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= 0034.0108.p (445 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... 895 0.0 gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [H... 350 1e-97 gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase smal... 241 1e-64 gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase smal... 166 5e-42 gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [H... 105 7e-24 >gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 436 Score = 895 bits (2314), Expect = 0.0, Method: Compositional matrix adjust. Identities = 431/436 (98%), Positives = 435/436 (99%) Query: 10 MKVIVLGAGIIGTASAWFLKKQGYDVTVIDRQPGAAQETSFANGCQISVSHAEPWANPAA 69 MKVIVLGAGIIGTASAWFLKKQGYDVTVIDRQPGAAQETSFANGCQISVSHAEPWANPAA Sbjct: 1 MKVIVLGAGIIGTASAWFLKKQGYDVTVIDRQPGAAQETSFANGCQISVSHAEPWANPAA 60 Query: 70 PMKVLKWLGKEDAPLLYRFRPEWLQWKWAVAFLRECTAARTDENIRNIVALCEYSRQTLQ 129 PMKVLKWLGKEDAPLLYRFRPEWLQWKWAVAFLRECTAARTDENIRNIVALCEYSRQTLQ Sbjct: 61 PMKVLKWLGKEDAPLLYRFRPEWLQWKWAVAFLRECTAARTDENIRNIVALCEYSRQTLQ 120 Query: 130 AVRADTGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRIEPALA 189 AVRA+TGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRIEPALA Sbjct: 121 AVRAETGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRIEPALA 180 Query: 190 SIRNKIVGGDFTATDESGDVFKLTTGLAKKSEEAGVEFRYSTSITRLITEGAGAAARVTG 249 SIRNKIVGGDFTATDESGDVFKLTTGLAKKS EAGVEFRYST+ITRLITEGAGAAARVTG Sbjct: 181 SIRNKIVGGDFTATDESGDVFKLTTGLAKKSAEAGVEFRYSTTITRLITEGAGAAARVTG 240 Query: 250 VEVINPDGRHEVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQITNPDAAPTV 309 VE+INPDGRHEVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQITNPDAAPTV Sbjct: 241 VEIINPDGRHEVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQITNPDAAPTV 300 Query: 310 SLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGCDYENPTY 369 SLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGCDYENPTY Sbjct: 301 SLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGCDYENPTY 360 Query: 370 WTGLRPLTPSNVPYVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAEIVSGHVPEIDFAFT 429 WTGLRPLTPSNVPYVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAEIV+GHVPEIDFAFT Sbjct: 361 WTGLRPLTPSNVPYVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAEIVAGHVPEIDFAFT 420 Query: 430 GLPRWNRARQVVTQAA 445 GLPRWNRARQVVTQAA Sbjct: 421 GLPRWNRARQVVTQAA 436 >gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 433 Score = 350 bits (899), Expect = 1e-97, Method: Compositional matrix adjust. Identities = 178/417 (42%), Positives = 251/417 (60%), Gaps = 11/417 (2%) Query: 10 MKVIVLGAGIIGTASAWFLKKQGYDVTVIDRQPGAAQETSFANGCQISVSHAEPWANPAA 69 M+V++LG+G+IG SAW+L + G+DVTV+DRQPG A ETSF N QIS +A PWA P Sbjct: 1 MRVVILGSGVIGVTSAWYLARAGHDVTVLDRQPGPALETSFGNAGQISPGYASPWAAPGI 60 Query: 70 PMKVLKWLGKEDAPLLYRFRPEWLQWKWAVAFLRECTAARTDENIRNIVALCEYSRQTLQ 129 P+K +KW+ +E APL R + Q +W LR C A R N +V L EYSR L+ Sbjct: 61 PLKAIKWMFQEHAPLAIRLDGSFNQLRWMWQMLRNCNAERYAVNKERMVRLAEYSRDCLR 120 Query: 130 AVRADTGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRIEPALA 189 +RAD GI Y+ +G L + +++ + + ++++ G P E + D++ EPALA Sbjct: 121 DLRADVGIPYEGRQQGTLQLFRSQEQLEGAAKDIAVLKEAGVPFELLTPDQLGNAEPALA 180 Query: 190 SIRNKIVGGDFTATDESGDVFKLTTGLAKKSEEAGVEFRYSTSITRLITEGAGAAARVTG 249 +R+K+ GG DE+GD TT LA +E+ GV+FRY I L G A V G Sbjct: 181 KVRDKLTGGLRLPNDETGDCQLFTTRLATMAEQIGVKFRYGVDIDALAMAGGKIAGVVCG 240 Query: 250 VEVINPDGRHEVLKADTFVVAMGSFSQQLVKPL-GIDLL-LYPGKGYSATYQITNPDAAP 307 E+++AD++VVA+GS+S QL+ + G+ + +YP KGYS T IT+ AAP Sbjct: 241 ---------KELVQADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDASAAP 291 Query: 308 TVSLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGCDYENP 367 ++ D+ YK+ V+R DR+RV G E+ GY L R + +LFP D Sbjct: 292 VSTILDETYKIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGAGDTAQA 351 Query: 368 TYWTGLRPLTPSNVPYVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAEIVSGHVPEI 424 ++WTGLRP+TP P VG T +NLY+NTGHGTLGWTM CGSG+ +A+++SG P I Sbjct: 352 SFWTGLRPMTPDGTPVVGATPVSNLYINTGHGTLGWTMSCGSGQLLADLISGRRPAI 408 >gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 421 Score = 241 bits (614), Expect = 1e-64, Method: Compositional matrix adjust. Identities = 152/425 (35%), Positives = 220/425 (51%), Gaps = 21/425 (4%) Query: 10 MKVIVLGAGIIGTASAWFLKKQGYDVTVIDR--QPGAAQETSFANGCQISVSHAEPWANP 67 M + V+GAG+IG +A+ L + G+ V++ID QPGA TS NG Q+S S+ P A+P Sbjct: 1 MHICVMGAGVIGVTTAYRLLQDGHQVSLIDERDQPGAG--TSQGNGAQLSYSYVAPLADP 58 Query: 68 AAPMKVLKWLGKEDAPLLYRFRPEWLQWKWAVAFLRECTAARTDENIRNIVALCEYSRQT 127 + K +L +D+PL + E Q++W FLR C A + +++ L YSR Sbjct: 59 SVWSKWAYYLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSVRQTTIDLLQLAFYSRDQ 118 Query: 128 LQAVRADTGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRIEPA 187 L + +DH G L +T+ + + + + GC +E + A + +RIEPA Sbjct: 119 LTQWNGRLKLSFDHQRSGKLVMFTDAQGLEAAAGQVRFQAQYGCQQEVLDAAQCIRIEPA 178 Query: 188 LASIRNKIVGGDFTATDESGDVFKLTTGLAKKSEEAGVEFRY--STSITRLITEGAGAAA 245 L + VGG +T ++E+GD L + +A FR+ IT + +G+ +A Sbjct: 179 LGRSQRDWVGGVYTRSEEAGDCPAFCRALV-AAMQADPNFRFIGGARITAVRRQGSALSA 237 Query: 246 RVTGVEVINPDGRHEVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQITNP-- 303 G +E + A FV+A+G+ S + L + L LYP KGYS T + + Sbjct: 238 VQAG---------NEWISAQRFVLALGADSADFARQLDLRLPLYPLKGYSITVPLEDEAS 288 Query: 304 -DAAPTVSLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGC 362 AAP VS+TD K+V +RLG RLRVAG EL G R + + + RELFPD Sbjct: 289 RAAAPQVSITDIARKIVYARLGQRLRVAGRIELVGQDRSIPPRAIAELKQGMRELFPDCV 348 Query: 363 DYENP--TYWTGLRPLTPSNVPYVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAEIVSGH 420 E+ + W G RP TPS VP VG NLYLN G G LGWT+ CGS IA+ ++G Sbjct: 349 LGEDARLSPWMGFRPATPSGVPIVGACPVDNLYLNIGQGALGWTLACGSAALIADQIAGR 408 Query: 421 VPEID 425 ID Sbjct: 409 PCSID 413 >gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 166 bits (419), Expect = 5e-42, Method: Compositional matrix adjust. Identities = 115/429 (26%), Positives = 213/429 (49%), Gaps = 22/429 (5%) Query: 11 KVIVLGAGIIGTASAWFLKKQGYDVTVIDRQPGAAQETSFANGCQISVSHAEPWANPAAP 70 ++ V+G G+ G SA+FL +GY+V VI+R+ A+E +F + ++ A P P A Sbjct: 7 QIAVIGGGLSGICSAYFLATKGYEVAVIERRAHVAEEATFGDSGLLAPGTAMPLTLPGA- 65 Query: 71 MKVLKWLGKEDAPLLYRFRPEWLQWKWAVAFLRECTAARTDENIRN---IVALCEYSRQT 127 + +++ +L ++ + +W +R AA+ ++ + L Y + Sbjct: 66 LATFACRFQDEPRVLLASGADFGRRRW----MRATRAAQQHHFAQHKLILSRLSAYGQDL 121 Query: 128 LQAVRADTGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADE--VVRIE 185 Q ++A +++++ + G+ H + + E LPA + C + + D + +E Sbjct: 122 TQQLQAHYNMEHEN-SAGVFHLFRQSAE-AARLPALQEAAS-QCEYKQLTLDAAGIRALE 178 Query: 186 PALASIRNKIVGGDFTATDESGDVFKLTTGLAKKSEEAGVEFRYSTSITRLITEGAGAAA 245 PA +S + G + D +G+ + ++ GV F ++++++ + +E G Sbjct: 179 PAFSS-EAALAGALYYPDDIAGNSVLFAKQMRNAAQALGVSFHFNSTVSSIRSEFGG--- 234 Query: 246 RVTGVEVINPD-GRHEVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQITNPD 304 RVT +EV +P H L D VVA G S L++PL L L + YSA + NPD Sbjct: 235 RVT-LEVQSPHLASH--LTMDAVVVAAGMASAALLQPLDTSLPLRALQSYSALVPVKNPD 291 Query: 305 AAPTVSLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGCDY 364 APT++L DD YK+ ++RLG R+R++G ++ L + + + +P+ +Y Sbjct: 292 DAPTMALYDDSYKVAMTRLGSRIRISGLLGFVPASQTLPPKALRNLLKIAGDYYPNAANY 351 Query: 365 ENPTYWTGLRPLTPSNVPYVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAEIVSGHVPEI 424 +W+ + P+ +P VG T+ N+++N GHG GW GS R ++++++G EI Sbjct: 352 NQAHFWSNSIAMMPTGLPVVGPTRQGNIFVNVGHGVTGWAASVGSARLLSDMMAGEETEI 411 Query: 425 DFAFTGLPR 433 A LPR Sbjct: 412 ATAGL-LPR 419 >gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 428 Score = 105 bits (262), Expect = 7e-24, Method: Compositional matrix adjust. Identities = 110/434 (25%), Positives = 183/434 (42%), Gaps = 45/434 (10%) Query: 13 IVLGAGIIGTASAWFLKKQGYDVTVIDRQP-GAAQETSFANGCQISVSHAEPWANPAAPM 71 +V+GAG +G SA QG +V+++D P G+ + S+ N +S P P Sbjct: 14 VVIGAGAVGLMSAIHALDQGLEVSLLDFNPVGSEEAASYGNAGWLSSHSVIPPVEPGMWK 73 Query: 72 KVLKWLGKEDAPLLYRFR--PEWLQWKWAVAFLRECTAARTDE---NIRNIVALCEYSRQ 126 KV +L PL R+R P W LR +AR + R + L +R Sbjct: 74 KVPGYLMDPIGPLSIRWRYLPRLTPW-----LLRNLASARRERIRATARALRTLVVDART 128 Query: 127 TLQAVRADTGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRIEP 186 + G+ + T G+LH Y ++F+ + R+LG + A+ + R EP Sbjct: 129 LHLDIARRAGVAHLIDTSGVLHVYRSRQQFEGDAFGWSVRRELGIQWSELEAEALRRREP 188 Query: 187 ALASIRNKIVGGDFTATDESGDVFKLTTGLAKKSEEAGVEFRYSTSITRLITEGAGAA-A 245 L G DE+G K+ A ++ + ++ R GA A Sbjct: 189 DL-----DPAFGFAVQVDEAGHC---------KNPAAYLQALQAYALAR----GAHRIDA 230 Query: 246 RVTGVEVINPDGRHEVL-------KADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATY 298 R TG + +GR + + D V+ G+ S+ L G + L +GY A Sbjct: 231 RATGFRI--EEGRLKAVLTETGEVACDAAVICAGARSKALAAQAGDRVQLESERGYHALI 288 Query: 299 QITNPDAAPTVSLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELF 358 + A + +K++ +++ LR+AG E + + R E + +LF Sbjct: 289 RGHEQAARARTPMMLSEFKVIATQMETGLRIAGQVEFASFEAAPDWRRGEIMRDIALKLF 348 Query: 359 PDGCDYENPT----YWTGLRPLTPSNVPYVGKTKFANLYLNT-GHGTLGWTMGCGSGRAI 413 P G + P YW G RP TP +P +G + ++ ++ GHG +G +GR + Sbjct: 349 P-GLPRDLPAADVRYWLGRRPSTPDGMPCIGYARASSDIVHAYGHGHIGLGCSARTGRIV 407 Query: 414 AEIVSGHVPEIDFA 427 A++++G PEID A Sbjct: 408 AQLLAGQTPEIDLA 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: 1,451,123 Number of extensions: 62750 Number of successful extensions: 233 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: 445 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 357 Effective length of database: 1,203,190 Effective search space: 429538830 Effective search space used: 429538830 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 (21.7 bits) S2: 132 (55.5 bits)