Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_065397571.1 BBI00_RS04080 acyl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >NCBI__GCF_001684965.1:WP_065397571.1 Length = 392 Score = 220 bits (560), Expect = 7e-62 Identities = 134/392 (34%), Positives = 211/392 (53%), Gaps = 4/392 (1%) Query: 40 TFPPCTS--DYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGA 97 ++ P TS DYY + LLT E + IR+ VR+ +E V P + + + + +LG Sbjct: 2 SYYPLTSIPDYYGIDALLTEEHKLIRQSVRDWVESFVMPQIDQAAQNHTDLPGLMRELGK 61 Query: 98 MGVAGGSIK-GYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQK 156 +G G I YG GL + + E+ R D++ + V SSL M I GSE QK Sbjct: 62 IGALGPYIPVEYGGSGLDQISYGLIMQELERGDSAVRSAASVQSSLVMFPINEFGSEEQK 121 Query: 157 EKYLPSLAQLNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLI 216 +KYLP LA + + LTEP++GSD + T + + +NG K WI NS D+ + Sbjct: 122 KKYLPKLAAGEMIGSFGLTEPNHGSDPGSMETYFKDMGDHYLLNGAKMWITNSPLCDIAV 181 Query: 217 IFARNTTTNQINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNS 276 ++A+N ++ G IV++ G + NK LR + G+++ +V VP E+ LPGV Sbjct: 182 VWAKNEE-GKVQGLIVERGMEGFTTPETHNKWSLRASKTGELVFNDVKVPKENLLPGVTG 240 Query: 277 FQDTSKVLAVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGN 336 + L +R ++W IG ++ Y +Y KERKQFG P+ ++QL Q+KL + L Sbjct: 241 LKGPLSCLNSARYGISWGVIGAAIDCYCTAVQYSKERKQFGKPIGSYQLQQKKLAEFLTE 300 Query: 337 VQAMFLMGWRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAK 396 + L+ +L L + TP Q S+ K A + A R++LGG GI+ +F + + Sbjct: 301 ITKAQLLCLQLGNLKNDHKATPAQISMAKRNNVKMAIDIARESRQILGGMGIMGEFPMMR 360 Query: 397 AFCDLEPIYTYEGTYDINTLVTGREVTGIASF 428 +LE + TYEGT+D++ L+TG ++TGI +F Sbjct: 361 HAANLESVITYEGTHDVHLLITGLDITGINAF 392 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: 381 Number of extensions: 10 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: 392 Length adjustment: 31 Effective length of query: 405 Effective length of database: 361 Effective search space: 146205 Effective search space used: 146205 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