GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism in Sinorhizobium fredii NGR234

Best path

bgl, gtsA, gtsB, gtsC, gtsD, glk

Rules

Overview: MetaCyc does not list any pathways for cellobiose utilization, but the major catabolic enzymes are believed to be intracellular cellobiase, periplasmic cellobiase, cellobiose-6-phosphate hydrolase, or cellobiose phosphorylase (PMID:28535986). These pathways all lead to glucose-6-phosphate, which is a central metabolic intermediate. There also may be a 3-ketoglucoside pathway in some Bacteroidetes, but this is not characterized.

73 steps (42 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgl cellobiase NGR_RS25855 NGR_RS14670
gtsA glucose ABC transporter, substrate-binding component (GtsA) NGR_RS27655 NGR_RS07700
gtsB glucose ABC transporter, permease component 1 (GtsB) NGR_RS27660 NGR_RS07695
gtsC glucose ABC transporter, permease component 2 (GtsC) NGR_RS07690 NGR_RS27665
gtsD glucose ABC transporter, ATPase component (GtsD) NGR_RS07685 NGR_RS05625
glk glucokinase NGR_RS28545 NGR_RS26390
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE) NGR_RS12915
aglF' glucose ABC transporter, permease component 1 (AglF) NGR_RS12920 NGR_RS30985
aglG' glucose ABC transporter, permease component 2 (AglG) NGR_RS12925 NGR_RS20150
aglK' glucose ABC transporter, ATPase component (AglK) NGR_RS12935 NGR_RS01305
ascB 6-phosphocellobiose hydrolase NGR_RS25855 NGR_RS01350
bglF glucose PTS, enzyme II (BCA components, BglF)
bglG cellobiose PTS system, EII-BC or EII-BCA components
bglT cellobiose transporter BglT
cbp cellobiose phosphorylase
cbpB cellobiose ABC transporter, substrate-binding component CpbB
cbpC cellobiose ABC transporter, substrate-binding component CbpC
cbtA cellobiose ABC transporter, substrate-binding component CbtA
cbtB cellobiose ABC transporter, permease component 1 (CbtB)
cbtC cellobiose ABC transporter, permease component 2 (CbtC) NGR_RS23365 NGR_RS03285
cbtD cellobiose ABC transporter, ATPase component 1 (CbtD) NGR_RS30455 NGR_RS08280
cbtF cellobiose ABC transporter, ATPase component 2 (CbtF) NGR_RS08285 NGR_RS30450
cdt cellobiose transporter cdt-1/cdt-2
cebE cellobiose ABC transporter, substrate-binding component CebE
cebF cellobiose ABC transporter, permease component 1 (CebF) NGR_RS01320 NGR_RS05360
cebG cellobiose ABC transporter, permease component 2 (CebG) NGR_RS08520 NGR_RS01315
celEIIA cellobiose PTS system, EII-A component
celEIIB cellobiose PTS system, EII-B component
celEIIC cellobiose PTS system, EII-C component
crr glucose PTS, enzyme IIA
eda 2-keto-3-deoxygluconate 6-phosphate aldolase NGR_RS25805 NGR_RS13545
edd phosphogluconate dehydratase NGR_RS12950 NGR_RS24345
gadh1 gluconate 2-dehydrogenase flavoprotein subunit NGR_RS00555
gadh2 gluconate 2-dehydrogenase cytochrome c subunit NGR_RS15000
gadh3 gluconate 2-dehydrogenase subunit 3 NGR_RS00550 NGR_RS00545
gdh quinoprotein glucose dehydrogenase NGR_RS15020 NGR_RS22565
glcS glucose ABC transporter, substrate-binding component (GlcS)
glcT glucose ABC transporter, permease component 1 (GlcT)
glcU glucose ABC transporter, permease component 2 (GlcU)
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) NGR_RS09940 NGR_RS01050
gnl gluconolactonase NGR_RS10695 NGR_RS02200
kguD 2-keto-6-phosphogluconate reductase NGR_RS25005 NGR_RS25725
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter NGR_RS09750
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
MFS-glucose glucose transporter, MFS superfamily
mglA glucose ABC transporter, ATP-binding component (MglA) NGR_RS23220 NGR_RS00525
mglB glucose ABC transporter, substrate-binding component NGR_RS23225 NGR_RS23260
mglC glucose ABC transporter, permease component (MglC) NGR_RS23215 NGR_RS23265
msdB1 cellobiose ABC transporter, permease component 1 (MsdB1) NGR_RS09950 NGR_RS30985
msdB2 cellobiose ABC transporter, permease component 2 (MsdB2) NGR_RS23885 NGR_RS09945
msdC1 cellobiose ABC transporter, permease component 1 (MsdC1) NGR_RS08650
msdC2 cellobiose ABC transporter, permease component 1 (MsdC2) NGR_RS08655 NGR_RS08520
msiK cellobiose ABC transporter, ATPase component NGR_RS09720 NGR_RS05345
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase NGR_RS25635 NGR_RS06645
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET
SMc04256 cellobiose ABC transporter, ATPase component NGR_RS20145 NGR_RS14665
SMc04257 cellobiose ABC transporter, permease component 1 NGR_RS20150 NGR_RS14660
SMc04258 cellobiose ABC transporter, permease component 2 NGR_RS20155 NGR_RS14655
SMc04259 cellobiose ABC transporter, substrate-binding protein NGR_RS20160 NGR_RS14650
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
TM0027 cellobiose ABC transporter, ATPase component 2 NGR_RS28510 NGR_RS05860
TM0028 cellobiose ABC transporter, ATPase component 1 NGR_RS30455 NGR_RS30450
TM0029 cellobiose ABC transporter, permease component 2
TM0030 cellobiose ABC transporter, permease component 1 NGR_RS03280 NGR_RS13105
TM0031 cellobiose ABC transporter, substrate-binding component

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