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= 0001.1091.p (412 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... 141 8e-35 gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase smal... 99 8e-22 gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [H... 90 4e-19 gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase smal... 87 3e-18 gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase smal... 63 5e-11 >gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 428 Score = 141 bits (356), Expect = 8e-35, Method: Compositional matrix adjust. Identities = 109/422 (25%), Positives = 187/422 (44%), Gaps = 17/422 (4%) Query: 3 KQIIVLGAGMVGVSTALALQERGYDVALIDRRAPGKE--TSYGNAGFIQREAVRPYAFPR 60 + +V+GAG VG+ +A+ ++G +V+L+D G E SYGNAG++ +V P P Sbjct: 11 RHAVVIGAGAVGLMSAIHALDQGLEVSLLDFNPVGSEEAASYGNAGWLSSHSVIPPVEPG 70 Query: 61 EWQTLCKVIAGSGNDVHYNLAATLKILPTLARYWHESAAVRYSRTIGSYAALIRHSISEH 120 W+ + + + ++ P L R + R T + L+ + + H Sbjct: 71 MWKKVPGYLMDPIGPLSIRWRYLPRLTPWLLRNLASARRERIRATARALRTLVVDARTLH 130 Query: 121 EKLIEAANAGELVRKDGWLEAYRNSEKFDKTIKHANSIAAEHGLNVAIYDSQGLQRAEPA 180 + A L+ G L YR+ ++F+ S+ E G+ + +++ L+R EP Sbjct: 131 LDIARRAGVAHLIDTSGVLHVYRSRQQFEGD-AFGWSVRRELGIQWSELEAEALRRREPD 189 Query: 181 LNNSLAGAIHWRDTWTISDPGELVERYAALFQRNGGTILNGDADTLRFNNNGWQ-VHTSD 239 L+ + A+ + +P ++ A G ++ A R + V T Sbjct: 190 LDPAFGFAVQVDEAGHCKNPAAYLQALQAYALARGAHRIDARATGFRIEEGRLKAVLTET 249 Query: 240 GSITASDAVVCLGPWASKVVEPLGYKIPLFIKRGYH---RHYKSESGLKLPLLDAERGYA 296 G + AV+C G + + G ++ L +RGYH R ++ + + P++ +E Sbjct: 250 GEVACDAAVICAGARSKALAAQAGDRVQLESERGYHALIRGHEQAARARTPMMLSEFKVI 309 Query: 297 LVPMKRGLRITTGAEFAELGAAPTPVQLNAAEVFADELLRL--GAP-----VESKPWVGA 349 M+ GLRI EFA AAP E+ D L+L G P + + W+G Sbjct: 310 ATQMETGLRIAGQVEFASFEAAP---DWRRGEIMRDIALKLFPGLPRDLPAADVRYWLGR 366 Query: 350 RPCVADMLPLVGSAGRHRGLWFHFGHGHQGFTLGPTTSRLLADLITGSSPYIDPRPYDPR 409 RP D +P +G A + +GHGH G T R++A L+ G +P ID P+ P+ Sbjct: 367 RPSTPDGMPCIGYARASSDIVHAYGHGHIGLGCSARTGRIVAQLLAGQTPEIDLAPFSPQ 426 Query: 410 RF 411 RF Sbjct: 427 RF 428 >gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 436 Score = 98.6 bits (244), Expect = 8e-22, Method: Compositional matrix adjust. Identities = 106/425 (24%), Positives = 178/425 (41%), Gaps = 36/425 (8%) Query: 4 QIIVLGAGMVGVSTALALQERGYDVALIDRRAPG--KETSYGNAGFIQREAVRPYAFPRE 61 ++IVLGAG++G ++A L+++GYDV +IDR+ PG +ETS+ N I P+A P Sbjct: 2 KVIVLGAGIIGTASAWFLKKQGYDVTVIDRQ-PGAAQETSFANGCQISVSHAEPWANPAA 60 Query: 62 WQTLCKVIAGSGNDVHYNLAATLKILPTLARYWHESAAVRYSRTIGSYAALIRHSISEHE 121 + K + + Y + E A R I + AL +S Sbjct: 61 PMKVLKWLGKEDAPLLYRFRPEWLQWKWAVAFLRECTAARTDENIRNIVALCEYS----R 116 Query: 122 KLIEAANAGELVRKD----GWLEAYRNSEKFDKTIKHANSIAAEHGLNVAIYDSQGLQRA 177 + ++A A ++ D G L Y ++F ++ A + + G + + R Sbjct: 117 QTLQAVRAETGIQYDHLTRGILHFYTEEKEFQDSLPAAK-LMRDLGCPRESIGADEVVRI 175 Query: 178 EPALNNSLAGAIHWRDTWTISDPGELVERYAALFQRNGGT-------------ILNGDAD 224 EPAL S+ I D + G++ + L +++ I G Sbjct: 176 EPAL-ASIRNKIVGGDFTATDESGDVFKLTTGLAKKSAEAGVEFRYSTTITRLITEGAGA 234 Query: 225 TLRFNNNGWQVHTSDGS---ITASDAVVCLGPWASKVVEPLGYKIPLFIKRGYHRHYKSE 281 R G ++ DG + A VV +G ++ ++V+PLG + L+ +GY Y+ Sbjct: 235 AARV--TGVEIINPDGRHEVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQIT 292 Query: 282 SGLKLPLLD-AERGYALVPMKRG--LRITTGAEFAELGAAPTPVQLNAAEVFADELLRLG 338 + P + + GY LV + G LR+ E + A EL G Sbjct: 293 NPDAAPTVSLTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDG 352 Query: 339 APVESKP-WVGARPCVADMLPLVGSAGRHRGLWFHFGHGHQGFTLGPTTSRLLADLITGS 397 E+ W G RP +P VG + L+ + GHG G+T+G + R +A+++ G Sbjct: 353 CDYENPTYWTGLRPLTPSNVPYVGKT-KFANLYLNTGHGTLGWTMGCGSGRAIAEIVAGH 411 Query: 398 SPYID 402 P ID Sbjct: 412 VPEID 416 >gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 433 Score = 89.7 bits (221), Expect = 4e-19, Method: Compositional matrix adjust. Identities = 103/410 (25%), Positives = 170/410 (41%), Gaps = 15/410 (3%) Query: 4 QIIVLGAGMVGVSTALALQERGYDVALIDRR-APGKETSYGNAGFIQREAVRPYAFPREW 62 ++++LG+G++GV++A L G+DV ++DR+ P ETS+GNAG I P+A P Sbjct: 2 RVVILGSGVIGVTSAWYLARAGHDVTVLDRQPGPALETSFGNAGQISPGYASPWAAPGIP 61 Query: 63 QTLCKVIAGSGNDVHYNLAATLKILPTLARYWHESAAVRYSRTIGSYAALIRHSISEHEK 122 K + + L + L + + A RY+ L +S Sbjct: 62 LKAIKWMFQEHAPLAIRLDGSFNQLRWMWQMLRNCNAERYAVNKERMVRLAEYSRDCLRD 121 Query: 123 LIEAANAGELVRKDGWLEAYRNSEKFDKTIKHANSIAAEHGLNVAIYDSQGLQRAEPAL- 181 L R+ G L+ +R+ E+ + K ++ E G+ + L AEPAL Sbjct: 122 LRADVGIPYEGRQQGTLQLFRSQEQLEGAAKDI-AVLKEAGVPFELLTPDQLGNAEPALA 180 Query: 182 --NNSLAGAIHWRDTWTISDPGELVERYAALFQRNGGTILNG-DADTLRFNNNGWQVHTS 238 + L G + + T D R A + ++ G G D D L Sbjct: 181 KVRDKLTGGLRLPNDET-GDCQLFTTRLATMAEQIGVKFRYGVDIDALAMAGGKIAGVVC 239 Query: 239 DGSITASDA-VVCLGPWASKVV--EPLGYKIPLFIKRGYHRHYKSESGLKLP---LLDAE 292 + +D+ VV LG ++ +++ P IP++ +GY P +LD Sbjct: 240 GKELVQADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDASAAPVSTILDET 299 Query: 293 RGYALVPMKRGLRITTGAEFAELGAAPTPVQLNAAEVFADELLR-LGAPVESKPWVGARP 351 A+ +R+ AE A + E+ ++L G ++ W G RP Sbjct: 300 YKIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGAGDTAQASFWTGLRP 359 Query: 352 CVADMLPLVGSAGRHRGLWFHFGHGHQGFTLGPTTSRLLADLITGSSPYI 401 D P+VG A L+ + GHG G+T+ + +LLADLI+G P I Sbjct: 360 MTPDGTPVVG-ATPVSNLYINTGHGTLGWTMSCGSGQLLADLISGRRPAI 408 >gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 421 Score = 87.0 bits (214), Expect = 3e-18, Method: Compositional matrix adjust. Identities = 106/436 (24%), Positives = 175/436 (40%), Gaps = 49/436 (11%) Query: 5 IIVLGAGMVGVSTALALQERGYDVALIDRR-APGKETSYGNAGFIQREAVRPYAFPREWQ 63 I V+GAG++GV+TA L + G+ V+LID R PG TS GN + V P A P W Sbjct: 3 ICVMGAGVIGVTTAYRLLQDGHQVSLIDERDQPGAGTSQGNGAQLSYSYVAPLADPSVWS 62 Query: 64 TLCKVIAGSGNDVHYNLAATLKILPTL--ARYWHESAAVRYSRTIGSYAALIRHSISEHE 121 + ++ + L I PTL A+Y + +RY A +R + + Sbjct: 63 KWAYYL--------FSKDSPLTIKPTLEAAQYRWLAGFLRYCN-----AGSVRQTTIDLL 109 Query: 122 KLIEAANAGELVRKDGWLEAYRNSEKFDKTIKHANS-----------IAAEHGLNVAIYD 170 +L + +L + +G L+ + ++ K + ++ A++G + D Sbjct: 110 QLAFYSR-DQLTQWNGRLKLSFDHQRSGKLVMFTDAQGLEAAAGQVRFQAQYGCQQEVLD 168 Query: 171 SQGLQRAEPALNNSL---AGAIHWRDTWTISDPGELVERYAALFQRNGGTILNGDADTLR 227 + R EPAL S G ++ R D A Q + G A Sbjct: 169 AAQCIRIEPALGRSQRDWVGGVYTRSE-EAGDCPAFCRALVAAMQADPNFRFIGGARITA 227 Query: 228 FNNNG---WQVHTSDGSITASDAVVCLGPWASKVVEPLGYKIPLFIKRGYHRHYKSE--- 281 G V + I+A V+ LG ++ L ++PL+ +GY E Sbjct: 228 VRRQGSALSAVQAGNEWISAQRFVLALGADSADFARQLDLRLPLYPLKGYSITVPLEDEA 287 Query: 282 ---SGLKLPLLDAERGYALVPMKRGLRITTGAEFAELGAAPTP-----VQLNAAEVFADE 333 + ++ + D R + + LR+ E + P ++ E+F D Sbjct: 288 SRAAAPQVSITDIARKIVYARLGQRLRVAGRIELVGQDRSIPPRAIAELKQGMRELFPDC 347 Query: 334 LLRLGAPVESKPWVGARPCVADMLPLVGSAGRHRGLWFHFGHGHQGFTLGPTTSRLLADL 393 + LG PW+G RP +P+VG+ L+ + G G G+TL ++ L+AD Sbjct: 348 V--LGEDARLSPWMGFRPATPSGVPIVGACPVD-NLYLNIGQGALGWTLACGSAALIADQ 404 Query: 394 ITGSSPYIDPRPYDPR 409 I G ID P+ R Sbjct: 405 IAGRPCSIDDTPFRYR 420 >gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 62.8 bits (151), Expect = 5e-11, Method: Compositional matrix adjust. Identities = 95/451 (21%), Positives = 177/451 (39%), Gaps = 81/451 (17%) Query: 3 KQIIVLGAGMVGVSTALALQERGYDVALIDRRA-PGKETSYGNAGFIQREAVRPYAFPRE 61 +QI V+G G+ G+ +A L +GY+VA+I+RRA +E ++G++G + P P Sbjct: 6 RQIAVIGGGLSGICSAYFLATKGYEVAVIERRAHVAEEATFGDSGLLAPGTAMPLTLPGA 65 Query: 62 WQTLC-------KVIAGSGNDVHYNLAATLKILPTLARYWHESAAVRYSRTIGSYAALIR 114 T +V+ SG D R W +R +R A + Sbjct: 66 LATFACRFQDEPRVLLASGADFGR-------------RRW-----MRATR------AAQQ 101 Query: 115 HSISEHEKLIE--AANAGELVRKDGWLEAYRNSEK---------FDKTIKHANSIAAEHG 163 H ++H+ ++ +A +L ++ L+A+ N E F ++ + A A + Sbjct: 102 HHFAQHKLILSRLSAYGQDLTQQ---LQAHYNMEHENSAGVFHLFRQSAEAARLPALQEA 158 Query: 164 LNVAIY-----DSQGLQRAEPALNN--SLAGAIHWRDTWTISDPGELVERYAALFQRNGG 216 + Y D+ G++ EPA ++ +LAGA+++ D + + LF + Sbjct: 159 ASQCEYKQLTLDAAGIRALEPAFSSEAALAGALYYPDD---------IAGNSVLFAKQMR 209 Query: 217 TILNGDADTLRFNNNGWQVHTSDGS--------------ITASDAVVCLGPWASKVVEPL 262 + FN+ + + G +T VV G ++ +++PL Sbjct: 210 NAAQALGVSFHFNSTVSSIRSEFGGRVTLEVQSPHLASHLTMDAVVVAAGMASAALLQPL 269 Query: 263 GYKIPLFIKRGYHRHY---KSESGLKLPLLDAERGYALVPMKRGLRITTGAEFAELGAAP 319 +PL + Y + + L D A+ + +RI+ F Sbjct: 270 DTSLPLRALQSYSALVPVKNPDDAPTMALYDDSYKVAMTRLGSRIRISGLLGFVPASQTL 329 Query: 320 TPVQL-NAAEVFADELLRLGAPVESKPWVGARPCVADMLPLVGSAGRHRGLWFHFGHGHQ 378 P L N ++ D ++ W + + LP+VG R ++ + GHG Sbjct: 330 PPKALRNLLKIAGDYYPNAANYNQAHFWSNSIAMMPTGLPVVGPT-RQGNIFVNVGHGVT 388 Query: 379 GFTLGPTTSRLLADLITGSSPYIDPRPYDPR 409 G+ ++RLL+D++ G I PR Sbjct: 389 GWAASVGSARLLSDMMAGEETEIATAGLLPR 419 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 0.419 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: 1,380,356 Number of extensions: 61662 Number of successful extensions: 256 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 246 Number of HSP's successfully gapped: 6 Length of query: 412 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 324 Effective length of database: 1,203,190 Effective search space: 389833560 Effective search space used: 389833560 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)