Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate Ga0059261_3648 Ga0059261_3648 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= SwissProt::Q9NKW1 (441 letters) >FitnessBrowser__Korea:Ga0059261_3648 Length = 298 Score = 254 bits (649), Expect = 3e-72 Identities = 141/296 (47%), Positives = 184/296 (62%), Gaps = 7/296 (2%) Query: 1 MALNFKDKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEI 60 MA+ F +V IVTGAGGG+G+ YALE A+RGA+VVVNDLGGS G G S AA KVVEEI Sbjct: 1 MAIRFDGRVAIVTGAGGGLGRAYALELARRGARVVVNDLGGSRDGTGHSDAAA-KVVEEI 59 Query: 61 KAAGGTAVANYDSVEDG---EKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLV 117 +A GG A+AN SV D E +V A + +GGV ILINNAG+LRD SF M D+ V Sbjct: 60 EALGGEALANGGSVTDYAQMEAMVAAAKEKWGGVHILINNAGVLRDKSFANMEPEDFRFV 119 Query: 118 YRVHAKGAYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLA 177 VH G+ +++A W+ MR++N+GRI+MT+S+ GLYGNFGQANYG+ K+ L GL+ TL Sbjct: 120 VDVHLNGSANVTKAVWSTMRDQNYGRILMTASSTGLYGNFGQANYGAAKLGLAGLTKTLY 179 Query: 178 QEGKSKNIHCNTIAPIAASRLTESVMPPEILEQMKPDYIVPLVLYLCHQDTTETGGVFEV 237 EG +I NTIAP A +R+TE + P + P+ + P L+L +D T + Sbjct: 180 LEGAKYDIRVNTIAPTAGTRMTEDIFPEAAFQAFTPESVAPAALFLVSED-APTNMIVGA 238 Query: 238 GAGWVSKVRLQRSAGVYM--KDLTPEKIKDNWAQIESFDNPSYPTSASESVSGILA 291 GAG + + GV + +DLTPE I NW+ I P S E I+A Sbjct: 239 GAGVFQAAYITLTPGVRLEGEDLTPEGIAANWSAITDRMGEIVPKSGGEQAMTIMA 294 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: 356 Number of extensions: 22 Number of successful extensions: 4 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: 298 Length adjustment: 29 Effective length of query: 412 Effective length of database: 269 Effective search space: 110828 Effective search space used: 110828 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