Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_011989348.1 CKL_RS03830 NAD(P)-dependent oxidoreductase
Query= uniprot:Q8EGC1 (252 letters) >NCBI__GCF_000016505.1:WP_011989348.1 Length = 247 Score = 125 bits (314), Expect = 8e-34 Identities = 83/254 (32%), Positives = 135/254 (53%), Gaps = 15/254 (5%) Query: 2 DLKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGYAL- 60 +L KV V+TG + G+G ++A N A+ GA + + + +K D+ G + Sbjct: 3 NLSGKVAVVTGASRGIGRSIAVNLARCGALVVINYIKNEKEACKTLDMVKQEGANGIIVQ 62 Query: 61 -DITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVIN 119 D++ L + GKI++LVNNAGI + G+ + ++ +++Q +I+ Sbjct: 63 GDVSLYNSAEKIMKNTLSNMGKIDILVNNAGISKVGLFIDMRE---------NEWQQIID 113 Query: 120 VNLTGTFLCGREAAAAMIESGQAGVIVNISSL-AKAGNVGQSNYAASKAGVAAMSVGWAK 178 +N G C MI S ++G IVNISS+ K G +S Y+ASK V + AK Sbjct: 114 INFKGVLNCTHCVLEHMI-SRKSGSIVNISSMWGKVGASCESIYSASKGAVNLFTKSIAK 172 Query: 179 ELARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFII--EN 236 E+ NIR AVAPGVI TEM + ++ E + L + +P+GR G +++I V F+ + Sbjct: 173 EMGPSNIRINAVAPGVIDTEMNSWLQEEERKNLIEEIPIGRFGKSDDIGKIVCFLAGESS 232 Query: 237 DYVNGRVFEVDGGI 250 Y+ G++ VDGG+ Sbjct: 233 QYITGQIITVDGGM 246 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: 162 Number of extensions: 13 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 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