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= 0001.3500.p (425 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309600|ref|YP_003773692.1| glycine/D-amino acid oxidase [H... 727 0.0 gi|300310459|ref|YP_003774551.1| glycine/D-amino acid oxidase [H... 440 e-124 gi|300310497|ref|YP_003774589.1| glycine/D-amino acid oxidase [H... 191 7e-50 gi|300310468|ref|YP_003774560.1| glycine/D-amino acid oxidase [H... 63 4e-11 >gi|300309600|ref|YP_003773692.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 425 Score = 727 bits (1877), Expect = 0.0, Method: Compositional matrix adjust. Identities = 357/425 (84%), Positives = 384/425 (90%) Query: 1 MMQLKSYWLDTSPAFVSQASSLPEGSCDVVVVGGGITGSAAALALARKGAKVVVCEADIV 60 MMQLKSYWLDTSPAFVSQ +LPEG+CDVVVVGGGITGSAAALALARKGA+VVVCEADIV Sbjct: 1 MMQLKSYWLDTSPAFVSQTQTLPEGACDVVVVGGGITGSAAALALARKGARVVVCEADIV 60 Query: 61 GGAASGRNGGMCNNGFAQDYATLSQRLGSEFANRIYRAFDAGVDTVERLVLEESIDCNFA 120 GGAASGRNGGMCNNGFAQDYATLSQRLG E+ANR+YRAFDAGVDTVERLV EESIDC+FA Sbjct: 61 GGAASGRNGGMCNNGFAQDYATLSQRLGVEWANRLYRAFDAGVDTVERLVREESIDCSFA 120 Query: 121 RYGKLKLAAKPEHFDKLARSHELLIRNVDAETRLLNRQQLQDELGSGCYYGAMLMEKSAG 180 R+GKLKLAAKPEH DKLARS ELL R+VD +TRLL+R QL+DELGS Y+G +LM KSAG Sbjct: 121 RHGKLKLAAKPEHVDKLARSQELLARHVDGDTRLLSRAQLRDELGSDRYHGGLLMHKSAG 180 Query: 181 MHVGRYVRGLAQAAQRRGATYLEHTPVLGLQARGSGYQVRTPAGELRANQVLLASGISQI 240 MHVGRYVRGLAQAAQRRGA YLE TPVLG++A+ Y VRT AG L A QVLLASGISQ+ Sbjct: 181 MHVGRYVRGLAQAAQRRGALYLERTPVLGIEAKNGRYAVRTSAGVLHAGQVLLASGISQV 240 Query: 241 GPFGWIRRRIVPVGAFLIVTEPLPTPLLEQLLPTRRMYTDTKNFVNYFRTTPDNRLLFGG 300 GPFGWIRRRIVPVGAFLIVTEPLP LL+QLLPT+RMYTDTKNFVNYFR TPD RLLFGG Sbjct: 241 GPFGWIRRRIVPVGAFLIVTEPLPGALLKQLLPTQRMYTDTKNFVNYFRATPDQRLLFGG 300 Query: 301 RARFAISNPRSDAKSGEILRGQMLTVFPQLANVRIDYCWGGMVDMTIGRLPRAGQRDGVY 360 RARFA SNP+SDA+SGEILR QML VFP LA RIDYCWGGMVDMT RLPRAGQRDG+Y Sbjct: 301 RARFAASNPQSDARSGEILRAQMLEVFPALAQTRIDYCWGGMVDMTTDRLPRAGQRDGLY 360 Query: 361 YSMGYSGHGTQMATLMGTMMADIMEGRADLNPWKEFKWPAIPGHVGTPWFLPFVGAWYRL 420 YSMGYSGHGT MATLMG+MMA+IM+G A+LNPWK+F WPAIPGH G PWFLPFVGAWYRL Sbjct: 361 YSMGYSGHGTHMATLMGSMMAEIMDGHAELNPWKDFDWPAIPGHFGKPWFLPFVGAWYRL 420 Query: 421 KDRFQ 425 KDR Q Sbjct: 421 KDRLQ 425 >gi|300310459|ref|YP_003774551.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 430 Score = 440 bits (1131), Expect = e-124, Method: Compositional matrix adjust. Identities = 234/430 (54%), Positives = 299/430 (69%), Gaps = 8/430 (1%) Query: 2 MQLKSYWLDTSPAFVSQASSLPEGSCDVVVVGGGITGSAAALALARKGAKVVVCEAD-IV 60 M+L+SYW D++P ++S LP DV +VGGG TG +AALALAR+GA VVV EA V Sbjct: 1 MKLESYWTDSAPLYISPTRDLP-AQVDVAIVGGGFTGLSAALALARRGASVVVLEAGPHV 59 Query: 61 GGAASGRNGGMCNNGFAQDYATLSQRLGSEFANRIYRAFDAGVDTVERLVLEESIDCNFA 120 ASGRNGG NNG A DYA L+ ++G E A Y A+D VDTV RLV EE IDC+F Sbjct: 60 AAEASGRNGGHVNNGLAVDYAELAAKVGVERARAWYHAYDDAVDTVARLVQEEQIDCDFL 119 Query: 121 RYGKLKLAAKPEHFDKLARSHELLIRN-VDAETRLLNRQQLQDELGSGCYYGAMLMEKSA 179 R+GKLK+A +P D L RS + LI + VD + +L+ Q++Q E+ S ++G +L ++S Sbjct: 120 RHGKLKMATRPYQMDALQRSADRLIADGVDLDVEILDAQRVQAEVQSERFHGGLLYKRSG 179 Query: 180 GMHVGRYVRGLAQAAQRRGATYLEHTPVLGLQARGS--GYQVRTPAGELRANQVLLASGI 237 MH+GR+ GLA AA+R+GA T V L+ G G+++ T G + A QVLLA+G Sbjct: 180 QMHMGRFAYGLAMAAERQGAAIHTGTEVRRLERIGQTHGHRLHTTRGAVLARQVLLATGA 239 Query: 238 SQ---IGPFGWIRRRIVPVGAFLIVTEPLPTPLLEQLLPTRRMYTDTKNFVNYFRTTPDN 294 S+ G FGW+RRRIVP+G+F++VTEPL LL +R YT N +YFR TPD Sbjct: 240 SRHGAYGSFGWLRRRIVPIGSFIVVTEPLGAQRAATLLKHQRTYTTVANIHHYFRMTPDT 299 Query: 295 RLLFGGRARFAISNPRSDAKSGEILRGQMLTVFPQLANVRIDYCWGGMVDMTIGRLPRAG 354 RL+FGGRARFAIS+P+SDA SGE+LR + FPQL VR+DYCWGG+VD+T RLP+AG Sbjct: 300 RLVFGGRARFAISSPQSDAASGEVLRRGLHETFPQLGQVRLDYCWGGLVDVTRDRLPQAG 359 Query: 355 QRDGVYYSMGYSGHGTQMATLMGTMMADIMEGRADLNPWKEFKWPAIPGHVGTPWFLPFV 414 +RDG+YYSMGYSGHGTQM+ MG MA +M G A NPW+E +WPAIPGH G PWFLP V Sbjct: 360 ERDGLYYSMGYSGHGTQMSVHMGQCMAKVMAGDALANPWREREWPAIPGHFGAPWFLPLV 419 Query: 415 GAWYRLKDRF 424 G +YRLKD+ Sbjct: 420 GLYYRLKDKL 429 >gi|300310497|ref|YP_003774589.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 433 Score = 191 bits (486), Expect = 7e-50, Method: Compositional matrix adjust. Identities = 139/428 (32%), Positives = 206/428 (48%), Gaps = 16/428 (3%) Query: 6 SYWLDTSPAFVSQASSLPEGSCDVVVVGGGITGSAAALALARKGAKVVVCEADIVGGAAS 65 S W T+ F DV +VG G TG + AL LA+ G V V +A G AS Sbjct: 12 SLWAATAGEFSGAPPLQASARYDVAIVGAGYTGLSTALHLAQAGVSVCVLDAHAPGWGAS 71 Query: 66 GRNGGMCNNGFAQDYATLSQRLGSEFANRIYRAFDAGVDTVERLVLEESIDCNFARYGKL 125 GRNGG G D L GS A+ + A + DTV L+ I+C R G + Sbjct: 72 GRNGGQVIPGLKYDPDQLRVMFGSAVADPLIAAIGSAADTVFDLIARHGIECEAQRAGWI 131 Query: 126 KLAAKPEHFDKLARSHELLIRNVDAE---TRLLNRQQLQDELGSGCYYGAMLMEKSAGMH 182 +P H K+ R+ E R AE +L++ ++ +G+G Y G E++ +H Sbjct: 132 ----QPTHSPKMMRALEARARQWMAEGAPAQLMDGAEVTRRIGTGAYVGGWKDERAGSLH 187 Query: 183 VGRYVRGLAQAAQRRGATYLEHTPVLGLQARGSGYQVRTPAGE----LRANQVLLASGIS 238 +Y RGLAQAAQR G T V L+ R G+++ P+GE + A +V+LA+ Sbjct: 188 PLKYCRGLAQAAQRLGVVIHGDTRVTRLERRQGGWRLHGPSGEQGPHIDAERVVLATNGY 247 Query: 239 QIGPFGWIRRRIVPVGAFLIVTEPLPTPLLEQLLPTRRMYTDTKNFVNYFRTTPDNRLLF 298 + +R+ ++ +F++ T PLP L +LP + +D++ + Y+R RLL Sbjct: 248 TDDLWPHLRQSVIAANSFIVATRPLPPALGASILPGGEVTSDSRRLLLYYRRDAQGRLLM 307 Query: 299 GGRARFAISNPRSDAKSGEILRGQMLTVFPQLANVRIDYCWGGMVDMTIGRLPRAGQ-RD 357 GGR F P+ A + R L +FPQLA V +Y W G V +T LP + Sbjct: 308 GGRGPFG--EPQGPADFAHLERSVAL-LFPQLAGVEYEYRWSGRVAITRDFLPHVHEPAP 364 Query: 358 GVYYSMGYSGHGTQMATLMGTMMADIMEGRADLN-PWKEFKWPAIPGHVGTPWFLPFVGA 416 G+ ++GY+G G MAT+MG +A + G A P+ IP H +++ A Sbjct: 365 GLSIALGYNGRGIAMATMMGQRLAQRLIGPAGTAFPFPVSTIAPIPLHGLQRFYIAAGVA 424 Query: 417 WYRLKDRF 424 WY + DRF Sbjct: 425 WYSVLDRF 432 >gi|300310468|ref|YP_003774560.1| glycine/D-amino acid oxidase [Herbaspirillum seropedicae SmR1] Length = 441 Score = 63.2 bits (152), Expect = 4e-11, Method: Compositional matrix adjust. Identities = 102/442 (23%), Positives = 159/442 (35%), Gaps = 87/442 (19%) Query: 12 SPAFVS-QASSLPEGSCDVVVVGGGITGSAAALALARKGAKVVVCEADIVGGAASGRNGG 70 SP V Q+ ++P S DVVV+GGGI G A LA++G V V E +G S RN G Sbjct: 2 SPPLVQVQSPTIPPASADVVVIGGGIIGIFTAYFLAKRGISVAVVEKGRIGAEQSSRNWG 61 Query: 71 MCNNGFAQDYATLSQRLGSEFANRIYRAF---DAGVDTVERLVLEESIDCNFARYGKLKL 127 C NR R +D E+ E D F R G L L Sbjct: 62 WCRQ-----------------QNRDARELPMATKSIDLWEQFSAETGEDTGFNRCGLLYL 104 Query: 128 AAKPEHFDKLARSHELLIRNVDAETRLLNRQQLQD--ELGSGCYYGAMLMEKSAGMHVGR 185 + E + A + + T +L+ +Q + + G + G+ Sbjct: 105 SNDEEEIARWAAWGD-FAKTAGVTTYMLDSKQAAERGHATGRAWKGGVFSPTDGTADPGK 163 Query: 186 YVRGLAQAAQRRGATYLEHTPVLGLQARGSGYQ-VRTPAGELRANQVLLASG------IS 238 +A+A + G ++ G+ G V T AG ++ ++A G Sbjct: 164 AAPAVARAIMKLGGHVIQQCAARGIDTEGGRVSGVITEAGVIKTKVAVMAGGAWASSFCH 223 Query: 239 QIG---PFGWIRRRIVPVGAFLIVTEPLPTPLLEQLLPTRRMYTDTKNF----------- 284 Q+G P +R+ I+ V + PLP L + R + Sbjct: 224 QLGIRFPQASVRQSIMSVAP---MEAPLPGALYTSGVAVTRRSDGSYALAISGRARVDPT 280 Query: 285 VNYFRTTPDNRLLFGGR------------------------------ARFAISNPRSDAK 314 + + R +P +F R R I + +D Sbjct: 281 MQFLRFSPQFLPMFAKRWRSLSPGGLEAWRSGHETLSRWRMDAPTPMERMRILDASADPA 340 Query: 315 SGEILRGQMLTVFPQLANVRIDYCWGGMVDMT------IGRLPRAGQRDGVYYSMGYSGH 368 S + + + PQLA ++ + W G VD T IG LP Q G+ + G+SGH Sbjct: 341 SIRATHRRAVELLPQLAQAKVTHTWAGYVDSTPDGVPGIGELP---QTPGLILAAGFSGH 397 Query: 369 GTQMATLMGTMMADIMEGRADL 390 G + G ++AD+ G A + Sbjct: 398 GFGIGPGAGHLIADLASGAAPI 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 0.322 0.138 0.423 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: 1,241,057 Number of extensions: 48478 Number of successful extensions: 164 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 157 Number of HSP's successfully gapped: 4 Length of query: 425 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 337 Effective length of database: 1,203,190 Effective search space: 405475030 Effective search space used: 405475030 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)