GapMind for catabolism of small carbon sources

 

L-serine catabolism in Klebsiella michiganensis M5al

Best path

Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB

Also see fitness data for the top candidates

Rules

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

19 steps (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Ac3H11_2396 L-tyrosine ABC transporter, substrate-binding component component BWI76_RS07260 BWI76_RS26350
Ac3H11_1695 L-tyrosine ABC transporter, permease component 1 BWI76_RS07280 BWI76_RS26345
Ac3H11_1694 L-tyrosine ABC transporter, permease component 2 BWI76_RS07275 BWI76_RS26340
Ac3H11_1693 L-tyrosine ABC transporter, ATPase component 1 BWI76_RS07270 BWI76_RS05980
Ac3H11_1692 L-tyrosine ABC transporter, ATPase component 2 BWI76_RS07265 BWI76_RS05975
sdaB L-serine ammonia-lyase BWI76_RS22880 BWI76_RS17875
Alternative steps:
AAP1 L-serine transporter AAP1
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) BWI76_RS26350 BWI76_RS26365
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BWI76_RS26345 BWI76_RS07280
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) BWI76_RS26340 BWI76_RS07275
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BWI76_RS26335 BWI76_RS05980
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BWI76_RS26330 BWI76_RS05975
dlsT L-serine transporter DlsT
sdaC L-serine transporter:H+ symporter sdaC BWI76_RS22875 BWI76_RS14475
sdhA FeS-containing L-serine dehydratase, alpha subunit BWI76_RS22880 BWI76_RS14470
sdhB FeS-containing L-serine dehydratase, beta subunit
serP L-serine permease SerP BWI76_RS02700 BWI76_RS07360
snatA L-serine transporter BWI76_RS17245
sstT L-serine:Na+ symporter SstT BWI76_RS24715

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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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