Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate WP_092349901.1 BLU87_RS14010 3-oxoacyl-[acyl-carrier-protein] reductase
Query= SwissProt::Q9NKW1 (441 letters) >NCBI__GCF_900107645.1:WP_092349901.1 Length = 245 Score = 131 bits (329), Expect = 3e-35 Identities = 79/201 (39%), Positives = 117/201 (58%), Gaps = 13/201 (6%) Query: 6 KDKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKAAGG 65 +DKV ++TG GIG+ A A GAK+V G++ +A + V E+KAAG Sbjct: 3 QDKVALITGTSRGIGRGIATALAANGAKIVA---------AGTNLQATEDFVAELKAAGT 53 Query: 66 TAVA---NYDSVEDGEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYRVHA 122 A+A + + E++V+TA ++FG +DIL+NNAGI RD +M + DWD V ++ Sbjct: 54 EAIAVRCDVSVAAEVEQLVKTAKETFGRIDILVNNAGITRDGLLLRMKEEDWDAVLDINL 113 Query: 123 KGAYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQEGKS 182 KGA+ +RA M ++ GRII S G GN GQANY + K L+GL+ + AQE Sbjct: 114 KGAFLCTRAVSKLMTKQRCGRIINIVSVVGQTGNPGQANYCASKAGLMGLTRSNAQELAK 173 Query: 183 KNIHCNTIAP-IAASRLTESV 202 +NI N +AP A+ +T+S+ Sbjct: 174 RNITVNAVAPGFIATDMTDSL 194 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: 252 Number of extensions: 10 Number of successful extensions: 2 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: 245 Length adjustment: 28 Effective length of query: 413 Effective length of database: 217 Effective search space: 89621 Effective search space used: 89621 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: 48 (23.1 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