Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_041929725.1 MPE_RS16000 acyl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >NCBI__GCF_000015725.1:WP_041929725.1 Length = 391 Score = 234 bits (597), Expect = 4e-66 Identities = 132/375 (35%), Positives = 211/375 (56%), Gaps = 2/375 (0%) Query: 55 LTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI-KGYGCPGL 113 L+ +E+A+R + +AP + E + + I ++G +G+ G ++ + YG GL Sbjct: 17 LSEDERAVRDAAQAYCRDRLAPRVLEAFRHEKTDPAIFREMGELGLLGATLPEAYGGAGL 76 Query: 114 SITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWA 173 + + E+ RVD+ + + V SSL M+ I G+EAQK+KYLP LA+ + C+ Sbjct: 77 NHVCYGLVAREVERVDSGYRSMMSVQSSLVMVPIHAFGTEAQKQKYLPKLARGEWIGCFG 136 Query: 174 LTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTNQINGFIVK 233 LTEP++GSD L T A V+GG+ ++G K WI NS AD+ +++A++ QI GFI+ Sbjct: 137 LTEPNHGSDPGSLATRARAVQGGYVLSGAKMWITNSPIADVFVVWAKD-DGGQIRGFILD 195 Query: 234 KDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVLAVSRVMVAW 293 K GL+A + K+GLR G+I++ VF P+E+ P V + L +R +AW Sbjct: 196 KGMKGLEAPAVHGKVGLRASLTGEIVMDEVFCPEENAFPEVRGLKGPFTCLNSARYGIAW 255 Query: 294 QPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCKLYET 353 +G + + +Y+ +R QFG PLAA QL Q+KL M + RL ++ + Sbjct: 256 GALGAAEDCFHRARQYVLDRPQFGRPLAANQLIQKKLADMQTEITLGLQGCLRLGRMKDE 315 Query: 354 GQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEGTYDI 413 G S+ K K+ E A + R+++GGNGI +F VA+ +LE + TYEGT+D+ Sbjct: 316 GTAAVEITSIMKRNSCGKSLEIARMARDMMGGNGISDEFGVARHLVNLEVVNTYEGTHDV 375 Query: 414 NTLVTGREVTGIASF 428 + L+ GR +TGI +F Sbjct: 376 HALILGRAITGIQAF 390 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: 366 Number of extensions: 20 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: 391 Length adjustment: 31 Effective length of query: 405 Effective length of database: 360 Effective search space: 145800 Effective search space used: 145800 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