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= 0006.0010.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... 284 8e-78 gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase smal... 252 5e-68 gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase smal... 211 1e-55 gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [H... 114 2e-26 >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 = 196/423 (46%), Positives = 269/423 (63%), Gaps = 10/423 (2%) Query: 1 MRIIVLGAGIVGVTTAYFLRERGHEVVVVERRAEVAAETSVGNAGHVCPSYATPWAAPGM 60 MR+++LG+G++GVT+A++L GH+V V++R+ A ETS GNAG + P YA+PWAAPG+ Sbjct: 1 MRVVILGSGVIGVTSAWYLARAGHDVTVLDRQPGPALETSFGNAGQISPGYASPWAAPGI 60 Query: 61 PAKSLKWSVQSWLGIEAALRFTPRLDA--HQWKWLKTFLAQCTPERYAVNKARMGRLARY 118 P K++KW Q A L RLD +Q +W+ L C ERYAVNK RM RLA Y Sbjct: 61 PLKAIKWMFQE----HAPLAI--RLDGSFNQLRWMWQMLRNCNAERYAVNKERMVRLAEY 114 Query: 119 SHSQLKQIRERLDIRYEQTTGGNLQLFRTQEGLDNAGLSTKVLAEAGVPFELLDADGCVA 178 S L+ +R + I YE G LQLFR+QE L+ A VL EAGVPFELL D Sbjct: 115 SRDCLRDLRADVGIPYEGRQQGTLQLFRSQEQLEGAAKDIAVLKEAGVPFELLTPDQLGN 174 Query: 179 FDPGLHAARHELKGGLLLPMDETGNCPLFARALAGWLQAHGVEFHLSTEVQAIEVAGGQV 238 +P L R +L GGL LP DETG+C LF LA + GV+F ++ A+ +AGG++ Sbjct: 175 AEPALAKVRDKLTGGLRLPNDETGDCQLFTTRLATMAEQIGVKFRYGVDIDALAMAGGKI 234 Query: 239 SGLRTPTGTLRADAYVVACASASVPMLKPL-GLD-LPIYPVKGYAITVPVADPKSAPRSG 296 +G+ ++AD+YVVA S S +L + GL +P+YP+KGY+ITVP+ D +AP S Sbjct: 235 AGVVCGKELVQADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDASAAPVST 294 Query: 297 VMDEYYKVAITRMGNHIRAAGTAEIGSWDTRVTPRDCATALKSLKNLYPQGADLAKVEYW 356 ++DE YK+A+TR + IR G AEI +DT + + AT + +L+P D A+ +W Sbjct: 295 ILDETYKIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGAGDTAQASFW 354 Query: 357 AGLRPMTPDGAPLIGATRYANLWLNAGHGSNGWTTACGSSAIIADKISGVASAIASADLE 416 GLRPMTPDG P++GAT +NL++N GHG+ GWT +CGS ++AD ISG AIA DL Sbjct: 355 TGLRPMTPDGTPVVGATPVSNLYINTGHGTLGWTMSCGSGQLLADLISGRRPAIAHEDLS 414 Query: 417 PQR 419 +R Sbjct: 415 VER 417 >gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 436 Score = 284 bits (727), Expect = 8e-78, Method: Compositional matrix adjust. Identities = 152/415 (36%), Positives = 230/415 (55%), Gaps = 15/415 (3%) Query: 1 MRIIVLGAGIVGVTTAYFLRERGHEVVVVERRAEVAAETSVGNAGHVCPSYATPWAAPGM 60 M++IVLGAGI+G +A+FL+++G++V V++R+ A ETS N + S+A PWA P Sbjct: 1 MKVIVLGAGIIGTASAWFLKKQGYDVTVIDRQPGAAQETSFANGCQISVSHAEPWANPAA 60 Query: 61 PAKSLKWSVQSWLGIE-AALRFTPRLDAHQWKWLKTFLAQCTPERYAVNKARMGRLARYS 119 P K LKW LG E A L + R + QWKW FL +CT R N + L YS Sbjct: 61 PMKVLKW-----LGKEDAPLLYRFRPEWLQWKWAVAFLRECTAARTDENIRNIVALCEYS 115 Query: 120 HSQLKQIRERLDIRYEQTTGGNLQLFRTQEGLDNAGLSTKVLAEAGVPFELLDADGCVAF 179 L+ +R I+Y+ T G L + ++ ++ + K++ + G P E + AD V Sbjct: 116 RQTLQAVRAETGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRI 175 Query: 180 DPGLHAARHELKGGLLLPMDETGNCPLFARALAGWLQAHGVEFHLSTEVQAIEVAGG--- 236 +P L + R+++ GG DE+G+ LA GVEF ST + + G Sbjct: 176 EPALASIRNKIVGGDFTATDESGDVFKLTTGLAKKSAEAGVEFRYSTTITRLITEGAGAA 235 Query: 237 -QVSGLR--TPTG---TLRADAYVVACASASVPMLKPLGLDLPIYPVKGYAITVPVADPK 290 +V+G+ P G L+AD +VVA S S ++KPLG+DL +YP KGY+ T + +P Sbjct: 236 ARVTGVEIINPDGRHEVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQITNPD 295 Query: 291 SAPRSGVMDEYYKVAITRMGNHIRAAGTAEIGSWDTRVTPRDCATALKSLKNLYPQGADL 350 +AP + D+ YK+ ++R+G+ +R AGT E+ + + C + + L+P G D Sbjct: 296 AAPTVSLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGCDY 355 Query: 351 AKVEYWAGLRPMTPDGAPLIGATRYANLWLNAGHGSNGWTTACGSSAIIADKISG 405 YW GLRP+TP P +G T++ANL+LN GHG+ GWT CGS IA+ ++G Sbjct: 356 ENPTYWTGLRPLTPSNVPYVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAEIVAG 410 >gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 421 Score = 252 bits (643), Expect = 5e-68, Method: Compositional matrix adjust. Identities = 147/417 (35%), Positives = 221/417 (52%), Gaps = 12/417 (2%) Query: 1 MRIIVLGAGIVGVTTAYFLRERGHEVVVVERRAEVAAETSVGNAGHVCPSYATPWAAPGM 60 M I V+GAG++GVTTAY L + GH+V +++ R + A TS GN + SY P A P + Sbjct: 1 MHICVMGAGVIGVTTAYRLLQDGHQVSLIDERDQPGAGTSQGNGAQLSYSYVAPLADPSV 60 Query: 61 PAKSLKWSVQSWLGIEAALRFTPRLDAHQWKWLKTFLAQCTPERYAVNKARMGRLARYSH 120 +K W+ ++ L P L+A Q++WL FL C + +LA YS Sbjct: 61 WSK---WAY-YLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSVRQTTIDLLQLAFYSR 116 Query: 121 SQLKQIRERLDIRYEQTTGGNLQLFRTQEGLDNAGLSTKVLAEAGVPFELLDADGCVAFD 180 QL Q RL + ++ G L +F +GL+ A + A+ G E+LDA C+ + Sbjct: 117 DQLTQWNGRLKLSFDHQRSGKLVMFTDAQGLEAAAGQVRFQAQYGCQQEVLDAAQCIRIE 176 Query: 181 PGLHAARHELKGGLLLPMDETGNCPLFARALAGWLQAH-GVEFHLSTEVQAIEVAGGQVS 239 P L ++ + GG+ +E G+CP F RAL +QA F + A+ G +S Sbjct: 177 PALGRSQRDWVGGVYTRSEEAGDCPAFCRALVAAMQADPNFRFIGGARITAVRRQGSALS 236 Query: 240 GLRTPTGTLRADAYVVACASASVPMLKPLGLDLPIYPVKGYAITVPVADPKS---APRSG 296 ++ + A +V+A + S + L L LP+YP+KGY+ITVP+ D S AP+ Sbjct: 237 AVQAGNEWISAQRFVLALGADSADFARQLDLRLPLYPLKGYSITVPLEDEASRAAAPQVS 296 Query: 297 VMDEYYKVAITRMGNHIRAAGTAEIGSWDTRVTPRDCATALKSLKNLYPQ---GADLAKV 353 + D K+ R+G +R AG E+ D + PR A + ++ L+P G D A++ Sbjct: 297 ITDIARKIVYARLGQRLRVAGRIELVGQDRSIPPRAIAELKQGMRELFPDCVLGED-ARL 355 Query: 354 EYWAGLRPMTPDGAPLIGATRYANLWLNAGHGSNGWTTACGSSAIIADKISGVASAI 410 W G RP TP G P++GA NL+LN G G+ GWT ACGS+A+IAD+I+G +I Sbjct: 356 SPWMGFRPATPSGVPIVGACPVDNLYLNIGQGALGWTLACGSAALIADQIAGRPCSI 412 >gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 211 bits (536), Expect = 1e-55, Method: Compositional matrix adjust. Identities = 138/426 (32%), Positives = 221/426 (51%), Gaps = 22/426 (5%) Query: 2 RIIVLGAGIVGVTTAYFLRERGHEVVVVERRAEVAAETSVGNAGHVCPSYATPWAAPGMP 61 +I V+G G+ G+ +AYFL +G+EV V+ERRA VA E + G++G + P A P PG Sbjct: 7 QIAVIGGGLSGICSAYFLATKGYEVAVIERRAHVAEEATFGDSGLLAPGTAMPLTLPGAL 66 Query: 62 AK-SLKWSVQSWLGIEAALRFTPRLDAHQWKWLKTFLAQCTPERYAVNKARMGRLARYSH 120 A + ++ + + + + F R +W++ A +A +K + RL+ Y Sbjct: 67 ATFACRFQDEPRVLLASGADFGRR------RWMRATRA-AQQHHFAQHKLILSRLSAYGQ 119 Query: 121 SQLKQIRERLDIRYEQTTGGNLQLFRTQEGLDNAGLSTKVLAEAGVPFEL----LDADGC 176 +Q++ ++ +E + G LFR + + A L L EA E LDA G Sbjct: 120 DLTQQLQAHYNMEHE-NSAGVFHLFR--QSAEAARL--PALQEAASQCEYKQLTLDAAGI 174 Query: 177 VAFDPGLHAARHELKGGLLLPMDETGNCPLFARALAGWLQAHGVEFHLSTEVQAIEVA-G 235 A +P ++ L G L P D GN LFA+ + QA GV FH ++ V +I G Sbjct: 175 RALEPAF-SSEAALAGALYYPDDIAGNSVLFAKQMRNAAQALGVSFHFNSTVSSIRSEFG 233 Query: 236 GQVS-GLRTP--TGTLRADAYVVACASASVPMLKPLGLDLPIYPVKGYAITVPVADPKSA 292 G+V+ +++P L DA VVA AS +L+PL LP+ ++ Y+ VPV +P A Sbjct: 234 GRVTLEVQSPHLASHLTMDAVVVAAGMASAALLQPLDTSLPLRALQSYSALVPVKNPDDA 293 Query: 293 PRSGVMDEYYKVAITRMGNHIRAAGTAEIGSWDTRVTPRDCATALKSLKNLYPQGADLAK 352 P + D+ YKVA+TR+G+ IR +G + P+ LK + YP A+ + Sbjct: 294 PTMALYDDSYKVAMTRLGSRIRISGLLGFVPASQTLPPKALRNLLKIAGDYYPNAANYNQ 353 Query: 353 VEYWAGLRPMTPDGAPLIGATRYANLWLNAGHGSNGWTTACGSSAIIADKISGVASAIAS 412 +W+ M P G P++G TR N+++N GHG GW + GS+ +++D ++G + IA+ Sbjct: 354 AHFWSNSIAMMPTGLPVVGPTRQGNIFVNVGHGVTGWAASVGSARLLSDMMAGEETEIAT 413 Query: 413 ADLEPQ 418 A L P+ Sbjct: 414 AGLLPR 419 >gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 428 Score = 114 bits (285), Expect = 2e-26, Method: Compositional matrix adjust. Identities = 113/427 (26%), Positives = 180/427 (42%), Gaps = 24/427 (5%) Query: 4 IVLGAGIVGVTTAYFLRERGHEVVVVERRAEVAAET-SVGNAGHVCPSYATPWAAPGMPA 62 +V+GAG VG+ +A ++G EV +++ + E S GNAG + P PGM Sbjct: 14 VVIGAGAVGLMSAIHALDQGLEVSLLDFNPVGSEEAASYGNAGWLSSHSVIPPVEPGMWK 73 Query: 63 KSLKWSVQSWLGIEAALRFTPRLDAHQWKWLKTFLAQCTPERYAVNKARMGRLARYSHSQ 122 K + + + R+ PRL WL LA ER + L + + Sbjct: 74 KVPGYLMDPIGPLSIRWRYLPRLT----PWLLRNLASARRERIRATARALRTLVVDARTL 129 Query: 123 LKQIRERLDIRYEQTTGGNLQLFRTQEGLDNAGLSTKVLAEAGVPFELLDADGCVAFDPG 182 I R + + T G L ++R+++ + V E G+ + L+A+ +P Sbjct: 130 HLDIARRAGVAHLIDTSGVLHVYRSRQQFEGDAFGWSVRRELGIQWSELEAEALRRREPD 189 Query: 183 LHAARHELKGGLLLPMDETGNCP---LFARALAGWLQAHGVEFHLSTEVQAIEVAGGQVS 239 L A G + +DE G+C + +AL + A G + + G++ Sbjct: 190 LDPA-----FGFAVQVDEAGHCKNPAAYLQALQAYALARGAH-RIDARATGFRIEEGRLK 243 Query: 240 GLRTPTGTLRADAYVVACASASVPMLKPLGLDLPIYPVKGYAITVPVADPKSAPRSGVMD 299 + T TG + DA V+ + S + G + + +GY + + + R+ +M Sbjct: 244 AVLTETGEVACDAAVICAGARSKALAAQAGDRVQLESERGYHALIRGHEQAARARTPMML 303 Query: 300 EYYKVAITRMGNHIRAAGTAEIGS------WDTRVTPRDCATALKSLKNLYPQGADLAKV 353 +KV T+M +R AG E S W RD ALK L P+ A V Sbjct: 304 SEFKVIATQMETGLRIAGQVEFASFEAAPDWRRGEIMRDI--ALKLFPGL-PRDLPAADV 360 Query: 354 EYWAGLRPMTPDGAPLIGATRYANLWLNA-GHGSNGWTTACGSSAIIADKISGVASAIAS 412 YW G RP TPDG P IG R ++ ++A GHG G + + I+A ++G I 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 0.319 0.134 0.414 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: 1,431,527 Number of extensions: 63338 Number of successful extensions: 245 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 232 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)