Align D-amino-acid oxidase (EC 1.4.3.3) (characterized)
to candidate AO356_15895 AO356_15895 D-amino acid oxidase
Query= BRENDA::A0PFJ3 (386 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_15895 Length = 366 Score = 76.3 bits (186), Expect = 1e-18 Identities = 106/389 (27%), Positives = 159/389 (40%), Gaps = 50/389 (12%) Query: 7 RRVVICGGGVVGACTAYFLATHAASPTVPTLVERCALACAASGKAGGFLA--LDWCDSTP 64 ++VVI GGGV+G TA+ LA+ L++R ++ +S GG ++ W S P Sbjct: 5 QQVVIVGGGVIGLLTAFNLASEGQRVV---LLDRSSVGQESSWAGGGIVSPLYPWRYS-P 60 Query: 65 ALSRLARASFALHRRLADALGGADAYGFRP-VHTLSVL---LPPHPAA---SSSPPHPLL 117 A++ LA S + +L + L A G P VH + L A + PL Sbjct: 61 AVTALAHWSQDFYPQLGERLFAAT--GIDPQVHVTGLYWLDLDDQDEALAWAEREGRPLR 118 Query: 118 PPWVDPSASAAPPRELGTPDT-----TAQVHPGLFTKAVLAASGA--EVVIGEVERVA-- 168 + A P G A V K++ AA A V + E V Sbjct: 119 AVDISTVHDAVPVLGAGFSRAIYMAGVANVRNPRLVKSLKAALQALPNVTLHEHCEVNGF 178 Query: 169 VAWDGRVAGVVVKGRDGVLDADAVVLALGPWSGRLEVVSEVLDVSGLKAHSIVFRPREPE 228 + GRV GV G + D VVLA G WSG E+L GLK + P + + Sbjct: 179 IRDGGRVVGV--DSSAGPMRGDQVVLAAGAWSG------ELLKTLGLK---LPVEPVKGQ 227 Query: 229 KVTPHCL--FLSYQPEPGAKMLDPEVYPRPTGEVYICGMSKDENPPDDPATITGEPDSIA 286 + C FLS + PR G + + + E P + Sbjct: 228 MILYKCASDFLSSMVLAKGRY----AIPRRDGHILVGSTLEREGFDKTPTEVA------- 276 Query: 287 MLHKIAGKVSSQLKKEEGAEVVAEQACYLPCTADGLPVIGEIPGVKGCYVATGHSCWGIL 346 L + + GAEVV A P + +G+P IGE+PGV G ++ GH G++ Sbjct: 277 -LESLKTSAQQLIPALAGAEVVGHWAGLRPGSPEGIPYIGEVPGVAGLWLNCGHYRNGLV 335 Query: 347 NGPATGAALAELILDGKAKIVDLEPFSPA 375 PA+ +L+L G+ ++D P++PA Sbjct: 336 LAPASCQLFTDLML-GREPVIDPVPYAPA 363 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: 372 Number of extensions: 25 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 386 Length of database: 366 Length adjustment: 30 Effective length of query: 356 Effective length of database: 336 Effective search space: 119616 Effective search space used: 119616 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