Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate Ga0059261_2164 Ga0059261_2164 Acyl-CoA dehydrogenases
Query= BRENDA::Q96329 (436 letters) >FitnessBrowser__Korea:Ga0059261_2164 Length = 394 Score = 233 bits (595), Expect = 6e-66 Identities = 136/385 (35%), Positives = 209/385 (54%), Gaps = 2/385 (0%) Query: 46 SDYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI 105 +D + + LT EE+ +R R ++ + P +T + F I ++G +G+ G +I Sbjct: 10 ADPFALDAQLTDEERMVRDAARAYAQERLLPRVTRAFLDENFDREIMSEMGQLGLLGPTI 69 Query: 106 -KGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLA 164 + YG GL A + E+ VD+ + + V SSL M I G+E QK KYLP L Sbjct: 70 PETYGGAGLGYVAYGLVAREVEAVDSGYRSAMSVQSSLVMHPINAYGTEEQKRKYLPKLL 129 Query: 165 QLNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTT 224 V C+ LTEPD GSD + T A K++GG++I G K WI NS AD+ +++A++ Sbjct: 130 SGEWVGCFGLTEPDAGSDPGSMRTRAEKIDGGYRITGSKMWITNSPIADVFVVWAKSDAH 189 Query: 225 NQ-INGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKV 283 I GF+++K GL A KI K+ LR G+I++ V V ++ LP V + Sbjct: 190 GGGIKGFVLEKGMKGLSAPKIEGKLSLRASITGEIVMDGVEVSEDALLPEVQGLKGPFGC 249 Query: 284 LAVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLM 343 L +R +AW +G + + +Y +R+QFG PLAA QL Q KL M + Sbjct: 250 LNRARYGIAWGSMGAAEACFHAARQYTLDRQQFGRPLAATQLVQLKLANMETEIALGLQA 309 Query: 344 GWRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEP 403 R ++++ G++ P S+ K KA E A + R++ GGNGI A+F V + +LE Sbjct: 310 ALRAGRMFDQGELAPEAISIIKRNNCGKALEIARVARDMHGGNGISAEFHVMRHAINLET 369 Query: 404 IYTYEGTYDINTLVTGREVTGIASF 428 + TYEGT+D++ L+ GR +TGIA+F Sbjct: 370 VNTYEGTHDVHGLILGRAITGIAAF 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: 338 Number of extensions: 14 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: 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 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