Finding step aspS2 for L-asparagine biosynthesis in Clostridium kluyveri DSM 555
2 candidates for aspS2: aspartyl-tRNA(Asp/Asn) synthetase
Confidence: high confidence medium confidence low confidence
? – known gap: despite the lack of a good candidate for this step, this organism (or a related organism) performs the pathway
GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.
Definition of step aspS2
- Curated proteins or TIGRFams with EC 6.1.1.23 (search)
- UniProt sequence A0A0H3C7V8_CAUVN: RecName: Full=Aspartate--tRNA(Asp/Asn) ligase {ECO:0000256|HAMAP-Rule:MF_00044}; EC=6.1.1.23 {ECO:0000256|HAMAP-Rule:MF_00044}; AltName: Full=Aspartyl-tRNA synthetase {ECO:0000256|HAMAP-Rule:MF_00044}; Short=AspRS {ECO:0000256|HAMAP-Rule:MF_00044}; AltName: Full=Non-discriminating aspartyl-tRNA synthetase {ECO:0000256|HAMAP-Rule:MF_00044}; Short=ND-AspRS {ECO:0000256|HAMAP-Rule:MF_00044};
- UniProt sequence SYDND_DINSH: RecName: Full=Aspartate--tRNA(Asp/Asn) ligase {ECO:0000255|HAMAP-Rule:MF_00044}; EC=6.1.1.23 {ECO:0000255|HAMAP-Rule:MF_00044}; AltName: Full=Aspartyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_00044}; Short=AspRS {ECO:0000255|HAMAP-Rule:MF_00044}; AltName: Full=Non-discriminating aspartyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_00044}; Short=ND-AspRS {ECO:0000255|HAMAP-Rule:MF_00044};
- UniProt sequence A0A2I7KAZ8: RecName: Full=Aspartate--tRNA(Asp/Asn) ligase {ECO:0000256|HAMAP-Rule:MF_00044}; EC=6.1.1.23 {ECO:0000256|HAMAP-Rule:MF_00044}; AltName: Full=Aspartyl-tRNA synthetase {ECO:0000256|HAMAP-Rule:MF_00044}; Short=AspRS {ECO:0000256|HAMAP-Rule:MF_00044}; AltName: Full=Non-discriminating aspartyl-tRNA synthetase {ECO:0000256|HAMAP-Rule:MF_00044}; Short=ND-AspRS {ECO:0000256|HAMAP-Rule:MF_00044};
- UniProt sequence B8DMM5_DESVM: RecName: Full=Aspartate--tRNA(Asp/Asn) ligase {ECO:0000256|HAMAP-Rule:MF_00044}; EC=6.1.1.23 {ECO:0000256|HAMAP-Rule:MF_00044}; AltName: Full=Aspartyl-tRNA synthetase {ECO:0000256|HAMAP-Rule:MF_00044}; Short=AspRS {ECO:0000256|HAMAP-Rule:MF_00044}; AltName: Full=Non-discriminating aspartyl-tRNA synthetase {ECO:0000256|HAMAP-Rule:MF_00044}; Short=ND-AspRS {ECO:0000256|HAMAP-Rule:MF_00044};
- UniProt sequence SYDND_DESVH: RecName: Full=Aspartate--tRNA(Asp/Asn) ligase {ECO:0000255|HAMAP-Rule:MF_00044}; EC=6.1.1.23 {ECO:0000255|HAMAP-Rule:MF_00044}; AltName: Full=Aspartyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_00044}; Short=AspRS {ECO:0000255|HAMAP-Rule:MF_00044}; AltName: Full=Non-discriminating aspartyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_00044}; Short=ND-AspRS {ECO:0000255|HAMAP-Rule:MF_00044};
- UniProt sequence SYDND_SYNE7: RecName: Full=Aspartate--tRNA(Asp/Asn) ligase {ECO:0000255|HAMAP-Rule:MF_00044}; EC=6.1.1.23 {ECO:0000255|HAMAP-Rule:MF_00044}; AltName: Full=Aspartyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_00044}; Short=AspRS {ECO:0000255|HAMAP-Rule:MF_00044}; AltName: Full=Non-discriminating aspartyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_00044}; Short=ND-AspRS {ECO:0000255|HAMAP-Rule:MF_00044};
- Ignore hits to P9WFW3 when looking for 'other' hits (aspartate-tRNA ligase (EC 6.1.1.12))
- Ignore hits to ASPS-MONOMER when looking for 'other' hits (Aspartate--tRNA ligase; Aspartyl-tRNA synthetase; AspRS; EC 6.1.1.12. aspartate—tRNA ligase (EC 6.1.1.12). aspartate—tRNA ligase (EC 6.1.1.12; EC 6.1.1.23))
- Ignore hits to MONOMER-124420 when looking for 'other' hits (aspartate--tRNA ligase/ergosteryl-3β-O-L-aspartate synthase (EC 6.1.1.23; EC 2.3.2.37))
- Comment: AspS2 forms both Asp-tRNA(Asp) and Asp-tRNA(Asn). It is difficult to distinguish the "non-discriminatory" synthase (aspS2) from the discriminatory synthase (aspRS) by similarity. Also, the presence of the tRNA-dependent amidotransferase gatABC is not sufficient to conclude that aspS2 is present because gatABC are also involved in tRNA-dependent synthesis of glutamine. However, if aspargine synthase and asparginyl-tRNA synthetase (asnRS) are absent, then we can conclude that the aspartyl-tRNA synthetase is non-discriminatory. This is the basis for annotating CCNA_01969 (A0A0H3C7V8_CAUVN), Dshi_2633 (SYDND_DINSH), and PGA1_c24530 (A0A2I7KAZ8). In Desulfovibrio vulgaris (2 strains) and in Synechococcus, the situation is more complicated -- there is an asnRS, but it is not essential, or even improtant for fitness in most conditions. This also indicates the presence of the tRNA-dependent pathway. (It is also doubtful whether any of those genomes encode asnB or asnA.) This is the basis for annotating DvMF_2038 (B8DMM5_DESVM), DVU3367 (SYDND_DESVH), and Synpcc7942_1313 (SYDND_SYNE7). Although the asp-tRNA synthetase from Mycobacterium tuberculosis (P9WFW3) is annotated as aspartate-specific in BRENDA, this organism seems to lack asparaginyl-tRNA synthetase, so this is ignored. MetaCyc annotates E.coli aspS (link) as both discriminating and non-discriminating, which is incorrect, so this is ignored. And MetaCyc gives erdS (link) this EC number, but it is not reported to act on asparagine.
Or cluster all characterized aspS2 proteins
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
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About GapMind
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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").
Otherwise, a candidate is "medium confidence" if either:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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