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= 0001.1263.p (436 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase smal... 890 0.0 gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [H... 347 1e-96 gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase smal... 242 5e-65 gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase smal... 169 4e-43 gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [H... 106 4e-24 >gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 436 Score = 890 bits (2300), Expect = 0.0, Method: Compositional matrix adjust. Identities = 431/436 (98%), Positives = 433/436 (99%) Query: 1 MKVIVLGAGIIGTASAWFLKKQGYDVTVIERQPGAAQETSFANGCQISVSHAEPWANPAA 60 MKVIVLGAGIIGTASAWFLKKQGYDVTVI+RQPGAAQETSFANGCQISVSHAEPWANPAA Sbjct: 1 MKVIVLGAGIIGTASAWFLKKQGYDVTVIDRQPGAAQETSFANGCQISVSHAEPWANPAA 60 Query: 61 PMKVLKWLGKEDAPLLYRFRTEWLQWKWALAFLRECTAARTDENIRNIVALCEYSRQTLQ 120 PMKVLKWLGKEDAPLLYRFR EWLQWKWA+AFLRECTAARTDENIRNIVALCEYSRQTLQ Sbjct: 61 PMKVLKWLGKEDAPLLYRFRPEWLQWKWAVAFLRECTAARTDENIRNIVALCEYSRQTLQ 120 Query: 121 AVRAETGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRIEPALA 180 AVRAETGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRIEPALA Sbjct: 121 AVRAETGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRIEPALA 180 Query: 181 SIRNKIVGGDFTATDESGDVFKLTTGLAKKSEEAGVEFRYSTTITRLITEGTGAAARVTG 240 SIRNKIVGGDFTATDESGDVFKLTTGLAKKS EAGVEFRYSTTITRLITEG GAAARVTG Sbjct: 181 SIRNKIVGGDFTATDESGDVFKLTTGLAKKSAEAGVEFRYSTTITRLITEGAGAAARVTG 240 Query: 241 VEIINPDGRHEVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQITNPDAAPTV 300 VEIINPDGRHEVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQITNPDAAPTV Sbjct: 241 VEIINPDGRHEVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQITNPDAAPTV 300 Query: 301 SLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGCDYENPTY 360 SLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGCDYENPTY Sbjct: 301 SLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGCDYENPTY 360 Query: 361 WTGLRPLTPSNVPYVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAEIVAGHVPEIDFAFT 420 WTGLRPLTPSNVPYVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAEIVAGHVPEIDFAFT Sbjct: 361 WTGLRPLTPSNVPYVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAEIVAGHVPEIDFAFT 420 Query: 421 GLPRWNRARQVVTQAA 436 GLPRWNRARQVVTQAA Sbjct: 421 GLPRWNRARQVVTQAA 436 >gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 433 Score = 347 bits (889), Expect = 1e-96, Method: Compositional matrix adjust. Identities = 175/417 (41%), Positives = 251/417 (60%), Gaps = 11/417 (2%) Query: 1 MKVIVLGAGIIGTASAWFLKKQGYDVTVIERQPGAAQETSFANGCQISVSHAEPWANPAA 60 M+V++LG+G+IG SAW+L + G+DVTV++RQPG A ETSF N QIS +A PWA P Sbjct: 1 MRVVILGSGVIGVTSAWYLARAGHDVTVLDRQPGPALETSFGNAGQISPGYASPWAAPGI 60 Query: 61 PMKVLKWLGKEDAPLLYRFRTEWLQWKWALAFLRECTAARTDENIRNIVALCEYSRQTLQ 120 P+K +KW+ +E APL R + Q +W LR C A R N +V L EYSR L+ Sbjct: 61 PLKAIKWMFQEHAPLAIRLDGSFNQLRWMWQMLRNCNAERYAVNKERMVRLAEYSRDCLR 120 Query: 121 AVRAETGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRIEPALA 180 +RA+ GI Y+ +G L + +++ + + ++++ G P E + D++ EPALA Sbjct: 121 DLRADVGIPYEGRQQGTLQLFRSQEQLEGAAKDIAVLKEAGVPFELLTPDQLGNAEPALA 180 Query: 181 SIRNKIVGGDFTATDESGDVFKLTTGLAKKSEEAGVEFRYSTTITRLITEGTGAAARVTG 240 +R+K+ GG DE+GD TT LA +E+ GV+FRY I L G A V G Sbjct: 181 KVRDKLTGGLRLPNDETGDCQLFTTRLATMAEQIGVKFRYGVDIDALAMAGGKIAGVVCG 240 Query: 241 VEIINPDGRHEVLKADTFVVAMGSFSQQLVKPL-GIDLL-LYPGKGYSATYQITNPDAAP 298 E++ +AD++VVA+GS+S QL+ + G+ + +YP KGYS T IT+ AAP Sbjct: 241 KELV---------QADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDASAAP 291 Query: 299 TVSLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGCDYENP 358 ++ D+ YK+ V+R DR+RV G E+ GY L R + +LFP D Sbjct: 292 VSTILDETYKIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGAGDTAQA 351 Query: 359 TYWTGLRPLTPSNVPYVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAEIVAGHVPEI 415 ++WTGLRP+TP P VG T +NLY+NTGHGTLGWTM CGSG+ +A++++G P I Sbjct: 352 SFWTGLRPMTPDGTPVVGATPVSNLYINTGHGTLGWTMSCGSGQLLADLISGRRPAI 408 >gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 421 Score = 242 bits (617), Expect = 5e-65, Method: Compositional matrix adjust. Identities = 152/425 (35%), Positives = 220/425 (51%), Gaps = 21/425 (4%) Query: 1 MKVIVLGAGIIGTASAWFLKKQGYDVTVIER--QPGAAQETSFANGCQISVSHAEPWANP 58 M + V+GAG+IG +A+ L + G+ V++I+ QPGA TS NG Q+S S+ P A+P Sbjct: 1 MHICVMGAGVIGVTTAYRLLQDGHQVSLIDERDQPGAG--TSQGNGAQLSYSYVAPLADP 58 Query: 59 AAPMKVLKWLGKEDAPLLYRFRTEWLQWKWALAFLRECTAARTDENIRNIVALCEYSRQT 118 + K +L +D+PL + E Q++W FLR C A + +++ L YSR Sbjct: 59 SVWSKWAYYLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSVRQTTIDLLQLAFYSRDQ 118 Query: 119 LQAVRAETGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRIEPA 178 L + +DH G L +T+ + + + + GC +E + A + +RIEPA Sbjct: 119 LTQWNGRLKLSFDHQRSGKLVMFTDAQGLEAAAGQVRFQAQYGCQQEVLDAAQCIRIEPA 178 Query: 179 LASIRNKIVGGDFTATDESGDVFKLTTGLAKKSEEAGVEFRY--STTITRLITEGTGAAA 236 L + VGG +T ++E+GD L + +A FR+ IT + +G+ +A Sbjct: 179 LGRSQRDWVGGVYTRSEEAGDCPAFCRALV-AAMQADPNFRFIGGARITAVRRQGSALSA 237 Query: 237 RVTGVEIINPDGRHEVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQITNP-- 294 G +E + A FV+A+G+ S + L + L LYP KGYS T + + Sbjct: 238 VQAG---------NEWISAQRFVLALGADSADFARQLDLRLPLYPLKGYSITVPLEDEAS 288 Query: 295 -DAAPTVSLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGC 353 AAP VS+TD K+V +RLG RLRVAG EL G R + + + RELFPD Sbjct: 289 RAAAPQVSITDIARKIVYARLGQRLRVAGRIELVGQDRSIPPRAIAELKQGMRELFPDCV 348 Query: 354 DYENP--TYWTGLRPLTPSNVPYVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAEIVAGH 411 E+ + W G RP TPS VP VG NLYLN G G LGWT+ CGS IA+ +AG Sbjct: 349 LGEDARLSPWMGFRPATPSGVPIVGACPVDNLYLNIGQGALGWTLACGSAALIADQIAGR 408 Query: 412 VPEID 416 ID Sbjct: 409 PCSID 413 >gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 169 bits (428), Expect = 4e-43, Method: Compositional matrix adjust. Identities = 117/429 (27%), Positives = 213/429 (49%), Gaps = 22/429 (5%) Query: 2 KVIVLGAGIIGTASAWFLKKQGYDVTVIERQPGAAQETSFANGCQISVSHAEPWANPAAP 61 ++ V+G G+ G SA+FL +GY+V VIER+ A+E +F + ++ A P P A Sbjct: 7 QIAVIGGGLSGICSAYFLATKGYEVAVIERRAHVAEEATFGDSGLLAPGTAMPLTLPGA- 65 Query: 62 MKVLKWLGKEDAPLLYRFRTEWLQWKWALAFLRECTAARTDENIRN---IVALCEYSRQT 118 + +++ +L ++ + +W +R AA+ ++ + L Y + Sbjct: 66 LATFACRFQDEPRVLLASGADFGRRRW----MRATRAAQQHHFAQHKLILSRLSAYGQDL 121 Query: 119 LQAVRAETGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADE--VVRIE 176 Q ++A +++++ + G+ H + + E LPA + C + + D + +E Sbjct: 122 TQQLQAHYNMEHEN-SAGVFHLFRQSAE-AARLPALQEAAS-QCEYKQLTLDAAGIRALE 178 Query: 177 PALASIRNKIVGGDFTATDESGDVFKLTTGLAKKSEEAGVEFRYSTTITRLITEGTGAAA 236 PA +S + G + D +G+ + ++ GV F +++T++ + +E G Sbjct: 179 PAFSS-EAALAGALYYPDDIAGNSVLFAKQMRNAAQALGVSFHFNSTVSSIRSEFGG--- 234 Query: 237 RVTGVEIINPD-GRHEVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQITNPD 295 RVT +E+ +P H L D VVA G S L++PL L L + YSA + NPD Sbjct: 235 RVT-LEVQSPHLASH--LTMDAVVVAAGMASAALLQPLDTSLPLRALQSYSALVPVKNPD 291 Query: 296 AAPTVSLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGCDY 355 APT++L DD YK+ ++RLG R+R++G ++ L + + + +P+ +Y Sbjct: 292 DAPTMALYDDSYKVAMTRLGSRIRISGLLGFVPASQTLPPKALRNLLKIAGDYYPNAANY 351 Query: 356 ENPTYWTGLRPLTPSNVPYVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAEIVAGHVPEI 415 +W+ + P+ +P VG T+ N+++N GHG GW GS R +++++AG EI Sbjct: 352 NQAHFWSNSIAMMPTGLPVVGPTRQGNIFVNVGHGVTGWAASVGSARLLSDMMAGEETEI 411 Query: 416 DFAFTGLPR 424 A LPR Sbjct: 412 ATAGL-LPR 419 >gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 428 Score = 106 bits (264), Expect = 4e-24, Method: Compositional matrix adjust. Identities = 109/431 (25%), Positives = 178/431 (41%), Gaps = 39/431 (9%) Query: 4 IVLGAGIIGTASAWFLKKQGYDVTVIERQP-GAAQETSFANGCQISVSHAEPWANPAAPM 62 +V+GAG +G SA QG +V++++ P G+ + S+ N +S P P Sbjct: 14 VVIGAGAVGLMSAIHALDQGLEVSLLDFNPVGSEEAASYGNAGWLSSHSVIPPVEPGMWK 73 Query: 63 KVLKWLGKEDAPLLYRFRTEWLQWKWALAFLRECTAARTDENIRNIVALCEYSRQTLQAV 122 KV +L PL R+R W L L R R + L +R + Sbjct: 74 KVPGYLMDPIGPLSIRWRYLPRLTPWLLRNLASARRERIRATARALRTLVVDARTLHLDI 133 Query: 123 RAETGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRIEPALASI 182 G+ + T G+LH Y ++F+ + R+LG + A+ + R EP L Sbjct: 134 ARRAGVAHLIDTSGVLHVYRSRQQFEGDAFGWSVRRELGIQWSELEAEALRRREPDL--- 190 Query: 183 RNKIVGGDFTATDESGDVFKLTTGLAKKSEEAGVEFRYSTTITRLITEGTGAA---ARVT 239 G DE+G K+ A ++ + + R GA AR T Sbjct: 191 --DPAFGFAVQVDEAGHC---------KNPAAYLQALQAYALAR------GAHRIDARAT 233 Query: 240 GVEIINPDGRHEVL-------KADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQIT 292 G I +GR + + D V+ G+ S+ L G + L +GY A + Sbjct: 234 GFRI--EEGRLKAVLTETGEVACDAAVICAGARSKALAAQAGDRVQLESERGYHALIRGH 291 Query: 293 NPDAAPTVSLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDG 352 A + +K++ +++ LR+AG E + + R E + +LFP G Sbjct: 292 EQAARARTPMMLSEFKVIATQMETGLRIAGQVEFASFEAAPDWRRGEIMRDIALKLFP-G 350 Query: 353 CDYENPT----YWTGLRPLTPSNVPYVGKTKFANLYLNT-GHGTLGWTMGCGSGRAIAEI 407 + P YW G RP TP +P +G + ++ ++ GHG +G +GR +A++ Sbjct: 351 LPRDLPAADVRYWLGRRPSTPDGMPCIGYARASSDIVHAYGHGHIGLGCSARTGRIVAQL 410 Query: 408 VAGHVPEIDFA 418 +AG PEID A Sbjct: 411 LAGQTPEIDLA 421 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 0.412 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: 1,436,366 Number of extensions: 61670 Number of successful extensions: 235 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 226 Number of HSP's successfully gapped: 6 Length of query: 436 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 348 Effective length of database: 1,203,190 Effective search space: 418710120 Effective search space used: 418710120 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)