Align D-amino-acid oxidase (EC 1.4.3.3) (characterized)
to candidate GFF749 PS417_03805 D-amino acid oxidase
Query= BRENDA::A0PFJ3 (386 letters) >FitnessBrowser__WCS417:GFF749 Length = 369 Score = 80.5 bits (197), Expect = 7e-20 Identities = 111/391 (28%), Positives = 161/391 (41%), Gaps = 50/391 (12%) Query: 4 APPRRVVICGGGVVGACTAYFLATHAASPTVPTLVERCALACAASGKAGGFLA--LDWCD 61 A ++VVI GGGV+G TA+ LAT + L+ER L +S GG ++ W Sbjct: 2 AEQQQVVIVGGGVIGLLTAFNLATQGQAVV---LLERAGLGQESSWAGGGIVSPLYPWRY 58 Query: 62 STPALSRLARASFALHRRLADALGGADAYGFRP-VHTLSVL---LPPHPAA---SSSPPH 114 S PA++ LA S + +LA L G P VHT + L A ++ Sbjct: 59 S-PAVTALAHWSQDFYPQLAQRLFAQT--GVDPEVHTTGLYWLDLDDEAEALAWAAREGR 115 Query: 115 PLLPPWVDPSASAAPPRELGTPDTTAQVH------PGLFT--KAVLAASGAEVVIGEVER 166 PL V + A P G + + P L KA L + + E Sbjct: 116 PLSKVDVSAAHDAVPVLGGGYANAIYMANVANVRNPRLVKSLKAALLTLPGVTIHEQCEV 175 Query: 167 VAVAWD-GRVAGVVVKGRDGVLDADAVVLALGPWSGRLEVVSEVLDVSGLKAHSIVFRPR 225 D G V GV DG + D VVLA G WSG E+L GL S+ P Sbjct: 176 TGFLLDAGNVVGVSTA--DGAIFGDQVVLAAGAWSG------ELLGTLGL---SLPVEPV 224 Query: 226 EPEKVTPHCL--FLSYQPEPGAKMLDPEVYPRPTGEVYICGMSKDENPPDDPATITGEPD 283 + + + C FLS + PR G + I G + + D T T Sbjct: 225 KGQMILYKCASDFLSSMVLAKGRY----AIPRRDGHILI-GSTLEHEGFDKTPTETA--- 276 Query: 284 SIAMLHKIAGKVSSQLKKEEGAEVVAEQACYLPCTADGLPVIGEIPGVKGCYVATGHSCW 343 L + + AEVV A P + +G+P IG++PG KG ++ GH Sbjct: 277 ----LESLKASAVELIPALADAEVVGHWAGLRPGSPEGIPYIGQVPGFKGLWLNCGHYRN 332 Query: 344 GILNGPATGAALAELILDGKAKIVDLEPFSP 374 G++ PA+ +L+L+ +A I+D P++P Sbjct: 333 GLVLAPASCQLFTDLLLE-RAPIIDPAPYAP 362 Lambda K H 0.318 0.136 0.423 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 363 Number of extensions: 23 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 386 Length of database: 369 Length adjustment: 30 Effective length of query: 356 Effective length of database: 339 Effective search space: 120684 Effective search space used: 120684 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: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory