Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate NP_350157.1 CA_C3574 3-ketoacyl-ACP reductase
Query= SwissProt::Q9NKW1 (441 letters) >NCBI__GCF_000008765.1:NP_350157.1 Length = 249 Score = 132 bits (332), Expect = 1e-35 Identities = 89/249 (35%), Positives = 135/249 (54%), Gaps = 22/249 (8%) Query: 8 KVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKAAGGTA 67 KV +VTGAG G+G+ AL+ A GA +VVN SS K+++EI+ G A Sbjct: 8 KVAVVTGAGRGLGRAIALKLAAEGANLVVN--------YRSSEAETQKLIKEIEELGSKA 59 Query: 68 VA---NYDSVEDGEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYRVHAKG 124 VA + ++ E I++ A+D +G VDIL+NNAGI +D +M + D+D V V+ KG Sbjct: 60 VAVKADISKYDEAETIIKKALDEYGTVDILVNNAGITKDNLLLRMKEEDFDSVINVNLKG 119 Query: 125 AYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQEGKSKN 184 A+ + M +K G+II SS GL GN GQ NY + K ++G++ ++A+E S+ Sbjct: 120 AFNCIKHTSRVMLKKKSGKIINISSVIGLIGNAGQVNYAAAKAGIIGMTKSVAKELASRG 179 Query: 185 IHCNTIAP-IAASRLT--------ESVMPPEILEQM-KPDYIVPLVLYLCHQ-DTTETGG 233 I N +AP I S +T ES++ L ++ + + + LVL+L + TG Sbjct: 180 ITVNAVAPGIIKSDMTDALTDKQRESIVAAVPLNKVGEAEDVANLVLFLASDLSSYITGQ 239 Query: 234 VFEVGAGWV 242 V V G V Sbjct: 240 VINVDGGMV 248 Score = 25.8 bits (55), Expect = 0.002 Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 4/71 (5%) Query: 371 ALDLKNGSGSIVVGAGSTKPNVTITVSDEDFVDIMTGKLNAQSAFTKGKLKISGNMGLAT 430 ALD +V AG TK N+ + + +EDF ++ +N + AF +K + + L Sbjct: 79 ALDEYGTVDILVNNAGITKDNLLLRMKEEDFDSVI--NVNLKGAF--NCIKHTSRVMLKK 134 Query: 431 KLGALMQGSKL 441 K G ++ S + Sbjct: 135 KSGKIINISSV 145 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: 14 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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 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