Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate H281DRAFT_01204 H281DRAFT_01204 hypothetical protein
Query= BRENDA::Q96329 (436 letters) >FitnessBrowser__Burk376:H281DRAFT_01204 Length = 377 Score = 174 bits (442), Expect = 3e-48 Identities = 117/373 (31%), Positives = 179/373 (47%), Gaps = 7/373 (1%) Query: 56 TPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSIKG-YGCPGLS 114 T E++ IR R+ + +AP ++ A+ P + ++G +G G + +G Sbjct: 6 TEEQRMIRDAARDFATERLAPNAAQWDRDAQLPADVVRQMGDLGFLGMIVPSQWGGSYTD 65 Query: 115 ITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWAL 174 A A+A EIA A+C+T + VH+S+G I GS+AQK++YL LA + + L Sbjct: 66 YVAYALALEEIAAGCAACATLMSVHNSVGCGPILNFGSDAQKDRYLHDLATGRRIGAFCL 125 Query: 175 TEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFA---RNTTTNQINGFI 231 TEP GS+A+ L T A +G W +NG K+++ N AD+ I+FA + ++ FI Sbjct: 126 TEPQAGSEANNLRTRAVLCDGKWILNGSKQFVTNGARADIAIVFAVTDPDRGKRGLSAFI 185 Query: 232 VKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRL--PGVNSFQDTSKVLAVSRV 289 V D PG K +K+G+R I L + VPD + L PG + L R+ Sbjct: 186 VPTDTPGFNVGKPEHKLGIRASDTCPISLDDCAVPDANLLGEPG-EGLRIALSNLEGGRI 244 Query: 290 MVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCK 349 +A Q +GI+ +D Y ER QFG L Q L M + A L+ + Sbjct: 245 GIAAQAVGIARAAFDAARAYASERMQFGKALKDHQTIANMLADMATRLNAARLLVHHAAR 304 Query: 350 LYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEG 409 L G+ +AS K + S A E S ++ GG G L D+ V + + D YEG Sbjct: 305 LRSAGEPCLSEASQAKLFASEVAEEVCSNAIQIHGGYGYLEDYAVERHYRDARITQIYEG 364 Query: 410 TYDINTLVTGREV 422 T ++ +V R V Sbjct: 365 TSEVQRMVIARHV 377 Lambda K H 0.319 0.133 0.399 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: 322 Number of extensions: 14 Number of successful extensions: 3 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: 436 Length of database: 377 Length adjustment: 31 Effective length of query: 405 Effective length of database: 346 Effective search space: 140130 Effective search space used: 140130 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 (21.7 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