Definition of L-serine catabolism
As rules and steps, or see full text
Rules
Overview: L-serine degradation in GapMind is based on the MetaCyc pathway (link)
- all: serine-transport and serine-ammonia-lyase
- Comment: Serine ammonia-lyase converts serine to pyruvate and ammonia via 2-aminoprop-2-enoate and 2-iminopropanoate.
- serine-ammonia-lyase:
- serine-transport:
Steps
braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB)
- Curated sequence P21175: Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein. Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein, component of Branched chain amino acid uptake transporter. Transports alanine
- Curated sequence Q55387: NatB aka SLR0559, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE
- Curated sequence Q8YVY4: NatB, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB)
- Comment: braC and natB are quite distantly related and were not clustered, but both are SBP
- Total: 3 characterized proteins
braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD)
- Curated sequence P21627: High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine
- Curated sequence P74318: NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE
- Curated sequence Q8YXD0: NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB)
- Total: 3 characterized proteins
braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC)
- Curated sequence P21628: High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine
- Curated sequence P74455: NatC aka SLL0146, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE
- Curated sequence Q8YY08: NatC, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB)
- Total: 3 characterized proteins
braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA)
- Curated sequence P21629: High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine
- Curated sequence Q55164: NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE
- Curated sequence Q7A2H0: NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB)
- Total: 3 characterized proteins
braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE)
- Curated sequence P21630: High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine
- Curated sequence P73650: NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE
- Curated sequence Q8YT15: NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB)
- Total: 3 characterized proteins
Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component
- UniProt sequence A0A165KTD4: SubName: Full=Branched chain amino acid ABC transporter substrate-binding protein {ECO:0000313|EMBL:KZT16064.1};
- Comment: 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.
- Total: 1 characterized proteins
Ac3H11_1695: L-tyrosine ABC transporter, permease component 1
Ac3H11_1694: L-tyrosine ABC transporter, permease component 2
Ac3H11_1693: L-tyrosine ABC transporter, ATPase component 1
Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2
serP: L-serine permease SerP
- Curated sequence A2RI87: Serine permease SerP1
- Curated sequence F2HQ24: Serine transporter, SerP2 or YdgB, of 459 aas and 12 TMSs (Trip et al. 2013). Transports L-alanine (Km = 20 μM), D-alanine (Km = 38 μM), L-serine, D-serine (Km = 356 μM) and glycine (Noens and Lolkema 2015). The encoding gene is adjacent to the one encoding SerP1 (TC# 2.A.3.1.21)
- Curated sequence F2HQ25: Serine uptake transporter, SerP1, of 259 aas and 12 TMSs (Trip et al. 2013). L-serine is the highest affinity substrate (Km = 18 μM), but SerP1 also transports L-threonine and L-cysteine (Km values = 20 - 40 μM)
- Ignore hits to A2RI86 when looking for 'other' hits (DL-alanine permease SerP2)
- Ignore hits to P0AAE0 when looking for 'other' hits (D-serine/D-alanine/glycine transporter. D-Serine/D-alanine/glycine/D-cycloserine:H+ symporter. D-serine/alanine/glycine/:H+symporter. D-serine/alanine/glycine/:H+symporter)
- Ignore hits to A0A0H2VDI7 when looking for 'other' hits (D-serine/D-alanine/glycine transporter)
- Comment: 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.
- Total: 3 characterized proteins
dlsT: L-serine transporter DlsT
sdaC: L-serine transporter:H+ symporter sdaC
- Curated sequence P0AAD6: Serine transporter. Serine permease. serine:H+ symporter SdaC. serine:H+ symporter SdaC
- Curated sequence P0AAD8: Threonine/serine transporter TdcC; H(+)/threonine-serine symporter. Threonine/Serine permease. threonine/serine:H+ symporter. threonine/serine:H+ symporter
- Total: 2 characterized proteins
AAP1: L-serine transporter AAP1
- Curated sequence CH_091601: amino acid transporter. Amino acid permease 1; Amino acid transporter AAP1; Neutral amino acid transporter II. General amino acid permease 1, AAP1 (transports most neutral and acidic amino acids but not aspartate or the basic amino acids). amino acid permease 1
- Total: 1 characterized proteins
sstT: L-serine:Na+ symporter SstT
- Curated sequence P0AGE4: Serine/threonine transporter SstT; Na(+)/serine-threonine symporter. Serine/threonine:Na+ symporter, SstT. serine/threonine:Na+ symporter
- Total: 1 characterized proteins
snatA: L-serine transporter
- Curated sequence Q8J305: The SnatA carrier. Transports glycine, L-alanine, L-serine, L-threonine and a variety of neutral L-amino acids
- Total: 1 characterized proteins
sdaB: L-serine ammonia-lyase
sdhA: FeS-containing L-serine dehydratase, alpha subunit
- UniProt sequence P33073: RecName: Full=L-serine dehydratase, alpha chain; Short=SDH; EC=4.3.1.17; AltName: Full=L-serine deaminase; Short=L-SD;
- Ignore hits to items matching 4.3.1.17 when looking for 'other' hits
- Comment: Heteromeric iron-cluster-containing form
- Total: 1 characterized proteins
sdhB: FeS-containing L-serine dehydratase, beta subunit
- UniProt sequence P33074: RecName: Full=L-serine dehydratase, beta chain; Short=SDH; EC=4.3.1.17; AltName: Full=L-serine deaminase; Short=L-SD;
- Ignore hits to items matching 4.3.1.17 when looking for 'other' hits
- Total: 1 characterized proteins
Links
Downloads
Related tools
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