Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_101588067.1 BJEO58_RS04410 acyl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >NCBI__GCF_900169175.1:WP_101588067.1 Length = 405 Score = 209 bits (533), Expect = 1e-58 Identities = 120/372 (32%), Positives = 198/372 (53%), Gaps = 9/372 (2%) Query: 66 VRECMEKEVAPIMTEYWEKAEFPFH-ITPKLGAMGVAGGSIKGYGCPGLSITANAIATAE 124 VR + + V + +++ P + LG +GV G ++GY C G + T +A E Sbjct: 32 VRSWLNEHVRDNIGDWYLDGTIPARELAEGLGELGVLGMHLEGYECAGSTATQYGLACRE 91 Query: 125 IARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWALTEPDNGSDAS 184 + VD+ + + V SL M +I GSE QK+++LP +A + C+ LTEPD GSD + Sbjct: 92 LEAVDSGLRSLVSVQGSLAMFSIHHWGSEEQKQEWLPQMAAGRAIGCFGLTEPDVGSDPA 151 Query: 185 GLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTNQ-------INGFIVKKDAP 237 G+ T ATK W +NG K WI NS +D+++++A+ ++ + GF+V D P Sbjct: 152 GMKTRATKDGSDWILNGAKMWITNSPVSDVMVVWAKTDEVDEKTGEKGVVRGFVVPTDTP 211 Query: 238 GLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVLAVSRVMVAWQPIG 297 G++ ++ K+ LR G+I+L NV +P+ LP + + L+ +R + + G Sbjct: 212 GVETPEVQRKLSLRASITGEIVLDNVRLPESAMLPKASGLKGPLSALSEARYGIVFGVTG 271 Query: 298 ISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCKLYETGQ-M 356 + + RY R QF PL++FQ++QQKL + G A+ L + +L ++ + Sbjct: 272 AARDSLEEALRYTDTRIQFDRPLSSFQISQQKLAKAFGEYSAITLTAAHIGRLKDSAAGV 331 Query: 357 TPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEGTYDINTL 416 P Q SLGK A A R L GG+GI +++ + +LE + TYEGT++++ L Sbjct: 332 RPEQISLGKMVNVDTAMNIARDLRALFGGSGITSEYSPLRHAINLETVLTYEGTHEVHQL 391 Query: 417 VTGREVTGIASF 428 GR +TGI +F Sbjct: 392 TLGRAMTGINAF 403 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: 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: 405 Length adjustment: 32 Effective length of query: 404 Effective length of database: 373 Effective search space: 150692 Effective search space used: 150692 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