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 6935814 Sama_0032 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)
Query= SwissProt::Q9JLZ3 (314 letters) >FitnessBrowser__SB2B:6935814 Length = 716 Score = 103 bits (257), Expect = 1e-26 Identities = 69/174 (39%), Positives = 94/174 (54%), Gaps = 7/174 (4%) Query: 64 IVVLGINRAYGKNALSKNLLKMLSKAVDALK-SDKKVRTIIIRSEVPGIFCAGADLKERA 122 I L N N + L L+ A+D LK SD K + + F GAD+ E Sbjct: 17 IARLCFNAPGSVNKFDRETLASLNAALDVLKDSDAKAAVLTSGKDT---FIVGADITEFL 73 Query: 123 KMHSSE---VGPFVSKIRSVINDIANLPVPTIAAIDGLALGGGLELALACDIRVAASSAK 179 + + E + ++++ V N + +LP PT++AI G ALGGG E LA D RVA +SAK Sbjct: 74 ALFAEEDAKLMEWIAQANVVFNKLEDLPFPTVSAIKGFALGGGCEAILATDFRVADTSAK 133 Query: 180 MGLVETKLAIIPGGGGTQRLPRAIGMSLAKELIFSARVLDGQEAKAVGLISHVL 233 +GL ETKL +IPG GGT RLPR IG A E I + + ++A VG I V+ Sbjct: 134 IGLPETKLGLIPGFGGTVRLPRLIGADNALEWITTGKDQRPEDALKVGAIDAVV 187 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: 382 Number of extensions: 21 Number of successful extensions: 1 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: 716 Length adjustment: 33 Effective length of query: 281 Effective length of database: 683 Effective search space: 191923 Effective search space used: 191923 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