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= 0027.0044.p (442 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase smal... 860 0.0 gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [H... 204 1e-53 gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase smal... 166 4e-42 gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase smal... 135 5e-33 gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [H... 64 2e-11 >gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 860 bits (2223), Expect = 0.0, Method: Compositional matrix adjust. Identities = 421/423 (99%), Positives = 422/423 (99%) Query: 20 VNSTHRQIAVIGGGLSGICSAYFLATKGYEVAVIERRAHVAEEATFGDSGLLAPGTAMPL 79 +NSTHRQIAVIGGGLSGICSAYFLATKGYEVAVIERRAHVAEEATFGDSGLLAPGTAMPL Sbjct: 1 MNSTHRQIAVIGGGLSGICSAYFLATKGYEVAVIERRAHVAEEATFGDSGLLAPGTAMPL 60 Query: 80 TLPGALATFACRFQDEPRVLLASGADFGRRRWMRATRAAQQHHFAQHKLILSRLSAYGQD 139 TLPGALATFACRFQDEPRVLLASGADFGRRRWMRATRAAQQHHFAQHKLILSRLSAYGQD Sbjct: 61 TLPGALATFACRFQDEPRVLLASGADFGRRRWMRATRAAQQHHFAQHKLILSRLSAYGQD 120 Query: 140 LTQQLQAHYNMEHENSAGVFHLFRQSAEAARLPALQEAASQCEYKQLTLDAAGIRALEPA 199 LTQQLQAHYNMEHENSAGVFHLFRQSAEAARLPALQEAASQCEYKQLTLDAAGIRALEPA Sbjct: 121 LTQQLQAHYNMEHENSAGVFHLFRQSAEAARLPALQEAASQCEYKQLTLDAAGIRALEPA 180 Query: 200 FSSEAALAGALYYPDDIAGNSVLFAKQMRNAAQALGVSFHFNSTVSSIRSEFGGRVTLEV 259 FSSEAALAGALYYPDDIAGNSVLFAKQMRNAAQALGVSFHFNSTVSSIRSEFGGRVTLEV Sbjct: 181 FSSEAALAGALYYPDDIAGNSVLFAKQMRNAAQALGVSFHFNSTVSSIRSEFGGRVTLEV 240 Query: 260 QSPHLASHLTMDAVVVAAGMASAALLQPLDTSLPLRALQSYSALVPVKNPDDAPTMALYD 319 QSPHLASHLTMDAVVVAAGMASAALLQPLDTSLPLRALQSYSALVPVKNPDDAPTMALYD Sbjct: 241 QSPHLASHLTMDAVVVAAGMASAALLQPLDTSLPLRALQSYSALVPVKNPDDAPTMALYD 300 Query: 320 DSYKVAMTRLGSRIRISGLLGFVPASQTLPPKALRNLLKIAGDYYPNAANYNQAHFWSNS 379 DSYKVAMTRLGSRIRISGLLGFVPASQTLPPKALRNLLKIAGDYYPNAANYNQAHFWSNS Sbjct: 301 DSYKVAMTRLGSRIRISGLLGFVPASQTLPPKALRNLLKIAGDYYPNAANYNQAHFWSNS 360 Query: 380 IAMMPTGLPVVGPTRQGNIFVNVGHGVTGWAASVGSARLLSDMMAGEETEIPTAGLLPRD 439 IAMMPTGLPVVGPTRQGNIFVNVGHGVTGWAASVGSARLLSDMMAGEETEI TAGLLPRD Sbjct: 361 IAMMPTGLPVVGPTRQGNIFVNVGHGVTGWAASVGSARLLSDMMAGEETEIATAGLLPRD 420 Query: 440 VLG 442 VLG Sbjct: 421 VLG 423 >gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 433 Score = 204 bits (520), Expect = 1e-53, Method: Compositional matrix adjust. Identities = 131/415 (31%), Positives = 209/415 (50%), Gaps = 18/415 (4%) Query: 26 QIAVIGGGLSGICSAYFLATKGYEVAVIERRAHVAEEATFGDSGLLAPGTAMPLTLPG-A 84 ++ ++G G+ G+ SA++LA G++V V++R+ A E +FG++G ++PG A P PG Sbjct: 2 RVVILGSGVIGVTSAWYLARAGHDVTVLDRQPGPALETSFGNAGQISPGYASPWAAPGIP 61 Query: 85 LATFACRFQDEPRVLLASGADFGRRRWM-RATRAAQQHHFAQHKLILSRLSAYGQDLTQQ 143 L FQ+ + + F + RWM + R +A +K + RL+ Y +D + Sbjct: 62 LKAIKWMFQEHAPLAIRLDGSFNQLRWMWQMLRNCNAERYAVNKERMVRLAEYSRDCLRD 121 Query: 144 LQAHYNMEHEN-SAGVFHLFRQSAE----AARLPALQEAASQCEYKQLTLDAAGIRALEP 198 L+A + +E G LFR + A + L+EA ++ LT D G EP Sbjct: 122 LRADVGIPYEGRQQGTLQLFRSQEQLEGAAKDIAVLKEAG--VPFELLTPDQLG--NAEP 177 Query: 199 AFSS-EAALAGALYYPDDIAGNSVLFAKQMRNAAQALGVSFHFNSTVSSIRSEFGGRVTL 257 A + L G L P+D G+ LF ++ A+ +GV F + + ++ + GG++ Sbjct: 178 ALAKVRDKLTGGLRLPNDETGDCQLFTTRLATMAEQIGVKFRYGVDIDAL-AMAGGKIAG 236 Query: 258 EVQSPHLASHLTMDAVVVAAGMASAALLQ--PLDTSLPLRALQSYSALVPVKNPDDAPTM 315 V L + D+ VVA G S LL P ++P+ L+ YS VP+ + AP Sbjct: 237 VVCGKEL---VQADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDASAAPVS 293 Query: 316 ALYDDSYKVAMTRLGSRIRISGLLGFVPASQTLPPKALRNLLKIAGDYYPNAANYNQAHF 375 + D++YK+A+TR RIR+ G+ V L K L + D +P A + QA F Sbjct: 294 TILDETYKIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGAGDTAQASF 353 Query: 376 WSNSIAMMPTGLPVVGPTRQGNIFVNVGHGVTGWAASVGSARLLSDMMAGEETEI 430 W+ M P G PVVG T N+++N GHG GW S GS +LL+D+++G I Sbjct: 354 WTGLRPMTPDGTPVVGATPVSNLYINTGHGTLGWTMSCGSGQLLADLISGRRPAI 408 >gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 436 Score = 166 bits (420), Expect = 4e-42, Method: Compositional matrix adjust. Identities = 116/429 (27%), Positives = 212/429 (49%), Gaps = 22/429 (5%) Query: 26 QIAVIGGGLSGICSAYFLATKGYEVAVIERRAHVAEEATFGDSGLLAPGTAMPLTLPGA- 84 ++ V+G G+ G SA+FL +GY+V VI+R+ A+E +F + ++ A P P A Sbjct: 2 KVIVLGAGIIGTASAWFLKKQGYDVTVIDRQPGAAQETSFANGCQISVSHAEPWANPAAP 61 Query: 85 LATFACRFQDEPRVLLASGADFGRRRW----MRATRAAQQHHFAQHKLILSRLSAYGQDL 140 + +++ +L ++ + +W +R AA+ ++ + L Y + Sbjct: 62 MKVLKWLGKEDAPLLYRFRPEWLQWKWAVAFLRECTAARTDENIRN---IVALCEYSRQT 118 Query: 141 TQQLQAHYNMEHEN-SAGVFHLFRQSAE-AARLPALQEAAS-QCEYKQLTLDAAGIRALE 197 Q ++A +++++ + G+ H + + E LPA + C + + D + +E Sbjct: 119 LQAVRAETGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADE--VVRIE 176 Query: 198 PAFSS-EAALAGALYYPDDIAGNSVLFAKQMRNAAQALGVSFHFNSTVSSIRSEFGG--- 253 PA +S + G + D +G+ + + GV F +++T++ + +E G Sbjct: 177 PALASIRNKIVGGDFTATDESGDVFKLTTGLAKKSAEAGVEFRYSTTITRLITEGAGAAA 236 Query: 254 RVT-LEVQSPHLASH--LTMDAVVVAAGMASAALLQPLDTSLPLRALQSYSALVPVKNPD 310 RVT +E+ +P H L D VVA G S L++PL L L + YSA + NPD Sbjct: 237 RVTGVEIINPD-GRHEVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQITNPD 295 Query: 311 DAPTMALYDDSYKVAMTRLGSRIRISGLLGFVPASQTLPPKALRNLLKIAGDYYPNAANY 370 APT++L DD YK+ ++RLG R+R++G ++ L + + + +P+ +Y Sbjct: 296 AAPTVSLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGCDY 355 Query: 371 NQAHFWSNSIAMMPTGLPVVGPTRQGNIFVNVGHGVTGWAASVGSARLLSDMMAGEETEI 430 +W+ + P+ +P VG T+ N+++N GHG GW GS R +++++AG EI Sbjct: 356 ENPTYWTGLRPLTPSNVPYVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAEIVAGHVPEI 415 Query: 431 PTAGL-LPR 438 A LPR Sbjct: 416 DFAFTGLPR 424 >gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 421 Score = 135 bits (341), Expect = 5e-33, Method: Compositional matrix adjust. Identities = 113/418 (27%), Positives = 196/418 (46%), Gaps = 22/418 (5%) Query: 27 IAVIGGGLSGICSAYFLATKGYEVAVIERRAHVAEEATFGDSGLLAPGTAMPLTLPGALA 86 I V+G G+ G+ +AY L G++V++I+ R + G+ L+ PL P + Sbjct: 3 ICVMGAGVIGVTTAYRLLQDGHQVSLIDERDQPGAGTSQGNGAQLSYSYVAPLADPSVWS 62 Query: 87 TFACR-FQDEPRVLLASGADFGRRRWMRA-TRAAQQHHFAQHKLILSRLSAYGQDLTQQL 144 +A F + + + + + RW+ R Q + L +L+ Y +D Q Sbjct: 63 KWAYYLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSVRQTTIDLLQLAFYSRDQLTQW 122 Query: 145 QAHYNM--EHENSAGVFHLFR--QSAEAARLPALQEAASQCEYKQLTLDAAGIRALEPAF 200 + +H+ S G +F Q EAA +A C+ Q LDAA +EPA Sbjct: 123 NGRLKLSFDHQRS-GKLVMFTDAQGLEAAAGQVRFQAQYGCQ--QEVLDAAQCIRIEPAL 179 Query: 201 S-SEAALAGALYYPDDIAGNSVLFAKQMRNAAQALGVSFHF--NSTVSSIRSEFGGRVTL 257 S+ G +Y + AG+ F + + A QA +F F + ++++R + G Sbjct: 180 GRSQRDWVGGVYTRSEEAGDCPAFCRALVAAMQA-DPNFRFIGGARITAVRRQ--GSALS 236 Query: 258 EVQSPHLASHLTMDAVVVAAGMASAALLQPLDTSLPLRALQSYSALVPVKNPDD---APT 314 VQ+ + ++ V+A G SA + LD LPL L+ YS VP+++ AP Sbjct: 237 AVQAGN--EWISAQRFVLALGADSADFARQLDLRLPLYPLKGYSITVPLEDEASRAAAPQ 294 Query: 315 MALYDDSYKVAMTRLGSRIRISGLLGFVPASQTLPPKALRNLLKIAGDYYPNAANYNQAH 374 +++ D + K+ RLG R+R++G + V +++PP+A+ L + + +P+ A Sbjct: 295 VSITDIARKIVYARLGQRLRVAGRIELVGQDRSIPPRAIAELKQGMRELFPDCVLGEDAR 354 Query: 375 F--WSNSIAMMPTGLPVVGPTRQGNIFVNVGHGVTGWAASVGSARLLSDMMAGEETEI 430 W P+G+P+VG N+++N+G G GW + GSA L++D +AG I Sbjct: 355 LSPWMGFRPATPSGVPIVGACPVDNLYLNIGQGALGWTLACGSAALIADQIAGRPCSI 412 >gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 428 Score = 63.9 bits (154), Expect = 2e-11, Method: Compositional matrix adjust. Identities = 101/438 (23%), Positives = 175/438 (39%), Gaps = 46/438 (10%) Query: 25 RQIAVIGGGLSGICSAYFLATKGYEVAVIERRAHVAEEA-TFGDSGLLAPGTAMPLTLPG 83 R VIG G G+ SA +G EV++++ +EEA ++G++G L+ + +P PG Sbjct: 11 RHAVVIGAGAVGLMSAIHALDQGLEVSLLDFNPVGSEEAASYGNAGWLSSHSVIPPVEPG 70 Query: 84 -----------ALATFACRFQDEPRV--LLASGADFGRRRWMRATRAAQQHHFAQHKLIL 130 + + R++ PR+ L RR +RAT A L Sbjct: 71 MWKKVPGYLMDPIGPLSIRWRYLPRLTPWLLRNLASARRERIRATARA-----------L 119 Query: 131 SRLSAYGQDLTQQLQAHYNMEHE-NSAGVFHLFRQSAEAARLPALQEAASQCEYKQLTLD 189 L + L + + H +++GV H++R + + + L+ Sbjct: 120 RTLVVDARTLHLDIARRAGVAHLIDTSGVLHVYRSRQQFEGDAFGWSVRRELGIQWSELE 179 Query: 190 AAGIRALEPAFSSEAALAGALYYPDDIAG---NSVLFAKQMRNAAQALGVSFHFNSTVSS 246 A +R EP A + D AG N + + ++ A A G + ++ + Sbjct: 180 AEALRRREPDLDPAFGFAVQV----DEAGHCKNPAAYLQALQAYALARG-AHRIDARATG 234 Query: 247 IRSEFGGRVTLEVQSPHLASHLTMDAVVVAAGMASAALLQPLDTSLPLRALQSYSALVPV 306 R E G + ++ +A DA V+ AG S AL + L + + Y AL+ Sbjct: 235 FRIEEGRLKAVLTETGEVAC----DAAVICAGARSKALAAQAGDRVQLESERGYHALIRG 290 Query: 307 KNPDDAPTMALYDDSYKVAMTRLGSRIRISGLLGFVPASQTLPPKALRN--LLKIAGDYY 364 + +KV T++ + +RI+G + F AS P R + IA + Sbjct: 291 HEQAARARTPMMLSEFKVIATQMETGLRIAGQVEF--ASFEAAPDWRRGEIMRDIALKLF 348 Query: 365 PNAANYNQA---HFWSNSIAMMPTGLPVVGPTRQGNIFVNV-GHGVTGWAASVGSARLLS 420 P A +W P G+P +G R + V+ GHG G S + R+++ Sbjct: 349 PGLPRDLPAADVRYWLGRRPSTPDGMPCIGYARASSDIVHAYGHGHIGLGCSARTGRIVA 408 Query: 421 DMMAGEETEIPTAGLLPR 438 ++AG+ EI A P+ Sbjct: 409 QLLAGQTPEIDLAPFSPQ 426 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 0.131 0.384 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: 1,383,099 Number of extensions: 57026 Number of successful extensions: 241 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 234 Number of HSP's successfully gapped: 5 Length of query: 442 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 354 Effective length of database: 1,203,190 Effective search space: 425929260 Effective search space used: 425929260 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)