From Plasmid R1 Adp Form
pdb|2QU4|A Chain A, Model For Bacterial Parm Filament
pdb|2ZGY|A Chain A, Parm With Gdp
pdb|2ZGY|B Chain B, Parm With Gdp
pdb|2ZGZ|A Chain A, Parm With Gmppnp
pdb|2ZGZ|B Chain B, Parm With Gmppnp
pdb|2ZHC|A Chain A, Parm Filament
pdb|3IKU|A Chain A, Structural Model Of Parm Filament In Closed State From
Cryo- Em
pdb|3IKU|B Chain B, Structural Model Of Parm Filament In Closed State From
Cryo- Em
pdb|3IKU|C Chain C, Structural Model Of Parm Filament In Closed State From
Cryo- Em
pdb|3IKU|D Chain D, Structural Model Of Parm Filament In Closed State From
Cryo- Em
pdb|3IKU|E Chain E, Structural Model Of Parm Filament In Closed State From
Cryo- Em
pdb|3IKU|F Chain F, Structural Model Of Parm Filament In Closed State From
Cryo- Em
pdb|3IKU|G Chain G, Structural Model Of Parm Filament In Closed State From
Cryo- Em
pdb|3IKU|H Chain H, Structural Model Of Parm Filament In Closed State From
Cryo- Em
pdb|3IKU|I Chain I, Structural Model Of Parm Filament In Closed State From
Cryo- Em
pdb|3IKU|J Chain J, Structural Model Of Parm Filament In Closed State From
Cryo- Em
pdb|3IKU|K Chain K, Structural Model Of Parm Filament In Closed State From
Cryo- Em
pdb|3IKU|L Chain L, Structural Model Of Parm Filament In Closed State From
Cryo- Em
pdb|3IKY|A Chain A, Structural Model Of Parm Filament In The Open State By
Cryo- Em
pdb|3IKY|B Chain B, Structural Model Of Parm Filament In The Open State By
Cryo- Em
pdb|3IKY|C Chain C, Structural Model Of Parm Filament In The Open State By
Cryo- Em
pdb|3IKY|D Chain D, Structural Model Of Parm Filament In The Open State By
Cryo- Em
pdb|3IKY|E Chain E, Structural Model Of Parm Filament In The Open State By
Cryo- Em
pdb|3IKY|F Chain F, Structural Model Of Parm Filament In The Open State By
Cryo- Em
pdb|3IKY|G Chain G, Structural Model Of Parm Filament In The Open State By
Cryo- Em
pdb|3IKY|H Chain H, Structural Model Of Parm Filament In The Open State By
Cryo- Em
pdb|3IKY|I Chain I, Structural Model Of Parm Filament In The Open State By
Cryo- Em
pdb|3IKY|J Chain J, Structural Model Of Parm Filament In The Open State By
Cryo- Em
pdb|3IKY|K Chain K, Structural Model Of Parm Filament In The Open State By
Cryo- Em
pdb|3IKY|L Chain L, Structural Model Of Parm Filament In The Open State By
Cryo- Em
pdb|4A6J|A Chain A, Structural Model Of Parm Filament Based On Cryoem Map
pdb|4A6J|B Chain B, Structural Model Of Parm Filament Based On Cryoem Map
pdb|4A6J|C Chain C, Structural Model Of Parm Filament Based On Cryoem Map
pdb|4A6J|D Chain D, Structural Model Of Parm Filament Based On Cryoem Map
pdb|4A6J|E Chain E, Structural Model Of Parm Filament Based On Cryoem Map
pdb|4A6J|F Chain F, Structural Model Of Parm Filament Based On Cryoem Map
pdb|4A6J|G Chain G, Structural Model Of Parm Filament Based On Cryoem Map
pdb|4A6J|H Chain H, Structural Model Of Parm Filament Based On Cryoem Map
pdb|4A6J|I Chain I, Structural Model Of Parm Filament Based On Cryoem Map
pdb|4A6J|J Chain J, Structural Model Of Parm Filament Based On Cryoem Map
Length = 320
Score = 28.9 bits (63), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 7/45 (15%)
Query: 221 FPDGSIFYGGGKNFVLEADEYDGCFLGLSPSVAVVTNLDWEHVDI 265
F D +F N+ L ++Y F +SP V TN+ W++ D+
Sbjct: 40 FGDKKVF-----NYTLNGEQY--SFDPISPDAVVTTNIAWQYSDV 77
>pdb|1F20|A Chain A, Crystal Structure Of Rat Neuronal Nitric-Oxide Synthase
FadNADP+ Domain At 1.9a Resolution
Length = 435
Score = 28.5 bits (62), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 3/65 (4%)
Query: 243 GCFLGLSPSVAVVTNLDWEHVDIFEDEDAVKSIFRRFLKQIRVGGHLVICGDSQCARSLL 302
G F L + + + ++V E +S++R +Q GGH+ +CGD A +L
Sbjct: 341 GVFRELYTAYSREPDRPKKYVQDVLQEQLAESVYRALKEQ---GGHIYVCGDVTMAADVL 397
Query: 303 DQIKQ 307
I++
Sbjct: 398 KAIQR 402
>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 = 9.8, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 144 VVASSAIPQDNVEILHAKSVGVPIYKRDYWLAKLTEKYNLIAVSGSHGKSTTASMLAYVL 203
+VAS I + + A G+ I D L + ++A++GS+GKST +++ +
Sbjct: 68 IVASPGIALAHPSLSAAADAGIEIVG-DIELFCREAQAPIVAITGSNGKSTVTTLVGEMA 126
Query: 204 KAMG 207
KA G
Sbjct: 127 KAAG 130
>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 = 9.9, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 144 VVASSAIPQDNVEILHAKSVGVPIYKRDYWLAKLTEKYNLIAVSGSHGKSTTASMLAYVL 203
+VAS I + + A G+ I D L + ++A++GS+GKST +++ +
Sbjct: 69 IVASPGIALAHPSLSAAADAGIEIVG-DIELFCREAQAPIVAITGSNGKSTVTTLVGEMA 127
Query: 204 KAMG 207
KA G
Sbjct: 128 KAAG 131
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 0.137 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,437,507
Number of Sequences: 62578
Number of extensions: 629301
Number of successful extensions: 1448
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 1390
Number of HSP's gapped (non-prelim): 35
length of query: 538
length of database: 14,973,337
effective HSP length: 103
effective length of query: 435
effective length of database: 8,527,803
effective search space: 3709594305
effective search space used: 3709594305
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: 54 (25.4 bits)