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= 0001.4464.p (428 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... 789 0.0 gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [H... 121 9e-29 gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase smal... 104 1e-23 gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase smal... 95 9e-21 gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase smal... 67 2e-12 >gi|300313873|ref|YP_003777965.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 428 Score = 789 bits (2038), Expect = 0.0, Method: Compositional matrix adjust. Identities = 384/428 (89%), Positives = 404/428 (94%) Query: 1 MPTSPEIVFPRHAVVIGAGAVGLMSAIHALDQGLQVSLLDFNPVGSEEAASYGNAGWLSS 60 M T P+I FPRHAVVIGAGAVGLMSAIHALDQGL+VSLLDFNPVGSEEAASYGNAGWLSS Sbjct: 1 MSTLPDISFPRHAVVIGAGAVGLMSAIHALDQGLEVSLLDFNPVGSEEAASYGNAGWLSS 60 Query: 61 HSVIPPVEPGMWKKVPGYLMDPLGPLSIRWRYLPRLTPWLLRNLASASRERIRSTARALR 120 HSVIPPVEPGMWKKVPGYLMDP+GPLSIRWRYLPRLTPWLLRNLASA RERIR+TARALR Sbjct: 61 HSVIPPVEPGMWKKVPGYLMDPIGPLSIRWRYLPRLTPWLLRNLASARRERIRATARALR 120 Query: 121 TLVVDARSLHLEVAQRAGVAHLIDTSGVLHVYRSRQHFDNDAFGWGVRRELGISWQELEG 180 TLVVDAR+LHL++A+RAGVAHLIDTSGVLHVYRSRQ F+ DAFGW VRRELGI W ELE Sbjct: 121 TLVVDARTLHLDIARRAGVAHLIDTSGVLHVYRSRQQFEGDAFGWSVRRELGIQWSELEA 180 Query: 181 EALREREPDLDPAFGFAVQVDEAGHCKNPAAYLQALQAYALARGATRIDGRATGFRVEQG 240 EALR REPDLDPAFGFAVQVDEAGHCKNPAAYLQALQAYALARGA RID RATGFR+E+G Sbjct: 181 EALRRREPDLDPAFGFAVQVDEAGHCKNPAAYLQALQAYALARGAHRIDARATGFRIEEG 240 Query: 241 RLKAVLTDAGEIVCDAAVICAGARSKALAAAAGDAVQLESERGYHAVIRGHEQQARARTP 300 RLKAVLT+ GE+ CDAAVICAGARSKALAA AGD VQLESERGYHA+IRGHEQ ARARTP Sbjct: 241 RLKAVLTETGEVACDAAVICAGARSKALAAQAGDRVQLESERGYHALIRGHEQAARARTP 300 Query: 301 MMVSEFKVIATQMETGLRIAGQVEFASFEAAPDWRRGEIMRDIACKLFPGLPRPLPAEDV 360 MM+SEFKVIATQMETGLRIAGQVEFASFEAAPDWRRGEIMRDIA KLFPGLPR LPA DV Sbjct: 301 MMLSEFKVIATQMETGLRIAGQVEFASFEAAPDWRRGEIMRDIALKLFPGLPRDLPAADV 360 Query: 361 QFWLGRRPSTPDGMPCIGHSRASGDIIHAYGHGHIGLGCSARTGRIAAQLLAGQAPEIDL 420 ++WLGRRPSTPDGMPCIG++RAS DI+HAYGHGHIGLGCSARTGRI AQLLAGQ PEIDL Sbjct: 361 RYWLGRRPSTPDGMPCIGYARASSDIVHAYGHGHIGLGCSARTGRIVAQLLAGQTPEIDL 420 Query: 421 APFSPQRF 428 APFSPQRF Sbjct: 421 APFSPQRF 428 >gi|300311013|ref|YP_003775105.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 433 Score = 121 bits (304), Expect = 9e-29, Method: Compositional matrix adjust. Identities = 106/424 (25%), Positives = 182/424 (42%), Gaps = 18/424 (4%) Query: 14 VVIGAGAVGLMSAIHALDQGLQVSLLDFNPVGSEEAASYGNAGWLSSHSVIPPVEPGMWK 73 V++G+G +G+ SA + G V++LD P G S+GNAG +S P PG+ Sbjct: 4 VILGSGVIGVTSAWYLARAGHDVTVLDRQP-GPALETSFGNAGQISPGYASPWAAPGIPL 62 Query: 74 KVPGYLMDPLGPLSIRWRYLPRLTPWLLRNLASASRERIRSTARALRTLVVDARSLHLEV 133 K ++ PL+IR W+ + L + + ER + L +R ++ Sbjct: 63 KAIKWMFQEHAPLAIRLDGSFNQLRWMWQMLRNCNAERYAVNKERMVRLAEYSRDCLRDL 122 Query: 134 AQRAGVAHLIDTSGVLHVYRSRQHFDNDAFGWGVRRELGISWQELEGEALREREPDLDP- 192 G+ + G L ++RS++ + A V +E G+ ++ L + L EP L Sbjct: 123 RADVGIPYEGRQQGTLQLFRSQEQLEGAAKDIAVLKEAGVPFELLTPDQLGNAEPALAKV 182 Query: 193 ----AFGFAVQVDEAGHCKNPAAYLQAL--QAYALARGATRIDGRATGFRVEQGRLKAVL 246 G + DE G C+ L + Q R ID A + G++ V+ Sbjct: 183 RDKLTGGLRLPNDETGDCQLFTTRLATMAEQIGVKFRYGVDIDALA----MAGGKIAGVV 238 Query: 247 TDAGEIVCDAAVICAGARSKALAAAAGD--AVQLESERGYHAVIRGHEQQARARTPMMVS 304 + D+ V+ G+ S L A+ + +GY + + A + ++ Sbjct: 239 CGKELVQADSYVVALGSYSPQLLGEVPGLPAIPVYPLKGYSITVPITDASAAPVSTILDE 298 Query: 305 EFKVIATQMETGLRIAGQVEFASFEAAPDWRRGEIMRDIACKLFPGLPRPLPAEDVQFWL 364 +K+ T+ + +R+ G E ++ A +R + + LFPG A FW Sbjct: 299 TYKIAVTRFDDRIRVGGMAEIVGYDTALKAKRRATLELVVNDLFPGAGDTAQAS---FWT 355 Query: 365 GRRPSTPDGMPCIGHSRASGDIIHAYGHGHIGLGCSARTGRIAAQLLAGQAPEIDLAPFS 424 G RP TPDG P +G + S I+ GHG +G S +G++ A L++G+ P I S Sbjct: 356 GLRPMTPDGTPVVGATPVSNLYINT-GHGTLGWTMSCGSGQLLADLISGRRPAIAHEDLS 414 Query: 425 PQRF 428 +R+ Sbjct: 415 VERY 418 >gi|300310779|ref|YP_003774871.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 436 Score = 104 bits (259), Expect = 1e-23, Method: Compositional matrix adjust. Identities = 101/420 (24%), Positives = 167/420 (39%), Gaps = 17/420 (4%) Query: 14 VVIGAGAVGLMSAIHALDQGLQVSLLDFNPVGSEEAASYGNAGWLSSHSVIPPVEPGMWK 73 +V+GAG +G SA QG V+++D P G+ + S+ N +S P P Sbjct: 4 IVLGAGIIGTASAWFLKKQGYDVTVIDRQP-GAAQETSFANGCQISVSHAEPWANPAAPM 62 Query: 74 KVPGYLMDPLGPLSIRWRYLPRLTPWLLRNLASASRERIRSTARALRTLVVDARSLHLEV 133 KV +L PL R+R W + L + R R + L +R V Sbjct: 63 KVLKWLGKEDAPLLYRFRPEWLQWKWAVAFLRECTAARTDENIRNIVALCEYSRQTLQAV 122 Query: 134 AQRAGVAHLIDTSGVLHVYRSRQHFDNDAFGWGVRRELGISWQELEGEALREREPDL--- 190 G+ + T G+LH Y + F + + R+LG + + + + EP L Sbjct: 123 RAETGIQYDHLTRGILHFYTEEKEFQDSLPAAKLMRDLGCPRESIGADEVVRIEPALASI 182 Query: 191 --DPAFGFAVQVDEAGHCKNPAAYLQALQA-----YALARGATRIDGRATGFRVEQGRLK 243 G DE+G L A + + TR+ G ++ Sbjct: 183 RNKIVGGDFTATDESGDVFKLTTGLAKKSAEAGVEFRYSTTITRLITEGAGAAARVTGVE 242 Query: 244 AVLTDAGEIV--CDAAVICAGARSKALAAAAGDAVQLESERGYHAVIRGHEQQARARTPM 301 + D V D V+ G+ S+ L G + L +GY A + A + Sbjct: 243 IINPDGRHEVLKADTFVVAMGSFSQQLVKPLGIDLLLYPGKGYSATYQITNPDAAPTVSL 302 Query: 302 MVSEFKVIATQMETGLRIAGQVEFASFEAAPDWRRGEIMRDIACKLFPGLPRPLPAEDVQ 361 +K++ +++ LR+AG E + + R E + +LFP E+ Sbjct: 303 TDDGYKLVVSRLGDRLRVAGTCELNGYTRELNTTRCEAITRRTRELFPD---GCDYENPT 359 Query: 362 FWLGRRPSTPDGMPCIGHSRASGDIIHAYGHGHIGLGCSARTGRIAAQLLAGQAPEIDLA 421 +W G RP TP +P +G ++ + ++ GHG +G +GR A+++AG PEID A Sbjct: 360 YWTGLRPLTPSNVPYVGKTKFANLYLNT-GHGTLGWTMGCGSGRAIAEIVAGHVPEIDFA 418 >gi|300309666|ref|YP_003773758.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 421 Score = 95.1 bits (235), Expect = 9e-21, Method: Compositional matrix adjust. Identities = 110/424 (25%), Positives = 174/424 (41%), Gaps = 20/424 (4%) Query: 12 HAVVIGAGAVGLMSAIHALDQGLQVSLLDFNPVGSEEAASYGNAGWLSSHSVIPPVEPGM 71 H V+GAG +G+ +A L G QVSL+D S GN LS V P +P + Sbjct: 2 HICVMGAGVIGVTTAYRLLQDGHQVSLIDERD-QPGAGTSQGNGAQLSYSYVAPLADPSV 60 Query: 72 WKKVPGYLMDPLGPLSIRWRYLPRLTPWLLRNLASASRERIRSTARALRTLVVDARSLHL 131 W K YL PL+I+ WL L + +R T L L +R Sbjct: 61 WSKWAYYLFSKDSPLTIKPTLEAAQYRWLAGFLRYCNAGSVRQTTIDLLQLAFYSRDQLT 120 Query: 132 EVAQRAGVAHLIDTSGVLHVYRSRQHFDNDAFGWGVRRELGISWQELEGEALREREPDL- 190 + R ++ SG L ++ Q + A + + G + L+ EP L Sbjct: 121 QWNGRLKLSFDHQRSGKLVMFTDAQGLEAAAGQVRFQAQYGCQQEVLDAAQCIRIEPALG 180 Query: 191 ----DPAFGFAVQVDEAGHCKNPAAYLQALQAYALARGATRIDG--RATGFRVEQGRLKA 244 D G + +EAG C A+ +AL A A R G R T R + L A Sbjct: 181 RSQRDWVGGVYTRSEEAGDCP---AFCRALVAAMQADPNFRFIGGARITAVRRQGSALSA 237 Query: 245 VLTDAGEIVCDAAVICAGARSKALAAAAGDAVQLESERGYHAVIRGHEQQARARTPMM-V 303 V I V+ GA S A + L +GY + ++ +RA P + + Sbjct: 238 VQAGNEWISAQRFVLALGADSADFARQLDLRLPLYPLKGYSITVPLEDEASRAAAPQVSI 297 Query: 304 SEF--KVIATQMETGLRIAGQVEFASFEAAPDWRRGEIMRDIACKLFPGLPRPLPAEDVQ 361 ++ K++ ++ LR+AG++E + + R ++ +LFP + ED + Sbjct: 298 TDIARKIVYARLGQRLRVAGRIELVGQDRSIPPRAIAELKQGMRELFPDC---VLGEDAR 354 Query: 362 F--WLGRRPSTPDGMPCIGHSRASGDIIHAYGHGHIGLGCSARTGRIAAQLLAGQAPEID 419 W+G RP+TP G+P +G ++ G G +G + + + A +AG+ ID Sbjct: 355 LSPWMGFRPATPSGVPIVGACPVD-NLYLNIGQGALGWTLACGSAALIADQIAGRPCSID 413 Query: 420 LAPF 423 PF Sbjct: 414 DTPF 417 >gi|300311555|ref|YP_003775647.1| D-amino acid dehydrogenase small subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 67.4 bits (163), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 101/439 (23%), Positives = 172/439 (39%), Gaps = 48/439 (10%) Query: 11 RHAVVIGAGAVGLMSAIHALDQGLQVSLLDFNPVGSEEAASYGNAGWLSSHSVIPPVEPG 70 R VIG G G+ SA +G +V++++ +EEA ++G++G L+ + +P PG Sbjct: 6 RQIAVIGGGLSGICSAYFLATKGYEVAVIERRAHVAEEA-TFGDSGLLAPGTAMPLTLPG 64 Query: 71 MWKKVPGYLMDPLGPLSIRWRYLPRLTPWLLRNLASASRERIRSTARA------------ 118 L + R++ PR+ LL + A R R RA Sbjct: 65 -----------ALATFACRFQDEPRV---LLASGADFGRRRWMRATRAAQQHHFAQHKLI 110 Query: 119 LRTLVVDARSLHLEVAQRAGVAHLIDTSGVLHVYRSRQHFDNDAFGWGVRRELGISWQEL 178 L L + L ++ + H +++GV H++R + L Sbjct: 111 LSRLSAYGQDLTQQLQAHYNMEH-ENSAGVFHLFRQSAEAARLPALQEAASQCEYKQLTL 169 Query: 179 EGEALREREPDLDPAFGFAVQV----DEAGHCKNPAAYLQALQAYALARGAT-RIDGRAT 233 + +R EP A + D AG N + + ++ A A G + + + Sbjct: 170 DAAGIRALEPAFSSEAALAGALYYPDDIAG---NSVLFAKQMRNAAQALGVSFHFNSTVS 226 Query: 234 GFRVE-QGRLKAVLTD---AGEIVCDAAVICAGARSKALAAAAGDAVQLESERGYHAVIR 289 R E GR+ + A + DA V+ AG S AL ++ L + + Y A++ Sbjct: 227 SIRSEFGGRVTLEVQSPHLASHLTMDAVVVAAGMASAALLQPLDTSLPLRALQSYSALVP 286 Query: 290 GHEQQARARTPMMVSEFKVIATQMETGLRIAGQVEF--ASFEAAPDWRRGEIMRDIACKL 347 + +KV T++ + +RI+G + F AS P R + IA Sbjct: 287 VKNPDDAPTMALYDDSYKVAMTRLGSRIRISGLLGFVPASQTLPPKALRN--LLKIAGDY 344 Query: 348 FPGLPRPLPAEDVQFWLGRRPSTPDGMPCIGHSRASGDIIHAYGHGHIGLGCSARTGRIA 407 +P FW P G+P +G +R G+I GHG G S + R+ Sbjct: 345 YPNAAN---YNQAHFWSNSIAMMPTGLPVVGPTR-QGNIFVNVGHGVTGWAASVGSARLL 400 Query: 408 AQLLAGQAPEIDLAPFSPQ 426 + ++AG+ EI A P+ Sbjct: 401 SDMMAGEETEIATAGLLPR 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 0.321 0.137 0.421 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: 1,402,331 Number of extensions: 60337 Number of successful extensions: 249 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 239 Number of HSP's successfully gapped: 5 Length of query: 428 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 340 Effective length of database: 1,203,190 Effective search space: 409084600 Effective search space used: 409084600 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 (21.9 bits) S2: 132 (55.5 bits)