Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate WP_015798850.1 AFER_RS07460 KR domain-containing protein
Query= SwissProt::Q9NKW1 (441 letters) >NCBI__GCF_000023265.1:WP_015798850.1 Length = 309 Score = 189 bits (481), Expect = 8e-53 Identities = 116/283 (40%), Positives = 169/283 (59%), Gaps = 26/283 (9%) Query: 8 KVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKAAGGTA 67 +VVIVTGAG GIG+ +AL FA++GA+VVVNDLG G GSS+ A +VV+ I++ GG A Sbjct: 8 RVVIVTGAGRGIGRAHALAFAEQGARVVVNDLGAEVDGSGSSTGPAGEVVDHIRSQGGAA 67 Query: 68 VANYDSV---EDGEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYRVHAKG 124 +AN D V E ++++ A++SFG +D+++NNAGILRD MT+ +WD V RVH KG Sbjct: 68 IANGDDVASWEGAQRLINAAIESFGRLDVVVNNAGILRDRMLVNMTESEWDDVIRVHLKG 127 Query: 125 AYKLSRAAWNHMREK------NFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQ 178 + ++R A + RE+ RII T+SA+G+YGN GQANYG+ K + L+ A Sbjct: 128 TFAMTRWAAAYFREQAKAGVAQDARIINTTSASGIYGNVGQANYGAAKAGIASLTIIAAM 187 Query: 179 EGKSKNIHCNTIAPIAASRLTES---VMPPEILEQ--MKPDYIVPLVLYLCHQDTTE-TG 232 E + N IAP+A +R+TE+ V P + Q + P+ I PLV++L + TG Sbjct: 188 ELARYGVTVNAIAPVALTRMTENLGIVAPDDRAAQAELAPENIAPLVVWLGSTHSAGITG 247 Query: 233 GVFEVG-----------AGWVSKVRLQRSAGVYMKDLTPEKIK 264 VF+V AG ++ R QR + D+ P ++ Sbjct: 248 RVFDVAGHHIDVAEGWHAGPSAEARGQRFTVDELDDVVPALVR 290 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: 355 Number of extensions: 19 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: 309 Length adjustment: 30 Effective length of query: 411 Effective length of database: 279 Effective search space: 114669 Effective search space used: 114669 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