Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate SMc03878 SMc03878 acetoacetyl-CoA reductase
Query= SwissProt::Q9NKW1 (441 letters) >FitnessBrowser__Smeli:SMc03878 Length = 241 Score = 112 bits (279), Expect = 2e-29 Identities = 77/258 (29%), Positives = 116/258 (44%), Gaps = 32/258 (12%) Query: 8 KVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKAAGGTA 67 +V +VTG GIG + G KV N G + ++ V + Sbjct: 3 RVALVTGGSRGIGAAICVALKAAGYKVAANYAGNDERAKAFEQESGIPVYK-------WD 55 Query: 68 VANYDSVEDGEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYRVHAKGAYK 127 V++Y + DG V+ + G VDIL+NNAGI RD F KMT W V + G + Sbjct: 56 VSSYQACVDGIARVEADL---GPVDILVNNAGITRDAMFHKMTPEQWGEVIGTNLTGVFN 112 Query: 128 LSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQEGKSKNIHC 187 ++ W+ MR++ FGRI+ SS G G GQ NY + K +GL+ LAQEG +K I Sbjct: 113 MTHPLWSGMRDRGFGRIVNISSINGQKGQMGQVNYSAAKAGDLGLTKALAQEGAAKGITV 172 Query: 188 NTIAP-----IAASRLTESVMPPEILEQM------KPDYIVPLVLYLCHQDTTETGGVFE 236 N I P + E V+ I+ Q+ +P+ + V++L D Sbjct: 173 NAICPGYIGTEMVRAVPEKVLNERIIPQIPVGRLGEPEEVARCVVFLASDD--------- 223 Query: 237 VGAGWVSKVRLQRSAGVY 254 AG+++ + + G Y Sbjct: 224 --AGFITGSTISANGGQY 239 Lambda K H 0.313 0.131 0.371 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: 223 Number of extensions: 12 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: 441 Length of database: 241 Length adjustment: 28 Effective length of query: 413 Effective length of database: 213 Effective search space: 87969 Effective search space used: 87969 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 48 (23.1 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