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= 0106.0007.p (377 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase smal... 371 e-104 gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [H... 176 3e-45 gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase smal... 119 4e-28 gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase smal... 69 4e-13 gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [H... 60 2e-10 >gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 436 Score = 371 bits (953), Expect = e-104, Method: Compositional matrix adjust. Identities = 178/204 (87%), Positives = 190/204 (93%), Gaps = 1/204 (0%) Query: 59 MKVIVLGAGIIGTASAWFLKREGHDVTVIDRQPGAAQETSFANGCQISVSHAEPWANPSA 118 MKVIVLGAGIIGTASAWFLK++G+DVTVIDRQPGAAQETSFANGCQISVSHAEPWANP+A Sbjct: 1 MKVIVLGAGIIGTASAWFLKKQGYDVTVIDRQPGAAQETSFANGCQISVSHAEPWANPAA 60 Query: 119 PLKVLKWLGKEDAPLLYRFRPEWLQWKWAVNFLRECTPARTDANIRQIVALCEYSRQTLV 178 P+KVLKWLGKEDAPLLYRFRPEWLQWKWAV FLRECT ARTD NIR IVALCEYSRQTL Sbjct: 61 PMKVLKWLGKEDAPLLYRFRPEWLQWKWAVAFLRECTAARTDENIRNIVALCEYSRQTLQ 120 Query: 179 ALRAETGIQYDHLNKGILHFYTEEKEFELSLPAAKLMRDLGCQRDSISADEVVRIEPALA 238 A+RAETGIQYDHL +GILHFYTEEKEF+ SLPAAKLMRDLGC R+SI ADEVVRIEPALA Sbjct: 121 AVRAETGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRIEPALA 180 Query: 239 GIRDKIVGGDFTATDEXLGDRLRV 262 IR+KIVGGDFTATDE GD ++ Sbjct: 181 SIRNKIVGGDFTATDES-GDVFKL 203 Score = 228 bits (582), Expect = 5e-61, Method: Compositional matrix adjust. Identities = 102/111 (91%), Positives = 107/111 (96%) Query: 256 LGDRLRVAGTCELNGYTRELNTTRCDAITRRTRELFPDGCDYDNPVYWTGLRPLTPSNIP 315 LGDRLRVAGTCELNGYTRELNTTRC+AITRRTRELFPDGCDY+NP YWTGLRPLTPSN+P Sbjct: 314 LGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGCDYENPTYWTGLRPLTPSNVP 373 Query: 316 YVGKTKFSNLYLNTGHGTLGWTMGCGSGRAIAEIIAGRQPEIDFGFTGLPR 366 YVGKTKF+NLYLNTGHGTLGWTMGCGSGRAIAEI+AG PEIDF FTGLPR Sbjct: 374 YVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAEIVAGHVPEIDFAFTGLPR 424 >gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 433 Score = 176 bits (445), Expect = 3e-45, Method: Compositional matrix adjust. Identities = 94/240 (39%), Positives = 131/240 (54%), Gaps = 15/240 (6%) Query: 59 MKVIVLGAGIIGTASAWFLKREGHDVTVIDRQPGAAQETSFANGCQISVSHAEPWANPSA 118 M+V++LG+G+IG SAW+L R GHDVTV+DRQPG A ETSF N QIS +A PWA P Sbjct: 1 MRVVILGSGVIGVTSAWYLARAGHDVTVLDRQPGPALETSFGNAGQISPGYASPWAAPGI 60 Query: 119 PLKVLKWLGKEDAPLLYRFRPEWLQWKWAVNFLRECTPARTDANIRQIVALCEYSRQTLV 178 PLK +KW+ +E APL R + Q +W LR C R N ++V L EYSR L Sbjct: 61 PLKAIKWMFQEHAPLAIRLDGSFNQLRWMWQMLRNCNAERYAVNKERMVRLAEYSRDCLR 120 Query: 179 ALRAETGIQYDHLNKGILHFYTEEKEFELSLPAAKLMRDLGCQRDSISADEVVRIEPALA 238 LRA+ GI Y+ +G L + +++ E + ++++ G + ++ D++ EPALA Sbjct: 121 DLRADVGIPYEGRQQGTLQLFRSQEQLEGAAKDIAVLKEAGVPFELLTPDQLGNAEPALA 180 Query: 239 GIRDKIVGGDFTATDEXLGDRLRVAGTCELNGYTRELNTTRCDAITRRTRELFPDGCDYD 298 +RDK+ GG DE G C +L TTR + + F G D D Sbjct: 181 KVRDKLTGGLRLPNDE--------TGDC-------QLFTTRLATMAEQIGVKFRYGVDID 225 Score = 113 bits (282), Expect = 3e-26, Method: Compositional matrix adjust. Identities = 51/100 (51%), Positives = 64/100 (64%) Query: 258 DRLRVAGTCELNGYTRELNTTRCDAITRRTRELFPDGCDYDNPVYWTGLRPLTPSNIPYV 317 DR+RV G E+ GY L R + +LFP D +WTGLRP+TP P V Sbjct: 309 DRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGAGDTAQASFWTGLRPMTPDGTPVV 368 Query: 318 GKTKFSNLYLNTGHGTLGWTMGCGSGRAIAEIIAGRQPEI 357 G T SNLY+NTGHGTLGWTM CGSG+ +A++I+GR+P I Sbjct: 369 GATPVSNLYINTGHGTLGWTMSCGSGQLLADLISGRRPAI 408 >gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 421 Score = 119 bits (298), Expect = 4e-28, Method: Compositional matrix adjust. Identities = 67/198 (33%), Positives = 103/198 (52%), Gaps = 4/198 (2%) Query: 59 MKVIVLGAGIIGTASAWFLKREGHDVTVIDR--QPGAAQETSFANGCQISVSHAEPWANP 116 M + V+GAG+IG +A+ L ++GH V++ID QPGA TS NG Q+S S+ P A+P Sbjct: 1 MHICVMGAGVIGVTTAYRLLQDGHQVSLIDERDQPGAG--TSQGNGAQLSYSYVAPLADP 58 Query: 117 SAPLKVLKWLGKEDAPLLYRFRPEWLQWKWAVNFLRECTPARTDANIRQIVALCEYSRQT 176 S K +L +D+PL + E Q++W FLR C ++ L YSR Sbjct: 59 SVWSKWAYYLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSVRQTTIDLLQLAFYSRDQ 118 Query: 177 LVALRAETGIQYDHLNKGILHFYTEEKEFELSLPAAKLMRDLGCQRDSISADEVVRIEPA 236 L + +DH G L +T+ + E + + GCQ++ + A + +RIEPA Sbjct: 119 LTQWNGRLKLSFDHQRSGKLVMFTDAQGLEAAAGQVRFQAQYGCQQEVLDAAQCIRIEPA 178 Query: 237 LAGIRDKIVGGDFTATDE 254 L + VGG +T ++E Sbjct: 179 LGRSQRDWVGGVYTRSEE 196 Score = 92.4 bits (228), Expect = 5e-20, Method: Compositional matrix adjust. Identities = 50/105 (47%), Positives = 58/105 (55%), Gaps = 2/105 (1%) Query: 256 LGDRLRVAGTCELNGYTRELNTTRCDAITRRTRELFPDGCDYDNPVY--WTGLRPLTPSN 313 LG RLRVAG EL G R + + + RELFPD ++ W G RP TPS Sbjct: 309 LGQRLRVAGRIELVGQDRSIPPRAIAELKQGMRELFPDCVLGEDARLSPWMGFRPATPSG 368 Query: 314 IPYVGKTKFSNLYLNTGHGTLGWTMGCGSGRAIAEIIAGRQPEID 358 +P VG NLYLN G G LGWT+ CGS IA+ IAGR ID Sbjct: 369 VPIVGACPVDNLYLNIGQGALGWTLACGSAALIADQIAGRPCSID 413 >gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 69.3 bits (168), Expect = 4e-13, Method: Compositional matrix adjust. Identities = 28/102 (27%), Positives = 55/102 (53%) Query: 256 LGDRLRVAGTCELNGYTRELNTTRCDAITRRTRELFPDGCDYDNPVYWTGLRPLTPSNIP 315 LG R+R++G ++ L + + + +P+ +Y+ +W+ + P+ +P Sbjct: 310 LGSRIRISGLLGFVPASQTLPPKALRNLLKIAGDYYPNAANYNQAHFWSNSIAMMPTGLP 369 Query: 316 YVGKTKFSNLYLNTGHGTLGWTMGCGSGRAIAEIIAGRQPEI 357 VG T+ N+++N GHG GW GS R +++++AG + EI Sbjct: 370 VVGPTRQGNIFVNVGHGVTGWAASVGSARLLSDMMAGEETEI 411 >gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 428 Score = 60.5 bits (145), Expect = 2e-10, Method: Compositional matrix adjust. Identities = 39/135 (28%), Positives = 64/135 (47%), Gaps = 6/135 (4%) Query: 230 VVRIEPALAGIRDKIVGGDFTATDEXLGDRLRVAGTCELNGYTRELNTTRCDAITRRTRE 289 ++R A R ++ +F + LR+AG E + + R + + + Sbjct: 287 LIRGHEQAARARTPMMLSEFKVIATQMETGLRIAGQVEFASFEAAPDWRRGEIMRDIALK 346 Query: 290 LFPDGCDYDNPV----YWTGLRPLTPSNIPYVGKTKFSNLYLNT-GHGTLGWTMGCGSGR 344 LFP G D P YW G RP TP +P +G + S+ ++ GHG +G +GR Sbjct: 347 LFP-GLPRDLPAADVRYWLGRRPSTPDGMPCIGYARASSDIVHAYGHGHIGLGCSARTGR 405 Query: 345 AIAEIIAGRQPEIDF 359 +A+++AG+ PEID Sbjct: 406 IVAQLLAGQTPEIDL 420 Score = 58.5 bits (140), Expect = 9e-10, Method: Compositional matrix adjust. Identities = 47/177 (26%), Positives = 76/177 (42%), Gaps = 1/177 (0%) Query: 62 IVLGAGIIGTASAWFLKREGHDVTVIDRQP-GAAQETSFANGCQISVSHAEPWANPSAPL 120 +V+GAG +G SA +G +V+++D P G+ + S+ N +S P P Sbjct: 14 VVIGAGAVGLMSAIHALDQGLEVSLLDFNPVGSEEAASYGNAGWLSSHSVIPPVEPGMWK 73 Query: 121 KVLKWLGKEDAPLLYRFRPEWLQWKWAVNFLRECTPARTDANIRQIVALCEYSRQTLVAL 180 KV +L PL R+R W + L R A R + L +R + + Sbjct: 74 KVPGYLMDPIGPLSIRWRYLPRLTPWLLRNLASARRERIRATARALRTLVVDARTLHLDI 133 Query: 181 RAETGIQYDHLNKGILHFYTEEKEFELSLPAAKLMRDLGCQRDSISADEVVRIEPAL 237 G+ + G+LH Y ++FE + R+LG Q + A+ + R EP L Sbjct: 134 ARRAGVAHLIDTSGVLHVYRSRQQFEGDAFGWSVRRELGIQWSELEAEALRRREPDL 190 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 0.318 0.135 0.417 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: 1,252,079 Number of extensions: 53554 Number of successful extensions: 209 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 209 Number of HSP's successfully gapped: 9 Length of query: 377 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 290 Effective length of database: 1,207,925 Effective search space: 350298250 Effective search space used: 350298250 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 131 (55.1 bits)