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= 0028.0031.p (485 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... 262 5e-71 gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [H... 111 2e-25 gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase smal... 97 4e-21 gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase smal... 62 9e-11 >gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 262 bits (669), Expect = 5e-71, Method: Compositional matrix adjust. Identities = 129/249 (51%), Positives = 175/249 (70%), Gaps = 1/249 (0%) Query: 20 LVQHLQEQHALEEENSQGLLHLFRNQADADRCAAIENSLKQFELPRQQLKGQDAIREVEP 79 L Q LQ + +E ENS G+ HLFR A+A R A++ + Q E + L IR +EP Sbjct: 121 LTQQLQAHYNMEHENSAGVFHLFRQSAEAARLPALQEAASQCEYKQLTLDAA-GIRALEP 179 Query: 80 AFQSATPIAGALYYPKDAAGNCVLFVKQLRAIAQSIGVQFHFSQSVKAVRPELGGRVSID 139 AF S +AGALYYP D AGN VLF KQ+R AQ++GV FHF+ +V ++R E GGRV+++ Sbjct: 180 AFSSEAALAGALYYPDDIAGNSVLFAKQMRNAAQALGVSFHFNSTVSSIRSEFGGRVTLE 239 Query: 140 VGSIDGDSTLTVDGVVLAAGMQNLPLLKPLGLSLPLCPVQSYNAMAAVKNLDEAPNTTLF 199 V S S LT+D VV+AAGM + LL+PL SLPL +QSY+A+ VKN D+AP L+ Sbjct: 240 VQSPHLASHLTMDAVVVAAGMASAALLQPLDTSLPLRALQSYSALVPVKNPDDAPTMALY 299 Query: 200 DETYKVAIARVGNRIRVSGLLGFLPRTELPHPKAIASLLKVANDYYPNAANFNTANFWSS 259 D++YKVA+ R+G+RIR+SGLLGF+P ++ PKA+ +LLK+A DYYPNAAN+N A+FWS+ Sbjct: 300 DDSYKVAMTRLGSRIRISGLLGFVPASQTLPPKALRNLLKIAGDYYPNAANYNQAHFWSN 359 Query: 260 TFALQPQHL 268 + A+ P L Sbjct: 360 SIAMMPTGL 368 Score = 155 bits (393), Expect = 5e-39, Method: Compositional matrix adjust. Identities = 82/166 (49%), Positives = 109/166 (65%), Gaps = 1/166 (0%) Query: 266 QHLQEQHALEEENSQGLLHLFRNQADADRCAAIENSLKQFELPRQQLKGQDAIREVEPAF 325 Q LQ + +E ENS G+ HLFR A+A R A++ + Q E + L IR +EPAF Sbjct: 123 QQLQAHYNMEHENSAGVFHLFRQSAEAARLPALQEAASQCEYKQLTLDAA-GIRALEPAF 181 Query: 326 QSATPIAGALYYPKDAAGNCVLFVKQLRAIAQSIGVQFHFSQSVKAVRPELGGRVSIDVG 385 S +AGALYYP D AGN VLF KQ+R AQ++GV FHF+ +V ++R E GGRV+++V Sbjct: 182 SSEAALAGALYYPDDIAGNSVLFAKQMRNAAQALGVSFHFNSTVSSIRSEFGGRVTLEVQ 241 Query: 386 SIDGDSTLTVDGVVLAAGMQNLPLLKPLGLSLPLCPVQSYNAMAAV 431 S S LT+D VV+AAGM + LL+PL SLPL +QSY+A+ V Sbjct: 242 SPHLASHLTMDAVVVAAGMASAALLQPLDTSLPLRALQSYSALVPV 287 >gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 433 Score = 111 bits (277), Expect = 2e-25, Method: Compositional matrix adjust. Identities = 74/237 (31%), Positives = 118/237 (49%), Gaps = 8/237 (3%) Query: 32 EENSQGLLHLFRNQADADRCAAIENSLKQFELPRQQLKGQDAIREVEPAFQSA-TPIAGA 90 E QG L LFR+Q + A LK+ +P + L D + EPA + G Sbjct: 131 EGRQQGTLQLFRSQEQLEGAAKDIAVLKEAGVPFELLT-PDQLGNAEPALAKVRDKLTGG 189 Query: 91 LYYPKDAAGNCVLFVKQLRAIAQSIGVQFHFSQSVKAVRPELGGRVSIDVGSIDGDSTLT 150 L P D G+C LF +L +A+ IGV+F + + A+ GG+++ G + G + Sbjct: 190 LRLPNDETGDCQLFTTRLATMAEQIGVKFRYGVDIDAL-AMAGGKIA---GVVCGKELVQ 245 Query: 151 VDGVVLAAGMQNLPLLKPL-GL-SLPLCPVQSYNAMAAVKNLDEAPNTTLFDETYKVAIA 208 D V+A G + LL + GL ++P+ P++ Y+ + + AP +T+ DETYK+A+ Sbjct: 246 ADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDASAAPVSTILDETYKIAVT 305 Query: 209 RVGNRIRVSGLLGFLPRTELPHPKAIASLLKVANDYYPNAANFNTANFWSSTFALQP 265 R +RIRV G+ + K A+L V ND +P A + A+FW+ + P Sbjct: 306 RFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGAGDTAQASFWTGLRPMTP 362 Score = 60.5 bits (145), Expect = 3e-10, Method: Compositional matrix adjust. Identities = 47/154 (30%), Positives = 76/154 (49%), Gaps = 8/154 (5%) Query: 276 EENSQGLLHLFRNQADADRCAAIENSLKQFELPRQQLKGQDAIREVEPAFQSA-TPIAGA 334 E QG L LFR+Q + A LK+ +P + L D + EPA + G Sbjct: 131 EGRQQGTLQLFRSQEQLEGAAKDIAVLKEAGVPFELLT-PDQLGNAEPALAKVRDKLTGG 189 Query: 335 LYYPKDAAGNCVLFVKQLRAIAQSIGVQFHFSQSVKAVRPELGGRVSIDVGSIDGDSTLT 394 L P D G+C LF +L +A+ IGV+F + + A+ GG+++ G + G + Sbjct: 190 LRLPNDETGDCQLFTTRLATMAEQIGVKFRYGVDIDAL-AMAGGKIA---GVVCGKELVQ 245 Query: 395 VDGVVLAAGMQNLPLLKPL-GL-SLPLCPVQSYN 426 D V+A G + LL + GL ++P+ P++ Y+ Sbjct: 246 ADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYS 279 >gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 436 Score = 96.7 bits (239), Expect = 4e-21, Method: Compositional matrix adjust. Identities = 60/240 (25%), Positives = 115/240 (47%), Gaps = 7/240 (2%) Query: 35 SQGLLHLFRNQADADRCAAIENSLKQFELPRQQLKGQDAIREVEPAFQSA-TPIAGALYY 93 ++G+LH + + + ++ PR+ + G D + +EPA S I G + Sbjct: 134 TRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESI-GADEVVRIEPALASIRNKIVGGDFT 192 Query: 94 PKDAAGNCVLFVKQLRAIAQSIGVQFHFSQSVKAVRPELGG---RVS-IDVGSIDG-DST 148 D +G+ L + GV+F +S ++ + E G RV+ +++ + DG Sbjct: 193 ATDESGDVFKLTTGLAKKSAEAGVEFRYSTTITRLITEGAGAAARVTGVEIINPDGRHEV 252 Query: 149 LTVDGVVLAAGMQNLPLLKPLGLSLPLCPVQSYNAMAAVKNLDEAPNTTLFDETYKVAIA 208 L D V+A G + L+KPLG+ L L P + Y+A + N D AP +L D+ YK+ ++ Sbjct: 253 LKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQITNPDAAPTVSLTDDGYKLVVS 312 Query: 209 RVGNRIRVSGLLGFLPRTELPHPKAIASLLKVANDYYPNAANFNTANFWSSTFALQPQHL 268 R+G+R+RV+G T + ++ + + +P+ ++ +W+ L P ++ Sbjct: 313 RLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGCDYENPTYWTGLRPLTPSNV 372 >gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 421 Score = 62.0 bits (149), Expect = 9e-11, Method: Compositional matrix adjust. Identities = 54/221 (24%), Positives = 98/221 (44%), Gaps = 10/221 (4%) Query: 32 EENSQGLLHLFRNQADADRCAAIENSLKQFELPRQQLKGQDAIREVEPAF-QSATPIAGA 90 + G L +F + + A Q+ ++ L IR +EPA +S G Sbjct: 131 DHQRSGKLVMFTDAQGLEAAAGQVRFQAQYGCQQEVLDAAQCIR-IEPALGRSQRDWVGG 189 Query: 91 LYYPKDAAGNCVLFVKQLRAIAQSI-GVQFHFSQSVKAVRPELGGRVSIDVGSIDGDSTL 149 +Y + AG+C F + L A Q+ +F + AVR + ++ G + + Sbjct: 190 VYTRSEEAGDCPAFCRALVAAMQADPNFRFIGGARITAVRRQGSALSAVQAG----NEWI 245 Query: 150 TVDGVVLAAGMQNLPLLKPLGLSLPLCPVQSYNAMAAVKN---LDEAPNTTLFDETYKVA 206 + VLA G + + L L LPL P++ Y+ +++ AP ++ D K+ Sbjct: 246 SAQRFVLALGADSADFARQLDLRLPLYPLKGYSITVPLEDEASRAAAPQVSITDIARKIV 305 Query: 207 IARVGNRIRVSGLLGFLPRTELPHPKAIASLLKVANDYYPN 247 AR+G R+RV+G + + + P+AIA L + + +P+ Sbjct: 306 YARLGQRLRVAGRIELVGQDRSIPPRAIAELKQGMRELFPD 346 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 0.320 0.134 0.396 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: 1,267,884 Number of extensions: 45209 Number of successful extensions: 134 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 128 Number of HSP's successfully gapped: 6 Length of query: 485 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 396 Effective length of database: 1,198,455 Effective search space: 474588180 Effective search space used: 474588180 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)