Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate GFF2715 PS417_13850 acyl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >FitnessBrowser__WCS417:GFF2715 Length = 375 Score = 158 bits (400), Expect = 2e-43 Identities = 111/375 (29%), Positives = 182/375 (48%), Gaps = 6/375 (1%) Query: 54 LLTPEEQA-IRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI-KGYGCP 111 +L EEQ I R+ ++ + P E+ + FP ++ +G G + + +G Sbjct: 1 MLPNEEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGC 60 Query: 112 GLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVAC 171 A A+A EIA D +CST + VH+S+G + + G++ QKE++L LA + Sbjct: 61 DTGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPVLKFGNDQQKEQFLKPLASGAMLGA 120 Query: 172 WALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTT---NQIN 228 +ALTEP GSDAS L T A + +NG K++I + A ++I+FA I+ Sbjct: 121 FALTEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPAAGKRGIS 180 Query: 229 GFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRL-PGVNSFQDTSKVLAVS 287 FIV D+PG ++ +K+G IL ++V VP +RL ++ L Sbjct: 181 AFIVPTDSPGYSVARVEDKLGQHASDTCQILFEDVKVPVANRLGEEGEGYKIALANLEGG 240 Query: 288 RVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRL 347 RV +A Q +G++ ++ Y +ER+ FG P+ Q +L M + M Sbjct: 241 RVGIASQAVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYA 300 Query: 348 CKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTY 407 L ++G+ +AS+ K + S A + S + LGG G L+DF + + + D+ Y Sbjct: 301 AALRDSGKPALVEASMAKLFASEMAEKVCSAALQTLGGYGYLSDFPLERIYRDVRVCQIY 360 Query: 408 EGTYDINTLVTGREV 422 EGT DI +V R + Sbjct: 361 EGTSDIQRMVISRNL 375 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: 314 Number of extensions: 15 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: 375 Length adjustment: 31 Effective length of query: 405 Effective length of database: 344 Effective search space: 139320 Effective search space used: 139320 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 17 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