Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate WP_046008144.1 OLEAN_RS03865 short chain dehydrogenase
Query= SwissProt::Q9NKW1 (441 letters) >NCBI__GCF_000967895.1:WP_046008144.1 Length = 252 Score = 103 bits (257), Expect = 6e-27 Identities = 77/252 (30%), Positives = 125/252 (49%), Gaps = 34/252 (13%) Query: 4 NFKDKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKAA 63 NF DKVV++TGAG GIG+ AL FA++GA VVV D+ + ++ I A Sbjct: 3 NFADKVVLITGAGNGIGRATALAFAQQGASVVVADINRAD---------GEETAAMITQA 53 Query: 64 GGTA---VANYDSVEDGEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGD---WDLV 117 GG A + + +D + +V+ ++++G +DI NNAGI ++ K+ DGD +D + Sbjct: 54 GGIATFMLCDVTKDQDVQSMVEGTVETYGKLDIAFNNAGI--EIEQSKLADGDEATYDKI 111 Query: 118 YRVHAKGAYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLA 177 V+ KG ++ + + +++ I+ T+S AGL + Y + K A++GL+ + A Sbjct: 112 MDVNVKGVWRCMKYQIPALLKQSTSAIVNTASIAGLGAAPKMSIYSASKHAVIGLTKSAA 171 Query: 178 QEGKSKNIHCNTIAPIAAS-----RLTESVMPPEILEQMK----------PDYIVPLVLY 222 E K + N I P R T++ P+ + +K PD + VLY Sbjct: 172 VEYGKKGLRVNAICPAVIDTEMFRRATQN--DPQKEQYVKSLHPVGRIGQPDEVAAAVLY 229 Query: 223 LCHQDTTETGGV 234 LC T GV Sbjct: 230 LCSDLAGFTTGV 241 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: 226 Number of extensions: 12 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: 252 Length adjustment: 28 Effective length of query: 413 Effective length of database: 224 Effective search space: 92512 Effective search space used: 92512 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