Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate N515DRAFT_2873 N515DRAFT_2873 3-oxoacyl-[acyl-carrier-protein] reductase
Query= uniprot:Q8EGC1 (252 letters) >FitnessBrowser__Dyella79:N515DRAFT_2873 Length = 247 Score = 115 bits (287), Expect = 1e-30 Identities = 82/251 (32%), Positives = 124/251 (49%), Gaps = 18/251 (7%) Query: 6 KVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGYA----LD 61 ++ ++TGG GGLG + A AG ++ D+ + +R A ++ G +D Sbjct: 3 RIAIVTGGIGGLGTEICRQLALAGRQVIAADLPA-RADRVAAFQAELADLDGAVRFEPVD 61 Query: 62 ITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINVN 121 ++D A + G+++VLVN AGI RD L K M +Q ++ VN Sbjct: 62 VSDFASCSELIARVEAAHGRVDVLVNAAGITRDTTLRK---------MDPQHWQELMRVN 112 Query: 122 LTGTFLCGREAAAAMIESGQAGVIVNISSL-AKAGNVGQSNYAASKAGVAAMSVGWAKEL 180 L G F R M G G IVN+SS+ + G GQ+NYAA+KAGV + A+E Sbjct: 113 LDGVFNMCRHVVEGMSARG-FGRIVNLSSVNGQTGQFGQTNYAAAKAGVHGFGMALARET 171 Query: 181 ARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIEND--Y 238 AR + V+PG T + A + E ++ + +PVGRLG +IA V F+ +D Y Sbjct: 172 ARKGVTVNTVSPGYCDTPLVARVPAEIRAQILEDIPVGRLGSPADIARAVCFLAADDAGY 231 Query: 239 VNGRVFEVDGG 249 + G V+GG Sbjct: 232 ITGANLPVNGG 242 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: 167 Number of extensions: 9 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: 247 Length adjustment: 24 Effective length of query: 228 Effective length of database: 223 Effective search space: 50844 Effective search space used: 50844 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