LBNL Hackathon: Dark Protein Atlas genes
A collection of gene reviews made during the LBNL hackathon. Each gene comes
from the KBase Dark Protein Atlas review queue
(https://gene-annotate-dashboard.kbase.us/review), where an LLM pipeline proposes
a function and GO terms for a poorly annotated bacterial protein and a curator
judges the call.
For each queue item we find the matching UniProt entry (an identical or
near-identical sequence), write a standard gene review, and record the verdict
on the dashboard's call in the gene notes file.
Genes
| Gene | Organism | UniProt | Dashboard item | Dashboard call | Verdict |
|---|---|---|---|---|---|
| LACLM/sufB | Lactococcus lactis subsp. cremoris MG1363 | A2RMK5 | NZ_LKLC01000161.1_58 | SufB Fe-S cluster assembly scaffold protein of the SUF system | supported |
| LACLA/yxcA | Lactococcus lactis subsp. lactis IL1403 | Q9CDI2 | NZ_VXKC01000008.1_19 | PlsA plasmalogen biosynthesis protein combining activation and reduction/dehydration functions for anaerobic plasmalogen production | supported (GO:0016836 hydro-lyase is an overreach) |
| SALTY/ybbO | Salmonella enterica serovar Typhimurium LT2 | Q7CR11 | AYCY01000026.1_161 | Short-chain dehydrogenase/reductase (SDR) family oxidoreductase, substrate undetermined | supported but under-specific (GO:0016491 correct, already in GOA); the protein is an NADPH-dependent aldehyde reductase (GO:0008106), by 1:1 orthology to ECOLI/ybbO |
| ECOLI/ybbO | Escherichia coli K-12 | P0AFP4 | not linked | n/a | NADPH-dependent aldehyde reductase (GO:0008106), direct assays |
| SYNE7/Synpcc7942_0873 | Synechococcus elongatus PCC 7942 (dashboard protein from PCC 6311, identical) | Q31PW6 | CP088958.1_900 | DUF4062 domain-containing protein, putative NACHT-family NTPase | wrong: GO:0017111 NTPase is NPI (no P-loop domain); probable DUF4062 TIR-like NAD+ nucleosidase (GO:0003953) |
| RHIME/dusA | Sinorhizobium meliloti 1021 | Q92P85 | NZ_RPHN01000062.1_55 | FMN-binding tRNA-dihydrouridine(20/20a) synthase DusA (EC 1.3.1.91) | supported |
Notes
- The dashboard sequence for CP088958.1_900 comes from the S. elongatus PCC 6311
chromosome (NCBI CP088958.1) and is 100% identical to PCC 7942 Q31PW6
(Synpcc7942_0873), so the review is filed under the PCC 7942 entry. - The dashboard sequence for NZ_LKLC01000161.1_58 is 100% identical to A2RMK5
(llmg_1969), so the review is filed under the MG1363 reference proteome. - The dashboard sequence for NZ_VXKC01000008.1_19 (UniParc UPI00072AC48C,
RefSeq WP_081041604) had no active UniProt entry: its two TrEMBL records,
A0A0V8CX59 and A0A2A5SIM0, were deleted as "Not part of a reference
proteome". The review is filed under the closest reference-proteome
entry, Q9CDI2 (IL1403 yxcA, 98.3% identical). The protein is the
single-chain anaerobic plasmalogen synthase PlsA, not HgdC. Reviewing it
turned up a GO labelling problem: GO:0047159 "plasmalogen synthase
activity" is an acyltransferase on lysoplasmalogen. It also showed that
GO has no MF term for the anaerobic, vinyl-ether-forming activity. Draft
GO issues for both points are pending. - SALTY/ybbO (STM0505) and its E. coli orthologue ECOLI/ybbO (b0493) were reviewed
during the hackathon on request rather than picked from the queue. The matching
Salmonella dashboard item, AYCY01000026.1_161, was located afterwards: its sequence
is 99.6% identical to Q7CR11 (one substitution, I244L, outside the catalytic
tetrad). Its call is reviewed in
genes/SALTY/ybbO/ybbO-dashboard-predictions-review.yamlas CNN for GO:0016491.
ECOLI/ybbO still has no dashboard item. The Salmonella
protein has no experiments of its own; its function rests on ECOLI/ybbO, whose
purified enzyme reduces C2-C18 aldehydes with NADPH. The transfer is supported by
reciprocal best hits across both proteomes, conserved gene order (ybbN-ybbO-tesA-ybbA),
90.6% identity and an invariant catalytic tetrad (N105-S133-Y146-K150), with only one
of 24 substitutions in the predicted active-site pocket. See
genes/SALTY/ybbO/ybbO-bioinformatics/RESULTS.md. - A sequence-only OpenScientist run on SALTY/ybbO reached the same activity call but
identified the protein from an exact UniParc checksum match. Hiding the gene name
therefore does not blind a sequence test; this matters for any dashboard-style
evaluation that relies on that kind of blinding. - For ECOLI/ybbO, a proposed retinol dehydrogenase annotation was withdrawn. Retinal
reduction is seen only in engineered strains, has not been assayed with purified
enzyme or a defined cofactor, and uses a substrate E. coli does not make. Studies in yeast
disagree on how efficient it is. - The dashboard sequence for NZ_RPHN01000062.1_55 (E. meliloti USDA1810) contains
Q92P85 (SMc04235) exactly as residues 40-398; the 39 extra N-terminal residues
come from an upstream start codon. The review is filed under the 1021 reference
proteome, and the truncated UniProt start is recorded as a gene model issue.