Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate WP_004514044.1 GMET_RS10390 3-oxoacyl-[acyl-carrier-protein] reductase
Query= SwissProt::Q9NKW1 (441 letters) >NCBI__GCF_000012925.1:WP_004514044.1 Length = 247 Score = 138 bits (347), Expect = 2e-37 Identities = 84/252 (33%), Positives = 128/252 (50%), Gaps = 22/252 (8%) Query: 3 LNFKDKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKA 62 ++ K K IVTGA GIG AL+ AK GA V +N S+ A+ + EI+ Sbjct: 1 MDLKGKNAIVTGASLGIGSAIALDLAKSGANVAIN--------YRKHSEEANAICAEIQK 52 Query: 63 AGGTAVA---NYDSVEDGEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYR 119 G A+A + S +D + +V FG VDIL+NNAG+ RD KMT+ WD Sbjct: 53 MGQKAIAVQADVASFKDAQAMVDKVAAEFGSVDILVNNAGVNRDAVIWKMTEEQWDECLA 112 Query: 120 VHAKGAYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQE 179 ++ KG + RA M+E+ G+I+ +S G+ G FGQ NY + K ++GL+ LA+E Sbjct: 113 INLKGYFNYCRAVAPLMKEQGSGKIVNVTSINGMRGKFGQTNYSAAKAGIIGLTKALARE 172 Query: 180 GKSKNIHCNTIAPIAASRLTESVMPPEILEQM----------KPDYIVPLVLYLCHQDTT 229 N++CN IAP + +P ++ ++ KP+ + LV +LC + + Sbjct: 173 LAKSNVNCNAIAPGLIETEMMAALPEDVKQKSLADIVLGRMGKPEEVAWLVTFLCSEKSR 232 Query: 230 E-TGGVFEVGAG 240 TG +V G Sbjct: 233 HITGECIKVDGG 244 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: 241 Number of extensions: 14 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: 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