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= 0001.0310.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 ... 891 0.0 gi|300309737|ref|YP_003773829.1| UDP-N-acetylmuramate:L-alanyl-g... 113 3e-26 >gi|300309679|ref|YP_003773771.1| UDP-N-acetylmuramate-L-alanine ligase [Herbaspirillum seropedicae SmR1] Length = 475 Score = 891 bits (2302), Expect = 0.0, Method: Compositional matrix adjust. Identities = 460/475 (96%), Positives = 465/475 (97%) Query: 1 MKHRVKNIHFVGIGGSGMSGIAEVLFNLGYGVSGSDLGSNAATQRLAQLGACIRYGHAAE 60 MKHRVKNIHFVGIGGSGMSGIAEVL NLGYGVSGSDLGSNAATQRLAQLGACIRYGHAA Sbjct: 1 MKHRVKNIHFVGIGGSGMSGIAEVLLNLGYGVSGSDLGSNAATQRLAQLGACIRYGHAAG 60 Query: 61 NIEGADAIVTSTAVKGDNPEVLAARKKHIPIVPRAVMLGELMRLKKGIAIAGTHGKTTTT 120 NIEGADAIVTSTAVKGDNPEVLAARKKHIPIVPRAVMLGELMRLKKGIAIAGTHGKTTTT Sbjct: 61 NIEGADAIVTSTAVKGDNPEVLAARKKHIPIVPRAVMLGELMRLKKGIAIAGTHGKTTTT 120 Query: 121 SLVASVLAQGGLDPTFVIGGRLTSAGANAKLGTGEFIVAEADESDASFLNLTPVIEVITN 180 SLVASVLAQGGLDPTFVIGGRLTSAGANAKLGTGEFIVAEADESDASFLNLTPVIEVITN Sbjct: 121 SLVASVLAQGGLDPTFVIGGRLTSAGANAKLGTGEFIVAEADESDASFLNLTPVIEVITN 180 Query: 181 IDADHMETYNHDFARLKQAFVEFTQRLPFYGVAVLCLDDPHVREIMPMVSKPILTYGFHA 240 IDADHMETYNHDFARLKQAFVEFTQRLPFYGVAVLCLDDPHVREIMPMVSKPILTYGFH Sbjct: 181 IDADHMETYNHDFARLKQAFVEFTQRLPFYGVAVLCLDDPHVREIMPMVSKPILTYGFHE 240 Query: 241 DADVRAIEASAVDGKMEFTVIQDGYAPMKVSLNQPGMHNVQNACAAIAIARELDVDDAAT 300 DADVRAI+A AVDGKMEFTVIQDGYAPM+VSLNQPGMHNVQNACAAIAIARELDVDDAAT Sbjct: 241 DADVRAIDAKAVDGKMEFTVIQDGYAPMQVSLNQPGMHNVQNACAAIAIARELDVDDAAT 300 Query: 301 QKALTEFNGVGRRFTRYGEVPITDAQGNPAGHFTLVDDYGHHPVETAATIAAARGAYPGR 360 QKALTEFNGVGRRFTRYGEVP+ DA+G PAGHFTLVDDYGHHPVETAATIAAARGAYPGR Sbjct: 301 QKALTEFNGVGRRFTRYGEVPLWDAEGKPAGHFTLVDDYGHHPVETAATIAAARGAYPGR 360 Query: 361 RLVLAFQPHRYTRTRDLFEDFVKVLSSPDVLVLGEVYAAGEAPIVAADGRSLAHALRAAG 420 RLVLAFQPHRYTRTRDLFEDFVKVLSSPDVLVL EVY+AGEAPIVAADGRSLAHALRAAG Sbjct: 361 RLVLAFQPHRYTRTRDLFEDFVKVLSSPDVLVLAEVYSAGEAPIVAADGRSLAHALRAAG 420 Query: 421 KVEPVFVDDIGDMPETIRNVVRDGDVVMTMGAGSISAVPGRLVAQAGGKNEQGAA 475 KVEPVFVDDIGDMPETIRNVVRDGDVVMTMGAGSISAVPGRL AQA KNEQGAA 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 = 113 bits (283), Expect = 3e-26, Method: Compositional matrix adjust. Identities = 133/476 (27%), Positives = 203/476 (42%), Gaps = 40/476 (8%) Query: 7 NIHFVGIGGSGMSGIAEVLFNLGYGVSGSD--LGSNAATQRLAQLGACIRYGHAAENIE- 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-LMRLKKGIAIAGTHGKTTTTSL 122 D V V NP + + +P V +GE +++ K +A+AGTHGKTTT+++ 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 ------EVITNIDADHMETYNHDFARLKQAFVEFTQRLPFYGVAVLCLDDPHVREIMPM- 228 V+ N++ DH + + D A ++ F + +P G ++ +P ++ ++ Sbjct: 181 HYRTRTAVLNNLEYDHADIFP-DLAAIETQFHHLVRTVPGIGRLIVNGREPALQRVLARG 239 Query: 229 VSKPILTYGFHADADVRAIEASAVDGKMEFTVIQDGYAPMKVSLNQPGMHNVQNACAAIA 288 +G A + DG+ F V DG V G HN NA AAIA Sbjct: 240 CWSEREDFGV-AQGQSGWSLLTHEDGR--FDVFFDGQTQGTVEWQLTGEHNRMNALAAIA 296 Query: 289 IARELDVDDAATQKALTEFNGVGRRFTRYGEVPITDAQGNPAGHFTLVDDYGHHPVETAA 348 AR + V A AL F V RR G A + DD+ HHP A Sbjct: 297 AARHVGVPVAQAIAALGAFQSVKRRMELRGS----------ANGVAVYDDFAHHPTAIAT 346 Query: 349 TIAAARGAYPGRRLVLAFQPHRYT-RTRDLFEDFVKVLSSPDVLVLGEVYAAGEAPIVAA 407 T+A R R++ +P T + + + L+ D+ V+ G A Sbjct: 347 TVAGLRKKVGAARILAVLEPRSNTMKLGTMKQALPGSLADADL-----VFGFGAHTGRDA 401 Query: 408 DGRSLAHALRAAGKVEPVFVDDIGDMPETIRNVVRDGDVVMTMGAGSISAVPGRLV 463 G L AL G F D + + ++ R GD V+ M G V +L+ Sbjct: 402 LGWDLGEALAPLGAKAAAFDDLAALV-QAVKAAARPGDHVLVMSNGGFGGVHQKLL 456 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 0.135 0.390 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: 1,528,429 Number of extensions: 66086 Number of successful extensions: 288 Number of sequences better than 1.0e-08: 2 Number of HSP's gapped: 284 Number of HSP's successfully gapped: 2 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 (21.8 bits) S2: 132 (55.5 bits)