Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate Echvi_1473 Echvi_1473 Acyl-CoA dehydrogenases
Query= BRENDA::Q96329 (436 letters) >FitnessBrowser__Cola:Echvi_1473 Length = 380 Score = 177 bits (448), Expect = 7e-49 Identities = 115/376 (30%), Positives = 186/376 (49%), Gaps = 5/376 (1%) Query: 52 NDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSIKG-YGC 110 N LT + I + +R+ KE+ P E+ + FP + KLG +G+ G I YG Sbjct: 3 NFQLTENQSMIAQMIRDFGAKEITPFRKEWDDHQTFPLPLFKKLGELGLMGVLIPSEYGG 62 Query: 111 PGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVA 170 G A E+A++D + H+SL I L GSE QK+KYLP LA + Sbjct: 63 SGFGYLEYVTAILELAKLDPGIGLSMAAHNSLCSGHIMLFGSEEQKQKYLPKLASCEFLG 122 Query: 171 CWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTNQING- 229 W LTEP+ GSDA+ + TTAT + +NG K +I + D+ ++ AR +G Sbjct: 123 AWGLTEPNTGSDAANMKTTATAEGDYFVLNGAKNFITHGVSGDVAVVIARTGEVGDKHGM 182 Query: 230 --FIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGV-NSFQDTSKVLAV 286 F+V+K G + + +K+G+R + +++ ++ V L V F + KVL Sbjct: 183 TAFVVEKGTEGFRGGRKEDKLGMRTSETAELIFEDCRVHKSQILGEVGEGFIQSMKVLDG 242 Query: 287 SRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWR 346 R+ +A +GI+ G ++ Y KER+QF P++A+Q KL M ++A L+ ++ Sbjct: 243 GRISIAALSLGIAEGAFEAALSYSKERQQFQKPISAYQGISFKLADMATKLEAAKLLTFK 302 Query: 347 LCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYT 406 L G+ ++ K + S A E A+ ++ GG G D+ V K + D++ Sbjct: 303 AADLKNRGEYVTLASAQAKYYASEIAVELANEAVQVYGGYGFTKDYPVEKYYRDVKLCTI 362 Query: 407 YEGTYDINTLVTGREV 422 EGT +I +V RE+ Sbjct: 363 GEGTSEIQKIVISREL 378 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: 339 Number of extensions: 14 Number of successful extensions: 4 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: 380 Length adjustment: 31 Effective length of query: 405 Effective length of database: 349 Effective search space: 141345 Effective search space used: 141345 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