GapMind for catabolism of small carbon sources

 

L-serine catabolism in Paraburkholderia phymatum STM815

Best path

Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB

Rules

Overview: L-serine degradation in GapMind is based on the MetaCyc pathway (link)

19 steps (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Ac3H11_2396 L-tyrosine ABC transporter, substrate-binding component component BPHY_RS00550 BPHY_RS02950
Ac3H11_1695 L-tyrosine ABC transporter, permease component 1 BPHY_RS02955 BPHY_RS11455
Ac3H11_1694 L-tyrosine ABC transporter, permease component 2 BPHY_RS02960
Ac3H11_1693 L-tyrosine ABC transporter, ATPase component 1 BPHY_RS02965 BPHY_RS15490
Ac3H11_1692 L-tyrosine ABC transporter, ATPase component 2 BPHY_RS02970 BPHY_RS15485
sdaB L-serine ammonia-lyase BPHY_RS15365 BPHY_RS16905
Alternative steps:
AAP1 L-serine transporter AAP1
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) BPHY_RS00550 BPHY_RS32955
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BPHY_RS02955 BPHY_RS15515
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) BPHY_RS02960
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BPHY_RS15530 BPHY_RS02965
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BPHY_RS02970 BPHY_RS15485
dlsT L-serine transporter DlsT
sdaC L-serine transporter:H+ symporter sdaC
sdhA FeS-containing L-serine dehydratase, alpha subunit
sdhB FeS-containing L-serine dehydratase, beta subunit BPHY_RS15365
serP L-serine permease SerP BPHY_RS03010 BPHY_RS32965
snatA L-serine transporter BPHY_RS14015 BPHY_RS13410
sstT L-serine:Na+ symporter SstT

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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:

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:

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