Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate WP_047005555.1 AAW01_RS01220 3-oxoacyl-[acyl-carrier-protein] reductase
Query= SwissProt::Q9NKW1 (441 letters) >NCBI__GCF_001010925.1:WP_047005555.1 Length = 254 Score = 116 bits (291), Expect = 7e-31 Identities = 72/195 (36%), Positives = 106/195 (54%), Gaps = 6/195 (3%) Query: 11 IVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKAAGGTA--V 68 +VTGA GGIG A AK+GA++ ++ G AD E AG Sbjct: 10 LVTGASGGIGSSIAYALAKQGARLALSGSNGDKLRAFREQLIADCGSPE---AGDHVEIT 66 Query: 69 ANYDSVEDGEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYRVHAKGAYKL 128 N E+++ A+D+ GG+DIL+NNAGI RD +M D +W+ V +V+ + ++L Sbjct: 67 CNLSDTTQVEELIPAAIDTLGGLDILVNNAGITRDNLAMRMKDEEWEQVIQVNLEAVFRL 126 Query: 129 SRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQEGKSKNIHCN 188 RA+ M + FGRII +S G GN GQ NY + K +VG+S +LAQE ++ I N Sbjct: 127 MRASARPMMKARFGRIINITSVVGTTGNPGQMNYCAAKAGVVGMSKSLAQELAARGITVN 186 Query: 189 TIAP-IAASRLTESV 202 +AP S +TE++ Sbjct: 187 CVAPGFIRSAMTEAL 201 Score = 25.8 bits (55), Expect = 0.002 Identities = 12/41 (29%), Positives = 22/41 (53%) Query: 371 ALDLKNGSGSIVVGAGSTKPNVTITVSDEDFVDIMTGKLNA 411 A+D G +V AG T+ N+ + + DE++ ++ L A Sbjct: 82 AIDTLGGLDILVNNAGITRDNLAMRMKDEEWEQVIQVNLEA 122 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: 248 Number of extensions: 9 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: 254 Length adjustment: 28 Effective length of query: 413 Effective length of database: 226 Effective search space: 93338 Effective search space used: 93338 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