Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_047092433.1 AAV99_RS03120 isovaleryl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >NCBI__GCF_001013305.1:WP_047092433.1 Length = 386 Score = 163 bits (412), Expect = 1e-44 Identities = 113/375 (30%), Positives = 180/375 (48%), Gaps = 5/375 (1%) Query: 55 LTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI-KGYGCPGL 113 L E Q IR V ++ +AP+ + + FP + P++GA+G+ G ++ + G GL Sbjct: 11 LGEEAQMIRDSVGRFADERIAPLAAKVDAEDWFPIELWPEMGALGLHGMTVSEDDGGTGL 70 Query: 114 SITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWA 173 + IA E++R AS HS+L + IA GS QK KYLP L V A Sbjct: 71 GYLEHTIAIEEVSRASASVGLSYGAHSNLCVNQIARWGSAEQKAKYLPGLISGEHVGSLA 130 Query: 174 LTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTT---NQINGF 230 ++E GSD + A V+GG+ +NG K WI N +A+ L+++A+ T I F Sbjct: 131 MSETGAGSDVVSMKLKADSVQGGYVLNGTKFWITNGHYAETLVVYAKTDATGGSKGITAF 190 Query: 231 IVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGV-NSFQDTSKVLAVSRV 289 +++KD PG + K+G++ +++ ++ VPD + L V Q L RV Sbjct: 191 LIEKDMPGFSCGQKIEKMGMKGSPTSELVFEDCEVPDANVLGEVGKGVQVLMSGLDYERV 250 Query: 290 MVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCK 349 +++ +GI D Y++ER QFG + FQL Q K+ M +Q+ + + K Sbjct: 251 VLSGVQLGIMQACLDTVIPYVRERNQFGKRIGDFQLIQAKVADMYVALQSARAYTYAVAK 310 Query: 350 LYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEG 409 + GQ T A+ S A A + LGG G D+ V + D + + G Sbjct: 311 ACDKGQTTRFDAAGTILLSSENAFRVAGEAIQALGGAGYTTDWPVERYLRDAKLLDIGAG 370 Query: 410 TYDINTLVTGREVTG 424 T +I ++ GRE+ G Sbjct: 371 TNEIRRMLIGRELIG 385 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: 362 Number of extensions: 16 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: 386 Length adjustment: 31 Effective length of query: 405 Effective length of database: 355 Effective search space: 143775 Effective search space used: 143775 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