Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate WP_097068497.1 CRO22_RS02400 beta-ketoacyl-ACP reductase
Query= SwissProt::Q9NKW1 (441 letters) >NCBI__GCF_900217815.1:WP_097068497.1 Length = 240 Score = 125 bits (314), Expect = 1e-33 Identities = 81/244 (33%), Positives = 114/244 (46%), Gaps = 21/244 (8%) Query: 8 KVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKAAGGTA 67 +V +VTG GIG ++ + G VV N G + + K V+ + Sbjct: 3 RVALVTGGTRGIGAAISMALKEAGYTVVANYAGNDEAAREFTHVTGIKTVK-------WS 55 Query: 68 VANYDSVEDGEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYRVHAKGAYK 127 VA+Y EDG + ++ D G +D+L+NNAGI RD F KM+ WD V + G + Sbjct: 56 VADYTGCEDGIRQIE---DEVGPIDVLVNNAGITRDAPFHKMSREQWDQVIGTNLNGLFN 112 Query: 128 LSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQEGKSKNIHC 187 ++ WN MRE+ FGRII SS G G FGQ NY + K +G + LAQEG I Sbjct: 113 MTHPLWNGMRERKFGRIINISSINGQKGQFGQVNYSAAKAGDIGFTKALAQEGARSGITV 172 Query: 188 NTIAPIAASRLTESVMPPEILEQM----------KPDYIVPLVLYLC-HQDTTETGGVFE 236 N I P + +P ++ E + +PD I V++L Q TG F Sbjct: 173 NAICPGYIATEMVMAVPEKVRESIIATIPVGRLGEPDEIARTVVFLASDQAGFITGATFT 232 Query: 237 VGAG 240 V G Sbjct: 233 VNGG 236 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: 230 Number of extensions: 11 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: 240 Length adjustment: 28 Effective length of query: 413 Effective length of database: 212 Effective search space: 87556 Effective search space used: 87556 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 24 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