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= 0025.0007.p (357 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... 482 e-137 gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [H... 89 5e-19 gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase smal... 79 6e-16 gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase smal... 74 2e-14 gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase smal... 65 1e-11 >gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 428 Score = 482 bits (1240), Expect = e-137, Method: Compositional matrix adjust. Identities = 240/359 (66%), Positives = 282/359 (78%), Gaps = 3/359 (0%) Query: 1 VWKKLPGFLADPLGPLSVRWRYLPRTLPWLLRYLVAGSTTARISATAAALRPLLQGAASL 60 +WKK+PG+L DP+GPLS+RWRYLPR PWLLR L A + RI ATA ALR L+ A +L Sbjct: 71 MWKKVPGYLMDPIGPLSIRWRYLPRLTPWLLRNL-ASARRERIRATARALRTLVVDARTL 129 Query: 61 HKAIADQAGVGDMIDLGGLLHIYRSREHFEADARGWGIRRKLGIGWQELSAQELHAREPD 120 H IA +AGV +ID G+LH+YRSR+ FE DA GW +RR+LGI W EL A+ L REPD Sbjct: 130 HLDIARRAGVAHLIDTSGVLHVYRSRQQFEGDAFGWSVRRELGIQWSELEAEALRRREPD 189 Query: 121 LDPAYGFGVLIPEAGHCRNPGAYIAALAAHACARGARLTAATATGFRFEGEKLAAVLTDA 180 LDPA+GF V + EAGHC+NP AY+ AL A+A ARGA A ATGFR E +L AVLT+ Sbjct: 190 LDPAFGFAVQVDEAGHCKNPAAYLQALQAYALARGAHRIDARATGFRIEEGRLKAVLTET 249 Query: 181 GEIACDAAVIAAGAQSKALAAKAGDKIPLETERGYHAMVLAPE--GRPRTPMMIMDRKVI 238 GE+ACDAAVI AGA+SKALAA+AGD++ LE+ERGYHA++ E R RTPMM+ + KVI Sbjct: 250 GEVACDAAVICAGARSKALAAQAGDRVQLESERGYHALIRGHEQAARARTPMMLSEFKVI 309 Query: 239 ATQTAEGLRVAGQVEIASFDAAPDWRRAEIMRDLALKLFPALPRDLPANRVRYWLGRRPS 298 ATQ GLR+AGQVE ASF+AAPDWRR EIMRD+ALKLFP LPRDLPA VRYWLGRRPS Sbjct: 310 ATQMETGLRIAGQVEFASFEAAPDWRRGEIMRDIALKLFPGLPRDLPAADVRYWLGRRPS 369 Query: 299 MPDGLPCIGPSSRSIDIIHAFGHGHIGLGSSARTGRLVGQLLAGQAPEIDLAPFSARRF 357 PDG+PCIG + S DI+HA+GHGHIGLG SARTGR+V QLLAGQ PEIDLAPFS +RF Sbjct: 370 TPDGMPCIGYARASSDIVHAYGHGHIGLGCSARTGRIVAQLLAGQTPEIDLAPFSPQRF 428 >gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 433 Score = 89.4 bits (220), Expect = 5e-19, Method: Compositional matrix adjust. Identities = 79/291 (27%), Positives = 128/291 (43%), Gaps = 19/291 (6%) Query: 78 GLLHIYRSREHFEADARGWGIRRKLGIGWQELSAQELHAREPDL----DPAYGFGVLIP- 132 G L ++RS+E E A+ + ++ G+ ++ L+ +L EP L D G G+ +P Sbjct: 136 GTLQLFRSQEQLEGAAKDIAVLKEAGVPFELLTPDQLGNAEPALAKVRDKLTG-GLRLPN 194 Query: 133 -EAGHCRNPGAYIAALAAHACARGARL-TAATATGFRFEGEKLAAVLTDAGEIACDAAVI 190 E G C+ + LA A G + G K+A V+ + D+ V+ Sbjct: 195 DETGDCQ---LFTTRLATMAEQIGVKFRYGVDIDALAMAGGKIAGVVCGKELVQADSYVV 251 Query: 191 AAGAQSKALAAKAGD--KIPLETERGYHAMVLAPEGRPRTPMMIMDR--KVIATQTAEGL 246 A G+ S L + IP+ +GY V + I+D K+ T+ + + Sbjct: 252 ALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDASAAPVSTILDETYKIAVTRFDDRI 311 Query: 247 RVAGQVEIASFDAAPDWRRAEIMRDLALKLFPALPRDLPANRVRYWLGRRPSMPDGLPCI 306 RV G EI +D A +R + + LFP A+ +W G RP PDG P + Sbjct: 312 RVGGMAEIVGYDTALKAKRRATLELVVNDLFPGAGDTAQAS---FWTGLRPMTPDGTPVV 368 Query: 307 GPSSRSIDIIHAFGHGHIGLGSSARTGRLVGQLLAGQAPEIDLAPFSARRF 357 G + S I+ GHG +G S +G+L+ L++G+ P I S R+ Sbjct: 369 GATPVSNLYINT-GHGTLGWTMSCGSGQLLADLISGRRPAIAHEDLSVERY 418 >gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 436 Score = 79.0 bits (193), Expect = 6e-16, Method: Compositional matrix adjust. Identities = 90/372 (24%), Positives = 142/372 (38%), Gaps = 40/372 (10%) Query: 10 ADPLGPLSV-RW----------RYLPRTLPW-----LLRYLVAGSTTARISATAAALRPL 53 A+P P+ V +W R+ P L W LR A T I A L Sbjct: 56 ANPAAPMKVLKWLGKEDAPLLYRFRPEWLQWKWAVAFLRECTAARTDENIRNIVA----L 111 Query: 54 LQGAASLHKAIADQAGVGDMIDLGGLLHIYRSREHFEADARGWGIRRKLGIGWQELSAQE 113 + + +A+ + G+ G+LH Y + F+ + R LG + + A E Sbjct: 112 CEYSRQTLQAVRAETGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADE 171 Query: 114 LHAREPDLDPAYG--FGVLIPEAGHCRNPGAYIAALAAHACARGARL-TAATATGFRFEG 170 + EP L G + LA + G + T T EG Sbjct: 172 VVRIEPALASIRNKIVGGDFTATDESGDVFKLTTGLAKKSAEAGVEFRYSTTITRLITEG 231 Query: 171 EKLAAVLTDAGEI---------ACDAAVIAAGAQSKALAAKAGDKIPLETERGYHA--MV 219 AA +T I D V+A G+ S+ L G + L +GY A + Sbjct: 232 AGAAARVTGVEIINPDGRHEVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQI 291 Query: 220 LAPEGRPRTPMMIMDRKVIATQTAEGLRVAGQVEIASFDAAPDWRRAEIMRDLALKLFP- 278 P+ P + K++ ++ + LRVAG E+ + + R E + +LFP Sbjct: 292 TNPDAAPTVSLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPD 351 Query: 279 ALPRDLPANRVRYWLGRRPSMPDGLPCIGPSSRSIDIIHAFGHGHIGLGSSARTGRLVGQ 338 + P YW G RP P +P +G ++ ++ GHG +G +GR + + Sbjct: 352 GCDYENPT----YWTGLRPLTPSNVPYVG-KTKFANLYLNTGHGTLGWTMGCGSGRAIAE 406 Query: 339 LLAGQAPEIDLA 350 ++AG PEID A Sbjct: 407 IVAGHVPEIDFA 418 >gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 421 Score = 73.6 bits (179), Expect = 2e-14, Method: Compositional matrix adjust. Identities = 103/378 (27%), Positives = 156/378 (41%), Gaps = 40/378 (10%) Query: 1 VWKKLPGFLADPLGPLSVRWRYLPRTLPWL---LRYLVAGS---TTARISATAAALRPLL 54 VW K +L PL+++ WL LRY AGS TT + A R L Sbjct: 60 VWSKWAYYLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSVRQTTIDLLQLAFYSRDQL 119 Query: 55 QGAASLHKAIADQAGVGDMIDLGGLLHIYRSREHFEADARGWGIRRKLGIGWQELSAQEL 114 K D G ++ ++ + EA A + + G + L A + Sbjct: 120 TQWNGRLKLSFDHQRSGKLV-------MFTDAQGLEAAAGQVRFQAQYGCQQEVLDAAQC 172 Query: 115 HAREPDL-----DPAYGFGVLIPEAGHCRNPG---AYIAALAAHACAR---GARLTAATA 163 EP L D G EAG C P A +AA+ A R GAR+TA Sbjct: 173 IRIEPALGRSQRDWVGGVYTRSEEAGDC--PAFCRALVAAMQADPNFRFIGGARITAV-- 228 Query: 164 TGFRFEGEKLAAVLTDAGEIACDAAVIAAGAQSKALAAKAGDKIPLETERGYHAMV-LAP 222 R +G L+AV I+ V+A GA S A + ++PL +GY V L Sbjct: 229 ---RRQGSALSAVQAGNEWISAQRFVLALGADSADFARQLDLRLPLYPLKGYSITVPLED 285 Query: 223 EGR----PRTPMMIMDRKVIATQTAEGLRVAGQVEIASFDAAPDWRRAEIMRDLALKLFP 278 E P+ + + RK++ + + LRVAG++E+ D + R ++ +LFP Sbjct: 286 EASRAAAPQVSITDIARKIVYARLGQRLRVAGRIELVGQDRSIPPRAIAELKQGMRELFP 345 Query: 279 ALPRDLPANRVRYWLGRRPSMPDGLPCIGPSSRSIDIIH-AFGHGHIGLGSSARTGRLVG 337 A R+ W+G RP+ P G+P +G +D ++ G G +G + + L+ Sbjct: 346 DCVLGEDA-RLSPWMGFRPATPSGVPIVGAC--PVDNLYLNIGQGALGWTLACGSAALIA 402 Query: 338 QLLAGQAPEIDLAPFSAR 355 +AG+ ID PF R Sbjct: 403 DQIAGRPCSIDDTPFRYR 420 >gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 64.7 bits (156), Expect = 1e-11, Method: Compositional matrix adjust. Identities = 50/173 (28%), Positives = 76/173 (43%), Gaps = 6/173 (3%) Query: 180 AGEIACDAAVIAAGAQSKALAAKAGDKIPLETERGYHAMV--LAPEGRPRTPMMIMDRKV 237 A + DA V+AAG S AL +PL + Y A+V P+ P + KV Sbjct: 246 ASHLTMDAVVVAAGMASAALLQPLDTSLPLRALQSYSALVPVKNPDDAPTMALYDDSYKV 305 Query: 238 IATQTAEGLRVAGQVEIASFDAAPDWRRAEIMRDLALKLFPALPRDLPANRVRYWLGRRP 297 T+ +R++G + F A + +R+L P N+ +W Sbjct: 306 AMTRLGSRIRISG---LLGFVPASQTLPPKALRNLLKIAGDYYPNAANYNQAHFWSNSIA 362 Query: 298 SMPDGLPCIGPSSRSIDIIHAFGHGHIGLGSSARTGRLVGQLLAGQAPEIDLA 350 MP GLP +GP+ R +I GHG G +S + RL+ ++AG+ EI A Sbjct: 363 MMPTGLPVVGPT-RQGNIFVNVGHGVTGWAASVGSARLLSDMMAGEETEIATA 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 0.322 0.138 0.427 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: 1,057,471 Number of extensions: 42237 Number of successful extensions: 170 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 160 Number of HSP's successfully gapped: 5 Length of query: 357 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 271 Effective length of database: 1,212,660 Effective search space: 328630860 Effective search space used: 328630860 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 (21.9 bits) S2: 131 (55.1 bits)