Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_029134232.1 A3GO_RS0115815 acyl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >NCBI__GCF_000428045.1:WP_029134232.1 Length = 397 Score = 248 bits (634), Expect = 2e-70 Identities = 143/376 (38%), Positives = 210/376 (55%), Gaps = 1/376 (0%) Query: 55 LTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSIKGYGCPGLS 114 LT EE+ +R ++ ++++ P + E F I ++G +G+ G +I GY C GL+ Sbjct: 23 LTEEERMVRDTAQKYCQEQLMPRVLEANRHEHFDREIMNEMGELGLLGVTIDGYDCAGLN 82 Query: 115 ITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWAL 174 + + E+ RVD+ + + V SSL M I G+E Q+EKYLP LA V C+ L Sbjct: 83 YVSYGLIAREVERVDSGYRSAMSVQSSLVMHPIYAYGTEEQREKYLPKLATGELVGCFGL 142 Query: 175 TEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTNQINGFIVKK 234 TEPD+GSD +G+ T A V+GG+ ++G K WI NS AD+ I++A++ I GFI++K Sbjct: 143 TEPDHGSDPAGMKTRARTVDGGYSLSGSKMWITNSPIADVFIVWAKD-DEGVIRGFILEK 201 Query: 235 DAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVLAVSRVMVAWQ 294 GL A KI K LR G+I++ VFVP E+ LP V L +R +AW Sbjct: 202 GMKGLSAPKIEGKFSLRASITGEIVMDEVFVPAENLLPNVKGLAGPFGCLNRARYGIAWG 261 Query: 295 PIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCKLYETG 354 +G + + Y +RKQFG PLAA QL Q KL M + +L +L++ G Sbjct: 262 VLGAAEDCWHRALTYTLDRKQFGRPLAANQLIQLKLANMQTEITLGLQGCLQLGRLFDAG 321 Query: 355 QMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEGTYDIN 414 Q P SL K + KA + A + R++ GGNGI +F V + +LE + TYEGT+D++ Sbjct: 322 QAAPEAISLMKRNNAGKALDIARIARDMHGGNGISDEFHVIRHAMNLEAVNTYEGTHDVH 381 Query: 415 TLVTGREVTGIASFKP 430 L+ GR TGI +F P Sbjct: 382 ALILGRAQTGIQAFAP 397 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: 356 Number of extensions: 16 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: 397 Length adjustment: 31 Effective length of query: 405 Effective length of database: 366 Effective search space: 148230 Effective search space used: 148230 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 Apr 09 2024. 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