Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate WP_058857527.1 AS188_RS02565 SDR family oxidoreductase
Query= SwissProt::Q9NKW1 (441 letters) >NCBI__GCF_001482365.1:WP_058857527.1 Length = 316 Score = 149 bits (376), Expect = 1e-40 Identities = 82/199 (41%), Positives = 117/199 (58%), Gaps = 13/199 (6%) Query: 8 KVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKAAGGTA 67 KV +VTG+G G+G YA E A++GA VV+ND+ + A+ V I +GG A Sbjct: 11 KVAVVTGSGQGLGLAYAQELARQGAAVVINDV---------DRQTAENAVATITRSGGRA 61 Query: 68 VA---NYDSVEDGEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYRVHAKG 124 VA S E +V A+++FG +D+L+ NAG+LRD S KMTD D+DLV +VH +G Sbjct: 62 VAVVAPVGSTETATALVDGAVEAFGRLDVLVTNAGVLRDKSLLKMTDEDFDLVIQVHLRG 121 Query: 125 AYKLSRAAWNHMREKNF-GRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQEGKSK 183 + R A+ + ++ GRII S G YGNFGQ NY + K +VG+ T A E K Sbjct: 122 TFTCVREAYRYFKDNGVAGRIITIGSPTGQYGNFGQTNYAAAKAGIVGMVRTWALEMKKA 181 Query: 184 NIHCNTIAPIAASRLTESV 202 + N + P+AA+ +TE+V Sbjct: 182 GVTANAVIPVAATAMTETV 200 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: 316 Number of extensions: 17 Number of successful extensions: 3 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: 316 Length adjustment: 30 Effective length of query: 411 Effective length of database: 286 Effective search space: 117546 Effective search space used: 117546 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: 50 (23.9 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