Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate WP_009544717.1 CCE_RS12275 7-alpha-hydroxysteroid dehydrogenase
Query= SwissProt::Q9NKW1 (441 letters) >NCBI__GCF_000017845.1:WP_009544717.1 Length = 255 Score = 94.7 bits (234), Expect = 3e-24 Identities = 82/254 (32%), Positives = 121/254 (47%), Gaps = 25/254 (9%) Query: 7 DKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKAAGGT 66 D V I+TGAG GIG+ A FA+ GA VVV+DL + A+ V E+IK+ GG Sbjct: 11 DHVAIITGAGAGIGRGIAELFAQAGAAVVVSDL---------KLETAEIVAEKIKSQGGK 61 Query: 67 AVA---NYDSVEDGEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYRVHAK 123 A+A + + E E +V + + +FG + IL+NNAG F D + Y+++ Sbjct: 62 AIAVSCDVTTNEALENLVNSTLTAFGKITILVNNAGGGGPKPFDMPMD-TFIWAYQLNVF 120 Query: 124 GAYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQEGKSK 183 + L + H+ G I+ SS +G N A+YGS K A+ L+ +A + K Sbjct: 121 SLFHLCQLCVPHIEAAGGGSILNISSMSGDNKNSNMASYGSSKAAVSHLTRNIAFDLGPK 180 Query: 184 NIHCNTIAPIA-ASRLTESVMPPEILEQM----------KPDYIVPLVLYLCHQDTT-ET 231 NI N IAP A + SV+ P+I M P I L+LC + + Sbjct: 181 NIRVNAIAPGAIKTDALASVLTPDIETAMLKHTPLARLGNPKDIAYAALFLCSPAASWIS 240 Query: 232 GGVFEVGAGWVSKV 245 G V V G V ++ Sbjct: 241 GQVLTVSGGGVQEL 254 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: 258 Number of extensions: 16 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: 255 Length adjustment: 28 Effective length of query: 413 Effective length of database: 227 Effective search space: 93751 Effective search space used: 93751 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 Apr 09 2024. 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