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= 0001.4631.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|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [H... 374 e-105 gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase smal... 288 7e-79 gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase smal... 248 9e-67 gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase smal... 215 5e-57 gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [H... 115 5e-27 >gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 433 Score = 374 bits (961), Expect = e-105, Method: Compositional matrix adjust. Identities = 192/425 (45%), Positives = 272/425 (64%), Gaps = 10/425 (2%) Query: 1 MRIIVLGAGIVGVTTAYFLRERGHDVVVVERRAEVAAETSVGNAGHVCPSYATPWAAPGM 60 MR+++LG+G++GVT+A++L GHDV V++R+ A ETS GNAG + P YA+PWAAPG+ Sbjct: 1 MRVVILGSGVIGVTSAWYLARAGHDVTVLDRQPGPALETSFGNAGQISPGYASPWAAPGI 60 Query: 61 PAKSLKWSLQSWLGIEAALRFTPRLDA--HQWKWLKAFLAQCTSERYAINKARMGRLARY 118 P K++KW Q A L RLD +Q +W+ L C +ERYA+NK RM RLA Y Sbjct: 61 PLKAIKWMFQE----HAPLAI--RLDGSFNQLRWMWQMLRNCNAERYAVNKERMVRLAEY 114 Query: 119 SHTQLKQIRERLDIRYEQTTVGNLQLFRTQEGLDNAGLSTSVLQEAGVPFELLDADGCVA 178 S L+ +R + I YE G LQLFR+QE L+ A +VL+EAGVPFELL D Sbjct: 115 SRDCLRDLRADVGIPYEGRQQGTLQLFRSQEQLEGAAKDIAVLKEAGVPFELLTPDQLGN 174 Query: 179 FDPGLHAARHEIKGGLLLPRDETGNCPLFARALASWLQAHGMEFHLSTEVQAIEVAGDQV 238 +P L R ++ GGL LP DETG+C LF LA+ + G++F ++ A+ +AG ++ Sbjct: 175 AEPALAKVRDKLTGGLRLPNDETGDCQLFTTRLATMAEQIGVKFRYGVDIDALAMAGGKI 234 Query: 239 SGLRTRSGTLRADAYVVACASASVPMLRPL-GL-ELPIYPVKGYAITVPVADPERAPRSG 296 +G+ ++AD+YVVA S S +L + GL +P+YP+KGY+ITVP+ D AP S Sbjct: 235 AGVVCGKELVQADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDASAAPVST 294 Query: 297 VMDEYYKVAITRMGQHIRAAGTAEIGSWDTRVRPRDCATALKSLNNLYPQGADLSRIEYW 356 ++DE YK+A+TR IR G AEI +DT ++ + AT +N+L+P D ++ +W Sbjct: 295 ILDETYKIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGAGDTAQASFW 354 Query: 357 AGLRPMTPDGAPLIGATRYSNLWLNAGHGSNGWTTACGSSRIIADRISGVTSEIESADLE 416 GLRPMTPDG P++GAT SNL++N GHG+ GWT +CGS +++AD ISG I DL Sbjct: 355 TGLRPMTPDGTPVVGATPVSNLYINTGHGTLGWTMSCGSGQLLADLISGRRPAIAHEDLS 414 Query: 417 PQRVI 421 +R + Sbjct: 415 VERYL 419 >gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 436 Score = 288 bits (736), Expect = 7e-79, Method: Compositional matrix adjust. Identities = 153/423 (36%), Positives = 232/423 (54%), Gaps = 15/423 (3%) Query: 1 MRIIVLGAGIVGVTTAYFLRERGHDVVVVERRAEVAAETSVGNAGHVCPSYATPWAAPGM 60 M++IVLGAGI+G +A+FL+++G+DV V++R+ A ETS N + S+A PWA P Sbjct: 1 MKVIVLGAGIIGTASAWFLKKQGYDVTVIDRQPGAAQETSFANGCQISVSHAEPWANPAA 60 Query: 61 PAKSLKWSLQSWLGIE-AALRFTPRLDAHQWKWLKAFLAQCTSERYAINKARMGRLARYS 119 P K LKW LG E A L + R + QWKW AFL +CT+ R N + L YS Sbjct: 61 PMKVLKW-----LGKEDAPLLYRFRPEWLQWKWAVAFLRECTAARTDENIRNIVALCEYS 115 Query: 120 HTQLKQIRERLDIRYEQTTVGNLQLFRTQEGLDNAGLSTSVLQEAGVPFELLDADGCVAF 179 L+ +R I+Y+ T G L + ++ ++ + ++++ G P E + AD V Sbjct: 116 RQTLQAVRAETGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRI 175 Query: 180 DPGLHAARHEIKGGLLLPRDETGNCPLFARALASWLQAHGMEFHLSTEVQ---------A 230 +P L + R++I GG DE+G+ LA G+EF ST + A Sbjct: 176 EPALASIRNKIVGGDFTATDESGDVFKLTTGLAKKSAEAGVEFRYSTTITRLITEGAGAA 235 Query: 231 IEVAGDQVSGLRTRSGTLRADAYVVACASASVPMLRPLGLELPIYPVKGYAITVPVADPE 290 V G ++ R L+AD +VVA S S +++PLG++L +YP KGY+ T + +P+ Sbjct: 236 ARVTGVEIINPDGRHEVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQITNPD 295 Query: 291 RAPRSGVMDEYYKVAITRMGQHIRAAGTAEIGSWDTRVRPRDCATALKSLNNLYPQGADL 350 AP + D+ YK+ ++R+G +R AGT E+ + + C + L+P G D Sbjct: 296 AAPTVSLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGCDY 355 Query: 351 SRIEYWAGLRPMTPDGAPLIGATRYSNLWLNAGHGSNGWTTACGSSRIIADRISGVTSEI 410 YW GLRP+TP P +G T+++NL+LN GHG+ GWT CGS R IA+ ++G EI Sbjct: 356 ENPTYWTGLRPLTPSNVPYVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAEIVAGHVPEI 415 Query: 411 ESA 413 + A Sbjct: 416 DFA 418 >gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 421 Score = 248 bits (632), Expect = 9e-67, Method: Compositional matrix adjust. Identities = 146/418 (34%), Positives = 219/418 (52%), Gaps = 12/418 (2%) Query: 1 MRIIVLGAGIVGVTTAYFLRERGHDVVVVERRAEVAAETSVGNAGHVCPSYATPWAAPGM 60 M I V+GAG++GVTTAY L + GH V +++ R + A TS GN + SY P A P + Sbjct: 1 MHICVMGAGVIGVTTAYRLLQDGHQVSLIDERDQPGAGTSQGNGAQLSYSYVAPLADPSV 60 Query: 61 PAKSLKWSLQSWLGIEAALRFTPRLDAHQWKWLKAFLAQCTSERYAINKARMGRLARYSH 120 +K W+ ++ L P L+A Q++WL FL C + + +LA YS Sbjct: 61 WSK---WAY-YLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSVRQTTIDLLQLAFYSR 116 Query: 121 TQLKQIRERLDIRYEQTTVGNLQLFRTQEGLDNAGLSTSVLQEAGVPFELLDADGCVAFD 180 QL Q RL + ++ G L +F +GL+ A + G E+LDA C+ + Sbjct: 117 DQLTQWNGRLKLSFDHQRSGKLVMFTDAQGLEAAAGQVRFQAQYGCQQEVLDAAQCIRIE 176 Query: 181 PGLHAARHEIKGGLLLPRDETGNCPLFARALASWLQAH-GMEFHLSTEVQAIEVAGDQVS 239 P L ++ + GG+ +E G+CP F RAL + +QA F + A+ G +S Sbjct: 177 PALGRSQRDWVGGVYTRSEEAGDCPAFCRALVAAMQADPNFRFIGGARITAVRRQGSALS 236 Query: 240 GLRTRSGTLRADAYVVACASASVPMLRPLGLELPIYPVKGYAITVPVADPER---APRSG 296 ++ + + A +V+A + S R L L LP+YP+KGY+ITVP+ D AP+ Sbjct: 237 AVQAGNEWISAQRFVLALGADSADFARQLDLRLPLYPLKGYSITVPLEDEASRAAAPQVS 296 Query: 297 VMDEYYKVAITRMGQHIRAAGTAEIGSWDTRVRPRDCATALKSLNNLYPQ---GADLSRI 353 + D K+ R+GQ +R AG E+ D + PR A + + L+P G D +R+ Sbjct: 297 ITDIARKIVYARLGQRLRVAGRIELVGQDRSIPPRAIAELKQGMRELFPDCVLGED-ARL 355 Query: 354 EYWAGLRPMTPDGAPLIGATRYSNLWLNAGHGSNGWTTACGSSRIIADRISGVTSEIE 411 W G RP TP G P++GA NL+LN G G+ GWT ACGS+ +IAD+I+G I+ Sbjct: 356 SPWMGFRPATPSGVPIVGACPVDNLYLNIGQGALGWTLACGSAALIADQIAGRPCSID 413 >gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 215 bits (548), Expect = 5e-57, Method: Compositional matrix adjust. Identities = 138/428 (32%), Positives = 219/428 (51%), Gaps = 20/428 (4%) Query: 2 RIIVLGAGIVGVTTAYFLRERGHDVVVVERRAEVAAETSVGNAGHVCPSYATPWAAPGMP 61 +I V+G G+ G+ +AYFL +G++V V+ERRA VA E + G++G + P A P PG Sbjct: 7 QIAVIGGGLSGICSAYFLATKGYEVAVIERRAHVAEEATFGDSGLLAPGTAMPLTLPGAL 66 Query: 62 AKSLKWSLQSWLGIEAALRFTPRLDAHQWKWLKAFLAQCTSERYAINKARMGRLARYSHT 121 A + Q E + D + +W++A A +A +K + RL+ Y Sbjct: 67 A-TFACRFQD----EPRVLLASGADFGRRRWMRATRA-AQQHHFAQHKLILSRLSAYGQD 120 Query: 122 QLKQIRERLDIRYEQTTVGNLQLFRTQEGLDNAGLSTSVLQEAGVPFEL----LDADGCV 177 +Q++ ++ +E + G LFR + + A L LQEA E LDA G Sbjct: 121 LTQQLQAHYNMEHE-NSAGVFHLFR--QSAEAARLP--ALQEAASQCEYKQLTLDAAGIR 175 Query: 178 AFDPGLHAARHEIKGGLLLPRDETGNCPLFARALASWLQAHGMEFHLSTEVQAIEVAGDQ 237 A +P ++ + G L P D GN LFA+ + + QA G+ FH ++ V +I Sbjct: 176 ALEPAF-SSEAALAGALYYPDDIAGNSVLFAKQMRNAAQALGVSFHFNSTVSSIRSEFGG 234 Query: 238 VSGLRTRS----GTLRADAYVVACASASVPMLRPLGLELPIYPVKGYAITVPVADPERAP 293 L +S L DA VVA AS +L+PL LP+ ++ Y+ VPV +P+ AP Sbjct: 235 RVTLEVQSPHLASHLTMDAVVVAAGMASAALLQPLDTSLPLRALQSYSALVPVKNPDDAP 294 Query: 294 RSGVMDEYYKVAITRMGQHIRAAGTAEIGSWDTRVRPRDCATALKSLNNLYPQGADLSRI 353 + D+ YKVA+TR+G IR +G + P+ LK + YP A+ ++ Sbjct: 295 TMALYDDSYKVAMTRLGSRIRISGLLGFVPASQTLPPKALRNLLKIAGDYYPNAANYNQA 354 Query: 354 EYWAGLRPMTPDGAPLIGATRYSNLWLNAGHGSNGWTTACGSSRIIADRISGVTSEIESA 413 +W+ M P G P++G TR N+++N GHG GW + GS+R+++D ++G +EI +A Sbjct: 355 HFWSNSIAMMPTGLPVVGPTRQGNIFVNVGHGVTGWAASVGSARLLSDMMAGEETEIATA 414 Query: 414 DLEPQRVI 421 L P+ V+ Sbjct: 415 GLLPRDVL 422 >gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 428 Score = 115 bits (289), Expect = 5e-27, Method: Compositional matrix adjust. Identities = 114/427 (26%), Positives = 184/427 (43%), Gaps = 24/427 (5%) Query: 4 IVLGAGIVGVTTAYFLRERGHDVVVVERRAEVAAET-SVGNAGHVCPSYATPWAAPGMPA 62 +V+GAG VG+ +A ++G +V +++ + E S GNAG + P PGM Sbjct: 14 VVIGAGAVGLMSAIHALDQGLEVSLLDFNPVGSEEAASYGNAGWLSSHSVIPPVEPGMWK 73 Query: 63 KSLKWSLQSWLGIEAALRFTPRLDAHQWKWLKAFLAQCTSERYAINKARMGRLARYSHTQ 122 K + + + R+ PRL WL LA ER + L + T Sbjct: 74 KVPGYLMDPIGPLSIRWRYLPRLT----PWLLRNLASARRERIRATARALRTLVVDARTL 129 Query: 123 LKQIRERLDIRYEQTTVGNLQLFRTQEGLDNAGLSTSVLQEAGVPFELLDADGCVAFDPG 182 I R + + T G L ++R+++ + SV +E G+ + L+A+ +P Sbjct: 130 HLDIARRAGVAHLIDTSGVLHVYRSRQQFEGDAFGWSVRRELGIQWSELEAEALRRREPD 189 Query: 183 LHAARHEIKGGLLLPRDETGNCP---LFARALASWLQAHGMEFHLSTEVQAIEVAGDQVS 239 L A G + DE G+C + +AL ++ A G + + ++ Sbjct: 190 LDPA-----FGFAVQVDEAGHCKNPAAYLQALQAYALARGAH-RIDARATGFRIEEGRLK 243 Query: 240 GLRTRSGTLRADAYVVACASASVPMLRPLGLELPIYPVKGYAITVPVADPERAPRSGVMD 299 + T +G + DA V+ + S + G + + +GY + + R+ +M Sbjct: 244 AVLTETGEVACDAAVICAGARSKALAAQAGDRVQLESERGYHALIRGHEQAARARTPMML 303 Query: 300 EYYKVAITRMGQHIRAAGTAEIGS------WDTRVRPRDCATALKSLNNLYPQGADLSRI 353 +KV T+M +R AG E S W RD A LK L P+ + + Sbjct: 304 SEFKVIATQMETGLRIAGQVEFASFEAAPDWRRGEIMRDIA--LKLFPGL-PRDLPAADV 360 Query: 354 EYWAGLRPMTPDGAPLIGATRYSNLWLNA-GHGSNGWTTACGSSRIIADRISGVTSEIES 412 YW G RP TPDG P IG R S+ ++A GHG G + + RI+A ++G T EI+ Sbjct: 361 RYWLGRRPSTPDGMPCIGYARASSDIVHAYGHGHIGLGCSARTGRIVAQLLAGQTPEIDL 420 Query: 413 ADLEPQR 419 A PQR Sbjct: 421 APFSPQR 427 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 0.320 0.134 0.413 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: 1,405,536 Number of extensions: 60793 Number of successful extensions: 233 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 220 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 (21.8 bits) S2: 132 (55.5 bits)