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= 0001.1555.p (433 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... 823 0.0 gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase smal... 335 5e-93 gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase smal... 261 5e-71 gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase smal... 207 1e-54 gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [H... 120 2e-28 >gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 433 Score = 823 bits (2127), Expect = 0.0, Method: Compositional matrix adjust. Identities = 401/433 (92%), Positives = 416/433 (96%) Query: 1 MRVVILGSGVIGVTSAWYLARAGHDVTVLDRQPGPALETSFGNAGQISPGYASPWAAPGI 60 MRVVILGSGVIGVTSAWYLARAGHDVTVLDRQPGPALETSFGNAGQISPGYASPWAAPGI Sbjct: 1 MRVVILGSGVIGVTSAWYLARAGHDVTVLDRQPGPALETSFGNAGQISPGYASPWAAPGI 60 Query: 61 PLKAIKWMFQEHAPLAIRPDGTLNQLRWMWQMLRNCNADSYAINKERMVRLAEYSRDCLR 120 PLKAIKWMFQEHAPLAIR DG+ NQLRWMWQMLRNCNA+ YA+NKERMVRLAEYSRDCLR Sbjct: 61 PLKAIKWMFQEHAPLAIRLDGSFNQLRWMWQMLRNCNAERYAVNKERMVRLAEYSRDCLR 120 Query: 121 ELRADVGIPYEGREQGTLQLFRSQEQLDGAAKDIAVLKEAGVPFELLTPEQLGGAEPALE 180 +LRADVGIPYEGR+QGTLQLFRSQEQL+GAAKDIAVLKEAGVPFELLTP+QLG AEPAL Sbjct: 121 DLRADVGIPYEGRQQGTLQLFRSQEQLEGAAKDIAVLKEAGVPFELLTPDQLGNAEPALA 180 Query: 181 KVRGKLTGGLRLPNDETGDCQLFTTRLAKMAEQLGVKFRYDVAIDALTMAGGKIAGVVCG 240 KVR KLTGGLRLPNDETGDCQLFTTRLA MAEQ+GVKFRY V IDAL MAGGKIAGVVCG Sbjct: 181 KVRDKLTGGLRLPNDETGDCQLFTTRLATMAEQIGVKFRYGVDIDALAMAGGKIAGVVCG 240 Query: 241 KELVQADSYVVALGSYSPQMLRDVPGLPAIPVYPLKGYSITVPITDATAAPVSTILDETY 300 KELVQADSYVVALGSYSPQ+L +VPGLPAIPVYPLKGYSITVPITDA+AAPVSTILDETY Sbjct: 241 KELVQADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDASAAPVSTILDETY 300 Query: 301 KIAVTRFDDRIRVGGMAEIVGYDTALRAKRRATLEMVVNDLFPGAGDTTQASFWTGLRPM 360 KIAVTRFDDRIRVGGMAEIVGYDTAL+AKRRATLE+VVNDLFPGAGDT QASFWTGLRPM Sbjct: 301 KIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGAGDTAQASFWTGLRPM 360 Query: 361 TPDGTPVVGATPVSNLFINTGHGTLGWTMSCGSGQLLADLISGRRPAIAHEDLSVARYMQ 420 TPDGTPVVGATPVSNL+INTGHGTLGWTMSCGSGQLLADLISGRRPAIAHEDLSV RY+ Sbjct: 361 TPDGTPVVGATPVSNLYINTGHGTLGWTMSCGSGQLLADLISGRRPAIAHEDLSVERYLS 420 Query: 421 SGAGVQTPRLAGA 433 SG QTPRLAGA Sbjct: 421 SGGRAQTPRLAGA 433 >gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 436 Score = 335 bits (858), Expect = 5e-93, Method: Compositional matrix adjust. Identities = 171/417 (41%), Positives = 247/417 (59%), Gaps = 11/417 (2%) Query: 1 MRVVILGSGVIGVTSAWYLARAGHDVTVLDRQPGPALETSFGNAGQISPGYASPWAAPGI 60 M+V++LG+G+IG SAW+L + G+DVTV+DRQPG A ETSF N QIS +A PWA P Sbjct: 1 MKVIVLGAGIIGTASAWFLKKQGYDVTVIDRQPGAAQETSFANGCQISVSHAEPWANPAA 60 Query: 61 PLKAIKWMFQEHAPLAIRPDGTLNQLRWMWQMLRNCNADSYAINKERMVRLAEYSRDCLR 120 P+K +KW+ +E APL R Q +W LR C A N +V L EYSR L+ Sbjct: 61 PMKVLKWLGKEDAPLLYRFRPEWLQWKWAVAFLRECTAARTDENIRNIVALCEYSRQTLQ 120 Query: 121 ELRADVGIPYEGREQGTLQLFRSQEQLDGAAKDIAVLKEAGVPFELLTPEQLGGAEPALE 180 +RA+ GI Y+ +G L + +++ + ++++ G P E + +++ EPAL Sbjct: 121 AVRAETGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRIEPALA 180 Query: 181 KVRGKLTGGLRLPNDETGDCQLFTTRLAKMAEQLGVKFRYDVAIDALTMAGGKIAGVVCG 240 +R K+ GG DE+GD TT LAK + + GV+FRY I L G A V G Sbjct: 181 SIRNKIVGGDFTATDESGDVFKLTTGLAKKSAEAGVEFRYSTTITRLITEGAGAAARVTG 240 Query: 241 KELV---------QADSYVVALGSYSPQMLRDVPGLPAIPVYPLKGYSITVPITDATAAP 291 E++ +AD++VVA+GS+S Q+++ + G+ + +YP KGYS T IT+ AAP Sbjct: 241 VEIINPDGRHEVLKADTFVVAMGSFSQQLVKPL-GIDLL-LYPGKGYSATYQITNPDAAP 298 Query: 292 VSTILDETYKIAVTRFDDRIRVGGMAEIVGYDTALRAKRRATLEMVVNDLFPGAGDTTQA 351 ++ D+ YK+ V+R DR+RV G E+ GY L R + +LFP D Sbjct: 299 TVSLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGCDYENP 358 Query: 352 SFWTGLRPMTPDGTPVVGATPVSNLFINTGHGTLGWTMSCGSGQLLADLISGRRPAI 408 ++WTGLRP+TP P VG T +NL++NTGHGTLGWTM CGSG+ +A++++G P I Sbjct: 359 TYWTGLRPLTPSNVPYVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAEIVAGHVPEI 415 >gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 421 Score = 261 bits (668), Expect = 5e-71, Method: Compositional matrix adjust. Identities = 153/414 (36%), Positives = 224/414 (54%), Gaps = 8/414 (1%) Query: 1 MRVVILGSGVIGVTSAWYLARAGHDVTVLDRQPGPALETSFGNAGQISPGYASPWAAPGI 60 M + ++G+GVIGVT+A+ L + GH V+++D + P TS GN Q+S Y +P A P + Sbjct: 1 MHICVMGAGVIGVTTAYRLLQDGHQVSLIDERDQPGAGTSQGNGAQLSYSYVAPLADPSV 60 Query: 61 PLKAIKWMFQEHAPLAIRPDGTLNQLRWMWQMLRNCNADSYAINKERMVRLAEYSRDCLR 120 K ++F + +PL I+P Q RW+ LR CNA S +++LA YSRD L Sbjct: 61 WSKWAYYLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSVRQTTIDLLQLAFYSRDQLT 120 Query: 121 ELRADVGIPYEGREQGTLQLFRSQEQLDGAAKDIAVLKEAGVPFELLTPEQLGGAEPALE 180 + + + ++ + G L +F + L+ AA + + G E+L Q EPAL Sbjct: 121 QWNGRLKLSFDHQRSGKLVMFTDAQGLEAAAGQVRFQAQYGCQQEVLDAAQCIRIEPALG 180 Query: 181 KVRGKLTGGLRLPNDETGDCQLFTTRL-AKMAEQLGVKFRYDVAIDALTMAGGKIAGVVC 239 + + GG+ ++E GDC F L A M +F I A+ G ++ V Sbjct: 181 RSQRDWVGGVYTRSEEAGDCPAFCRALVAAMQADPNFRFIGGARITAVRRQGSALSAVQA 240 Query: 240 GKELVQADSYVVALGSYSPQMLRDVPGLPAIPVYPLKGYSITVPITDA---TAAPVSTIL 296 G E + A +V+ALG+ S R + +P+YPLKGYSITVP+ D AAP +I Sbjct: 241 GNEWISAQRFVLALGADSADFARQLD--LRLPLYPLKGYSITVPLEDEASRAAAPQVSIT 298 Query: 297 DETYKIAVTRFDDRIRVGGMAEIVGYDTALRAKRRATLEMVVNDLFPGA--GDTTQASFW 354 D KI R R+RV G E+VG D ++ + A L+ + +LFP G+ + S W Sbjct: 299 DIARKIVYARLGQRLRVAGRIELVGQDRSIPPRAIAELKQGMRELFPDCVLGEDARLSPW 358 Query: 355 TGLRPMTPDGTPVVGATPVSNLFINTGHGTLGWTMSCGSGQLLADLISGRRPAI 408 G RP TP G P+VGA PV NL++N G G LGWT++CGS L+AD I+GR +I Sbjct: 359 MGFRPATPSGVPIVGACPVDNLYLNIGQGALGWTLACGSAALIADQIAGRPCSI 412 >gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 207 bits (528), Expect = 1e-54, Method: Compositional matrix adjust. Identities = 131/416 (31%), Positives = 211/416 (50%), Gaps = 18/416 (4%) Query: 2 RVVILGSGVIGVTSAWYLARAGHDVTVLDRQPGPALETSFGNAGQISPGYASPWAAPGIP 61 ++ ++G G+ G+ SA++LA G++V V++R+ A E +FG++G ++PG A P PG Sbjct: 7 QIAVIGGGLSGICSAYFLATKGYEVAVIERRAHVAEEATFGDSGLLAPGTAMPLTLPG-A 65 Query: 62 LKAIKWMFQEHAPLAIRPDGTLNQLRWMWQMLRNCNADSYAINKERMVRLAEYSRDCLRE 121 L FQ+ + + + RWM + R +A +K + RL+ Y +D ++ Sbjct: 66 LATFACRFQDEPRVLLASGADFGRRRWM-RATRAAQQHHFAQHKLILSRLSAYGQDLTQQ 124 Query: 122 LRADVGIPYEGREQGTLQLFRSQEQLDGAAKDIAVLKEAG--VPFELLTPEQLG--GAEP 177 L+A + +E G LFR + A + L+EA ++ LT + G EP Sbjct: 125 LQAHYNMEHEN-SAGVFHLFRQSAE----AARLPALQEAASQCEYKQLTLDAAGIRALEP 179 Query: 178 ALEKVRGKLTGGLRLPNDETGDCQLFTTRLAKMAEQLGVKFRYDVAIDAL-TMAGGKIAG 236 A L G L P+D G+ LF ++ A+ LGV F ++ + ++ + GG++ Sbjct: 180 AFSS-EAALAGALYYPDDIAGNSVLFAKQMRNAAQALGVSFHFNSTVSSIRSEFGGRVTL 238 Query: 237 VVCGKEL---VQADSYVVALGSYSPQMLRDVPGLPAIPVYPLKGYSITVPITDATAAPVS 293 V L + D+ VVA G S +L+ P ++P+ L+ YS VP+ + AP Sbjct: 239 EVQSPHLASHLTMDAVVVAAGMASAALLQ--PLDTSLPLRALQSYSALVPVKNPDDAPTM 296 Query: 294 TILDETYKIAVTRFDDRIRVGGMAEIVGYDTALRAKRRATLEMVVNDLFPGAGDTTQASF 353 + D++YK+A+TR RIR+ G+ V L K L + D +P A + QA F Sbjct: 297 ALYDDSYKVAMTRLGSRIRISGLLGFVPASQTLPPKALRNLLKIAGDYYPNAANYNQAHF 356 Query: 354 WTGLRPMTPDGTPVVGATPVSNLFINTGHGTLGWTMSCGSGQLLADLISGRRPAIA 409 W+ M P G PVVG T N+F+N GHG GW S GS +LL+D+++G IA Sbjct: 357 WSNSIAMMPTGLPVVGPTRQGNIFVNVGHGVTGWAASVGSARLLSDMMAGEETEIA 412 >gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 428 Score = 120 bits (302), Expect = 2e-28, Method: Compositional matrix adjust. Identities = 104/423 (24%), Positives = 183/423 (43%), Gaps = 16/423 (3%) Query: 4 VILGSGVIGVTSAWYLARAGHDVTVLDRQP-GPALETSFGNAGQISPGYASPWAAPGIPL 62 V++G+G +G+ SA + G +V++LD P G S+GNAG +S P PG+ Sbjct: 14 VVIGAGAVGLMSAIHALDQGLEVSLLDFNPVGSEEAASYGNAGWLSSHSVIPPVEPGMWK 73 Query: 63 KAIKWMFQEHAPLAIRPDGTLNQLRWMWQMLRNCNADSYAINKERMVRLAEYSRDCLREL 122 K ++ PL+IR W+ + L + + + L +R ++ Sbjct: 74 KVPGYLMDPIGPLSIRWRYLPRLTPWLLRNLASARRERIRATARALRTLVVDARTLHLDI 133 Query: 123 RADVGIPYEGREQGTLQLFRSQEQLDGAAKDIAVLKEAGVPFELLTPEQLGGAEPALEKV 182 G+ + G L ++RS++Q +G A +V +E G+ + L E L EP L+ Sbjct: 134 ARRAGVAHLIDTSGVLHVYRSRQQFEGDAFGWSVRRELGIQWSELEAEALRRREPDLDP- 192 Query: 183 RGKLTGGLRLPNDETGDCQ---LFTTRLAKMAEQLGVKFRYDVAIDALTMAGGKIAGVVC 239 G + DE G C+ + L A G R D + G++ V+ Sbjct: 193 ----AFGFAVQVDEAGHCKNPAAYLQALQAYALARGAH-RIDARATGFRIEEGRLKAVLT 247 Query: 240 GKELVQADSYVVALGSYSPQMLRDVPGLPAIPVYPLKGYSITVPITDATAAPVSTILDET 299 V D+ V+ G+ S + + + +GY + + A + ++ Sbjct: 248 ETGEVACDAAVICAGARSKALAAQAGD--RVQLESERGYHALIRGHEQAARARTPMMLSE 305 Query: 300 YKIAVTRFDDRIRVGGMAEIVGYDTALRAKRRATLEMVVNDLFPGAGDTTQAS---FWTG 356 +K+ T+ + +R+ G E ++ A +R + + LFPG A+ +W G Sbjct: 306 FKVIATQMETGLRIAGQVEFASFEAAPDWRRGEIMRDIALKLFPGLPRDLPAADVRYWLG 365 Query: 357 LRPMTPDGTPVVG-ATPVSNLFINTGHGTLGWTMSCGSGQLLADLISGRRPAIAHEDLSV 415 RP TPDG P +G A S++ GHG +G S +G+++A L++G+ P I S Sbjct: 366 RRPSTPDGMPCIGYARASSDIVHAYGHGHIGLGCSARTGRIVAQLLAGQTPEIDLAPFSP 425 Query: 416 ARY 418 R+ Sbjct: 426 QRF 428 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 0.136 0.411 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: 1,557,938 Number of extensions: 72657 Number of successful extensions: 272 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 263 Number of HSP's successfully gapped: 5 Length of query: 433 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 345 Effective length of database: 1,203,190 Effective search space: 415100550 Effective search space used: 415100550 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 (21.7 bits) S2: 132 (55.5 bits)