Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_047093223.1 AAV99_RS06380 acyl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >NCBI__GCF_001013305.1:WP_047093223.1 Length = 394 Score = 226 bits (577), Expect = 7e-64 Identities = 134/385 (34%), Positives = 207/385 (53%), Gaps = 2/385 (0%) Query: 46 SDYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI 105 +D ++ +D L+ EE+ +R + E+ P + E + K + P +GA G+ G +I Sbjct: 10 ADPFNLDDQLSEEERMVRDAAHGFAQGELQPRVIEAYSKEIDAPELFPLMGAAGLLGVTI 69 Query: 106 -KGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLA 164 + YG G + A + EI RVD+ + V SSL M I GS+ Q+ +YLP LA Sbjct: 70 PEEYGGAGANYVAYGLVAREIERVDSGYRSMASVQSSLVMHPIHAYGSDEQRARYLPGLA 129 Query: 165 QLNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTT 224 + C+ LTEPD GSD SG+ T A K G+ ++G K WI NS FAD+ +++A++ Sbjct: 130 SGQLIGCFGLTEPDAGSDPSGMRTYAKKDGDGYSLSGAKTWISNSPFADVFVVWAKSEAH 189 Query: 225 -NQINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKV 283 +++ GFI++K GL A KI K+ LR G I + V +P + LP V + Sbjct: 190 GDKVRGFILEKGMEGLAAPKIGGKLSLRASTTGMIQMDEVKLPADALLPNVEGMKGPFGC 249 Query: 284 LAVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLM 343 L +R ++W IG + Y +Y +R QFG PLA+ QL Q KL M + Sbjct: 250 LNRARYGISWGSIGAAEFCYSAARQYGLDRHQFGVPLASKQLYQLKLADMATEIALGLQA 309 Query: 344 GWRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEP 403 R+ +L + G+ P S+ K KA + A R++ GGNGI ++ V + +LE Sbjct: 310 SLRVGRLLDEGRYAPEMISVVKRNNVGKALDVARTARDMHGGNGISEEYQVMRHMANLET 369 Query: 404 IYTYEGTYDINTLVTGREVTGIASF 428 + TYEGT+D++ L+ GR +TGI++F Sbjct: 370 VNTYEGTHDVHALILGRAITGISAF 394 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: 348 Number of extensions: 15 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: 394 Length adjustment: 31 Effective length of query: 405 Effective length of database: 363 Effective search space: 147015 Effective search space used: 147015 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 24 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