Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate GFF4186 PS417_21440 3-ketoacyl-ACP reductase
Query= SwissProt::Q9NKW1 (441 letters) >FitnessBrowser__WCS417:GFF4186 Length = 247 Score = 109 bits (273), Expect = 8e-29 Identities = 81/260 (31%), Positives = 123/260 (47%), Gaps = 21/260 (8%) Query: 3 LNFKDKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKA 62 ++ + KV +VTGA GIG+ ALE ++GA V+ G +S+ A+++ +K Sbjct: 1 MSLQGKVALVTGASRGIGQAIALELGRQGAVVI---------GTATSASGAERIAATLKE 51 Query: 63 AG--GTAVA-NYDSVEDGEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYR 119 G GT + N S E ++ FG IL+NNAGI RD +M D +W V Sbjct: 52 NGVQGTGLELNVTSDESVAAVLAEITAQFGAPAILVNNAGITRDNLMMRMKDDEWYDVVD 111 Query: 120 VHAKGAYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQE 179 + ++LS+ M + +GRII S G GN GQ NY S K L G S LA+E Sbjct: 112 TNLNSLFRLSKGVLRGMTKARWGRIINIGSVVGAMGNAGQVNYASAKAGLEGFSRALARE 171 Query: 180 GKSKNIHCNTIAPIAASRLTESVMPPEILEQMKPDYIVPLVLYLCHQDTTETGGVFEV-- 237 S++I N++AP ++ M E+ E + + + L Q E V Sbjct: 172 VGSRSITVNSVAP----GFIDTDMTRELPEAQREALLTQIPLGRLGQ-AQEIANVVTFLA 226 Query: 238 --GAGWVSKVRLQRSAGVYM 255 GA +V+ + + G+YM Sbjct: 227 SDGAAYVTGATIPVNGGMYM 246 Score = 29.6 bits (65), Expect = 1e-04 Identities = 22/101 (21%), Positives = 45/101 (44%), Gaps = 7/101 (6%) Query: 328 GYNASKIFTTIQGNIGAKGAELVKKINGIY----LINIKKGTNTQAWALDLKNGSGS--- 380 G + + T GA+ K NG+ +N+ + A ++ G+ Sbjct: 26 GRQGAVVIGTATSASGAERIAATLKENGVQGTGLELNVTSDESVAAVLAEITAQFGAPAI 85 Query: 381 IVVGAGSTKPNVTITVSDEDFVDIMTGKLNAQSAFTKGKLK 421 +V AG T+ N+ + + D+++ D++ LN+ +KG L+ Sbjct: 86 LVNNAGITRDNLMMRMKDDEWYDVVDTNLNSLFRLSKGVLR 126 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: 250 Number of extensions: 11 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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 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