Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate 5210113 Shew_2557 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= SwissProt::Q9NKW1 (441 letters) >FitnessBrowser__PV4:5210113 Length = 306 Score = 152 bits (384), Expect = 1e-41 Identities = 93/292 (31%), Positives = 147/292 (50%), Gaps = 9/292 (3%) Query: 3 LNFKDKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLG-GSHTGQGSSSKAADKVVEEIK 61 + F ++V +VTGAG G+G+ YA+ A+RGA++ + D G G Q + +K + Sbjct: 2 MRFDEQVAVVTGAGAGLGRAYAIALAERGARLAIIDSGSGDSRCQSYAGAGLNKTARTLA 61 Query: 62 AAGGTAVANYDSVEDGEKI---VQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVY 118 G ++ V D + + ++T + +G +DI INNAGI VSF ++ W Sbjct: 62 ELGADCLSFQLDVTDSQALKSAIETVLKRWGRIDIAINNAGIHTPVSFDSLSFEQWQRQL 121 Query: 119 RVHAKGAYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQ 178 V G++ L++ W M+ +N+GRI+MT+ A+GLYG+ + Y + KMALVGL N+LA+ Sbjct: 122 DVDLNGSFHLTKLVWPQMKRQNYGRIVMTAGASGLYGDMHETPYSTSKMALVGLVNSLAK 181 Query: 179 EGKSKNIHCNTIAPIAASRLTESVMPPEILEQMKPDYIVPLVLYLCHQDTTETGGVFEVG 238 EG+ NI NT+ P A + +T + P + + +LYLC T +G Sbjct: 182 EGRDYNISVNTLVPEALTAMTAHHLSPLVKPLFSTSSVNATLLYLC-SSTACSGQHLLAA 240 Query: 239 AGWVSK---VRLQRSAGVYMKDLTPEKIKDNWAQIESFDNPSYPTSASESVS 287 AG VS V Q + PE I W ++ + S E V+ Sbjct: 241 AGSVSHGMFVEFQ-PLRIVEDGCKPEVIAQRWDELYRAQPCHFHESGEEQVT 291 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: 298 Number of extensions: 14 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: 306 Length adjustment: 30 Effective length of query: 411 Effective length of database: 276 Effective search space: 113436 Effective search space used: 113436 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