Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate CA265_RS14465 CA265_RS14465 acyl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >FitnessBrowser__Pedo557:CA265_RS14465 Length = 453 Score = 376 bits (966), Expect = e-109 Identities = 191/389 (49%), Positives = 258/389 (66%), Gaps = 2/389 (0%) Query: 42 PPCTSDYYHFND-LLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGV 100 PP D+YH D L E++ ++ KVR +EKEV PI+ YW KAEFPF I PKL + + Sbjct: 64 PPIEGDFYHLGDEALKDEDRELQLKVRAFLEKEVKPIVNHYWNKAEFPFEIIPKLAELNI 123 Query: 101 AGGSIKGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYL 160 G + KGYGCPG S I E+AR+D S STF V S L M +I LCGSE QK+++L Sbjct: 124 CGLTYKGYGCPGKSNLMEGILAMEMARIDTSISTFFGVQSGLAMGSIYLCGSEEQKQQWL 183 Query: 161 PSLAQLNTVACWALTEPDNGSDASG-LGTTATKVEGGWKINGQKRWIGNSTFADLLIIFA 219 P + Q + + LTEP+ GS A+G L TT KV+G W +NGQK+WIGN+TFAD+LII+A Sbjct: 184 PLMQQFKIIGAFGLTEPEVGSAAAGGLTTTCKKVDGKWVLNGQKKWIGNATFADILIIWA 243 Query: 220 RNTTTNQINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQD 279 R+ + ++ GFIVKKD PG K+ +K+ LR+VQNG I L N V + DRL NSF+D Sbjct: 244 RDEESGEVKGFIVKKDNPGFAVEKMQDKMALRIVQNGIITLTNCEVEEADRLQNANSFKD 303 Query: 280 TSKVLAVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQA 339 T+KVL ++R VAWQ +G + G Y+ Y + RKQFG P+A+FQL Q LV+ML N+ A Sbjct: 304 TAKVLQMTRAGVAWQAVGCARGAYENALDYTRTRKQFGKPIASFQLIQNHLVEMLSNLTA 363 Query: 340 MFLMGWRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFC 399 M + +RL +L + G + ASL K + S + R+ S RE++GGNGIL ++ VA+ Sbjct: 364 MQTLCFRLSQLQDQGLLKDEHASLAKVFCSLRTRDVVSRAREVMGGNGILLEYNVARFVA 423 Query: 400 DLEPIYTYEGTYDINTLVTGREVTGIASF 428 D E IY+YEGT +INTL+ GR +TG ++F Sbjct: 424 DAEAIYSYEGTKEINTLIVGRAITGFSAF 452 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: 449 Number of extensions: 18 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: 453 Length adjustment: 32 Effective length of query: 404 Effective length of database: 421 Effective search space: 170084 Effective search space used: 170084 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: 51 (24.3 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