Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate WP_084056375.1 B9A12_RS03625 3-oxoacyl-[acyl-carrier-protein] reductase
Query= SwissProt::Q9NKW1 (441 letters) >NCBI__GCF_900176285.1:WP_084056375.1 Length = 247 Score = 128 bits (321), Expect = 2e-34 Identities = 86/248 (34%), Positives = 125/248 (50%), Gaps = 22/248 (8%) Query: 7 DKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKAAGGT 66 +KVV+VTGA GIG+ AL FA+ VVVN G +AA + ++ GG Sbjct: 4 NKVVLVTGASRGIGRAVALAFAEPETTVVVNYRSGQ--------EAAQETARAVEKQGGK 55 Query: 67 AVANYDSVEDGE---KIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYRVHAK 123 AV V D + K + +DS G +D+L+NNAG+ RD F ++ DWDLV V+ K Sbjct: 56 AVLCPFDVADPDAVKKAFKEVVDSLGRLDVLVNNAGMTRDNVFPRLKTEDWDLVLDVNLK 115 Query: 124 GAYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQEGKSK 183 G + S+AA M ++ GRII +S G GN GQ NY + K ++GL+ +LA+E S+ Sbjct: 116 GIFLCSQAAVRPMLKQRHGRIINITSVVGFTGNPGQCNYAAAKAGIMGLTRSLARELISR 175 Query: 184 NIHCNTIAPIAASRLTESVMPPEILEQM----------KPDYIVPLVLYLCHQDTTE-TG 232 NI N +AP +P + E + +P+ + V +L + TG Sbjct: 176 NITVNAVAPGYIETEMTHALPEKAREALVAQIPAGRTGRPEEVAAAVRFLASEQAAYITG 235 Query: 233 GVFEVGAG 240 V V G Sbjct: 236 QVLHVNGG 243 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: 216 Number of extensions: 10 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: 441 Length of database: 247 Length adjustment: 28 Effective length of query: 413 Effective length of database: 219 Effective search space: 90447 Effective search space used: 90447 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: 49 (23.5 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