GapMind for catabolism of small carbon sources

 

L-serine catabolism in Nocardioides dokdonensis FR1436

Best path

braC, braD, braE, braF, braG, sdaB

Rules

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

19 steps (10 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) I601_RS18165
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) I601_RS18185 I601_RS10450
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) I601_RS18180 I601_RS05895
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) I601_RS18175 I601_RS19350
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) I601_RS18170 I601_RS10465
sdaB L-serine ammonia-lyase I601_RS09980 I601_RS07215
Alternative steps:
AAP1 L-serine transporter AAP1
Ac3H11_1692 L-tyrosine ABC transporter, ATPase component 2 I601_RS10465 I601_RS19345
Ac3H11_1693 L-tyrosine ABC transporter, ATPase component 1 I601_RS02125 I601_RS09180
Ac3H11_1694 L-tyrosine ABC transporter, permease component 2 I601_RS05895
Ac3H11_1695 L-tyrosine ABC transporter, permease component 1 I601_RS05905 I601_RS02135
Ac3H11_2396 L-tyrosine ABC transporter, substrate-binding component component
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
serP L-serine permease SerP
snatA L-serine transporter
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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:

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