Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_003939770.1 C1M55_RS24690 acyl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >NCBI__GCF_002893965.1:WP_003939770.1 Length = 390 Score = 233 bits (594), Expect = 8e-66 Identities = 136/394 (34%), Positives = 212/394 (53%), Gaps = 9/394 (2%) Query: 40 TFPPCTSDYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFH-ITPKLGAM 98 T P S+ + + LL EE AIR VR+ ++ + P + E++E A P + +LGA+ Sbjct: 2 TTPQSLSELFAIDTLLDAEEIAIRDTVRKMVDDRIRPHVGEWFEAAALPARELAKELGAL 61 Query: 99 GVAGGSIKGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEK 158 GV G ++GYGC G+S TA +A E+ VD+ + + V SL M I GSE QKE+ Sbjct: 62 GVLGMHLEGYGCAGMSATAYGLACQELEAVDSGIRSLVSVQGSLAMFAIHHNGSEEQKEE 121 Query: 159 YLPSLAQLNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIF 218 +LP +A + C+ LTEPD GS+ G+ T A + W +NG K WI N + AD+ +++ Sbjct: 122 WLPRMAAGEAIGCFGLTEPDFGSNPGGMRTNAKRDGDDWILNGTKMWITNGSIADVAVVW 181 Query: 219 ARNTTTNQINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQ 278 AR T + + GF+V D PG A +I NK+ LR +++L++V +P LP Sbjct: 182 AR--TDDGVRGFVVPTDTPGFSAPEIKNKMSLRASVTSELVLEDVRLPASAMLPKARGLS 239 Query: 279 DTSKVLAVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQ 338 L +R + + +G + + Y ++RK F LAA+Q+ Q K+ M + Sbjct: 240 GPLGCLNEARFGIIFGAMGAARDCLETAISYARDRKVFDKSLAAYQITQAKIADMAVELG 299 Query: 339 AMFLMGWRLCKLYETGQMTPGQASLGKAWISSKARETASLGRE---LLGGNGILADFLVA 395 L+ L +L + G + P Q S GK + RE + RE +LG NGI ++ V Sbjct: 300 KGQLLAIHLGRLKDAGTVRPEQVSTGKL---NNVREAIKIARECRTILGANGITLEYPVI 356 Query: 396 KAFCDLEPIYTYEGTYDINTLVTGREVTGIASFK 429 + +LE + TYEGT +++ LV GR +TG +F+ Sbjct: 357 RHANNLESVLTYEGTSEVHQLVIGRALTGEEAFR 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: 333 Number of extensions: 13 Number of successful extensions: 2 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: 390 Length adjustment: 31 Effective length of query: 405 Effective length of database: 359 Effective search space: 145395 Effective search space used: 145395 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