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= 0029.0209.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... 881 0.0 gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase smal... 345 4e-96 gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase smal... 261 8e-71 gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase smal... 206 3e-54 gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [H... 130 3e-31 >gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 433 Score = 881 bits (2277), Expect = 0.0, Method: Compositional matrix adjust. Identities = 433/433 (100%), Positives = 433/433 (100%) Query: 1 MRVVILGSGVIGVTSAWYLARAGHDVTVLDRQPGPALETSFGNAGQISPGYASPWAAPGI 60 MRVVILGSGVIGVTSAWYLARAGHDVTVLDRQPGPALETSFGNAGQISPGYASPWAAPGI Sbjct: 1 MRVVILGSGVIGVTSAWYLARAGHDVTVLDRQPGPALETSFGNAGQISPGYASPWAAPGI 60 Query: 61 PLKAIKWMFQEHAPLAIRLDGSFNQLRWMWQMLRNCNAERYAVNKERMVRLAEYSRDCLR 120 PLKAIKWMFQEHAPLAIRLDGSFNQLRWMWQMLRNCNAERYAVNKERMVRLAEYSRDCLR Sbjct: 61 PLKAIKWMFQEHAPLAIRLDGSFNQLRWMWQMLRNCNAERYAVNKERMVRLAEYSRDCLR 120 Query: 121 DLRADVGIPYEGRQQGTLQLFRSQEQLEGAAKDIAVLKEAGVPFELLTPDQLGNAEPALA 180 DLRADVGIPYEGRQQGTLQLFRSQEQLEGAAKDIAVLKEAGVPFELLTPDQLGNAEPALA Sbjct: 121 DLRADVGIPYEGRQQGTLQLFRSQEQLEGAAKDIAVLKEAGVPFELLTPDQLGNAEPALA 180 Query: 181 KVRDKLTGGLRLPNDETGDCQLFTTRLATMAEQIGVKFRYGVDIDALAMAGGKIAGVVCG 240 KVRDKLTGGLRLPNDETGDCQLFTTRLATMAEQIGVKFRYGVDIDALAMAGGKIAGVVCG Sbjct: 181 KVRDKLTGGLRLPNDETGDCQLFTTRLATMAEQIGVKFRYGVDIDALAMAGGKIAGVVCG 240 Query: 241 KELVQADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDASAAPVSTILDETY 300 KELVQADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDASAAPVSTILDETY Sbjct: 241 KELVQADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDASAAPVSTILDETY 300 Query: 301 KIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGAGDTAQASFWTGLRPM 360 KIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGAGDTAQASFWTGLRPM Sbjct: 301 KIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGAGDTAQASFWTGLRPM 360 Query: 361 TPDGTPVVGATPVSNLYINTGHGTLGWTMSCGSGQLLADLISGRRPAIAHEDLSVERYLS 420 TPDGTPVVGATPVSNLYINTGHGTLGWTMSCGSGQLLADLISGRRPAIAHEDLSVERYLS Sbjct: 361 TPDGTPVVGATPVSNLYINTGHGTLGWTMSCGSGQLLADLISGRRPAIAHEDLSVERYLS 420 Query: 421 SGGRAQTPRLAGA 433 SGGRAQTPRLAGA Sbjct: 421 SGGRAQTPRLAGA 433 >gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 436 Score = 345 bits (885), Expect = 4e-96, Method: Compositional matrix adjust. Identities = 175/417 (41%), Positives = 250/417 (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 PLKAIKWMFQEHAPLAIRLDGSFNQLRWMWQMLRNCNAERYAVNKERMVRLAEYSRDCLR 120 P+K +KW+ +E APL R + Q +W LR C A R N +V L EYSR L+ Sbjct: 61 PMKVLKWLGKEDAPLLYRFRPEWLQWKWAVAFLRECTAARTDENIRNIVALCEYSRQTLQ 120 Query: 121 DLRADVGIPYEGRQQGTLQLFRSQEQLEGAAKDIAVLKEAGVPFELLTPDQLGNAEPALA 180 +RA+ GI Y+ +G L + +++ + + ++++ G P E + D++ EPALA Sbjct: 121 AVRAETGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRIEPALA 180 Query: 181 KVRDKLTGGLRLPNDETGDCQLFTTRLATMAEQIGVKFRYGVDIDALAMAGGKIAGVVCG 240 +R+K+ GG DE+GD TT LA + + GV+FRY I L G A V G Sbjct: 181 SIRNKIVGGDFTATDESGDVFKLTTGLAKKSAEAGVEFRYSTTITRLITEGAGAAARVTG 240 Query: 241 KELV---------QADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDASAAP 291 E++ +AD++VVA+GS+S QL+ + G+ + +YP KGYS T IT+ AAP Sbjct: 241 VEIINPDGRHEVLKADTFVVAMGSFSQQLVKPL-GIDLL-LYPGKGYSATYQITNPDAAP 298 Query: 292 VSTILDETYKIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGAGDTAQA 351 ++ D+ YK+ V+R DR+RV G E+ GY L R + +LFP D Sbjct: 299 TVSLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGCDYENP 358 Query: 352 SFWTGLRPMTPDGTPVVGATPVSNLYINTGHGTLGWTMSCGSGQLLADLISGRRPAI 408 ++WTGLRP+TP P VG T +NLY+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 (667), Expect = 8e-71, Method: Compositional matrix adjust. Identities = 154/414 (37%), Positives = 225/414 (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 PLKAIKWMFQEHAPLAIRLDGSFNQLRWMWQMLRNCNAERYAVNKERMVRLAEYSRDCLR 120 K ++F + +PL I+ Q RW+ LR CNA +++LA YSRD L Sbjct: 61 WSKWAYYLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSVRQTTIDLLQLAFYSRDQLT 120 Query: 121 DLRADVGIPYEGRQQGTLQLFRSQEQLEGAAKDIAVLKEAGVPFELLTPDQLGNAEPALA 180 + + ++ ++ G L +F + LE AA + + G E+L Q EPAL Sbjct: 121 QWNGRLKLSFDHQRSGKLVMFTDAQGLEAAAGQVRFQAQYGCQQEVLDAAQCIRIEPALG 180 Query: 181 KVRDKLTGGLRLPNDETGDCQLFTTRL-ATMAEQIGVKFRYGVDIDALAMAGGKIAGVVC 239 + + GG+ ++E GDC F L A M +F G I A+ G ++ V Sbjct: 181 RSQRDWVGGVYTRSEEAGDCPAFCRALVAAMQADPNFRFIGGARITAVRRQGSALSAVQA 240 Query: 240 GKELVQADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDA---SAAPVSTIL 296 G E + A +V+ALG+ S ++ +P+YPLKGYSITVP+ D +AAP +I Sbjct: 241 GNEWISAQRFVLALGADSADFARQLD--LRLPLYPLKGYSITVPLEDEASRAAAPQVSIT 298 Query: 297 DETYKIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGA--GDTAQASFW 354 D KI R R+RV G E+VG D ++ + A L+ + +LFP G+ A+ S W Sbjct: 299 DIARKIVYARLGQRLRVAGRIELVGQDRSIPPRAIAELKQGMRELFPDCVLGEDARLSPW 358 Query: 355 TGLRPMTPDGTPVVGATPVSNLYINTGHGTLGWTMSCGSGQLLADLISGRRPAI 408 G RP TP G P+VGA PV NLY+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 = 206 bits (523), Expect = 3e-54, Method: Compositional matrix adjust. Identities = 132/416 (31%), Positives = 210/416 (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 LKAIKWMFQEHAPLAIRLDGSFNQLRWMWQMLRNCNAERYAVNKERMVRLAEYSRDCLRD 121 L FQ+ + + F + RWM + R +A +K + RL+ Y +D + Sbjct: 66 LATFACRFQDEPRVLLASGADFGRRRWM-RATRAAQQHHFAQHKLILSRLSAYGQDLTQQ 124 Query: 122 LRADVGIPYEGRQQGTLQLFRSQEQLEGAAKDIAVLKEAG--VPFELLTPDQLG--NAEP 177 L+A + +E G LFR + A + L+EA ++ LT D G EP Sbjct: 125 LQAHYNMEHEN-SAGVFHLFRQSAE----AARLPALQEAASQCEYKQLTLDAAGIRALEP 179 Query: 178 ALAKVRDKLTGGLRLPNDETGDCQLFTTRLATMAEQIGVKFRYGVDIDAL-AMAGGKIAG 236 A + L G L P+D G+ LF ++ A+ +GV F + + ++ + GG++ Sbjct: 180 AFSS-EAALAGALYYPDDIAGNSVLFAKQMRNAAQALGVSFHFNSTVSSIRSEFGGRVTL 238 Query: 237 VVCGKEL---VQADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDASAAPVS 293 V L + D+ VVA G S LL P ++P+ L+ YS VP+ + AP Sbjct: 239 EVQSPHLASHLTMDAVVVAAGMASAALLQ--PLDTSLPLRALQSYSALVPVKNPDDAPTM 296 Query: 294 TILDETYKIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGAGDTAQASF 353 + D++YK+A+TR RIR+ G+ V L K L + D +P A + QA F Sbjct: 297 ALYDDSYKVAMTRLGSRIRISGLLGFVPASQTLPPKALRNLLKIAGDYYPNAANYNQAHF 356 Query: 354 WTGLRPMTPDGTPVVGATPVSNLYINTGHGTLGWTMSCGSGQLLADLISGRRPAIA 409 W+ M P G PVVG T N+++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 = 130 bits (326), Expect = 3e-31, Method: Compositional matrix adjust. Identities = 106/422 (25%), Positives = 186/422 (44%), Gaps = 14/422 (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 KAIKWMFQEHAPLAIRLDGSFNQLRWMWQMLRNCNAERYAVNKERMVRLAEYSRDCLRDL 122 K ++ PL+IR W+ + L + ER + L +R D+ Sbjct: 74 KVPGYLMDPIGPLSIRWRYLPRLTPWLLRNLASARRERIRATARALRTLVVDARTLHLDI 133 Query: 123 RADVGIPYEGRQQGTLQLFRSQEQLEGAAKDIAVLKEAGVPFELLTPDQLGNAEPALAKV 182 G+ + G L ++RS++Q EG A +V +E G+ + L + L EP L Sbjct: 134 ARRAGVAHLIDTSGVLHVYRSRQQFEGDAFGWSVRRELGIQWSELEAEALRRREPDLDP- 192 Query: 183 RDKLTGGLRLPNDETGDCQLFTTRLATMAEQIGVKFRYGVDIDA--LAMAGGKIAGVVCG 240 G + DE G C+ L + + + +D A + G++ V+ Sbjct: 193 ----AFGFAVQVDEAGHCKNPAAYLQALQAYALARGAHRIDARATGFRIEEGRLKAVLTE 248 Query: 241 KELVQADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDASAAPVSTILDETY 300 V D+ V+ G+ S L + + + +GY + + +A + ++ + Sbjct: 249 TGEVACDAAVICAGARSKALAAQAGD--RVQLESERGYHALIRGHEQAARARTPMMLSEF 306 Query: 301 KIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGAGD---TAQASFWTGL 357 K+ T+ + +R+ G E ++ A +R + + LFPG A +W G Sbjct: 307 KVIATQMETGLRIAGQVEFASFEAAPDWRRGEIMRDIALKLFPGLPRDLPAADVRYWLGR 366 Query: 358 RPMTPDGTPVVG-ATPVSNLYINTGHGTLGWTMSCGSGQLLADLISGRRPAIAHEDLSVE 416 RP TPDG P +G A S++ GHG +G S +G+++A L++G+ P I S + Sbjct: 367 RPSTPDGMPCIGYARASSDIVHAYGHGHIGLGCSARTGRIVAQLLAGQTPEIDLAPFSPQ 426 Query: 417 RY 418 R+ Sbjct: 427 RF 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 0.410 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: 1,546,633 Number of extensions: 72167 Number of successful extensions: 279 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 269 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)