Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate Synpcc7942_0684 Synpcc7942_0684 3-oxoacyl-[acyl-carrier-protein] reductase
Query= SwissProt::Q9NKW1 (441 letters) >FitnessBrowser__SynE:Synpcc7942_0684 Length = 249 Score = 134 bits (338), Expect = 2e-36 Identities = 89/237 (37%), Positives = 127/237 (53%), Gaps = 21/237 (8%) Query: 2 ALNFKDKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIK 61 AL D++ +VTGA GIG+ ALE A GAKV VN SS+ AAD+VV I Sbjct: 3 ALPLTDRIALVTGASRGIGRAIALELAAAGAKVAVN--------YASSAGAADEVVAAIA 54 Query: 62 AAGGTAVA---NYDSVEDGEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVY 118 AAGG A A + + E + ++ +G +D+L+NNAGI RD +M DW V Sbjct: 55 AAGGEAFAVKADVSQESEVEALFAAVIERWGRLDVLVNNAGITRDTLLLRMKRDDWQSVL 114 Query: 119 RVHAKGAYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQ 178 ++ G + SRAA M ++ GRII +S G GN GQANY + K ++GL+ T+A+ Sbjct: 115 DLNLGGVFLCSRAAAKIMLKQRSGRIINIASVVGEMGNPGQANYSAAKAGVIGLTKTVAK 174 Query: 179 EGKSKNIHCNTIAP-IAASRLTESVMPPEILEQMKPDYIVPLVLYLCHQDTTETGGV 234 E S+ I N +AP A+ +T + ++LE ++PL Y + E GV Sbjct: 175 ELASRGITVNAVAPGFIATDMTSELAAEKLLE------VIPLGRY---GEAAEVAGV 222 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: 230 Number of extensions: 13 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: 249 Length adjustment: 28 Effective length of query: 413 Effective length of database: 221 Effective search space: 91273 Effective search space used: 91273 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