Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_036834462.1 N784_RS09610 acyl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >NCBI__GCF_000775615.1:WP_036834462.1 Length = 379 Score = 182 bits (462), Expect = 2e-50 Identities = 123/372 (33%), Positives = 187/372 (50%), Gaps = 5/372 (1%) Query: 56 TPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI-KGYGCPGLS 114 T E+ +RK VR+ KEVAPI+ + ++ FP + ++G +G+ G I + YG G+ Sbjct: 6 TEEQHMMRKMVRDFANKEVAPIVQQMDQEDYFPIELIKQMGDIGLMGIPIPEQYGGSGMD 65 Query: 115 ITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWAL 174 + IA E+++V AS + VH+S+G I G+E QK+KY+P LA + +AL Sbjct: 66 FPSYIIAIHELSKVSASVGVILSVHTSVGTNPILYFGTEEQKQKYIPKLASGEFLGAFAL 125 Query: 175 TEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFAR---NTTTNQINGFI 231 TEP GSDA L A + + +NG K +I N AD I+FAR N + FI Sbjct: 126 TEPGAGSDAGSLKMKAVREGEEYILNGSKVFITNGEKADTFIVFARTDSNAGNKGVTAFI 185 Query: 232 VKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRL-PGVNSFQDTSKVLAVSRVM 290 V+++ G + K +K+G+ + N +P E RL F+ L V R+ Sbjct: 186 VERNTSGFEIGKKEHKMGMNGSGTVTLNFDNCRIPAEQRLGEEGEGFKIAMANLNVGRIG 245 Query: 291 VAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCKL 350 +A Q +GI+ + Y KER+QFG P+A Q KL M +V+A L+ + L Sbjct: 246 IAAQSLGIAEAALEHAVGYAKEREQFGKPIARNQGISFKLADMATSVEAAKLLTYHAANL 305 Query: 351 YETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEGT 410 G +AS+ K S A A+ ++ GG G D+ V + F D + YEGT Sbjct: 306 RHQGIDCGKEASMAKMTASQAAMNVATEAIQVYGGYGYTEDYPVERFFRDAKVCEIYEGT 365 Query: 411 YDINTLVTGREV 422 +I +V G+ V Sbjct: 366 NEIQRVVIGKHV 377 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: 337 Number of extensions: 15 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