Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate BWI76_RS20455 BWI76_RS20455 multifunctional fatty acid oxidation complex subunit alpha
Query= BRENDA::F4JML5 (301 letters) >FitnessBrowser__Koxy:BWI76_RS20455 Length = 714 Score = 113 bits (282), Expect = 1e-29 Identities = 73/201 (36%), Positives = 102/201 (50%), Gaps = 4/201 (1%) Query: 41 EFVKLNRLSGSDSGIIEVNLDRPVTK-NAINKEMLKSLQNAFESIHQDNSARVVMIRSLV 99 E V L I + +D P K N + E ++ I + R + S Sbjct: 2 ETVSAFTLEVRPDNIAVITIDAPGEKMNTLKAEFASEVRGIIRQIRDNKELRGAVFISAK 61 Query: 100 PGVFCAGADLKE-RRTMSPSEVHTYVNSLRYMFSFIEALSIPTIAAIEGAALGGGLEMAL 158 P F AGAD+ R S E + + + I LSIP IAAI GA LGGGLE+AL Sbjct: 62 PDNFIAGADINMIARCHSAQEAEALARQGQQIMAEIHGLSIPVIAAIHGACLGGGLELAL 121 Query: 159 ACDLRICGEN--AVFGLPETGLAIIPGAGGTQRLSRLVGRSVSKELIFTGRKIDAIEAAN 216 AC R+C ++ GLPE L ++PG+GGTQRL RL+G S + E+I TG+++ +A Sbjct: 122 ACHGRVCSDDDKTRLGLPEVQLGLLPGSGGTQRLPRLIGVSGALEMILTGKQLRPRQALK 181 Query: 217 KGLVNICVTAGEAHEKAIEMA 237 GLV+ V + A+E+A Sbjct: 182 AGLVDEVVAQTILLQTAVELA 202 Lambda K H 0.318 0.134 0.373 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: 399 Number of extensions: 15 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: 301 Length of database: 714 Length adjustment: 33 Effective length of query: 268 Effective length of database: 681 Effective search space: 182508 Effective search space used: 182508 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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