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= 0001.0297.p (421 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase smal... 723 0.0 gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [H... 269 4e-73 gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase smal... 241 9e-65 gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase smal... 151 8e-38 gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [H... 108 1e-24 >gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 421 Score = 723 bits (1867), Expect = 0.0, Method: Compositional matrix adjust. Identities = 356/421 (84%), Positives = 377/421 (89%) Query: 1 MHICVLGAGVIGVTTAYRLLQDGHQVSLIDAHEHPGAGTSYGNGAQLSYSYVAPLADPSV 60 MHICV+GAGVIGVTTAYRLLQDGHQVSLID + PGAGTS GNGAQLSYSYVAPLADPSV Sbjct: 1 MHICVMGAGVIGVTTAYRLLQDGHQVSLIDERDQPGAGTSQGNGAQLSYSYVAPLADPSV 60 Query: 61 WSKWAYYLFSKDSPLTIRPTADAAQYRWLLGFLRCCNSPRVRQTTIDLLQLAFYSRDQLN 120 WSKWAYYLFSKDSPLTI+PT +AAQYRWL GFLR CN+ VRQTTIDLLQLAFYSRDQL Sbjct: 61 WSKWAYYLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSVRQTTIDLLQLAFYSRDQLT 120 Query: 121 QWNERLQLSFDYQRSGKLVMFTDVQGLDAAARQVQFQAQYGCKQEVLSAADCLRIEPALA 180 QWN RL+LSFD+QRSGKLVMFTD QGL+AAA QV+FQAQYGC+QEVL AA C+RIEPAL Sbjct: 121 QWNGRLKLSFDHQRSGKLVMFTDAQGLEAAAGQVRFQAQYGCQQEVLDAAQCIRIEPALG 180 Query: 181 GSQRAWTGGVYTPSEAAGDCPQFCRALVNAMQADPNFRFIGNTRVTAVRRAGRALRAVQA 240 SQR W GGVYT SE AGDCP FCRALV AMQADPNFRFIG R+TAVRR G AL AVQA Sbjct: 181 RSQRDWVGGVYTRSEEAGDCPAFCRALVAAMQADPNFRFIGGARITAVRRQGSALSAVQA 240 Query: 241 GEQWLEADRFVLALGADSTDFARQLDLRLPLYPLKGYSITVPLEDEASRAAAPQVSITDI 300 G +W+ A RFVLALGADS DFARQLDLRLPLYPLKGYSITVPLEDEASRAAAPQVSITDI Sbjct: 241 GNEWISAQRFVLALGADSADFARQLDLRLPLYPLKGYSITVPLEDEASRAAAPQVSITDI 300 Query: 301 ARKIVYARLGQRLRVAGRIELVGQDRRIPQAAIDQLKHGMRELFPACTLGEEATLSPWMG 360 ARKIVYARLGQRLRVAGRIELVGQDR IP AI +LK GMRELFP C LGE+A LSPWMG Sbjct: 301 ARKIVYARLGQRLRVAGRIELVGQDRSIPPRAIAELKQGMRELFPDCVLGEDARLSPWMG 360 Query: 361 FRPATPSGVPIVGASPVDNLYLNLGQGALGWTLACGSAALLADQIAGRKRAIDDAPFQYR 420 FRPATPSGVPIVGA PVDNLYLN+GQGALGWTLACGSAAL+ADQIAGR +IDD PF+YR Sbjct: 361 FRPATPSGVPIVGACPVDNLYLNIGQGALGWTLACGSAALIADQIAGRPCSIDDTPFRYR 420 Query: 421 S 421 + Sbjct: 421 T 421 >gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 433 Score = 269 bits (687), Expect = 4e-73, Method: Compositional matrix adjust. Identities = 157/415 (37%), Positives = 229/415 (55%), Gaps = 10/415 (2%) Query: 1 MHICVLGAGVIGVTTAYRLLQDGHQVSLIDAHEHPGAGTSYGNGAQLSYSYVAPLADPSV 60 M + +LG+GVIGVT+A+ L + GH V+++D P TS+GN Q+S Y +P A P + Sbjct: 1 MRVVILGSGVIGVTSAWYLARAGHDVTVLDRQPGPALETSFGNAGQISPGYASPWAAPGI 60 Query: 61 WSKWAYYLFSKDSPLTIRPTADAAQYRWLLGFLRCCNSPRVRQTTIDLLQLAFYSRDQLN 120 K ++F + +PL IR Q RW+ LR CN+ R +++LA YSRD L Sbjct: 61 PLKAIKWMFQEHAPLAIRLDGSFNQLRWMWQMLRNCNAERYAVNKERMVRLAEYSRDCLR 120 Query: 121 QWNERLQLSFDYQRSGKLVMFTDVQGLDAAARQVQFQAQYGCKQEVLSAADCLRIEPALA 180 + + ++ ++ G L +F + L+ AA+ + + G E+L+ EPALA Sbjct: 121 DLRADVGIPYEGRQQGTLQLFRSQEQLEGAAKDIAVLKEAGVPFELLTPDQLGNAEPALA 180 Query: 181 GSQRAWTGGVYTPSEAAGDCPQFCRALVN-AMQADPNFRFIGNTRVTAVRRAGRALRAVQ 239 + TGG+ P++ GDC F L A Q FR+ + A+ AG + V Sbjct: 181 KVRDKLTGGLRLPNDETGDCQLFTTRLATMAEQIGVKFRY--GVDIDALAMAGGKIAGVV 238 Query: 240 AGEQWLEADRFVLALGADSTDFARQLD--LRLPLYPLKGYSITVPLEDEASRAAAPQVSI 297 G++ ++AD +V+ALG+ S ++ +P+YPLKGYSITVP+ D +AAP +I Sbjct: 239 CGKELVQADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDA---SAAPVSTI 295 Query: 298 TDIARKIVYARLGQRLRVAGRIELVGQDRRIPQAAIDQLKHGMRELFPACTLGEEATLSP 357 D KI R R+RV G E+VG D + L+ + +LFP G+ A S Sbjct: 296 LDETYKIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGA--GDTAQASF 353 Query: 358 WMGFRPATPSGVPIVGASPVDNLYLNLGQGALGWTLACGSAALLADQIAGRKRAI 412 W G RP TP G P+VGA+PV NLY+N G G LGWT++CGS LLAD I+GR+ AI Sbjct: 354 WTGLRPMTPDGTPVVGATPVSNLYINTGHGTLGWTMSCGSGQLLADLISGRRPAI 408 >gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 436 Score = 241 bits (614), Expect = 9e-65, Method: Compositional matrix adjust. Identities = 151/425 (35%), Positives = 217/425 (51%), Gaps = 17/425 (4%) Query: 1 MHICVLGAGVIGVTTAYRLLQDGHQVSLIDAHEHPGAG--TSYGNGAQLSYSYVAPLADP 58 M + VLGAG+IG +A+ L + G+ V++ID PGA TS+ NG Q+S S+ P A+P Sbjct: 1 MKVIVLGAGIIGTASAWFLKKQGYDVTVID--RQPGAAQETSFANGCQISVSHAEPWANP 58 Query: 59 SVWSKWAYYLFSKDSPLTIRPTADAAQYRWLLGFLRCCNSPRVRQTTIDLLQLAFYSRDQ 118 + K +L +D+PL R + Q++W + FLR C + R + +++ L YSR Sbjct: 59 AAPMKVLKWLGKEDAPLLYRFRPEWLQWKWAVAFLRECTAARTDENIRNIVALCEYSRQT 118 Query: 119 LNQWNERLQLSFDYQRSGKLVMFTDVQGLDAAARQVQFQAQYGCKQEVLSAADCLRIEPA 178 L + +D+ G L +T+ + + + GC +E + A + +RIEPA Sbjct: 119 LQAVRAETGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRIEPA 178 Query: 179 LAGSQRAWTGGVYTPSEAAGDCPQFCRALV-NAMQADPNFRFIGNTRVTAVRRAGRALRA 237 LA + GG +T ++ +GD + L + +A FR+ AG A R Sbjct: 179 LASIRNKIVGGDFTATDESGDVFKLTTGLAKKSAEAGVEFRYSTTITRLITEGAGAAARV 238 Query: 238 V-------QAGEQWLEADRFVLALGADSTDFARQLDLRLPLYPLKGYSITVPLEDEASRA 290 + L+AD FV+A+G+ S + L + L LYP KGYS T + + Sbjct: 239 TGVEIINPDGRHEVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQITNP---D 295 Query: 291 AAPQVSITDIARKIVYARLGQRLRVAGRIELVGQDRRIPQAAIDQLKHGMRELFPACTLG 350 AAP VS+TD K+V +RLG RLRVAG EL G R + + + RELFP Sbjct: 296 AAPTVSLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGCDY 355 Query: 351 EEATLSPWMGFRPATPSGVPIVGASPVDNLYLNLGQGALGWTLACGSAALLADQIAGRKR 410 E T W G RP TPS VP VG + NLYLN G G LGWT+ CGS +A+ +AG Sbjct: 356 ENPTY--WTGLRPLTPSNVPYVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAEIVAGHVP 413 Query: 411 AIDDA 415 ID A Sbjct: 414 EIDFA 418 >gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 151 bits (382), Expect = 8e-38, Method: Compositional matrix adjust. Identities = 120/421 (28%), Positives = 199/421 (47%), Gaps = 22/421 (5%) Query: 3 ICVLGAGVIGVTTAYRLLQDGHQVSLIDAHEHPGAGTSYGNGAQLSYSYVAPLADPSVWS 62 I V+G G+ G+ +AY L G++V++I+ H ++G+ L+ PL P + Sbjct: 8 IAVIGGGLSGICSAYFLATKGYEVAVIERRAHVAEEATFGDSGLLAPGTAMPLTLPGALA 67 Query: 63 KWAYYLFSKDSPLTIRPTADAAQYRWLLGFLRCCNSPRVRQTTIDLLQLAFYSRDQLNQW 122 +A F + + + AD + RW+ R Q + L +L+ Y +D Sbjct: 68 TFACR-FQDEPRVLLASGADFGRRRWMRA-TRAAQQHHFAQHKLILSRLSAYGQD----L 121 Query: 123 NERLQLSFDYQRSGKLVMFTDVQGLDAAARQVQFQ---AQYGCKQEVLSAADCLRIEPAL 179 ++LQ ++ + +F + AAR Q +Q KQ L AA +EPA Sbjct: 122 TQQLQAHYNMEHENSAGVFHLFRQSAEAARLPALQEAASQCEYKQLTLDAAGIRALEPAF 181 Query: 180 AGSQRAWTGGVYTPSEAAGDCPQFCRALVNAMQA-DPNFRFIGNTRVTAVRR--AGRALR 236 + S+ A G +Y P + AG+ F + + NA QA +F F N+ V+++R GR Sbjct: 182 S-SEAALAGALYYPDDIAGNSVLFAKQMRNAAQALGVSFHF--NSTVSSIRSEFGGRVTL 238 Query: 237 AVQAGE--QWLEADRFVLALGADSTDFARQLDLRLPLYPLKGYSITVPLEDEASRAAAPQ 294 VQ+ L D V+A G S + LD LPL L+ YS VP+++ AP Sbjct: 239 EVQSPHLASHLTMDAVVVAAGMASAALLQPLDTSLPLRALQSYSALVPVKNPDD---APT 295 Query: 295 VSITDIARKIVYARLGQRLRVAGRIELVGQDRRIPQAAIDQLKHGMRELFPACTLGEEAT 354 +++ D + K+ RLG R+R++G + V + +P A+ L + +P +A Sbjct: 296 MALYDDSYKVAMTRLGSRIRISGLLGFVPASQTLPPKALRNLLKIAGDYYPNAANYNQAH 355 Query: 355 LSPWMGFRPATPSGVPIVGASPVDNLYLNLGQGALGWTLACGSAALLADQIAGRKRAIDD 414 W P+G+P+VG + N+++N+G G GW + GSA LL+D +AG + I Sbjct: 356 F--WSNSIAMMPTGLPVVGPTRQGNIFVNVGHGVTGWAASVGSARLLSDMMAGEETEIAT 413 Query: 415 A 415 A Sbjct: 414 A 414 >gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 428 Score = 108 bits (269), Expect = 1e-24, Method: Compositional matrix adjust. Identities = 114/421 (27%), Positives = 178/421 (42%), Gaps = 14/421 (3%) Query: 2 HICVLGAGVIGVTTAYRLLQDGHQVSLIDAHE-HPGAGTSYGNGAQLSYSYVAPLADPSV 60 H V+GAG +G+ +A L G +VSL+D + SYGN LS V P +P + Sbjct: 12 HAVVIGAGAVGLMSAIHALDQGLEVSLLDFNPVGSEEAASYGNAGWLSSHSVIPPVEPGM 71 Query: 61 WSKWAYYLFSKDSPLTIRPTADAAQYRWLLGFLRCCNSPRVRQTTIDLLQLAFYSRDQLN 120 W K YL PL+IR WLL L R+R T L L +R Sbjct: 72 WKKVPGYLMDPIGPLSIRWRYLPRLTPWLLRNLASARRERIRATARALRTLVVDARTLHL 131 Query: 121 QWNERLQLSFDYQRSGKLVMFTDVQGLDAAARQVQFQAQYGCKQEVLSAADCLRIEPALA 180 R ++ SG L ++ Q + A + + G + L A R EP L Sbjct: 132 DIARRAGVAHLIDTSGVLHVYRSRQQFEGDAFGWSVRRELGIQWSELEAEALRRREPDLD 191 Query: 181 GSQRAWTGGVYTPSEAAGDCPQFCRALVNAMQADPNFRFIG--NTRVTAVRRAGRALRAV 238 + G + AG C A + A+QA R + R T R L+AV Sbjct: 192 PAF-----GFAVQVDEAGHCKNPA-AYLQALQAYALARGAHRIDARATGFRIEEGRLKAV 245 Query: 239 QAGEQWLEADRFVLALGADSTDFARQLDLRLPLYPLKGYSITVPLEDEASRAAAPQVSIT 298 + D V+ GA S A Q R+ L +GY + ++A+RA P + ++ Sbjct: 246 LTETGEVACDAAVICAGARSKALAAQAGDRVQLESERGYHALIRGHEQAARARTPMM-LS 304 Query: 299 DIARKIVYARLGQRLRVAGRIELVGQDRRIPQAAIDQLKHGMRELFPACTLG-EEATLSP 357 + K++ ++ LR+AG++E + + ++ +LFP A + Sbjct: 305 EF--KVIATQMETGLRIAGQVEFASFEAAPDWRRGEIMRDIALKLFPGLPRDLPAADVRY 362 Query: 358 WMGFRPATPSGVPIVG-ASPVDNLYLNLGQGALGWTLACGSAALLADQIAGRKRAIDDAP 416 W+G RP+TP G+P +G A ++ G G +G + + ++A +AG+ ID AP Sbjct: 363 WLGRRPSTPDGMPCIGYARASSDIVHAYGHGHIGLGCSARTGRIVAQLLAGQTPEIDLAP 422 Query: 417 F 417 F Sbjct: 423 F 423 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 0.322 0.136 0.419 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: 1,399,413 Number of extensions: 61064 Number of successful extensions: 233 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 219 Number of HSP's successfully gapped: 5 Length of query: 421 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 333 Effective length of database: 1,203,190 Effective search space: 400662270 Effective search space used: 400662270 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)