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= 0020.0142.p (475 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309679|ref|YP_003773771.1| UDP-N-acetylmuramate-L-alanine ... 890 0.0 gi|300309737|ref|YP_003773829.1| UDP-N-acetylmuramate:L-alanyl-g... 93 4e-20 >gi|300309679|ref|YP_003773771.1| UDP-N-acetylmuramate-L-alanine ligase [Herbaspirillum seropedicae SmR1] Length = 475 Score = 890 bits (2301), Expect = 0.0, Method: Compositional matrix adjust. Identities = 462/475 (97%), Positives = 464/475 (97%) Query: 1 MKHRVKNIHFVGIGGSGMSGIAEVLLNLGYGVSGSDLGSNAATQRLAQLGACIRYGHAAG 60 MKHRVKNIHFVGIGGSGMSGIAEVLLNLGYGVSGSDLGSNAATQRLAQLGACIRYGHAAG Sbjct: 1 MKHRVKNIHFVGIGGSGMSGIAEVLLNLGYGVSGSDLGSNAATQRLAQLGACIRYGHAAG 60 Query: 61 NIEGADAIVTSTAVKGDNPEVLAARKKHIPIVPRAVMLGELMRLKNA*CVRFFFNGPTTT 120 NIEGADAIVTSTAVKGDNPEVLAARKKHIPIVPRAVMLGELMRLK + TTT Sbjct: 61 NIEGADAIVTSTAVKGDNPEVLAARKKHIPIVPRAVMLGELMRLKKGIAIAGTHGKTTTT 120 Query: 121 SLVASVLAQGGLDPTFVIGGRLTSAGANAKLGTGEFIVAEADESDASFLNLTPVIEVITN 180 SLVASVLAQGGLDPTFVIGGRLTSAGANAKLGTGEFIVAEADESDASFLNLTPVIEVITN Sbjct: 121 SLVASVLAQGGLDPTFVIGGRLTSAGANAKLGTGEFIVAEADESDASFLNLTPVIEVITN 180 Query: 181 IDADHMETYNHDFARLKQAFVEFTQRLPFYGVAVLCLDDPHVREIMPMVSKPILTYGFHE 240 IDADHMETYNHDFARLKQAFVEFTQRLPFYGVAVLCLDDPHVREIMPMVSKPILTYGFHE Sbjct: 181 IDADHMETYNHDFARLKQAFVEFTQRLPFYGVAVLCLDDPHVREIMPMVSKPILTYGFHE 240 Query: 241 DADVRAIDAKAVDGKMEFTVIQDGYAPMQVSLNQPGMHNVQNACAAIAIARELDVDDAAT 300 DADVRAIDAKAVDGKMEFTVIQDGYAPMQVSLNQPGMHNVQNACAAIAIARELDVDDAAT Sbjct: 241 DADVRAIDAKAVDGKMEFTVIQDGYAPMQVSLNQPGMHNVQNACAAIAIARELDVDDAAT 300 Query: 301 QKALTEFNGVGRRFTRYGEVPLWDAEGKPAGHFTLVDDYGHHPVETAATIAAARGAYPGR 360 QKALTEFNGVGRRFTRYGEVPLWDAEGKPAGHFTLVDDYGHHPVETAATIAAARGAYPGR Sbjct: 301 QKALTEFNGVGRRFTRYGEVPLWDAEGKPAGHFTLVDDYGHHPVETAATIAAARGAYPGR 360 Query: 361 RLVLAFQPHRYTRTRDLFEDFVKVLSSPDVLVLAEVYSAGEAPIVAADGRSLAHALRAAG 420 RLVLAFQPHRYTRTRDLFEDFVKVLSSPDVLVLAEVYSAGEAPIVAADGRSLAHALRAAG Sbjct: 361 RLVLAFQPHRYTRTRDLFEDFVKVLSSPDVLVLAEVYSAGEAPIVAADGRSLAHALRAAG 420 Query: 421 KVEPVFVDDIGDMPETIRNVVRDGDVVMTMGAGSISAVPGRLTAQADVKSEQGAA 475 KVEPVFVDDIGDMPETIRNVVRDGDVVMTMGAGSISAVPGRLTAQADVK+EQGAA Sbjct: 421 KVEPVFVDDIGDMPETIRNVVRDGDVVMTMGAGSISAVPGRLTAQADVKNEQGAA 475 >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 = 93.2 bits (230), Expect = 4e-20, Method: Compositional matrix adjust. Identities = 127/479 (26%), Positives = 193/479 (40%), Gaps = 48/479 (10%) Query: 7 NIHFVGIGGSGMSGIAEVLLNLGYGVSGSDLG--SNAATQRLAQLGACIRYGHAAGNIE- 63 +IH +GI G+ M G+A + G+ V+G D +TQ AQ G + G A +E Sbjct: 2 HIHILGICGTFMGGLAVLAKEAGHTVTGCDANVYPPMSTQLEAQ-GITLTQGFDAAQVEL 60 Query: 64 GADAIVTSTAVKGDNPEVLAARKKHIPIVPRAVMLGE-LMRLKNA*CVRFFFNGPTTTSL 122 D V V NP + + +P V +GE +++ K V TT+++ Sbjct: 61 EPDLFVIGNVVSRGNPLMEEILNRGLPYVSGPQWMGENILQDKWVLAVAGTHGKTTTSAM 120 Query: 123 VASVLAQGGLDPTFVIGGRLTSAGANAKLGT------GEFIVAEADESDASFLNLTPVI- 175 +A VL G P F+IGG + G +A+LG+ F V EADE D +F + Sbjct: 121 LAWVLEHAGYQPGFLIGGVPMNFGVSARLGSDGQGGPAPFFVIEADEYDTAFFDKRSKFV 180 Query: 176 ------EVITNIDADHMETYNHDFARLKQAFVEFTQRLPFYGVAVLCLDDPHVREIMPMV 229 V+ N++ DH + + D A ++ F + +P G ++ +P ++ ++ Sbjct: 181 HYRTRTAVLNNLEYDHADIFP-DLAAIETQFHHLVRTVPGIGRLIVNGREPALQRVLARG 239 Query: 230 SKPILTYGFHEDADVRAIDAKAV-----DGKMEFTVIQDGYAPMQVSLNQPGMHNVQNAC 284 + ED V + DG+ F V DG V G HN NA Sbjct: 240 C-----WSEREDFGVAQGQSGWSLLTHEDGR--FDVFFDGQTQGTVEWQLTGEHNRMNAL 292 Query: 285 AAIAIARELDVDDAATQKALTEFNGVGRRFTRYGEVPLWDAEGKPAGHFTLVDDYGHHPV 344 AAIA AR + V A AL F V RR G A + DD+ HHP Sbjct: 293 AAIAAARHVGVPVAQAIAALGAFQSVKRRMELRGS----------ANGVAVYDDFAHHPT 342 Query: 345 ETAATIAAARGAYPGRRLVLAFQPHRYT-RTRDLFEDFVKVLSSPDVLVLAEVYSAGEAP 403 A T+A R R++ +P T + + + L+ D+ V+ G Sbjct: 343 AIATTVAGLRKKVGAARILAVLEPRSNTMKLGTMKQALPGSLADADL-----VFGFGAHT 397 Query: 404 IVAADGRSLAHALRAAGKVEPVFVDDIGDMPETIRNVVRDGDVVMTMGAGSISAVPGRL 462 A G L AL G F D + + ++ R GD V+ M G V +L Sbjct: 398 GRDALGWDLGEALAPLGAKAAAFDDLAALV-QAVKAAARPGDHVLVMSNGGFGGVHQKL 455 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 0.321 0.137 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: 1,509,341 Number of extensions: 64945 Number of successful extensions: 251 Number of sequences better than 1.0e-08: 2 Number of HSP's gapped: 248 Number of HSP's successfully gapped: 3 Length of query: 475 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 386 Effective length of database: 1,198,455 Effective search space: 462603630 Effective search space used: 462603630 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 (21.9 bits) S2: 132 (55.5 bits)