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= 0001.0304.p (508 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309673|ref|YP_003773765.1| UDP-N-acetylmuramoylalanyl-D-gl... 904 0.0 gi|300309674|ref|YP_003773766.1| UDP-N-acetylmuramoyl-tripeptide... 78 1e-15 >gi|300309673|ref|YP_003773765.1| UDP-N-acetylmuramoylalanyl-D-glutamate-2,6- diaminopimelate ligase [Herbaspirillum seropedicae SmR1] Length = 508 Score = 904 bits (2337), Expect = 0.0, Method: Compositional matrix adjust. Identities = 457/508 (89%), Positives = 478/508 (94%) Query: 1 MAERVLDLQDILAWLRQVAPSAQLSSDSRRVAPGDVFLAYVGDADGRSYIADAVERGAAA 60 M ER L+L DI AWLRQ APSAQL+SDSRRVAPGDVF AYVGDADGRSYIADAVERGAAA Sbjct: 1 MPERALNLHDIQAWLRQAAPSAQLTSDSRRVAPGDVFFAYVGDADGRSYIADAVERGAAA 60 Query: 61 VLYEAEGYTWPAQIDEPHLAVPDLKQQAGQIAAAWYGQPDQSMLSVAVTGTNGKTSCAYW 120 V+YEA G+TWPAQID PHLAV DLK AG+IAA+WYGQPDQ ML+VAVTGTNGKTSCAYW Sbjct: 61 VVYEAAGFTWPAQIDVPHLAVTDLKSHAGEIAASWYGQPDQGMLTVAVTGTNGKTSCAYW 120 Query: 121 LGSALSRLPGATAAGVVGTLGVGSFINGKSQGFDVTGYTTPDAVLLQRSLAKLAQARVGA 180 LG ALSRL GA+ AGV+GTLGVGSF+NGK QGFDVTGYTTPDAVLLQRSL KLAQ RVGA Sbjct: 121 LGIALSRLAGASTAGVIGTLGVGSFVNGKPQGFDVTGYTTPDAVLLQRSLFKLAQGRVGA 180 Query: 181 LAIEASSIGLAQGRMNGMHVDVALFTNFTRDHLDFHGDMQTYEEAKRKLFQWPGLKHAVL 240 LAIEASSIGLAQGRMNGMHVDVAL TNFTRDHLDFHGDMQTYE+AKRKLFQWPGLKHAV+ Sbjct: 181 LAIEASSIGLAQGRMNGMHVDVALLTNFTRDHLDFHGDMQTYEDAKRKLFQWPGLKHAVV 240 Query: 241 NLDDPMGLRLLPLLAGRQVPVIGYSIAEQIDAQAAHVATLRASQLRSSHTGTVFHVDSPF 300 NLDD MG RLLPLLA R+VPVIGY+IA++ V TLRASQLRSSHTGTVFHVDSPF Sbjct: 241 NLDDDMGQRLLPLLAERKVPVIGYAIADEQGGDPHGVPTLRASQLRSSHTGTVFHVDSPF 300 Query: 301 GSGQVKTQLVGRFNVSNVLGIMGVLLTQGLAWDAVVAAAAALTPAPGRMQQFGGPDVPLI 360 GSGQVKTQLVGRFNVSNVLGIMGVLLTQG+AWDAVVAAAAAL+PAPGRMQQFGGPDVPLI Sbjct: 301 GSGQVKTQLVGRFNVSNVLGIMGVLLTQGVAWDAVVAAAAALSPAPGRMQQFGGPDVPLI 360 Query: 361 VIDYAHTPDALDKTLSTLRQVATQRGGQLWCVFGCGGDRDPGKRPQMGQIAEQADQVVLT 420 VIDYAHTPDALDKTLSTLRQ+ATQRGGQLWCVFGCGGDRDPGKRPQMGQIAEQADQVVLT Sbjct: 361 VIDYAHTPDALDKTLSTLRQLATQRGGQLWCVFGCGGDRDPGKRPQMGQIAEQADQVVLT 420 Query: 421 SDNPRSEDPQAIIDQIRAGMSRIEPVVLPDRAGAILWAIRHATRADVVLLAGKGHESYQE 480 SDNPRSEDPQAIIDQIRAGMSR+EPVVLPDRAGAILWAIRHAT+ADVVLLAGKGHESYQE Sbjct: 421 SDNPRSEDPQAIIDQIRAGMSRVEPVVLPDRAGAILWAIRHATKADVVLLAGKGHESYQE 480 Query: 481 IAGKKLPFLDADHVALALAARSTMMGGA 508 IAGKKLPFLDADHVALALAARSTMMGGA Sbjct: 481 IAGKKLPFLDADHVALALAARSTMMGGA 508 >gi|300309674|ref|YP_003773766.1| UDP-N-acetylmuramoyl-tripeptide---D-alanyl-D-alanine ligase [Herbaspirillum seropedicae SmR1] Length = 486 Score = 78.2 bits (191), Expect = 1e-15, Method: Compositional matrix adjust. Identities = 116/432 (26%), Positives = 180/432 (41%), Gaps = 61/432 (14%) Query: 6 LDLQDILAWLRQV--------------APSAQLS-----SDSRRVAPGDVFLAYVGDA-D 45 D + +L WLR AP+ L+ +DSR V PG+VF+A G+ D Sbjct: 4 FDFRQMLEWLRTAEAAASAHTVPGVVNAPAGLLALNDVVTDSRAVKPGNVFVALRGERFD 63 Query: 46 GRSYIADAVERGAAAVLYEAEGYTWPAQIDEPHLAVPDLKQQAGQIAAAWYGQPDQSMLS 105 ++ ++GAAAV+ E P + P + VPD + GQIA W Q + + Sbjct: 64 AHDFLDAVADQGAAAVVVE----RVPPGLALPAIVVPDTRAALGQIAHGWRMQ--RQIPV 117 Query: 106 VAVTGTNGKTSCAYWLGSALSRLPGATAAGVVGTLGV-GSFINGKSQGFDVTGYTTPDAV 164 + VTG+NGKT+ + + L A A G G LG G+F N G +T + Sbjct: 118 IGVTGSNGKTTVKEMIATIL-----AAAFGEEGYLGTRGNFNN--EIGVPLTLFRL--RA 168 Query: 165 LLQRSLAKLAQARVGALAIEASSIGLAQGRMNGMHVDVALFTNFTRDHLDFHGDMQTYEE 224 Q ++ ++ G +A+ + G +N N R+H +F M T E Sbjct: 169 QHQAAVIEMGMNHPGEIAVLSRIAAPTLGLVN----------NAQREHQEF---MATVEA 215 Query: 225 AKRK----LFQWPGLKHAVLNLDDPMGLRLLPLLAGRQVPVIGYSIAEQIDAQAAHVATL 280 R+ + P AV DD R+V + + ++ Q D A++ AT Sbjct: 216 VARENGAVIRHLPADGVAVFPADDDFTPLWREEAGARRV--LSFGLSAQADVSASYQATA 273 Query: 281 RASQLRSSHTGTVFHVDSPFGSGQVKTQLVGRFNVSNVLGIMGVLLTQGLAWDAVVAAAA 340 S L+ + G P +V+ VG NV N L L G+A +AVV Sbjct: 274 FGSTLQVAVKGLAV----PPAQFKVELAAVGEHNVRNALAAAACALGAGIAIEAVVRGLE 329 Query: 341 ALTPAPGRMQQFGGPDVPLIVID-YAHTPDALDKTLSTLRQVATQRGGQLWCVFGCGGDR 399 + P GR+Q+ L++ D Y PD++ + L +A R L + G GD+ Sbjct: 330 SFAPVNGRLQRKEARSGALVIDDTYNANPDSVRAAIDVLAAIAGPRVLVLGDM-GEVGDQ 388 Query: 400 DPGKRPQMGQIA 411 P ++G A Sbjct: 389 GPQFHAEIGAYA 400 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 0.319 0.134 0.399 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: 1,674,429 Number of extensions: 73324 Number of successful extensions: 260 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 257 Number of HSP's successfully gapped: 3 Length of query: 508 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 419 Effective length of database: 1,198,455 Effective search space: 502152645 Effective search space used: 502152645 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: 133 (55.8 bits)