Definition of L-serine catabolism

GapMind for catabolism of small carbon sources

Definition of L-serine catabolism

# 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

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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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources