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= 0001.2013.p (377 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311475|ref|YP_003775567.1| succinyl-diaminopimelate desucc... 769 0.0 gi|300312087|ref|YP_003776179.1| peptidase [Herbaspirillum serop... 83 5e-17 gi|300312510|ref|YP_003776602.1| acetylornithine deacetylase [He... 73 3e-14 gi|300314019|ref|YP_003778111.1| amino acid deacylase [Herbaspir... 60 4e-10 >gi|300311475|ref|YP_003775567.1| succinyl-diaminopimelate desuccinylase [Herbaspirillum seropedicae SmR1] Length = 377 Score = 769 bits (1987), Expect = 0.0, Method: Compositional matrix adjust. Identities = 370/376 (98%), Positives = 375/376 (99%) Query: 1 MIMSKTLALTQELMSLSSVTPEDKGCQARLAELLTPLGFVCETIQSGEVTNLWARKGTAQ 60 MIMSKTLALTQELMSLSSVTPEDKGCQARLAELLTPLGFVCETIQSGEVTNLWARKGTAQ Sbjct: 1 MIMSKTLALTQELMSLSSVTPEDKGCQARLAELLTPLGFVCETIQSGEVTNLWARKGTAQ 60 Query: 61 PLVVFAGHTDVVPTGPLEKWQSHPFQPTLRDGRLYGRGASDMKTSIAAMVVACEEFTAAH 120 PLVVFAGHTDVVPTGPLEKWQSHPFQPTLR+GRLYGRGASDMKTSIAAMVVACEEFTAAH Sbjct: 61 PLVVFAGHTDVVPTGPLEKWQSHPFQPTLREGRLYGRGASDMKTSIAAMVVACEEFTAAH 120 Query: 121 PEHKGSIGFLITSDEEGPATDGTVVVCNALKARGEQLDYCIVGEPTSAKTLGDMIKNGRR 180 P+HKGSIGFLITSDEEGPA DGTVVVCNALKARGEQLDYCIVGEPTSAKTLGDMIKNGRR Sbjct: 121 PDHKGSIGFLITSDEEGPAIDGTVVVCNALKARGEQLDYCIVGEPTSAKTLGDMIKNGRR 180 Query: 181 GTMSGKLTVKGIQGHIAYPQLARNPIHQAAPALAELVAEQWDAGNEYYLPTSWQISNIHG 240 GTMSGKLTVKGIQGHIAYPQLARNPIHQAAPALAELVAEQWDAGNEYYLPTSWQISNIHG Sbjct: 181 GTMSGKLTVKGIQGHIAYPQLARNPIHQAAPALAELVAEQWDAGNEYYLPTSWQISNIHG 240 Query: 241 GTGASNVIPGEVVIDFNFRFSTASTVEGLQQRVHAILDKHGLEYDLKWTVGGLPFLTPRG 300 GTGASNVIPGEV+IDFNFRFSTASTVEGLQQRVHAILDKHGLEYDLKWTVGGLPFLTPRG Sbjct: 241 GTGASNVIPGEVMIDFNFRFSTASTVEGLQQRVHAILDKHGLEYDLKWTVGGLPFLTPRG 300 Query: 301 DLSDALSKAIKDETGLETELSTTGGTSDGRFIAQICPQVIEFGPPNDSIHKINEHIEVRY 360 DLSDALSKAIKDETGL+TELSTTGGTSDGRFIAQICPQVIEFGPPNDSIHKI+EHIEVRY Sbjct: 301 DLSDALSKAIKDETGLDTELSTTGGTSDGRFIAQICPQVIEFGPPNDSIHKIDEHIEVRY 360 Query: 361 IDPLKNIYRKTLENLL 376 IDPLKNIYRKTLENLL Sbjct: 361 IDPLKNIYRKTLENLL 376 >gi|300312087|ref|YP_003776179.1| peptidase [Herbaspirillum seropedicae SmR1] Length = 395 Score = 82.8 bits (203), Expect = 5e-17, Method: Compositional matrix adjust. Identities = 94/335 (28%), Positives = 143/335 (42%), Gaps = 28/335 (8%) Query: 57 GTAQPLVVFAGHTDVVPTGPLEKWQSHPFQPTLRDGRLYGRGASDMKTSIAAMVVACEEF 116 G+ + +V +GHTDVVP +KW + PF+ T +DG LY RG+ DMK IA + E+ Sbjct: 70 GSTEGGIVLSGHTDVVPVDG-QKWDTDPFKLTEKDGALYARGSCDMKGFIATALALVPEY 128 Query: 117 TAAHPEHKGSIGFLITSDEEGPATDGTVVVCNALKARGEQLDYCIVGEPTSAKTLGDMIK 176 A P K I + DEE G V+ + RG ++D C+VGEPTS + Sbjct: 129 LAM-PRVK-PIHLAFSFDEE-IGCIGAPVMLEEIVKRGIKVDGCVVGEPTSMNVV----- 180 Query: 177 NGRRGTMSGKLTVKGIQGHIAYPQLARNPIHQAAPALAEL--VAEQWDAGNEY----YLP 230 +G V G H + N I AA + + A+ + A Y +P Sbjct: 181 VAHKGINVFACKVHGKSAHSSLTPQGCNAIEHAARLICAIRDFADGYKANGPYDQFFDVP 240 Query: 231 TSWQISNIHGGTGASNVIPGEVVIDFNFRFSTASTVEGLQQRV-----HAILDKHGLEY- 284 S +N G A N IP + FR +V +Q ++ +L K E+ Sbjct: 241 FSTMTTNQIRGGIAVNTIPELCEFTYEFRNLPGMSVADIQAQIDKYIAEVLLPKMRTEFP 300 Query: 285 DLKWTV---GGLPFLTPRGDLSDALSKAIKDETGLETELSTTGGTSDGRFIAQICPQVIE 341 D + + G P L A+++ ++ TG GT G F QI I Sbjct: 301 DARVEIDNFAGSPAL--EAVEQAAITELVRALTGDRQTRKVAYGTEAGLF-QQIGIPTIV 357 Query: 342 FGPPN-DSIHKINEHIEVRYIDPLKNIYRKTLENL 375 GP + + HK NE + + ++ + RK ++L Sbjct: 358 CGPGDIGNAHKPNEFVTLAQMEHCEQFLRKLGKSL 392 >gi|300312510|ref|YP_003776602.1| acetylornithine deacetylase [Herbaspirillum seropedicae SmR1] Length = 400 Score = 73.2 bits (178), Expect = 3e-14, Method: Compositional matrix adjust. Identities = 70/223 (31%), Positives = 100/223 (44%), Gaps = 26/223 (11%) Query: 51 NLWARKGTAQPL---VVFAGHTDVVP-TGPLEKWQSHPFQPTLRDGRLYGRGASDMKTSI 106 NL+A G A P VF+GHTDVVP TG +KW + PF + DG+L+GRGA DMK I Sbjct: 64 NLFATLGDAGPGRFGTVFSGHTDVVPVTG--QKWDTDPFVAHVADGKLFGRGACDMKGFI 121 Query: 107 AAMVVACEEFTAAH---PEHKGSIGFLITSDEEGPATDGTVVVCNALKARGEQLDYCIVG 163 A + A P H F + DEE G + L+ + I+G Sbjct: 122 AICMARLPAIDLARLHTPLH-----FSFSYDEE-VGCLGVRELLADLQQNDIRPTGVIIG 175 Query: 164 EPTSAKTLGDMIKNGRRGTMSGKLTVKGIQGHIAYPQLARNPIHQAAP---ALAELVAEQ 220 EPT + + +G S + +V G H + P L N I AA + E+ Sbjct: 176 EPTMMQPV-----IAHKGKRSYRCSVHGHAAHSSCPHLGINSIDFAAMMQLKIREIALRV 230 Query: 221 WDAG---NEYYLPTSWQISNIHGGTGASNVIPGEVVIDFNFRF 260 +G +++ +P S + + G A N+IP + F RF Sbjct: 231 RHSGVQDDDFDVPYSSIATTLTSGGNAPNIIPDKAEFVFEHRF 273 >gi|300314019|ref|YP_003778111.1| amino acid deacylase [Herbaspirillum seropedicae SmR1] Length = 414 Score = 59.7 bits (143), Expect = 4e-10, Method: Compositional matrix adjust. Identities = 72/284 (25%), Positives = 115/284 (40%), Gaps = 45/284 (15%) Query: 3 MSKTLALTQELMSLSSVTPEDKGC--QARLAELLTPLGFVCET------------IQSGE 48 + + + Q+L+ + + TP +AEL+ G+ E +QS Sbjct: 18 FDEEVGVLQQLIRIPTDTPPGNNAPHADAVAELVAGWGWAAEKHVVPAQQVADYGMQS-- 75 Query: 49 VTNLWARK--GTAQPLVVFAGHTDVVPTGPLEKWQSHPFQPTLRDGRLYGRGASDMKTSI 106 +TNL R+ G P + H DVVP G E W P+ + DGR+YGR A+ K+ Sbjct: 76 ITNLIVRRPYGDGGPTLALNAHGDVVPPG--EGWTHDPYGGEIADGRIYGRAAAVSKSDF 133 Query: 107 AAMVVACEEFTAAHPEHKGSIGFLITSDEEGPATDGTVVVCNALKARGEQLDYCIVGEPT 166 A+ + A A +G + T DEE G + L+ + + DY + Sbjct: 134 ASYLFATRALEAVGASLRGGVELHFTYDEE---FGGLLGPGWLLEQKLTRPDYVL----- 185 Query: 167 SAKTLGDMIKNGRRGTMSGKLTVKGIQGHIAYPQLAR----------NPIHQAAPALAEL 216 A + + ++TV G H + P+ N I+ A P L E+ Sbjct: 186 -AAGFSYNVVTAHNACLQFEITVHGRATHGSMPETGHDALQAATAILNAIYGALPGLKEI 244 Query: 217 VAEQWDAGNEYYLPTSWQISNIHGGTGASNVIPGEVVIDFNFRF 260 + A PT + I GGT +NV+PG+VV+ + R Sbjct: 245 RS----AIPGITHPTMI-VGRIDGGTN-TNVVPGKVVLKMDRRM 282 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 0.316 0.134 0.401 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: 1,182,428 Number of extensions: 48930 Number of successful extensions: 126 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 123 Number of HSP's successfully gapped: 4 Length of query: 377 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 290 Effective length of database: 1,207,925 Effective search space: 350298250 Effective search space used: 350298250 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 131 (55.1 bits)