Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate Pf6N2E2_5603 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= uniprot:Q8EGC1 (252 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5603 Length = 252 Score = 277 bits (709), Expect = 1e-79 Identities = 141/253 (55%), Positives = 188/253 (74%), Gaps = 2/253 (0%) Query: 1 MDLKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSS-TEVQGYA 59 M L DKV++ITGG GLG +MA A GAKLAL+D++Q+KL++A A + E + Y Sbjct: 1 MQLTDKVIIITGGCQGLGRSMAEYLAGKGAKLALVDLNQEKLDQAVAACAAKGVEARAYL 60 Query: 60 LDITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVIN 119 ++ +EE V A + EDFG I+ L+NNAGILRDG+L+K KDG++T +MS Q+Q+VI+ Sbjct: 61 CNVANEEQVSDMVARVAEDFGAIHGLINNAGILRDGLLLKVKDGEMT-KMSLAQWQAVID 119 Query: 120 VNLTGTFLCGREAAAAMIESGQAGVIVNISSLAKAGNVGQSNYAASKAGVAAMSVGWAKE 179 VNLTG FLC RE AA M+E +G I+NISS+++AGNVGQ+NY+A+KAGVAA +V WAKE Sbjct: 120 VNLTGVFLCTREVAAKMVELKNSGAIINISSISRAGNVGQTNYSAAKAGVAAATVTWAKE 179 Query: 180 LARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIENDYV 239 LARY IR A +APG I TEMT MKPEALE++ +P+ R+G EEIA + +I ENDY Sbjct: 180 LARYGIRVAGIAPGFIETEMTLGMKPEALEKMTSGIPLKRMGKPEEIAHSAAYIFENDYY 239 Query: 240 NGRVFEVDGGIRL 252 GR+ E+DGG+R+ Sbjct: 240 TGRILEMDGGLRI 252 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: 217 Number of extensions: 5 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: 252 Length adjustment: 24 Effective length of query: 228 Effective length of database: 228 Effective search space: 51984 Effective search space used: 51984 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