Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate PfGW456L13_1761 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= uniprot:Q8EGC1 (252 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1761 Length = 232 Score = 253 bits (647), Expect = 2e-72 Identities = 130/233 (55%), Positives = 170/233 (72%), Gaps = 2/233 (0%) Query: 21 MAHNFAQAGAKLALIDVDQDKLERACADL-GSSTEVQGYALDITDEEDVVAGFAYILEDF 79 MA FA GAKLAL+D++Q+KL+ A A E + Y ++ +EE V A + EDF Sbjct: 1 MAEYFAGLGAKLALVDLNQEKLDDAVAACKAQGVEARAYLCNVANEEQVTHMVAQVAEDF 60 Query: 80 GKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINVNLTGTFLCGREAAAAMIES 139 G I+ L+NNAGILRDG+L+K KDG++ +MS Q+Q+VI+VNLTG FLC RE AA M+E Sbjct: 61 GAIHGLINNAGILRDGLLLKVKDGEMI-KMSLAQWQAVIDVNLTGVFLCTREVAAKMVEL 119 Query: 140 GQAGVIVNISSLAKAGNVGQSNYAASKAGVAAMSVGWAKELARYNIRSAAVAPGVIATEM 199 G I+NISS+++AGNVGQ+NY+A+KAGVAA +V WAKELARY IR A +APG I TEM Sbjct: 120 NNTGAIINISSISRAGNVGQTNYSAAKAGVAAATVTWAKELARYGIRVAGIAPGFIETEM 179 Query: 200 TAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIENDYVNGRVFEVDGGIRL 252 T MKPEALE++ +P+ R+G EEIA + +I ENDY GR+ E+DGG+RL Sbjct: 180 TLGMKPEALEKMTAGIPLKRMGKPEEIAHSAAYIFENDYYTGRILEMDGGLRL 232 Lambda K H 0.317 0.134 0.369 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: 204 Number of extensions: 6 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: 252 Length of database: 232 Length adjustment: 23 Effective length of query: 229 Effective length of database: 209 Effective search space: 47861 Effective search space used: 47861 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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