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= 0002.0009.p (460 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309737|ref|YP_003773829.1| UDP-N-acetylmuramate:L-alanyl-g... 850 0.0 gi|300309679|ref|YP_003773771.1| UDP-N-acetylmuramate-L-alanine ... 108 9e-25 >gi|300309737|ref|YP_003773829.1| UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso- diaminopimelate ligase transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 460 Score = 850 bits (2196), Expect = 0.0, Method: Compositional matrix adjust. Identities = 428/460 (93%), Positives = 445/460 (96%) Query: 1 MHIHILGICGTFMGGLAVLAKEAGHTVTGCDANVYPPMSTQLEAQGITLTQGFEPSQVEI 60 MHIHILGICGTFMGGLAVLAKEAGHTVTGCDANVYPPMSTQLEAQGITLTQGF+ +QVE+ Sbjct: 1 MHIHILGICGTFMGGLAVLAKEAGHTVTGCDANVYPPMSTQLEAQGITLTQGFDAAQVEL 60 Query: 61 KPDLFVIGNVVSRGNPLMEEILNRGLPYVSGPQWMGENILQDKWVLSVAGTHGKTTTSAM 120 +PDLFVIGNVVSRGNPLMEEILNRGLPYVSGPQWMGENILQDKWVL+VAGTHGKTTTSAM Sbjct: 61 EPDLFVIGNVVSRGNPLMEEILNRGLPYVSGPQWMGENILQDKWVLAVAGTHGKTTTSAM 120 Query: 121 LAWVLEHAGYQPGFLIGGVPMNFGISARLGSDGQGGPSPFFVIEADEYDTAFFDKRSKFV 180 LAWVLEHAGYQPGFLIGGVPMNFG+SARLGSDGQGGP+PFFVIEADEYDTAFFDKRSKFV Sbjct: 121 LAWVLEHAGYQPGFLIGGVPMNFGVSARLGSDGQGGPAPFFVIEADEYDTAFFDKRSKFV 180 Query: 181 HYRSRTAVLNNLEYDHADIFPDLAAIETQFHHLVRTVPGIGRVIANGREAALQRVLARGC 240 HYR+RTAVLNNLEYDHADIFPDLAAIETQFHHLVRTVPGIGR+I NGRE ALQRVLARGC Sbjct: 181 HYRTRTAVLNNLEYDHADIFPDLAAIETQFHHLVRTVPGIGRLIVNGREPALQRVLARGC 240 Query: 241 WSEREDFGVAAGQPGWSLQTHEDGRFEVFFEGQSQGTVDWSLTGEHNRMNALAAIAAARH 300 WSEREDFGVA GQ GWSL THEDGRF+VFF+GQ+QGTV+W LTGEHNRMNALAAIAAARH Sbjct: 241 WSEREDFGVAQGQSGWSLLTHEDGRFDVFFDGQTQGTVEWQLTGEHNRMNALAAIAAARH 300 Query: 301 VGVPAAQAIEALGAFQSVKRRMELRGSANGVAVYDDFAHHPTAIATTVAGLRKKVGAARI 360 VGVP AQAI ALGAFQSVKRRMELRGSANGVAVYDDFAHHPTAIATTVAGLRKKVGAARI Sbjct: 301 VGVPVAQAIAALGAFQSVKRRMELRGSANGVAVYDDFAHHPTAIATTVAGLRKKVGAARI 360 Query: 361 LAVLEPRSNTMKLGTMKEALPGSLTDADLVFGFGAQSGRDALGWDLAEALAPLGQKAAAF 420 LAVLEPRSNTMKLGTMK+ALPGSL DADLVFGFGA +GRDALGWDL EALAPLG KAAAF Sbjct: 361 LAVLEPRSNTMKLGTMKQALPGSLADADLVFGFGAHTGRDALGWDLGEALAPLGAKAAAF 420 Query: 421 HDIDALVQAVKAAAQPGDHVLVMSNGGFGGVHQKLLDALA 460 D+ ALVQAVKAAA+PGDHVLVMSNGGFGGVHQKLLDALA Sbjct: 421 DDLAALVQAVKAAARPGDHVLVMSNGGFGGVHQKLLDALA 460 >gi|300309679|ref|YP_003773771.1| UDP-N-acetylmuramate-L-alanine ligase [Herbaspirillum seropedicae SmR1] Length = 475 Score = 108 bits (270), Expect = 9e-25, Method: Compositional matrix adjust. Identities = 123/464 (26%), Positives = 190/464 (40%), Gaps = 62/464 (13%) Query: 24 GHTVTGCDANVYPPMSTQLEAQ-GITLTQGFEPSQVEIKPDLFVIGNVVSRGNPLMEEIL 82 G+ V+G D +TQ AQ G + G +E D V V NP + Sbjct: 29 GYGVSGSDLG--SNAATQRLAQLGACIRYGHAAGNIE-GADAIVTSTAVKGDNPEVLAAR 85 Query: 83 NRGLPYVSGPQWMGENILQDKWVLSVAGTHGKTTTSAMLAWVLEHAGYQPGFLIGGVPMN 142 + +P V +GE +++ K +++AGTHGKTTT++++A VL G P F+IGG + Sbjct: 86 KKHIPIVPRAVMLGE-LMRLKKGIAIAGTHGKTTTTSLVASVLAQGGLDPTFVIGGRLTS 144 Query: 143 FGISARLGSDGQGGPSPFFVIEADEYDTAFFDKRSKFVHYRSRTAVLNNLEYDHADIFP- 201 G +A+LG+ F V EADE D +F + V+ N++ DH + + Sbjct: 145 AGANAKLGT------GEFIVAEADESDASFLN-------LTPVIEVITNIDADHMETYNH 191 Query: 202 DLAAIETQFHHLVRTVPGIGRVIANGREAALQRVLARGCWSEREDFGVAAGQPGWSLQTH 261 D A ++ F + +P G + + ++ ++ +P + H Sbjct: 192 DFARLKQAFVEFTQRLPFYGVAVLCLDDPHVREIMP------------MVSKPILTYGFH 239 Query: 262 EDG--------------RFEVFFEGQSQGTVDWSLTGEHNRMNALAAIAAARHVGVPAAQ 307 ED F V +G + V + G HN NA AAIA AR + V A Sbjct: 240 EDADVRAIDAKAVDGKMEFTVIQDGYAPMQVSLNQPGMHNVQNACAAIAIARELDVDDAA 299 Query: 308 AIEALGAFQSVKRRMELRGS----------ANGVAVYDDFAHHPTAIATTVAGLRKKVGA 357 +AL F V RR G A + DD+ HHP A T+A R Sbjct: 300 TQKALTEFNGVGRRFTRYGEVPLWDAEGKPAGHFTLVDDYGHHPVETAATIAAARGAYPG 359 Query: 358 ARILAVLEPRSNTMKLGTMKEALPGSLTDADL-----VFGFGAQSGRDALGWDLAEALAP 412 R++ +P T + + E L+ D+ V+ G A G LA AL Sbjct: 360 RRLVLAFQPHRYT-RTRDLFEDFVKVLSSPDVLVLAEVYSAGEAPIVAADGRSLAHALRA 418 Query: 413 LGQKAAAF-HDIDALVQAVKAAAQPGDHVLVMSNGGFGGVHQKL 455 G+ F DI + + ++ + GD V+ M G V +L Sbjct: 419 AGKVEPVFVDDIGDMPETIRNVVRDGDVVMTMGAGSISAVPGRL 462 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 0.136 0.411 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: 1,520,554 Number of extensions: 66369 Number of successful extensions: 223 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 219 Number of HSP's successfully gapped: 3 Length of query: 460 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 372 Effective length of database: 1,203,190 Effective search space: 447586680 Effective search space used: 447586680 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)