Definition of L-asparagine biosynthesis
As rules and steps, or see full text
Rules
Overview: Asparagine biosynthesis in GapMind is based on MetaCyc pathways L-asparagine biosynthesis I (link), II (link), or III (tRNA-dependent) (link). In pathways I or II, aspartate is amidated directly, with glutamine or ammonia as the nitrogen source. In pathway III, aspartate is ligated to tRNA(Asn) and then amidated to Asn-tRNA(Asn).
- all:
- to_asn_tRNA
- or to_asparagine
- to_asn_tRNA: aspS2 and transamidation
- transamidation: gatA, gatB and gatC
- Comment: Some organisms have gatDE instead of gatABC. GatDE are thought to form glutaminyl-tRNA only, so they are not described here (but TIGRFam suggests that gatD might replace gatB in some archaea). In the step definitions of gatABC, metacyc entries are added separately because they have HTML tags in their descriptions. Also there are no hits for some of the terms -- often, only gatB is annotated as a aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit.
- to_asparagine:
Steps
asnB: asparagine synthase (glutamine-hydrolysing)
- Curated proteins or TIGRFams with EC 6.3.5.4
- Ignore hits to A4I213 when looking for 'other' hits (asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4))
- Ignore hits to items matching EC 6.3.1.1 when looking for 'other' hits
- Ignore hits to CH_123066 when looking for 'other' hits (asparagine synthetase)
- Comment: In BRENDA, A4I213 is misannotated as asnB. Many asparagine synthases are bifunctional (obtaining nitrogen from either ammonia or glutamine) so similarity to EC 6.3.1.1 is ignored. CH_123066 has a vague annotation and it is not clear if it is actually characterized.
- Total: 1 HMMs and 32 characterized proteins
asnA: aspartate--ammonia ligase
- Curated proteins or TIGRFams with EC 6.3.1.1
- Curated sequence A4I213: asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4)
- Ignore hits to items matching EC 6.3.5.4 when looking for 'other' hits
- Ignore hits to CH_123066 when looking for 'other' hits (asparagine synthetase)
- Comment: In BRENDA, A4I213 (asnA) is misannotated as asnB. Many asparagine synthases are bifunctional (obtaining nitrogen from either ammonia or glutamine) so similarity to EC 6.3.5.4 is ignored. CH_123066 has a vague annotation and it is not clear if it is actually characterized.
- Total: 1 HMMs and 5 characterized proteins
aspS2: aspartyl-tRNA(Asp/Asn) synthetase
- Curated proteins or TIGRFams with EC 6.1.1.23
- 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.
- Total: 1 HMMs and 24 characterized proteins
gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A
gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
gatC: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C
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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