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= 0001.2089.p (422 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... 720 0.0 gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [H... 203 3e-53 gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase smal... 160 1e-40 gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase smal... 134 2e-32 gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [H... 61 2e-10 >gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 720 bits (1858), Expect = 0.0, Method: Compositional matrix adjust. Identities = 349/422 (82%), Positives = 380/422 (90%), Gaps = 1/422 (0%) Query: 1 VNSTHRQIAVIGGGLSGICSAYFLAAKGYEVAVIERRAHVAEEATFGDTGLLAPGVATPL 60 +NSTHRQIAVIGGGLSGICSAYFLA KGYEVAVIERRAHVAEEATFGD+GLLAPG A PL Sbjct: 1 MNSTHRQIAVIGGGLSGICSAYFLATKGYEVAVIERRAHVAEEATFGDSGLLAPGTAMPL 60 Query: 61 TLPGAMATFACRFQDEPRVLLASGTDFGRRRWMGRTRQAQQY-FAQNKLRLSRLSAYGQA 119 TLPGA+ATFACRFQDEPRVLLASG DFGRRRWM TR AQQ+ FAQ+KL LSRLSAYGQ Sbjct: 61 TLPGALATFACRFQDEPRVLLASGADFGRRRWMRATRAAQQHHFAQHKLILSRLSAYGQD 120 Query: 120 LTLQLQTHYNLEHENGNGVFHLFRLPAEAARMGQMQEAAEQCEFKHQALDTEAIRALEPA 179 LT QLQ HYN+EHEN GVFHLFR AEAAR+ +QEAA QCE+K LD IRALEPA Sbjct: 121 LTQQLQAHYNMEHENSAGVFHLFRQSAEAARLPALQEAASQCEYKQLTLDAAGIRALEPA 180 Query: 180 FSSGAALAGALYYPDDIAGNCVLFAKQMRNAAQELGVRFHFDSTVTAIQAEFGGRVMLQL 239 FSS AALAGALYYPDDIAGN VLFAKQMRNAAQ LGV FHF+STV++I++EFGGRV L++ Sbjct: 181 FSSEAALAGALYYPDDIAGNSVLFAKQMRNAAQALGVSFHFNSTVSSIRSEFGGRVTLEV 240 Query: 240 QSPHLASQMRVDAVVVTAGMSSAELLRPLDTDLPLRALQSYSALVPVKNPDDAPSMALYD 299 QSPHLAS + +DAVVV AGM+SA LL+PLDT LPLRALQSYSALVPVKNPDDAP+MALYD Sbjct: 241 QSPHLASHLTMDAVVVAAGMASAALLQPLDTSLPLRALQSYSALVPVKNPDDAPTMALYD 300 Query: 300 DSYKVAMTRLGGRIRISGLLGFVQPSQTLPPKALRNLLKIAGDYYPNAANYNQAHFWSNT 359 DSYKVAMTRLG RIRISGLLGFV SQTLPPKALRNLLKIAGDYYPNAANYNQAHFWSN+ Sbjct: 301 DSYKVAMTRLGSRIRISGLLGFVPASQTLPPKALRNLLKIAGDYYPNAANYNQAHFWSNS 360 Query: 360 MALLPHGLPLIGPTRQGNVFVNVGHGATGWAASVGSARLLADLVAGEETEIPTEGLLPRD 419 +A++P GLP++GPTRQGN+FVNVGHG TGWAASVGSARLL+D++AGEETEI T GLLPRD Sbjct: 361 IAMMPTGLPVVGPTRQGNIFVNVGHGVTGWAASVGSARLLSDMMAGEETEIATAGLLPRD 420 Query: 420 VL 421 VL Sbjct: 421 VL 422 >gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 433 Score = 203 bits (516), Expect = 3e-53, Method: Compositional matrix adjust. Identities = 132/421 (31%), Positives = 212/421 (50%), Gaps = 21/421 (4%) Query: 7 QIAVIGGGLSGICSAYFLAAKGYEVAVIERRAHVAEEATFGDTGLLAPGVATPLTLPG-A 65 ++ ++G G+ G+ SA++LA G++V V++R+ A E +FG+ G ++PG A+P PG Sbjct: 2 RVVILGSGVIGVTSAWYLARAGHDVTVLDRQPGPALETSFGNAGQISPGYASPWAAPGIP 61 Query: 66 MATFACRFQDEPRVLLASGTDFGRRRWMG---RTRQAQQYFAQNKLRLSRLSAYGQALTL 122 + FQ+ + + F + RWM R A++Y A NK R+ RL+ Y + Sbjct: 62 LKAIKWMFQEHAPLAIRLDGSFNQLRWMWQMLRNCNAERY-AVNKERMVRLAEYSRDCLR 120 Query: 123 QLQTHYNLEHEN-GNGVFHLFR----LPAEAARMGQMQEAAEQCEFKHQALDTEAIRALE 177 L+ + +E G LFR L A + ++EA E L + + E Sbjct: 121 DLRADVGIPYEGRQQGTLQLFRSQEQLEGAAKDIAVLKEAGVPFEL----LTPDQLGNAE 176 Query: 178 PAFSS-GAALAGALYYPDDIAGNCVLFAKQMRNAAQELGVRFHFDSTVTAIQAEFGGRVM 236 PA + L G L P+D G+C LF ++ A+++GV+F + + A+ A GG++ Sbjct: 177 PALAKVRDKLTGGLRLPNDETGDCQLFTTRLATMAEQIGVKFRYGVDIDAL-AMAGGKIA 235 Query: 237 LQLQSPHLASQMRVDAVVVTAGMSSAELL--RPLDTDLPLRALQSYSALVPVKNPDDAPS 294 + L ++ D+ VV G S +LL P +P+ L+ YS VP+ + AP Sbjct: 236 GVVCGKEL---VQADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDASAAPV 292 Query: 295 MALYDDSYKVAMTRLGGRIRISGLLGFVQPSQTLPPKALRNLLKIAGDYYPNAANYNQAH 354 + D++YK+A+TR RIR+ G+ V L K L + D +P A + QA Sbjct: 293 STILDETYKIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGAGDTAQAS 352 Query: 355 FWSNTMALLPHGLPLIGPTRQGNVFVNVGHGATGWAASVGSARLLADLVAGEETEIPTEG 414 FW+ + P G P++G T N+++N GHG GW S GS +LLADL++G I E Sbjct: 353 FWTGLRPMTPDGTPVVGATPVSNLYINTGHGTLGWTMSCGSGQLLADLISGRRPAIAHED 412 Query: 415 L 415 L Sbjct: 413 L 413 >gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 436 Score = 160 bits (406), Expect = 1e-40, Method: Compositional matrix adjust. Identities = 104/414 (25%), Positives = 198/414 (47%), Gaps = 10/414 (2%) Query: 7 QIAVIGGGLSGICSAYFLAAKGYEVAVIERRAHVAEEATFGDTGLLAPGVATPLTLPGA- 65 ++ V+G G+ G SA+FL +GY+V VI+R+ A+E +F + ++ A P P A Sbjct: 2 KVIVLGAGIIGTASAWFLKKQGYDVTVIDRQPGAAQETSFANGCQISVSHAEPWANPAAP 61 Query: 66 MATFACRFQDEPRVLLASGTDFGRRRW-MGRTRQAQQYFAQNKLR-LSRLSAYGQALTLQ 123 M +++ +L ++ + +W + R+ +R + L Y + Sbjct: 62 MKVLKWLGKEDAPLLYRFRPEWLQWKWAVAFLRECTAARTDENIRNIVALCEYSRQTLQA 121 Query: 124 LQTHYNLEHEN-GNGVFHLFRLPAEAARMGQMQEAAEQCEFKHQALDTEAIRALEPAFSS 182 ++ +++++ G+ H + E + +++ + + +EPA +S Sbjct: 122 VRAETGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRIEPALAS 181 Query: 183 -GAALAGALYYPDDIAGNCVLFAKQMRNAAQELGVRFHFDSTVTAIQAEFGG---RVM-L 237 + G + D +G+ + + E GV F + +T+T + E G RV + Sbjct: 182 IRNKIVGGDFTATDESGDVFKLTTGLAKKSAEAGVEFRYSTTITRLITEGAGAAARVTGV 241 Query: 238 QLQSPHLASQ-MRVDAVVVTAGMSSAELLRPLDTDLPLRALQSYSALVPVKNPDDAPSMA 296 ++ +P + ++ D VV G S +L++PL DL L + YSA + NPD AP+++ Sbjct: 242 EIINPDGRHEVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQITNPDAAPTVS 301 Query: 297 LYDDSYKVAMTRLGGRIRISGLLGFVQPSQTLPPKALRNLLKIAGDYYPNAANYNQAHFW 356 L DD YK+ ++RLG R+R++G ++ L + + + +P+ +Y +W Sbjct: 302 LTDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPDGCDYENPTYW 361 Query: 357 SNTMALLPHGLPLIGPTRQGNVFVNVGHGATGWAASVGSARLLADLVAGEETEI 410 + L P +P +G T+ N+++N GHG GW GS R +A++VAG EI Sbjct: 362 TGLRPLTPSNVPYVGKTKFANLYLNTGHGTLGWTMGCGSGRAIAEIVAGHVPEI 415 >gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 421 Score = 134 bits (336), Expect = 2e-32, Method: Compositional matrix adjust. Identities = 108/415 (26%), Positives = 190/415 (45%), Gaps = 17/415 (4%) Query: 8 IAVIGGGLSGICSAYFLAAKGYEVAVIERRAHVAEEATFGDTGLLAPGVATPLTLPGAMA 67 I V+G G+ G+ +AY L G++V++I+ R + G+ L+ PL P + Sbjct: 3 ICVMGAGVIGVTTAYRLLQDGHQVSLIDERDQPGAGTSQGNGAQLSYSYVAPLADPSVWS 62 Query: 68 TFACR-FQDEPRVLLASGTDFGRRRWM-GRTRQAQQ-YFAQNKLRLSRLSAYGQALTLQL 124 +A F + + + + + RW+ G R Q + L +L+ Y + Q Sbjct: 63 KWAYYLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSVRQTTIDLLQLAFYSRDQLTQW 122 Query: 125 QTHYNL--EHENGNGVFHLFRLPAEAARMGQMQEAAEQCEFKHQALDTEAIRALEPAFS- 181 L +H+ + A GQ++ A Q + + LD +EPA Sbjct: 123 NGRLKLSFDHQRSGKLVMFTDAQGLEAAAGQVRFQA-QYGCQQEVLDAAQCIRIEPALGR 181 Query: 182 SGAALAGALYYPDDIAGNCVLFAKQMRNAAQ-ELGVRFHFDSTVTAIQAEFGGRVMLQLQ 240 S G +Y + AG+C F + + A Q + RF + +TA++ + +Q Sbjct: 182 SQRDWVGGVYTRSEEAGDCPAFCRALVAAMQADPNFRFIGGARITAVRRQGSALSAVQAG 241 Query: 241 SPHLASQMRVDAVVVTAGMSSAELLRPLDTDLPLRALQSYSALVPVKNPDD---APSMAL 297 + +++Q V+ G SA+ R LD LPL L+ YS VP+++ AP +++ Sbjct: 242 NEWISAQR----FVLALGADSADFARQLDLRLPLYPLKGYSITVPLEDEASRAAAPQVSI 297 Query: 298 YDDSYKVAMTRLGGRIRISGLLGFVQPSQTLPPKALRNLLKIAGDYYPNAANYNQAHF-- 355 D + K+ RLG R+R++G + V +++PP+A+ L + + +P+ A Sbjct: 298 TDIARKIVYARLGQRLRVAGRIELVGQDRSIPPRAIAELKQGMRELFPDCVLGEDARLSP 357 Query: 356 WSNTMALLPHGLPLIGPTRQGNVFVNVGHGATGWAASVGSARLLADLVAGEETEI 410 W P G+P++G N+++N+G GA GW + GSA L+AD +AG I Sbjct: 358 WMGFRPATPSGVPIVGACPVDNLYLNIGQGALGWTLACGSAALIADQIAGRPCSI 412 >gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 428 Score = 60.8 bits (146), Expect = 2e-10, Method: Compositional matrix adjust. Identities = 96/427 (22%), Positives = 162/427 (37%), Gaps = 41/427 (9%) Query: 6 RQIAVIGGGLSGICSAYFLAAKGYEVAVIERRAHVAEEA-TFGDTGLLAPGVATPLTLPG 64 R VIG G G+ SA +G EV++++ +EEA ++G+ G L+ P PG Sbjct: 11 RHAVVIGAGAVGLMSAIHALDQGLEVSLLDFNPVGSEEAASYGNAGWLSSHSVIPPVEPG 70 Query: 65 -----------AMATFACRFQDEPRV--LLASGTDFGRRRWMGRTRQAQQYFAQNKLRLS 111 + + R++ PR+ L RR + T +A L Sbjct: 71 MWKKVPGYLMDPIGPLSIRWRYLPRLTPWLLRNLASARRERIRATARA----------LR 120 Query: 112 RLSAYGQALTLQLQTHYNLEH-ENGNGVFHLFRLPAEAARMGQMQEAAEQCEFKHQALDT 170 L + L L + + H + +GV H++R + + + L+ Sbjct: 121 TLVVDARTLHLDIARRAGVAHLIDTSGVLHVYRSRQQFEGDAFGWSVRRELGIQWSELEA 180 Query: 171 EAIRALEPAFSSGAALAGALYYPDDIAGNC---VLFAKQMRNAAQELGVRFHFDSTVTAI 227 EA+R EP A + D AG+C + + ++ A G D+ T Sbjct: 181 EALRRREPDLDPAFGFAVQV----DEAGHCKNPAAYLQALQAYALARGA-HRIDARATGF 235 Query: 228 QAEFGGRVMLQLQSPHLASQMRVDAVVVTAGMSSAELLRPLDTDLPLRALQSYSALVPVK 287 + E G + ++ +A DA V+ AG S L + L + + Y AL+ Sbjct: 236 RIEEGRLKAVLTETGEVA----CDAAVICAGARSKALAAQAGDRVQLESERGYHALIRGH 291 Query: 288 NPDDAPSMALYDDSYKVAMTRLGGRIRISGLLGFVQPSQTLPPKALRNLLKIAGDYYPNA 347 + +KV T++ +RI+G + F + + IA +P Sbjct: 292 EQAARARTPMMLSEFKVIATQMETGLRIAGQVEFASFEAAPDWRRGEIMRDIALKLFPGL 351 Query: 348 AN---YNQAHFWSNTMALLPHGLPLIGPTRQGNVFVNV-GHGATGWAASVGSARLLADLV 403 +W P G+P IG R + V+ GHG G S + R++A L+ Sbjct: 352 PRDLPAADVRYWLGRRPSTPDGMPCIGYARASSDIVHAYGHGHIGLGCSARTGRIVAQLL 411 Query: 404 AGEETEI 410 AG+ EI Sbjct: 412 AGQTPEI 418 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: 1,189,271 Number of extensions: 45671 Number of successful extensions: 207 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 199 Number of HSP's successfully gapped: 5 Length of query: 422 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 334 Effective length of database: 1,203,190 Effective search space: 401865460 Effective search space used: 401865460 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)