As text, or see rules and steps
# L-serine degradation in GapMind is based on the MetaCyc pathway (metacyc:SERDEG-PWY) # ABC transporters for L-serine are NatABCDE or BraCDEFG, with two ATPase and two permease components. # These also transport alanine. # I could not find experimental evidence for serine transport by BraCDEFG from Pseudomonas aeruginosa, # which is included in these, but the subtrate-binding # component (braC or PA1074) has high affinity for similar compounds # (alanine, threonine, homserine; PMC6829864) so it seems likely. # (TCDB also annotates LivJFGHM from Streptococcus pneumoniae as a serine # transporter, but PMC2715661 does not mention serine and suggests that the transporter is specific # for branched-chain amino acids.) import alanine.steps:braC braD braE braF braG # Transporters were identified using # query: transporter:L-serine:serine # (D-serine transporters and serine protease autotransporters were removed). serine-transport: braC braD braE braF braG # A 5-part ABC transporter for serine and other amino acids was identified in Acidovorax sp. GW101-3H11. # It is related to branched-amino-acid transporters. # The substrate-binding component (Ac3H11_2396) is not nearby but is cofit. Ac3H11_2396 L-tyrosine ABC transporter, substrate-binding component component uniprot:A0A165KTD4 Ac3H11_1695 L-tyrosine ABC transporter, permease component 1 uniprot:A0A165KC95 Ac3H11_1694 L-tyrosine ABC transporter, permease component 2 uniprot:A0A165KER0 Ac3H11_1693 L-tyrosine ABC transporter, ATPase component 1 uniprot:A0A165KC86 Ac3H11_1692 L-tyrosine ABC transporter, ATPase component 2 uniprot:A0A165KC78 serine-transport: Ac3H11_2396 Ac3H11_1695 Ac3H11_1694 Ac3H11_1693 Ac3H11_1692 # This cluster also includes cycA (P0AAE0 or A0A0H2VDI7), but that may only transport D-serine. # A close homolog of SerP2, A2RI87, is annotated as a D,L-alanine permease # and is reported to have weak affinity for L-serine (see SwissProt); it is also marked ignore. serP L-serine permease SerP curated:SwissProt::A2RI87 curated:TCDB::F2HQ24 curated:TCDB::F2HQ25 ignore:SwissProt::A2RI86 ignore:SwissProt::P0AAE0 ignore:SwissProt::A0A0H2VDI7 serine-transport: serP dlsT L-serine transporter DlsT curated:SwissProt::P42628 curated:SwissProt::Q8XAF5 serine-transport: dlsT sdaC L-serine transporter:H+ symporter sdaC curated:SwissProt::P0AAD6 curated:SwissProt::P0AAD8 serine-transport: sdaC AAP1 L-serine transporter AAP1 curated:CharProtDB::CH_091601 serine-transport: AAP1 sstT L-serine:Na+ symporter SstT curated:SwissProt::P0AGE4 serine-transport: sstT snatA L-serine transporter curated:TCDB::Q8J305 serine-transport: snatA # Exporters, porins, and metazoan solute carriers were also ignored. # Monomeric form (the heteromeric form is not in the database) sdaB L-serine ammonia-lyase EC:4.3.1.17 # Heteromeric iron-cluster-containing form sdhA FeS-containing L-serine dehydratase, alpha subunit uniprot:P33073 ignore_other:4.3.1.17 sdhB FeS-containing L-serine dehydratase, beta subunit uniprot:P33074 ignore_other:4.3.1.17 serine-ammonia-lyase: sdaB serine-ammonia-lyase: sdhA sdhB # Serine ammonia-lyase converts serine to pyruvate and ammonia # via 2-aminoprop-2-enoate and 2-iminopropanoate. all: serine-transport serine-ammonia-lyase
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