GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Herbaspirillum seropedicae SmR1

Best path

gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF

Also see fitness data for the top candidates

Rules

Overview: L-arabinose utilization in GapMind is based on MetaCyc pathways L-arabinose degradation I, via xylulose 5-phosphate (link); III, oxidation to 2-oxoglutarate (link); and IV, via glycolaldehyde (link). Pathway II via xylitol and xylulose is not represented in GapMind because it is not reported in prokaryotes (link).

40 steps (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gguA L-arabinose ABC transporter, ATPase component GguA HSERO_RS05195 HSERO_RS22465
gguB L-arabinose ABC transporter, permease component GguB HSERO_RS05200 HSERO_RS22470
chvE L-arabinose ABC transporter, substrate-binding component ChvE HSERO_RS05190 HSERO_RS22460
xacB L-arabinose 1-dehydrogenase HSERO_RS05210 HSERO_RS13590
xacC L-arabinono-1,4-lactonase HSERO_RS05225 HSERO_RS19370
xacD L-arabinonate dehydratase HSERO_RS05205 HSERO_RS16705
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase HSERO_RS06870 HSERO_RS19330
xacF alpha-ketoglutarate semialdehyde dehydrogenase HSERO_RS00735 HSERO_RS07235
Alternative steps:
aldA (glycol)aldehyde dehydrogenase HSERO_RS05395 HSERO_RS05645
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit HSERO_RS16320
aldox-small (glycol)aldehyde oxidoreductase, small subunit HSERO_RS06620 HSERO_RS16320
araA L-arabinose isomerase
araB ribulokinase
araD L-ribulose-5-phosphate epimerase
araE L-arabinose:H+ symporter
araF L-arabinose ABC transporter, substrate-binding component AraF
araG L-arabinose ABC transporter, ATPase component AraG HSERO_RS03640 HSERO_RS05250
araH L-arabinose ABC transporter, permease component AraH HSERO_RS03645 HSERO_RS05325
araS L-arabinose ABC transporter, substrate-binding component AraS
araT L-arabinose ABC transporter, permease component 1 (AraT)
araU L-arabinose ABC transporter, permease component 2 (AraU)
araUsh L-arabinose ABC transporter, substrate-binding component AraU(Sh) HSERO_RS05170 HSERO_RS11480
araV L-arabinose ABC transporter, ATPase component AraV HSERO_RS16715 HSERO_RS22645
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) HSERO_RS05175 HSERO_RS05250
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) HSERO_RS05180 HSERO_RS03645
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) HSERO_RS05185 HSERO_RS05325
BT0355 L-arabinose:Na+ symporter
Echvi_1880 L-arabinose:Na+ symporter
glcB malate synthase HSERO_RS15200
gyaR glyoxylate reductase HSERO_RS08110 HSERO_RS19280
KDG-aldolase 2-dehydro-3-deoxy-L-arabinonate aldolase
xacG L-arabinose ABC transporter, substrate-binding component XacG
xacH L-arabinose ABC transporter, permease component 1 (XacH)
xacI L-arabinose ABC transporter, permease component 2 (XacI)
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) HSERO_RS16715 HSERO_RS02210
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) HSERO_RS16715 HSERO_RS22750
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG HSERO_RS12120 HSERO_RS05175
xylHsa L-arabinose ABC transporter, permease component XylH HSERO_RS05325

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 (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