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= 0030.0015.p (400 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... 310 1e-85 gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase smal... 230 2e-61 gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase smal... 203 2e-53 gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase smal... 194 9e-51 gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [H... 125 5e-30 >gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 433 Score = 310 bits (794), Expect = 1e-85, Method: Compositional matrix adjust. Identities = 166/366 (45%), Positives = 227/366 (62%), Gaps = 7/366 (1%) Query: 2 IAPGYVTPWAAPGMPGKILKYLFKASSPVVFRPRMSARQWRWISQWLGNCTLERYRRNKL 61 I+PGY +PWAAPG+P K +K++F+ +P+ R S Q RW+ Q L NC ERY NK Sbjct: 47 ISPGYASPWAAPGIPLKAIKWMFQEHAPLAIRLDGSFNQLRWMWQMLRNCNAERYAVNKE 106 Query: 62 RMQRIAYYSRDCLHEFLAQHPFDY-GRSQGYLQLFRSRFDEDMAAPALALLEEAGIAHQR 120 RM R+A YSRDCL + A Y GR QG LQLFRS+ + AA +A+L+EAG+ + Sbjct: 107 RMVRLAEYSRDCLRDLRADVGIPYEGRQQGTLQLFRSQEQLEGAAKDIAVLKEAGVPFEL 166 Query: 121 LSAAQCVATEPGLQHARIEPRSGLYLPDDEAGDCAVFARQLRRLCEEMGVQFRFGTQVSG 180 L+ Q EP L R + GL LP+DE GDC +F +L + E++GV+FR+G + Sbjct: 167 LTPDQLGNAEPALAKVRDKLTGGLRLPNDETGDCQLFTTRLATMAEQIGVKFRYGVDIDA 226 Query: 181 LRVQGGQVQGLQVSSAGQAGQLACDALVVAAGVDSHALLAPL-GI-RVPLYPVKGYSATI 238 L + GG++ G+ + D+ VVA G S LL + G+ +P+YP+KGYS T+ Sbjct: 227 LAMAGGKIAGVVCGKE----LVQADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITV 282 Query: 239 PVRFPEAAPRAAVMDESLKTAITRMGDVVRVAGTAELGDDRLQLRAACLHTLRQVMRDWF 298 P+ AAP + ++DE+ K A+TR D +RV G AE+ L+A TL V+ D F Sbjct: 283 PITDASAAPVSTILDETYKIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLF 342 Query: 299 PLAGDLDDAQFWVGRRPMTPDGPPLLGPTPVRNLFLNLGHGSTGWAMSLGSGRVVADLIT 358 P AGD A FW G RPMTPDG P++G TPV NL++N GHG+ GW MS GSG+++ADLI+ Sbjct: 343 PGAGDTAQASFWTGLRPMTPDGTPVVGATPVSNLYINTGHGTLGWTMSCGSGQLLADLIS 402 Query: 359 GTPPAI 364 G PAI Sbjct: 403 GRRPAI 408 >gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 436 Score = 230 bits (586), Expect = 2e-61, Method: Compositional matrix adjust. Identities = 127/373 (34%), Positives = 192/373 (51%), Gaps = 6/373 (1%) Query: 2 IAPGYVTPWAAPGMPGKILKYLFKASSPVVFRPRMSARQWRWISQWLGNCTLERYRRNKL 61 I+ + PWA P P K+LK+L K +P+++R R QW+W +L CT R N Sbjct: 47 ISVSHAEPWANPAAPMKVLKWLGKEDAPLLYRFRPEWLQWKWAVAFLRECTAARTDENIR 106 Query: 62 RMQRIAYYSRDCLHEFLAQHPFDYGR-SQGYLQLFRSRFDEDMAAPALALLEEAGIAHQR 120 + + YSR L A+ Y ++G L + + + PA L+ + G + Sbjct: 107 NIVALCEYSRQTLQAVRAETGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRES 166 Query: 121 LSAAQCVATEPGLQHARIEPRSGLYLPDDEAGDCAVFARQLRRLCEEMGVQFRFGTQVSG 180 + A + V EP L R + G + DE+GD L + E GV+FR+ T ++ Sbjct: 167 IGADEVVRIEPALASIRNKIVGGDFTATDESGDVFKLTTGLAKKSAEAGVEFRYSTTITR 226 Query: 181 LRVQGG----QVQGLQV-SSAGQAGQLACDALVVAAGVDSHALLAPLGIRVPLYPVKGYS 235 L +G +V G+++ + G+ L D VVA G S L+ PLGI + LYP KGYS Sbjct: 227 LITEGAGAAARVTGVEIINPDGRHEVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYS 286 Query: 236 ATIPVRFPEAAPRAAVMDESLKTAITRMGDVVRVAGTAELGDDRLQLRAACLHTLRQVMR 295 AT + P+AAP ++ D+ K ++R+GD +RVAGT EL +L + + R Sbjct: 287 ATYQITNPDAAPTVSLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTR 346 Query: 296 DWFPLAGDLDDAQFWVGRRPMTPDGPPLLGPTPVRNLFLNLGHGSTGWAMSLGSGRVVAD 355 + FP D ++ +W G RP+TP P +G T NL+LN GHG+ GW M GSGR +A+ Sbjct: 347 ELFPDGCDYENPTYWTGLRPLTPSNVPYVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAE 406 Query: 356 LITGTPPAIDIXW 368 ++ G P ID + Sbjct: 407 IVAGHVPEIDFAF 419 >gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 421 Score = 203 bits (516), Expect = 2e-53, Method: Compositional matrix adjust. Identities = 134/372 (36%), Positives = 200/372 (53%), Gaps = 21/372 (5%) Query: 6 YVTPWAAPGMPGKILKYLFKASSPVVFRPRMSARQWRWISQWLGNCTLERYRRNKLRMQR 65 YV P A P + K YLF SP+ +P + A Q+RW++ +L C R+ + + + Sbjct: 51 YVAPLADPSVWSKWAYYLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSVRQTTIDLLQ 110 Query: 66 IAYYSRDCLHEFLA--QHPFDYGRSQGYLQLFRSRFDEDMAAPALALLEEAGIAHQRLSA 123 +A+YSRD L ++ + FD+ RS G L +F + AA + + G + L A Sbjct: 111 LAFYSRDQLTQWNGRLKLSFDHQRS-GKLVMFTDAQGLEAAAGQVRFQAQYGCQQEVLDA 169 Query: 124 AQCVATEPGLQHARIEPRSGLYLPDDEAGDCAVFARQLRRLCEEMGVQFRF--GTQVSGL 181 AQC+ EP L ++ + G+Y +EAGDC F R L + FRF G +++ + Sbjct: 170 AQCIRIEPALGRSQRDWVGGVYTRSEEAGDCPAFCRALV-AAMQADPNFRFIGGARITAV 228 Query: 182 RVQGGQVQGLQVSSAGQAGQ--LACDALVVAAGVDSHALLAPLGIRVPLYPVKGYSATIP 239 R QG + SA QAG ++ V+A G DS L +R+PLYP+KGYS T+P Sbjct: 229 RRQGSAL------SAVQAGNEWISAQRFVLALGADSADFARQLDLRLPLYPLKGYSITVP 282 Query: 240 VRFPE---AAPRAAVMDESLKTAITRMGDVVRVAGTAEL-GDDRLQLRAACLHTLRQVMR 295 + AAP+ ++ D + K R+G +RVAG EL G DR + + L+Q MR Sbjct: 283 LEDEASRAAAPQVSITDIARKIVYARLGQRLRVAGRIELVGQDR-SIPPRAIAELKQGMR 341 Query: 296 DWFPLAGDLDDAQF--WVGRRPMTPDGPPLLGPTPVRNLFLNLGHGSTGWAMSLGSGRVV 353 + FP +DA+ W+G RP TP G P++G PV NL+LN+G G+ GW ++ GS ++ Sbjct: 342 ELFPDCVLGEDARLSPWMGFRPATPSGVPIVGACPVDNLYLNIGQGALGWTLACGSAALI 401 Query: 354 ADLITGTPPAID 365 AD I G P +ID Sbjct: 402 ADQIAGRPCSID 413 >gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 194 bits (494), Expect = 9e-51, Method: Compositional matrix adjust. Identities = 122/370 (32%), Positives = 187/370 (50%), Gaps = 15/370 (4%) Query: 1 VIAPGYVTPWAAPGMPGKILKYL--FKASSPVVFRPRMSARQWRWISQWLGNCTLERYRR 58 ++APG P +PG + + F+ V+ + RW+ + + Sbjct: 51 LLAPGTAMPLT---LPGALATFACRFQDEPRVLLASGADFGRRRWMRATRA-AQQHHFAQ 106 Query: 59 NKLRMQRIAYYSRDCLHEFLAQHPFDYGRSQGYLQLFRSRFDEDMAAPALALLEEAG--- 115 +KL + R++ Y +D + A + ++ S G LFR + A L L+EA Sbjct: 107 HKLILSRLSAYGQDLTQQLQAHYNMEHENSAGVFHLFR----QSAEAARLPALQEAASQC 162 Query: 116 -IAHQRLSAAQCVATEPGLQHARIEPRSGLYLPDDEAGDCAVFARQLRRLCEEMGVQFRF 174 L AA A EP + LY PDD AG+ +FA+Q+R + +GV F F Sbjct: 163 EYKQLTLDAAGIRALEPAFS-SEAALAGALYYPDDIAGNSVLFAKQMRNAAQALGVSFHF 221 Query: 175 GTQVSGLRVQGGQVQGLQVSSAGQAGQLACDALVVAAGVDSHALLAPLGIRVPLYPVKGY 234 + VS +R + G L+V S A L DA+VVAAG+ S ALL PL +PL ++ Y Sbjct: 222 NSTVSSIRSEFGGRVTLEVQSPHLASHLTMDAVVVAAGMASAALLQPLDTSLPLRALQSY 281 Query: 235 SATIPVRFPEAAPRAAVMDESLKTAITRMGDVVRVAGTAELGDDRLQLRAACLHTLRQVM 294 SA +PV+ P+ AP A+ D+S K A+TR+G +R++G L L L ++ Sbjct: 282 SALVPVKNPDDAPTMALYDDSYKVAMTRLGSRIRISGLLGFVPASQTLPPKALRNLLKIA 341 Query: 295 RDWFPLAGDLDDAQFWVGRRPMTPDGPPLLGPTPVRNLFLNLGHGSTGWAMSLGSGRVVA 354 D++P A + + A FW M P G P++GPT N+F+N+GHG TGWA S+GS R+++ Sbjct: 342 GDYYPNAANYNQAHFWSNSIAMMPTGLPVVGPTRQGNIFVNVGHGVTGWAASVGSARLLS 401 Query: 355 DLITGTPPAI 364 D++ G I Sbjct: 402 DMMAGEETEI 411 >gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 428 Score = 125 bits (315), Expect = 5e-30, Method: Compositional matrix adjust. Identities = 117/376 (31%), Positives = 169/376 (44%), Gaps = 34/376 (9%) Query: 7 VTPWAAPGMPGKILKYLFKASSPVVFRPRMSARQWRWISQWLGNCTLERYRRNKLRMQRI 66 V P PGM K+ YL P+ R R R W+ + L + ER R ++ + Sbjct: 63 VIPPVEPGMWKKVPGYLMDPIGPLSIRWRYLPRLTPWLLRNLASARRERIRATARALRTL 122 Query: 67 AYYSRDCLHEFLAQ-----HPFDYGRSQGYLQLFRSRFDEDMAAPALALLEEAGIAHQRL 121 +R LH +A+ H D + G L ++RSR + A ++ E GI L Sbjct: 123 VVDAR-TLHLDIARRAGVAHLID---TSGVLHVYRSRQQFEGDAFGWSVRRELGIQWSEL 178 Query: 122 SAAQCVATEPGLQHARIEPRSGLYLPDDEAGDC---AVFARQLRRLCEEMGVQFRFGTQV 178 A EP L +P G + DEAG C A + + L+ G R + Sbjct: 179 EAEALRRREPDL-----DPAFGFAVQVDEAGHCKNPAAYLQALQAYALARGAH-RIDARA 232 Query: 179 SGLRVQGGQVQGLQVSSAGQAGQLACDALVVAAGVDSHALLAPLGIRVPLYPVKGYSATI 238 +G R++ G+++ + + G++ACDA V+ AG S AL A G RV L +GY A I Sbjct: 233 TGFRIEEGRLKAVLT----ETGEVACDAAVICAGARSKALAAQAGDRVQLESERGYHALI 288 Query: 239 PVRFPEAAPRAAVMDESLKTAITRMGDVVRVAGTAELGDDRLQLRAACLHTLRQVMRD-- 296 A R +M K T+M +R+AG E AA ++MRD Sbjct: 289 RGHEQAARARTPMMLSEFKVIATQMETGLRIAGQVEFA----SFEAAPDWRRGEIMRDIA 344 Query: 297 --WFP-LAGDL--DDAQFWVGRRPMTPDGPPLLGPTPVRNLFLN-LGHGSTGWAMSLGSG 350 FP L DL D ++W+GRRP TPDG P +G + ++ GHG G S +G Sbjct: 345 LKLFPGLPRDLPAADVRYWLGRRPSTPDGMPCIGYARASSDIVHAYGHGHIGLGCSARTG 404 Query: 351 RVVADLITGTPPAIDI 366 R+VA L+ G P ID+ Sbjct: 405 RIVAQLLAGQTPEIDL 420 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 0.324 0.139 0.445 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: 1,246,853 Number of extensions: 48715 Number of successful extensions: 153 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 142 Number of HSP's successfully gapped: 5 Length of query: 400 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 313 Effective length of database: 1,207,925 Effective search space: 378080525 Effective search space used: 378080525 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 132 (55.5 bits)