Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_065397801.1 BBI00_RS05370 acyl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >NCBI__GCF_001684965.1:WP_065397801.1 Length = 379 Score = 177 bits (448), Expect = 7e-49 Identities = 114/367 (31%), Positives = 174/367 (47%), Gaps = 5/367 (1%) Query: 62 IRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI-KGYGCPGLSITANAI 120 I + +E EK + P + E+ E FP + +LG MG G + + YG GL Sbjct: 12 IAETAKEFAEKNIRPNIMEWDESQTFPKDLFHQLGEMGFMGIVVPEQYGGSGLGYHEYVA 71 Query: 121 ATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWALTEPDNG 180 EI++VD S + H+SL I G+E Q+ K+LP LA + W LTE + G Sbjct: 72 ILDEISQVDPSIGLSVAAHNSLCTNHIYEFGNEEQRNKWLPQLATGKVIGAWGLTEHNTG 131 Query: 181 SDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFAR---NTTTNQINGFIVKKDAP 237 SD+ G+ TTA K W ING K +I ++ D+ ++ R N F+++K Sbjct: 132 SDSGGMSTTAVKDGDEWIINGAKNFITHAISGDIAVVMTRTGEKGAKNNSTAFVLEKGML 191 Query: 238 GLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGV-NSFQDTSKVLAVSRVMVAWQPI 296 G + K NK+G+R + +++ NV VPD RL V F+ K+L R+ +A + Sbjct: 192 GFTSGKKENKLGMRASETAELIFDNVRVPDSHRLGEVGEGFKQAMKILDGGRISIAALSL 251 Query: 297 GISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCKLYETGQM 356 G + G Y +Y KER QFG ++ FQ L M + A L+ R L Q Sbjct: 252 GTARGAYKAALKYAKERHQFGKSISEFQAINFMLADMATEIDAAELLIQRAATLKNAKQK 311 Query: 357 TPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEGTYDINTL 416 + ++ K + S ++ ++ GG G DF K + D + EGT +I L Sbjct: 312 MTKEGAMAKLYASEACVRISNNAVQIFGGYGYTKDFPAEKFYRDSKLCTIGEGTSEIQRL 371 Query: 417 VTGREVT 423 V GR++T Sbjct: 372 VIGRDIT 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: 319 Number of extensions: 12 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: 379 Length adjustment: 31 Effective length of query: 405 Effective length of database: 348 Effective search space: 140940 Effective search space used: 140940 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