As text, or see rules and steps
# Asparagine biosynthesis in GapMind is based on MetaCyc pathways # L-asparagine biosynthesis I (metacyc:ASPARAGINE-BIOSYNTHESIS), # II (metacyc:ASPARAGINESYN-PWY), # or III (tRNA-dependent) (metacyc:PWY490-4). # 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). # In BRENDA, uniprot: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. asnB asparagine synthase (glutamine-hydrolysing) EC:6.3.5.4 ignore:BRENDA::A4I213 ignore_other:EC 6.3.1.1 ignore:CharProtDB::CH_123066 # In BRENDA, uniprot: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. asnA aspartate--ammonia ligase EC:6.3.1.1 curated:BRENDA::A4I213 ignore_other:EC 6.3.5.4 ignore:CharProtDB::CH_123066 to_asparagine: asnB to_asparagine: asnA # 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 (uniprot:A0A0H3C7V8_CAUVN), Dshi_2633 (uniprot:SYDND_DINSH), # and PGA1_c24530 (uniprot: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 (uniprot:B8DMM5_DESVM), # DVU3367 (uniprot:SYDND_DESVH), and Synpcc7942_1313 (uniprot:SYDND_SYNE7). # # Although the asp-tRNA synthetase from Mycobacterium # tuberculosis (uniprot: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 (metacyc:ASPS-MONOMER) as both discriminating and non-discriminating, # which is incorrect, so this is ignored. # And MetaCyc gives erdS (metacyc:MONOMER-124420) this EC number, but it is not reported to act on asparagine. aspS2 aspartyl-tRNA(Asp/Asn) synthetase EC:6.1.1.23 uniprot:A0A0H3C7V8_CAUVN uniprot:SYDND_DINSH uniprot:A0A2I7KAZ8 uniprot:B8DMM5_DESVM uniprot:SYDND_DESVH uniprot:SYDND_SYNE7 ignore:BRENDA::P9WFW3 ignore:metacyc::ASPS-MONOMER ignore:metacyc::MONOMER-124420 import gln.steps:gatA gatB gatC # aspartyl-tRNA(Asn) amidotransferase complex # 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. transamidation: gatA gatB gatC to_asn_tRNA: aspS2 transamidation all: to_asn_tRNA all: to_asparagine
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