BLASTP 2.2.18 [Mar-02-2008] 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= 0035.0035.p (478 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309674|ref|YP_003773766.1| UDP-N-acetylmuramoyl-tripeptide... 598 e-172 gi|300309673|ref|YP_003773765.1| UDP-N-acetylmuramoylalanyl-D-gl... 68 1e-12 >gi|300309674|ref|YP_003773766.1| UDP-N-acetylmuramoyl-tripeptide---D-alanyl-D-alanine ligase [Herbaspirillum seropedicae SmR1] Length = 486 Score = 598 bits (1542), Expect = e-172, Method: Compositional matrix adjust. Identities = 330/490 (67%), Positives = 376/490 (76%), Gaps = 17/490 (3%) Query: 1 MQTTLEQLKQWLDGA-----------TVHNDAGALADVSINGATTDSRAVVPGNLFIALR 49 M+ Q+ +WL A V+ AG LA +N TDSRAV PGN+F+ALR Sbjct: 2 MRFDFRQMLEWLRTAEAAASAHTVPGVVNAPAGLLA---LNDVVTDSRAVKPGNVFVALR 58 Query: 50 GERFDAHDFLDAVAAQGAAAVVVERVPAGLKIPAIVVSDTRVALGRIARHWRQQFKLPLI 109 GERFDAHDFLDAVA QGAAAVVVERVP GL +PAIVV DTR ALG+IA WR Q ++P+I Sbjct: 59 GERFDAHDFLDAVADQGAAAVVVERVPPGLALPAIVVPDTRAALGQIAHGWRMQRQIPVI 118 Query: 110 AVTGSNGKTTVKEMIASILAADFGEDRSMATRGNFNNEIGVPLTLFRLQPQHQAAVVELG 169 VTGSNGKTTVKEMIA+ILAA FGE+ + TRGNFNNEIGVPLTLFRL+ QHQAAV+E+G Sbjct: 119 GVTGSNGKTTVKEMIATILAAAFGEEGYLGTRGNFNNEIGVPLTLFRLRAQHQAAVIEMG 178 Query: 170 MNHPGEIAVLAEIARPTLALVNNAQREHQEFMATVEAVARENGAVFAALPADGIAVFPAE 229 MNHPGEIAVL+ IA PTL LVNNAQREHQEFMATVEAVARENGAV LPADG+AVFPA+ Sbjct: 179 MNHPGEIAVLSRIAAPTLGLVNNAQREHQEFMATVEAVARENGAVIRHLPADGVAVFPAD 238 Query: 230 DDYAWVWREIAGARPVISFGLNPDANVSATYQVREFGSAIAVNAD-IDGRSQQFGIKLAA 288 DD+ +WRE AGAR V+SFGL+ A+VSA+YQ FGS + V + QF ++LAA Sbjct: 239 DDFTPLWREEAGARRVLSFGLSAQADVSASYQATAFGSTLQVAVKGLAVPPAQFKVELAA 298 Query: 289 VGEHNVRNALAATACALGAGIAVAAIVRGLEAFAPVNGRLQRKAAASGALVIDDTYNANP 348 VGEHNVRNALAA ACALGAGIA+ A+VRGLE+FAPVNGRLQRK A SGALVIDDTYNANP Sbjct: 299 VGEHNVRNALAAAACALGAGIAIEAVVRGLESFAPVNGRLQRKEARSGALVIDDTYNANP 358 Query: 349 DSVRAAIDVLAQTVAPRVLALGDMGEVGNEGPKFHREIGAYARARGIEHFFGFGDAMRDA 408 DSVRAAIDVLA PRVL LGDMGEVG++GP+FH EIGAYAR+RGI FFG G+ + A Sbjct: 359 DSVRAAIDVLAAIAGPRVLVLGDMGEVGDQGPQFHAEIGAYARSRGIPLFFGLGELTKHA 418 Query: 409 IEAYNSAPGAAFPARHFDTVDAIGAATREVAVAAATVLVKGSRFMKMERVVQHLVGAQLQ 468 + AY + P A HFD + A+ AA + A ATVLVKGSRFMKMERVVQHLV + Sbjct: 419 VTAYGATPQGVAQALHFDDIAALNAAVEQAAPQGATVLVKGSRFMKMERVVQHLVNVESP 478 Query: 469 TGAPLHQETH 478 T QETH Sbjct: 479 TQH--QQETH 486 >gi|300309673|ref|YP_003773765.1| UDP-N-acetylmuramoylalanyl-D-glutamate-2,6- diaminopimelate ligase [Herbaspirillum seropedicae SmR1] Length = 508 Score = 68.2 bits (165), Expect = 1e-12, Method: Compositional matrix adjust. Identities = 97/372 (26%), Positives = 152/372 (40%), Gaps = 50/372 (13%) Query: 33 TTDSRAVVPGNLFIALRGERFDAHDFLDAVAAQGAAAVVVERV----PAGLKIPAIVVSD 88 T+DSR V PG++F A G+ D ++ +GAAAVV E PA + +P + V+D Sbjct: 25 TSDSRRVAPGDVFFAYVGDA-DGRSYIADAVERGAAAVVYEAAGFTWPAQIDVPHLAVTD 83 Query: 89 TRVALGRIARHWRQQFK--LPLIAVTGSNGKTTVKEMIASILAADFGEDRSMATRGNFNN 146 + G IA W Q + +AVTG+NGKT+ + L+ G A+ Sbjct: 84 LKSHAGEIAASWYGQPDQGMLTVAVTGTNGKTSCAYWLGIALSRLAG-----ASTAGVIG 138 Query: 147 EIGVPLTLFRLQPQH--------------QAAVVELGMNHPGEIAVLAE---IARPTL-- 187 +GV + +PQ Q ++ +L G +A+ A +A+ + Sbjct: 139 TLGVG-SFVNGKPQGFDVTGYTTPDAVLLQRSLFKLAQGRVGALAIEASSIGLAQGRMNG 197 Query: 188 -----ALVNNAQREHQEFMATVEAVARENGAVFAALPADGIAVFPAEDDYAWVWREIAGA 242 AL+ N R+H +F ++ +F P AV +DD + Sbjct: 198 MHVDVALLTNFTRDHLDFHGDMQTYEDAKRKLF-QWPGLKHAVVNLDDDMGQRLLPLLAE 256 Query: 243 R--PVISF------GLNPDANVSA-TYQVREFGSAIAVNADIDGRSQQFGIKLAAVGEHN 293 R PVI + G +P + Q+R + + D S Q +K VG N Sbjct: 257 RKVPVIGYAIADEQGGDPHGVPTLRASQLRSSHTGTVFHVDSPFGSGQ--VKTQLVGRFN 314 Query: 294 VRNALAATACALGAGIAVAAIVRGLEAFAPVNGRLQRKAAASGALVIDDTYNANPDSVRA 353 V N L L G+A A+V A +P GR+Q+ L++ D Y PD++ Sbjct: 315 VSNVLGIMGVLLTQGVAWDAVVAAAAALSPAPGRMQQFGGPDVPLIVID-YAHTPDALDK 373 Query: 354 AIDVLAQTVAPR 365 + L Q R Sbjct: 374 TLSTLRQLATQR 385 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.320 0.133 0.383 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 1,441,073 Number of extensions: 58048 Number of successful extensions: 242 Number of sequences better than 1.0e-08: 2 Number of HSP's gapped: 241 Number of HSP's successfully gapped: 2 Length of query: 478 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 389 Effective length of database: 1,198,455 Effective search space: 466198995 Effective search space used: 466198995 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 132 (55.5 bits)