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= 0002.0449.p (435 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [H... 566 e-162 gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase smal... 114 1e-26 gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [H... 114 2e-26 gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase smal... 110 2e-25 gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase smal... 68 2e-12 >gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 428 Score = 566 bits (1459), Expect = e-162, Method: Compositional matrix adjust. Identities = 284/422 (67%), Positives = 330/422 (78%), Gaps = 4/422 (0%) Query: 17 SAARHVVVIGAGAVGLMSALHALDQGFQVTIVDPGQPGGEQASSYGNAGWLSSHSVLPPS 76 S RH VVIGAGAVGLMSA+HALDQG +V+++D G E+A+SYGNAGWLSSHSV+PP Sbjct: 8 SFPRHAVVIGAGAVGLMSAIHALDQGLEVSLLDFNPVGSEEAASYGNAGWLSSHSVIPPV 67 Query: 77 EPGVWKKVPGFLADPLGPLSVRWRYLPRTLPWLLRYLAAGSTTARISATAAAL-XLLHGA 135 EPG+WKKVPG+L DP+GPLS+RWRYLPR PWLLR LA+ + RI ATA AL L+ A Sbjct: 68 EPGMWKKVPGYLMDPIGPLSIRWRYLPRLTPWLLRNLAS-ARRERIRATARALRTLVVDA 126 Query: 136 APLHKAIAEQAGVGDLIDLGGLLHIYRSRAHFEADARGWGIRRKLGIGWQELSAQELHAR 195 LH IA +AGV LID G+LH+YRSR FE DA GW +RR+LGI W EL A+ L R Sbjct: 127 RTLHLDIARRAGVAHLIDTSGVLHVYRSRQQFEGDAFGWSVRRELGIQWSELEAEALRRR 186 Query: 196 EPDLDPAYGFGVLIPEAGHCRNPGAYIAALAAHACARGARLTAVTATGFRFEGNGLAAVQ 255 EPDLDPA+GF V + EAGHC+NP AY+ AL A+A ARGA ATGFR E L AV Sbjct: 187 EPDLDPAFGFAVQVDEAGHCKNPAAYLQALQAYALARGAHRIDARATGFRIEEGRLKAVL 246 Query: 256 TDAGDILCDAAVIAAGAQSKALAAKAGDKVPLETERGYHAMVLAPE--GRPRTPMMIMDR 313 T+ G++ CDAAVI AGA+SKALAA+AGD+V LE+ERGYHA++ E R RTPMM+ + Sbjct: 247 TETGEVACDAAVICAGARSKALAAQAGDRVQLESERGYHALIRGHEQAARARTPMMLSEF 306 Query: 314 KVIATQTEEGLRVAGQVEIASFDAAPDWRRAEIMRDLALKLFPALPRDLPANRVRYWLGR 373 KVIATQ E GLR+AGQVE ASF+AAPDWRR EIMRD+ALKLFP LPRDLPA VRYWLGR Sbjct: 307 KVIATQMETGLRIAGQVEFASFEAAPDWRRGEIMRDIALKLFPGLPRDLPAADVRYWLGR 366 Query: 374 RPSMPDGLPCIGRSSHSVDIIHAFGHGHIGLGSSARTGRLVGQLLAGQLPEIDMAPFSAQ 433 RPS PDG+PCIG + S DI+HA+GHGHIGLG SARTGR+V QLLAGQ PEID+APFS Q Sbjct: 367 RPSTPDGMPCIGYARASSDIVHAYGHGHIGLGCSARTGRIVAQLLAGQTPEIDLAPFSPQ 426 Query: 434 RF 435 RF Sbjct: 427 RF 428 >gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 436 Score = 114 bits (286), Expect = 1e-26, Method: Compositional matrix adjust. Identities = 116/430 (26%), Positives = 176/430 (40%), Gaps = 35/430 (8%) Query: 21 HVVVIGAGAVGLMSALHALDQGFQVTIVDPGQPGGEQASSYGNAGWLSSHSVLPPSEPGV 80 V+V+GAG +G SA QG+ VT++D QPG Q +S+ N +S P + P Sbjct: 2 KVIVLGAGIIGTASAWFLKKQGYDVTVIDR-QPGAAQETSFANGCQISVSHAEPWANPAA 60 Query: 81 WKKVPGFLADPLGPLSVRWRYLPRTLPW-----LLRYLAAGSTTARISATAAALXLLHGA 135 KV +L PL R+R P L W LR A T I A L + Sbjct: 61 PMKVLKWLGKEDAPLLYRFR--PEWLQWKWAVAFLRECTAARTDENIRNIVA---LCEYS 115 Query: 136 APLHKAIAEQAGVGDLIDLGGLLHIYRSRAHFEADARGWGIRRKLGIGWQELSAQELHAR 195 +A+ + G+ G+LH Y F+ + R LG + + A E+ Sbjct: 116 RQTLQAVRAETGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRI 175 Query: 196 EPDLDPAY-----GFGVLIPEAGHCRNPGAYIAALAAHACARGARLTAVTATGFRFEGNG 250 EP L G E+G +A +A A T +T EG G Sbjct: 176 EPALASIRNKIVGGDFTATDESGDVFKLTTGLAKKSAEAGVEFRYSTTITR--LITEGAG 233 Query: 251 LAAVQTDAGDI---------LCDAAVIAAGAQSKALAAKAGDKVPLETERGYHA--MVLA 299 AA T I D V+A G+ S+ L G + L +GY A + Sbjct: 234 AAARVTGVEIINPDGRHEVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQITN 293 Query: 300 PEGRPRTPMMIMDRKVIATQTEEGLRVAGQVEIASFDAAPDWRRAEIMRDLALKLFP-AL 358 P+ P + K++ ++ + LRVAG E+ + + R E + +LFP Sbjct: 294 PDAAPTVSLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGC 353 Query: 359 PRDLPANRVRYWLGRRPSMPDGLPCIGRSSHSVDIIHAFGHGHIGLGSSARTGRLVGQLL 418 + P YW G RP P +P +G++ + ++ GHG +G +GR + +++ Sbjct: 354 DYENPT----YWTGLRPLTPSNVPYVGKTKFA-NLYLNTGHGTLGWTMGCGSGRAIAEIV 408 Query: 419 AGQLPEIDMA 428 AG +PEID A Sbjct: 409 AGHVPEIDFA 418 >gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 433 Score = 114 bits (285), Expect = 2e-26, Method: Compositional matrix adjust. Identities = 109/426 (25%), Positives = 185/426 (43%), Gaps = 20/426 (4%) Query: 21 HVVVIGAGAVGLMSALHALDQGFQVTIVDPGQPGGEQASSYGNAGWLSSHSVLPPSEPGV 80 VV++G+G +G+ SA + G VT++D QPG +S+GNAG +S P + PG+ Sbjct: 2 RVVILGSGVIGVTSAWYLARAGHDVTVLDR-QPGPALETSFGNAGQISPGYASPWAAPGI 60 Query: 81 WKKVPGFLADPLGPLSVRWRYLPRTLPWLLRYLAAGSTTARISATAAALXLLHGAAPLHK 140 K ++ PL++R L W+ + L + + L + + Sbjct: 61 PLKAIKWMFQEHAPLAIRLDGSFNQLRWMWQMLRNCNAERYAVNKERMVRLAEYSRDCLR 120 Query: 141 AIAEQAGVGDLIDLGGLLHIYRSRAHFEADARGWGIRRKLGIGWQELSAQELHAREPDL- 199 + G+ G L ++RS+ E A+ + ++ G+ ++ L+ +L EP L Sbjct: 121 DLRADVGIPYEGRQQGTLQLFRSQEQLEGAAKDIAVLKEAGVPFELLTPDQLGNAEPALA 180 Query: 200 ---DPAYGFGVLIP--EAGHCRNPGAYIAALAAHACARGARL-TAVTATGFRFEGNGLAA 253 D G G+ +P E G C+ + LA A G + V G +A Sbjct: 181 KVRDKLTG-GLRLPNDETGDCQ---LFTTRLATMAEQIGVKFRYGVDIDALAMAGGKIAG 236 Query: 254 VQTDAGDILCDAAVIAAGAQSKALAAKAGD--KVPLETERGYHAMVLAPEGRPRTPMMIM 311 V + D+ V+A G+ S L + +P+ +GY V + I+ Sbjct: 237 VVCGKELVQADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDASAAPVSTIL 296 Query: 312 DR--KVIATQTEEGLRVAGQVEIASFDAAPDWRRAEIMRDLALKLFPALPRDLPANRVRY 369 D K+ T+ ++ +RV G EI +D A +R + + LFP A+ + Sbjct: 297 DETYKIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGAGDTAQAS---F 353 Query: 370 WLGRRPSMPDGLPCIGRSSHSVDIIHAFGHGHIGLGSSARTGRLVGQLLAGQLPEIDMAP 429 W G RP PDG P +G + S I+ GHG +G S +G+L+ L++G+ P I Sbjct: 354 WTGLRPMTPDGTPVVGATPVSNLYINT-GHGTLGWTMSCGSGQLLADLISGRRPAIAHED 412 Query: 430 FSAQRF 435 S +R+ Sbjct: 413 LSVERY 418 >gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 421 Score = 110 bits (275), Expect = 2e-25, Method: Compositional matrix adjust. Identities = 127/434 (29%), Positives = 190/434 (43%), Gaps = 42/434 (9%) Query: 21 HVVVIGAGAVGLMSALHALDQGFQVTIVDP-GQPGGEQASSYGNAGWLSSHSVLPPSEPG 79 H+ V+GAG +G+ +A L G QV+++D QPG +S GN LS V P ++P Sbjct: 2 HICVMGAGVIGVTTAYRLLQDGHQVSLIDERDQPGA--GTSQGNGAQLSYSYVAPLADPS 59 Query: 80 VWKKVPGFLADPLGPLSVRWRYLPRTLPWL---LRYLAAGSTTARISATAAALXLLHGAA 136 VW K +L PL+++ WL LRY AGS + LL A Sbjct: 60 VWSKWAYYLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSV------RQTTIDLLQLAF 113 Query: 137 PLHKAIAEQAGVGDLI---DLGGLLHIYRSRAHFEADARGWGIRRKLGIGWQELSAQELH 193 + + G L G L ++ EA A + + G + L A + Sbjct: 114 YSRDQLTQWNGRLKLSFDHQRSGKLVMFTDAQGLEAAAGQVRFQAQYGCQQEVLDAAQCI 173 Query: 194 AREPDL-----DPAYGFGVLIPEAGHCRNPG---AYIAALAAHACAR---GARLTAVTAT 242 EP L D G EAG C P A +AA+ A R GAR+TAV Sbjct: 174 RIEPALGRSQRDWVGGVYTRSEEAGDC--PAFCRALVAAMQADPNFRFIGGARITAV--- 228 Query: 243 GFRFEGNGLAAVQTDAGDILCDAAVIAAGAQSKALAAKAGDKVPLETERGYHAMV-LAPE 301 R +G+ L+AVQ I V+A GA S A + ++PL +GY V L E Sbjct: 229 --RRQGSALSAVQAGNEWISAQRFVLALGADSADFARQLDLRLPLYPLKGYSITVPLEDE 286 Query: 302 GR----PRTPMMIMDRKVIATQTEEGLRVAGQVEIASFDAAPDWRRAEIMRDLALKLFPA 357 P+ + + RK++ + + LRVAG++E+ D + R ++ +LFP Sbjct: 287 ASRAAAPQVSITDIARKIVYARLGQRLRVAGRIELVGQDRSIPPRAIAELKQGMRELFPD 346 Query: 358 LPRDLPANRVRYWLGRRPSMPDGLPCIGRSSHSVDIIH-AFGHGHIGLGSSARTGRLVGQ 416 A R+ W+G RP+ P G+P +G + VD ++ G G +G + + L+ Sbjct: 347 CVLGEDA-RLSPWMGFRPATPSGVPIVG--ACPVDNLYLNIGQGALGWTLACGSAALIAD 403 Query: 417 LLAGQLPEIDMAPF 430 +AG+ ID PF Sbjct: 404 QIAGRPCSIDDTPF 417 >gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 67.8 bits (164), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 106/442 (23%), Positives = 178/442 (40%), Gaps = 58/442 (13%) Query: 16 TSAARHVVVIGAGAVGLMSALHALDQGFQVTIVDPGQPGGEQASSYGNAGWLSSHSVLPP 75 S R + VIG G G+ SA +G++V +++ E+A+ +G++G L+ + +P Sbjct: 2 NSTHRQIAVIGGGLSGICSAYFLATKGYEVAVIERRAHVAEEAT-FGDSGLLAPGTAMPL 60 Query: 76 SEPGVWKKVPGFLADPLGPLSVRWRYLPRTLPWLLRYLAAGSTTAR---ISATAAALXLL 132 + PG L + R++ PR L LA+G+ R + AT AA Sbjct: 61 TLPGA-----------LATFACRFQDEPRVL------LASGADFGRRRWMRATRAAQQ-- 101 Query: 133 HGAAPLHKAIAEQAGVG-DLI------------DLGGLLHIYRSRAHFEADARGWGIRRK 179 H A ++ + G DL + G+ H++R A AR ++ Sbjct: 102 HHFAQHKLILSRLSAYGQDLTQQLQAHYNMEHENSAGVFHLFRQSAE---AARLPALQEA 158 Query: 180 LG-IGWQELSAQELHAREPDLDPAYGFGVLIPEAGHCRNPGAYIAALAAHACARGARLTA 238 +++L+ R L+PA+ + A + + A + L A A+ Sbjct: 159 ASQCEYKQLTLDAAGIRA--LEPAFSSEAALAGALYYPDDIAGNSVLFAKQMRNAAQALG 216 Query: 239 V------TATGFRFEGNGLAAVQTD----AGDILCDAAVIAAGAQSKALAAKAGDKVPLE 288 V T + R E G ++ A + DA V+AAG S AL +PL Sbjct: 217 VSFHFNSTVSSIRSEFGGRVTLEVQSPHLASHLTMDAVVVAAGMASAALLQPLDTSLPLR 276 Query: 289 TERGYHAMV--LAPEGRPRTPMMIMDRKVIATQTEEGLRVAGQVEIASFDAAPDWRRAEI 346 + Y A+V P+ P + KV T+ +R++G + F A + Sbjct: 277 ALQSYSALVPVKNPDDAPTMALYDDSYKVAMTRLGSRIRISG---LLGFVPASQTLPPKA 333 Query: 347 MRDLALKLFPALPRDLPANRVRYWLGRRPSMPDGLPCIGRSSHSVDIIHAFGHGHIGLGS 406 +R+L P N+ +W MP GLP +G + +I GHG G + Sbjct: 334 LRNLLKIAGDYYPNAANYNQAHFWSNSIAMMPTGLPVVGPTRQG-NIFVNVGHGVTGWAA 392 Query: 407 SARTGRLVGQLLAGQLPEIDMA 428 S + RL+ ++AG+ EI A Sbjct: 393 SVGSARLLSDMMAGEETEIATA 414 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 0.135 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: 1,285,769 Number of extensions: 52748 Number of successful extensions: 261 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 247 Number of HSP's successfully gapped: 6 Length of query: 435 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 347 Effective length of database: 1,203,190 Effective search space: 417506930 Effective search space used: 417506930 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)