Align Methylglutaconyl-CoA hydratase, mitochondrial; AU-specific RNA-binding enoyl-CoA hydratase; AU-binding enoyl-CoA hydratase; muAUH; Itaconyl-CoA hydratase; EC 4.2.1.18; EC 4.2.1.56 (characterized)
to candidate BWI76_RS01365 BWI76_RS01365 multifunctional fatty acid oxidation complex subunit alpha
Query= SwissProt::Q9JLZ3 (314 letters) >FitnessBrowser__Koxy:BWI76_RS01365 Length = 729 Score = 112 bits (281), Expect = 2e-29 Identities = 66/190 (34%), Positives = 106/190 (55%), Gaps = 4/190 (2%) Query: 56 HLEEENRGIVVLGINRAYGKNALSKNLLKMLSKAVDALKSDKKVRTIIIRSEVPGIFCAG 115 +L+ GI L + N L + L +A+D L+ K ++ +++RSE F G Sbjct: 9 YLDWREDGIAELVFDAPGSVNKLDTATVASLGEALDVLEKQKDLKGLLLRSE-KAAFIVG 67 Query: 116 ADLKERAKMH---SSEVGPFVSKIRSVINDIANLPVPTIAAIDGLALGGGLELALACDIR 172 AD+ E + ++ ++ SV N + +LPVPTI+A++G ALGGG E LA D R Sbjct: 68 ADITEFLSLFLVPEEQLSQWLHFANSVFNRLEDLPVPTISAVNGYALGGGCECVLATDYR 127 Query: 173 VAASSAKMGLVETKLAIIPGGGGTQRLPRAIGMSLAKELIFSARVLDGQEAKAVGLISHV 232 +A ++GL ETKL I+PG GG+ R+PR +G A E+I + + L ++A +GL+ V Sbjct: 128 LATPDLRIGLPETKLGIMPGFGGSVRMPRMLGADSALEIIAAGKDLGAEQALKIGLVDGV 187 Query: 233 LEQNQEGDAA 242 ++ + D A Sbjct: 188 VKHEKLIDGA 197 Lambda K H 0.318 0.135 0.377 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: 410 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: 314 Length of database: 729 Length adjustment: 33 Effective length of query: 281 Effective length of database: 696 Effective search space: 195576 Effective search space used: 195576 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