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= 0009.0178.p (247 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [H... 296 1e-81 gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase smal... 160 6e-41 gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase smal... 150 1e-37 gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase smal... 125 2e-30 gi|300309957|ref|YP_003774049.1| chemotaxis histidine kinase [He... 76 2e-15 >gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 433 Score = 296 bits (758), Expect = 1e-81, Method: Compositional matrix adjust. Identities = 144/188 (76%), Positives = 163/188 (86%), Gaps = 3/188 (1%) Query: 52 GSVVIDVFDKELVRGDAYVVALGSYSANFLRRIVD---IPVYPLKGYSITVPVVDSRAAP 108 G + V KELV+ D+YVVALGSYS L + IPVYPLKGYSITVP+ D+ AAP Sbjct: 232 GKIAGVVCGKELVQADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDASAAP 291 Query: 109 VSTILDETYKIAVTRFDNRIRVGGMAEVVGFNKELNPKRRATLELVVNDLFPGAGNTAQA 168 VSTILDETYKIAVTRFD+RIRVGGMAE+VG++ L KRRATLELVVNDLFPGAG+TAQA Sbjct: 292 VSTILDETYKIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGAGDTAQA 351 Query: 169 SFWTGLRPMTPDGTPIVGATPLNNLFLNTGHGTLGWTMSCGSGQLLADLISGKRPAIAAD 228 SFWTGLRPMTPDGTP+VGATP++NL++NTGHGTLGWTMSCGSGQLLADLISG+RPAIA + Sbjct: 352 SFWTGLRPMTPDGTPVVGATPVSNLYINTGHGTLGWTMSCGSGQLLADLISGRRPAIAHE 411 Query: 229 DLSMARYL 236 DLS+ RYL Sbjct: 412 DLSVERYL 419 >gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 436 Score = 160 bits (406), Expect = 6e-41, Method: Compositional matrix adjust. Identities = 74/180 (41%), Positives = 113/180 (62%), Gaps = 1/180 (0%) Query: 62 ELVRGDAYVVALGSYSANFLRRI-VDIPVYPLKGYSITVPVVDSRAAPVSTILDETYKIA 120 E+++ D +VVA+GS+S ++ + +D+ +YP KGYS T + + AAP ++ D+ YK+ Sbjct: 251 EVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQITNPDAAPTVSLTDDGYKLV 310 Query: 121 VTRFDNRIRVGGMAEVVGFNKELNPKRRATLELVVNDLFPGAGNTAQASFWTGLRPMTPD 180 V+R +R+RV G E+ G+ +ELN R + +LFP + ++WTGLRP+TP Sbjct: 311 VSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGCDYENPTYWTGLRPLTPS 370 Query: 181 GTPIVGATPLNNLFLNTGHGTLGWTMSCGSGQLLADLISGKRPAIAADDLSMARYLGQRQ 240 P VG T NL+LNTGHGTLGWTM CGSG+ +A++++G P I + R+ RQ Sbjct: 371 NVPYVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAEIVAGHVPEIDFAFTGLPRWNRARQ 430 >gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 421 Score = 150 bits (379), Expect = 1e-37, Method: Compositional matrix adjust. Identities = 80/170 (47%), Positives = 111/170 (65%), Gaps = 6/170 (3%) Query: 62 ELVRGDAYVVALGSYSANFLRRI-VDIPVYPLKGYSITVPVVD--SRAA-PVSTILDETY 117 E + +V+ALG+ SA+F R++ + +P+YPLKGYSITVP+ D SRAA P +I D Sbjct: 243 EWISAQRFVLALGADSADFARQLDLRLPLYPLKGYSITVPLEDEASRAAAPQVSITDIAR 302 Query: 118 KIAVTRFDNRIRVGGMAEVVGFNKELNPKRRATLELVVNDLFPGA--GNTAQASFWTGLR 175 KI R R+RV G E+VG ++ + P+ A L+ + +LFP G A+ S W G R Sbjct: 303 KIVYARLGQRLRVAGRIELVGQDRSIPPRAIAELKQGMRELFPDCVLGEDARLSPWMGFR 362 Query: 176 PMTPDGTPIVGATPLNNLFLNTGHGTLGWTMSCGSGQLLADLISGKRPAI 225 P TP G PIVGA P++NL+LN G G LGWT++CGS L+AD I+G+ +I Sbjct: 363 PATPSGVPIVGACPVDNLYLNIGQGALGWTLACGSAALIADQIAGRPCSI 412 >gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 125 bits (315), Expect = 2e-30, Method: Compositional matrix adjust. Identities = 70/183 (38%), Positives = 100/183 (54%), Gaps = 4/183 (2%) Query: 52 GSVVIDVFDKELVRG---DAYVVALGSYSANFLRRI-VDIPVYPLKGYSITVPVVDSRAA 107 G V ++V L DA VVA G SA L+ + +P+ L+ YS VPV + A Sbjct: 234 GRVTLEVQSPHLASHLTMDAVVVAAGMASAALLQPLDTSLPLRALQSYSALVPVKNPDDA 293 Query: 108 PVSTILDETYKIAVTRFDNRIRVGGMAEVVGFNKELNPKRRATLELVVNDLFPGAGNTAQ 167 P + D++YK+A+TR +RIR+ G+ V ++ L PK L + D +P A N Q Sbjct: 294 PTMALYDDSYKVAMTRLGSRIRISGLLGFVPASQTLPPKALRNLLKIAGDYYPNAANYNQ 353 Query: 168 ASFWTGLRPMTPDGTPIVGATPLNNLFLNTGHGTLGWTMSCGSGQLLADLISGKRPAIAA 227 A FW+ M P G P+VG T N+F+N GHG GW S GS +LL+D+++G+ IA Sbjct: 354 AHFWSNSIAMMPTGLPVVGPTRQGNIFVNVGHGVTGWAASVGSARLLSDMMAGEETEIAT 413 Query: 228 DDL 230 L Sbjct: 414 AGL 416 >gi|300309957|ref|YP_003774049.1| chemotaxis histidine kinase [Herbaspirillum seropedicae SmR1] Length = 725 Score = 76.3 bits (186), Expect = 2e-15, Method: Compositional matrix adjust. Identities = 42/80 (52%), Positives = 47/80 (58%), Gaps = 8/80 (10%) Query: 1 MHIVRNAMDHGIESAEARREAGKPEIGVLRLNATHESGSVVIDVFDDGRGXGSVVIDVFD 60 MHIVRNA+DHGIE A R AGKP L+LNA HESGSVVI+V DDGRG D Sbjct: 442 MHIVRNAIDHGIEPAAERLAAGKPAKASLQLNAIHESGSVVIEVMDDGRG--------MD 493 Query: 61 KELVRGDAYVVALGSYSANF 80 +E + A L S A Sbjct: 494 REAILAKAVAQGLASPDAEL 513 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 0.137 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: 837,591 Number of extensions: 38246 Number of successful extensions: 93 Number of sequences better than 1.0e-08: 11 Number of HSP's gapped: 89 Number of HSP's successfully gapped: 11 Length of query: 247 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 164 Effective length of database: 1,226,865 Effective search space: 201205860 Effective search space used: 201205860 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: 129 (54.3 bits)