Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate Echvi_2990 Echvi_2990 Acyl-CoA dehydrogenases
Query= BRENDA::Q96329 (436 letters) >FitnessBrowser__Cola:Echvi_2990 Length = 402 Score = 256 bits (654), Expect = 9e-73 Identities = 145/384 (37%), Positives = 214/384 (55%), Gaps = 2/384 (0%) Query: 47 DYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSIK 106 D+Y +DL T E IR+ +R+ ++KEV+P + E+ + A FP I PK G +G G I Sbjct: 20 DFYGLDDLFTAEHLLIRQSLRDFVKKEVSPYIEEWAQDAHFPSEIVPKFGEIGAFGPQIP 79 Query: 107 G-YGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQ 165 YG GL + + EI R D+ + + V SL M I GSE Q+EK+LP LA Sbjct: 80 AKYGGGGLDYISYGLIMQEIERGDSGMRSTVSVQGSLVMYPIHAFGSEEQREKFLPKLAS 139 Query: 166 LNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTN 225 + C+ LTEPD+GS+ GL T+ + +NG K WI N+ AD+ +++A++ Sbjct: 140 GEWLGCFGLTEPDHGSNPGGLTTSFKDNGDHYLLNGAKMWISNAPEADIAVVWAKDEN-G 198 Query: 226 QINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVLA 285 +I+G IV++ G +K LR G+++ NV VP E+ LPG + L Sbjct: 199 RIHGLIVERGMEGFTTPTTHHKWSLRASCTGELVFDNVKVPKENLLPGKSGLSAPLMCLD 258 Query: 286 VSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGW 345 +R +AW IG +M Y+ RY ER QF P+AAFQL Q+KL +ML + L+ W Sbjct: 259 AARYGIAWGAIGAAMDCYESAKRYAMERIQFDKPIAAFQLVQKKLAEMLTEITKAQLLAW 318 Query: 346 RLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIY 405 RL L + G+ T Q S+ K + A E A R++ GG GI D+ + + +LE + Sbjct: 319 RLGTLKDQGKATSAQISMAKRNNVAMALEIAREARQIHGGMGITGDYPIMRHMMNLESVI 378 Query: 406 TYEGTYDINTLVTGREVTGIASFK 429 TYEGT+DI+ L+ G+E+TGI +FK Sbjct: 379 TYEGTHDIHLLILGQEITGIPAFK 402 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: 387 Number of extensions: 14 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: 402 Length adjustment: 32 Effective length of query: 404 Effective length of database: 370 Effective search space: 149480 Effective search space used: 149480 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