Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_017601831.1 D471_RS0128820 beta-ketoacyl-ACP reductase
Query= uniprot:Q8EGC1 (252 letters) >NCBI__GCF_000341125.1:WP_017601831.1 Length = 234 Score = 137 bits (345), Expect = 2e-37 Identities = 90/245 (36%), Positives = 125/245 (51%), Gaps = 21/245 (8%) Query: 8 VVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGYALDITDEED 67 V++TGG G+GLA+A A G +A+ + E + G DITD Sbjct: 5 VLVTGGNRGIGLAIARELAAGGDDVAVTHRSGEPPEG----------LLGVRCDITDSAQ 54 Query: 68 VVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINVNLTGTFL 127 V A F + E G + VLV NAGI +D +L MS D F SV++ NLTG F Sbjct: 55 VDAAFKEVEEAQGPVEVLVANAGITKDQLLAL---------MSEDDFSSVLDTNLTGAFR 105 Query: 128 CGREAAAAMIESGQAGVIVNISSLAKAGNVGQSNYAASKAGVAAMSVGWAKELARYNIRS 187 + A M+ +I+ S + G+ GQ+NYAASKAG+ A+EL NI Sbjct: 106 VAKRAVRGMMRKRGGRIILISSVVGLLGSGGQANYAASKAGLVGFGRSLARELGSRNITV 165 Query: 188 AAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIEND--YVNGRVFE 245 VAPG I T+MTA + + ++K +P+GR+G E+IA TV F+ Y+ G V Sbjct: 166 NVVAPGFIETDMTAQLGEDRQAEIKKNIPLGRIGGTEDIAKTVGFLAGPGAAYITGAVIP 225 Query: 246 VDGGI 250 VDGG+ Sbjct: 226 VDGGM 230 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: 151 Number of extensions: 8 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: 252 Length of database: 234 Length adjustment: 23 Effective length of query: 229 Effective length of database: 211 Effective search space: 48319 Effective search space used: 48319 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 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