Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_068463187.1 APY04_RS12550 beta-ketoacyl-ACP reductase
Query= uniprot:Q8EGC1 (252 letters) >NCBI__GCF_001541235.1:WP_068463187.1 Length = 242 Score = 129 bits (325), Expect = 4e-35 Identities = 84/248 (33%), Positives = 132/248 (53%), Gaps = 17/248 (6%) Query: 6 KVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGYALDITDE 65 +V ++TGG G+G A++ AG ++A D A + T + + ++ D Sbjct: 3 RVALVTGGTRGIGHAISVALKNAGYRVAANYAGNDA---AAQQFQAETGIPVFKWNVGDY 59 Query: 66 EDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINVNLTGT 125 + AG + ++ G +++LVNNAGI RD ML RM+ +Q+ VINV+L Sbjct: 60 DACAAGIEQVTKEVGPVDILVNNAGITRDAML---------HRMTKEQWNEVINVDLDSL 110 Query: 126 FLCGREAAAAMIESGQAGVIVNISSL-AKAGNVGQSNYAASKAGVAAMSVGWAKELARYN 184 F R M + G I+N+SS+ + G +GQ+NY+A+KAG + A E A Sbjct: 111 FNMSRPVIDGM-RARNFGRIINVSSINGRKGQMGQTNYSAAKAGAHGFTKALAAESAAKG 169 Query: 185 IRSAAVAPGVIATEMTAAMKPEALE-RLEKLVPVGRLGHAEEIASTVRFIIEND--YVNG 241 I +APG IATEM AA+ E L+ ++ +P GRLG A+EIA V F+ + ++ G Sbjct: 170 ITVNTIAPGYIATEMVAAVPKEVLDTKIIPQIPAGRLGEADEIARAVVFLAADSAGFITG 229 Query: 242 RVFEVDGG 249 F+++GG Sbjct: 230 ACFDINGG 237 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: 163 Number of extensions: 11 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: 242 Length adjustment: 24 Effective length of query: 228 Effective length of database: 218 Effective search space: 49704 Effective search space used: 49704 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