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= 0020.0156.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... 843 0.0 gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [H... 268 8e-73 gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase smal... 243 1e-65 gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase smal... 136 4e-33 gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [H... 105 5e-24 >gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 421 Score = 843 bits (2179), Expect = 0.0, Method: Compositional matrix adjust. Identities = 417/421 (99%), Positives = 418/421 (99%) Query: 1 MHICVMGAGVIGVTTAYRLLQDGHQVSLIDERDQPGAGTSQGNGAQLSYSYVAPLADPSV 60 MHICVMGAGVIGVTTAYRLLQDGHQVSLIDERDQPGAGTSQGNGAQLSYSYVAPLADPSV Sbjct: 1 MHICVMGAGVIGVTTAYRLLQDGHQVSLIDERDQPGAGTSQGNGAQLSYSYVAPLADPSV 60 Query: 61 WSKWAYYLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSVRQTTIDLLQLAFYSRDQLT 120 WSKWAYYLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSVRQTTIDLLQLAFYSRDQLT Sbjct: 61 WSKWAYYLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSVRQTTIDLLQLAFYSRDQLT 120 Query: 121 QWNGRLKLPFDHQRSGKLVMFTDAQGLEAAAGQVRFQAQYGCQQEVLDAAQCIRIEPALG 180 QWNGRLKL FDHQRSGKLVMFTDAQGLEAAAGQVRFQAQYGCQQEVLDAAQCIRIEPALG Sbjct: 121 QWNGRLKLSFDHQRSGKLVMFTDAQGLEAAAGQVRFQAQYGCQQEVLDAAQCIRIEPALG 180 Query: 181 RSQRDWVGGVYTPSEEAGDCPAFCRALVAAMQADPNFRFIGGARITAVRRQGSALSAVQA 240 RSQRDWVGGVYT SEEAGDCPAFCRALVAAMQADPNFRFIGGARITAVRRQGSALSAVQA Sbjct: 181 RSQRDWVGGVYTRSEEAGDCPAFCRALVAAMQADPNFRFIGGARITAVRRQGSALSAVQA 240 Query: 241 GNEWISAQRFVLALGADSADFARRLDLRLPLYPLKGYSITVPLEDEASRAAAPQVSITDI 300 GNEWISAQRFVLALGADSADFAR+LDLRLPLYPLKGYSITVPLEDEASRAAAPQVSITDI Sbjct: 241 GNEWISAQRFVLALGADSADFARQLDLRLPLYPLKGYSITVPLEDEASRAAAPQVSITDI 300 Query: 301 ARKIVYARLGQRLRVAGRIELVGQDRSIPSRAIAELKQGMRELFPDCVLGEDARLSPWMG 360 ARKIVYARLGQRLRVAGRIELVGQDRSIP RAIAELKQGMRELFPDCVLGEDARLSPWMG Sbjct: 301 ARKIVYARLGQRLRVAGRIELVGQDRSIPPRAIAELKQGMRELFPDCVLGEDARLSPWMG 360 Query: 361 FRPATPSGVPIVGACPVDNLYLNIGQGALGWTLACGSAALIADQIAGRPCSIDDTPFRYR 420 FRPATPSGVPIVGACPVDNLYLNIGQGALGWTLACGSAALIADQIAGRPCSIDDTPFRYR Sbjct: 361 FRPATPSGVPIVGACPVDNLYLNIGQGALGWTLACGSAALIADQIAGRPCSIDDTPFRYR 420 Query: 421 T 421 T Sbjct: 421 T 421 >gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 433 Score = 268 bits (684), Expect = 8e-73, Method: Compositional matrix adjust. Identities = 156/414 (37%), Positives = 227/414 (54%), Gaps = 8/414 (1%) Query: 1 MHICVMGAGVIGVTTAYRLLQDGHQVSLIDERDQPGAGTSQGNGAQLSYSYVAPLADPSV 60 M + ++G+GVIGVT+A+ L + GH V+++D + P TS GN Q+S Y +P A P + Sbjct: 1 MRVVILGSGVIGVTSAWYLARAGHDVTVLDRQPGPALETSFGNAGQISPGYASPWAAPGI 60 Query: 61 WSKWAYYLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSVRQTTIDLLQLAFYSRDQLT 120 K ++F + +PL I+ Q RW+ LR CNA +++LA YSRD L Sbjct: 61 PLKAIKWMFQEHAPLAIRLDGSFNQLRWMWQMLRNCNAERYAVNKERMVRLAEYSRDCLR 120 Query: 121 QWNGRLKLPFDHQRSGKLVMFTDAQGLEAAAGQVRFQAQYGCQQEVLDAAQCIRIEPALG 180 + +P++ ++ G L +F + LE AA + + G E+L Q EPAL Sbjct: 121 DLRADVGIPYEGRQQGTLQLFRSQEQLEGAAKDIAVLKEAGVPFELLTPDQLGNAEPALA 180 Query: 181 RSQRDWVGGVYTPSEEAGDCPAFCRALVAAMQADPNFRFIGGARITAVRRQGSALSAVQA 240 + + GG+ P++E GDC F L A M +F G I A+ G ++ V Sbjct: 181 KVRDKLTGGLRLPNDETGDCQLFTTRL-ATMAEQIGVKFRYGVDIDALAMAGGKIAGVVC 239 Query: 241 GNEWISAQRFVLALGADSADFARRLD--LRLPLYPLKGYSITVPLEDEASRAAAPQVSIT 298 G E + A +V+ALG+ S + +P+YPLKGYSITVP+ D +AAP +I Sbjct: 240 GKELVQADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDA---SAAPVSTIL 296 Query: 299 DIARKIVYARLGQRLRVAGRIELVGQDRSIPSRAIAELKQGMRELFPDCVLGEDARLSPW 358 D KI R R+RV G E+VG D ++ ++ A L+ + +LFP G+ A+ S W Sbjct: 297 DETYKIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGA--GDTAQASFW 354 Query: 359 MGFRPATPSGVPIVGACPVDNLYLNIGQGALGWTLACGSAALIADQIAGRPCSI 412 G RP TP G P+VGA PV NLY+N G G LGWT++CGS L+AD I+GR +I Sbjct: 355 TGLRPMTPDGTPVVGATPVSNLYINTGHGTLGWTMSCGSGQLLADLISGRRPAI 408 >gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 436 Score = 243 bits (621), Expect = 1e-65, Method: Compositional matrix adjust. Identities = 153/424 (36%), Positives = 219/424 (51%), Gaps = 19/424 (4%) Query: 1 MHICVMGAGVIGVTTAYRLLQDGHQVSLIDERDQPGAG--TSQGNGAQLSYSYVAPLADP 58 M + V+GAG+IG +A+ L + G+ V++ID QPGA TS NG Q+S S+ P A+P Sbjct: 1 MKVIVLGAGIIGTASAWFLKKQGYDVTVIDR--QPGAAQETSFANGCQISVSHAEPWANP 58 Query: 59 SVWSKWAYYLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSVRQTTIDLLQLAFYSRDQ 118 + K +L +D+PL + E Q++W FLR C A + +++ L YSR Sbjct: 59 AAPMKVLKWLGKEDAPLLYRFRPEWLQWKWAVAFLRECTAARTDENIRNIVALCEYSRQT 118 Query: 119 LTQWNGRLKLPFDHQRSGKLVMFTDAQGLEAAAGQVRFQAQYGCQQEVLDAAQCIRIEPA 178 L + +DH G L +T+ + + + + GC +E + A + +RIEPA Sbjct: 119 LQAVRAETGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRIEPA 178 Query: 179 LGRSQRDWVGGVYTPSEEAGDCPAFCRALVAAMQADPNFRFIGGARITAVRRQGSALSAV 238 L + VGG +T ++E+GD L A A+ F IT + +G+ +A Sbjct: 179 LASIRNKIVGGDFTATDESGDVFKLTTGL-AKKSAEAGVEFRYSTTITRLITEGAGAAAR 237 Query: 239 QAG---------NEWISAQRFVLALGADSADFARRLDLRLPLYPLKGYSITVPLEDEASR 289 G +E + A FV+A+G+ S + L + L LYP KGYS T + + Sbjct: 238 VTGVEIINPDGRHEVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQITNP--- 294 Query: 290 AAAPQVSITDIARKIVYARLGQRLRVAGRIELVGQDRSIPSRAIAELKQGMRELFPDCVL 349 AAP VS+TD K+V +RLG RLRVAG EL G R + + + + RELFPD Sbjct: 295 DAAPTVSLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGCD 354 Query: 350 GEDARLSPWMGFRPATPSGVPIVGACPVDNLYLNIGQGALGWTLACGSAALIADQIAGRP 409 E+ + W G RP TPS VP VG NLYLN G G LGWT+ CGS IA+ +AG Sbjct: 355 YENP--TYWTGLRPLTPSNVPYVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAEIVAGHV 412 Query: 410 CSID 413 ID Sbjct: 413 PEID 416 >gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 136 bits (342), Expect = 4e-33, Method: Compositional matrix adjust. Identities = 113/418 (27%), Positives = 196/418 (46%), Gaps = 22/418 (5%) Query: 3 ICVMGAGVIGVTTAYRLLQDGHQVSLIDERDQPGAGTSQGNGAQLSYSYVAPLADPSVWS 62 I V+G G+ G+ +AY L G++V++I+ R + G+ L+ PL P + Sbjct: 8 IAVIGGGLSGICSAYFLATKGYEVAVIERRAHVAEEATFGDSGLLAPGTAMPLTLPGALA 67 Query: 63 KWAYYLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSVRQTTIDLLQLAFYSRDQLTQW 122 +A F + + + + + RW+ R Q + L +L+ Y +D Q Sbjct: 68 TFACR-FQDEPRVLLASGADFGRRRWMRA-TRAAQQHHFAQHKLILSRLSAYGQDLTQQL 125 Query: 123 NGRLKLPFDHQRS-GKLVMFTDAQGLEAAAGQVRFQAQYGCQ--QEVLDAAQCIRIEPAL 179 + +H+ S G +F Q EAA +A C+ Q LDAA +EPA Sbjct: 126 QAHYNM--EHENSAGVFHLFR--QSAEAARLPALQEAASQCEYKQLTLDAAGIRALEPAF 181 Query: 180 GRSQRDWVGGVYTPSEEAGDCPAFCRALVAAMQA-DPNFRFIGGARITAVRRQ--GSALS 236 S+ G +Y P + AG+ F + + A QA +F F + ++++R + G Sbjct: 182 S-SEAALAGALYYPDDIAGNSVLFAKQMRNAAQALGVSFHF--NSTVSSIRSEFGGRVTL 238 Query: 237 AVQAGN--EWISAQRFVLALGADSADFARRLDLRLPLYPLKGYSITVPLEDEASRAAAPQ 294 VQ+ + ++ V+A G SA + LD LPL L+ YS VP+++ AP Sbjct: 239 EVQSPHLASHLTMDAVVVAAGMASAALLQPLDTSLPLRALQSYSALVPVKNPDD---APT 295 Query: 295 VSITDIARKIVYARLGQRLRVAGRIELVGQDRSIPSRAIAELKQGMRELFPDCVLGEDAR 354 +++ D + K+ RLG R+R++G + V +++P +A+ L + + +P+ A Sbjct: 296 MALYDDSYKVAMTRLGSRIRISGLLGFVPASQTLPPKALRNLLKIAGDYYPNAANYNQAH 355 Query: 355 LSPWMGFRPATPSGVPIVGACPVDNLYLNIGQGALGWTLACGSAALIADQIAGRPCSI 412 W P+G+P+VG N+++N+G G GW + GSA L++D +AG I Sbjct: 356 F--WSNSIAMMPTGLPVVGPTRQGNIFVNVGHGVTGWAASVGSARLLSDMMAGEETEI 411 >gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 428 Score = 105 bits (263), Expect = 5e-24, Method: Compositional matrix adjust. Identities = 115/424 (27%), Positives = 177/424 (41%), Gaps = 20/424 (4%) Query: 2 HICVMGAGVIGVTTAYRLLQDGHQVSLIDERD-QPGAGTSQGNGAQLSYSYVAPLADPSV 60 H V+GAG +G+ +A L G +VSL+D S GN LS V P +P + Sbjct: 12 HAVVIGAGAVGLMSAIHALDQGLEVSLLDFNPVGSEEAASYGNAGWLSSHSVIPPVEPGM 71 Query: 61 WSKWAYYLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSVRQTTIDLLQLAFYSRDQLT 120 W K YL PL+I+ WL L +R T L L +R Sbjct: 72 WKKVPGYLMDPIGPLSIRWRYLPRLTPWLLRNLASARRERIRATARALRTLVVDARTLHL 131 Query: 121 QWNGRLKLPFDHQRSGKLVMFTDAQGLEAAAGQVRFQAQYGCQQEVLDAAQCIRIEPALG 180 R + SG L ++ Q E A + + G Q L+A R EP L Sbjct: 132 DIARRAGVAHLIDTSGVLHVYRSRQQFEGDAFGWSVRRELGIQWSELEAEALRRREPDL- 190 Query: 181 RSQRDWVGGVYTPSEEAGDCP---AFCRALVAAMQADPNFRFIGGARITAVRRQGSALSA 237 D G +EAG C A+ +AL A A R AR T R + L A Sbjct: 191 ----DPAFGFAVQVDEAGHCKNPAAYLQALQAYALARGAHRI--DARATGFRIEEGRLKA 244 Query: 238 VQAGNEWISAQRFVLALGADSADFARRLDLRLPLYPLKGYSITVPLEDEASRAAAPQVSI 297 V ++ V+ GA S A + R+ L +GY + ++A+RA P + + Sbjct: 245 VLTETGEVACDAAVICAGARSKALAAQAGDRVQLESERGYHALIRGHEQAARARTPMM-L 303 Query: 298 TDIARKIVYARLGQRLRVAGRIELVGQDRSIPSRAIAELKQGMRELFPDC---VLGEDAR 354 ++ K++ ++ LR+AG++E + + R ++ +LFP + D R Sbjct: 304 SEF--KVIATQMETGLRIAGQVEFASFEAAPDWRRGEIMRDIALKLFPGLPRDLPAADVR 361 Query: 355 LSPWMGFRPATPSGVPIVG-ACPVDNLYLNIGQGALGWTLACGSAALIADQIAGRPCSID 413 W+G RP+TP G+P +G A ++ G G +G + + ++A +AG+ ID Sbjct: 362 Y--WLGRRPSTPDGMPCIGYARASSDIVHAYGHGHIGLGCSARTGRIVAQLLAGQTPEID 419 Query: 414 DTPF 417 PF Sbjct: 420 LAPF 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 0.137 0.422 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: 1,416,407 Number of extensions: 62515 Number of successful extensions: 219 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 204 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)