GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Sinorhizobium fredii NGR234

Best path

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

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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gguA L-arabinose ABC transporter, ATPase component GguA NGR_RS23220 NGR_RS00525
gguB L-arabinose ABC transporter, permease component GguB NGR_RS23215 NGR_RS00530
chvE L-arabinose ABC transporter, substrate-binding component ChvE NGR_RS23225
xacB L-arabinose 1-dehydrogenase NGR_RS15815 NGR_RS13555
xacC L-arabinono-1,4-lactonase NGR_RS13540 NGR_RS02200
xacD L-arabinonate dehydratase NGR_RS23200 NGR_RS13535
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase NGR_RS23210
xacF alpha-ketoglutarate semialdehyde dehydrogenase NGR_RS23205 NGR_RS27930
Alternative steps:
aldA (glycol)aldehyde dehydrogenase NGR_RS06845 NGR_RS03080
aldox-large (glycol)aldehyde oxidoreductase, large subunit NGR_RS26490 NGR_RS14300
aldox-med (glycol)aldehyde oxidoreductase, medium subunit NGR_RS14315 NGR_RS26485
aldox-small (glycol)aldehyde oxidoreductase, small subunit NGR_RS01010 NGR_RS14310
araA L-arabinose isomerase
araB ribulokinase NGR_RS14485
araD L-ribulose-5-phosphate epimerase NGR_RS14480
araE L-arabinose:H+ symporter
araF L-arabinose ABC transporter, substrate-binding component AraF
araG L-arabinose ABC transporter, ATPase component AraG NGR_RS00525 NGR_RS09875
araH L-arabinose ABC transporter, permease component AraH NGR_RS00530 NGR_RS14475
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) NGR_RS07690 NGR_RS08910
araUsh L-arabinose ABC transporter, substrate-binding component AraU(Sh) NGR_RS07415
araV L-arabinose ABC transporter, ATPase component AraV NGR_RS09940 NGR_RS21950
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) NGR_RS07420 NGR_RS00525
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) NGR_RS07425 NGR_RS14580
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) NGR_RS07430 NGR_RS14580
BT0355 L-arabinose:Na+ symporter
Echvi_1880 L-arabinose:Na+ symporter
glcB malate synthase NGR_RS28165 NGR_RS26910
gyaR glyoxylate reductase NGR_RS28600 NGR_RS02230
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) NGR_RS27660 NGR_RS07695
xacI L-arabinose ABC transporter, permease component 2 (XacI) NGR_RS07690 NGR_RS27665
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) NGR_RS09940 NGR_RS09335
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) NGR_RS09720 NGR_RS30975
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG NGR_RS00605 NGR_RS11930
xylHsa L-arabinose ABC transporter, permease component XylH NGR_RS09880 NGR_RS14580

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.

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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