GapMind for catabolism of small carbon sources

 

L-proline catabolism in Klebsiella michiganensis M5al

Best path

HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA

Also see fitness data for the top candidates

Rules

Overview: Proline degradation in GapMind is based on MetaCyc pathway I via glutamate semialdehyde dehydrogenase (link) and pathway II via 5-aminopentanoate (link). (MetaCyc describes 5-aminopentanoate, also known as 5-aminovalerate, as a fermentative end product, but it is further degraded

53 steps (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
HSERO_RS00870 proline ABC transporter, substrate-binding component BWI76_RS07260 BWI76_RS26350
HSERO_RS00885 proline ABC transporter, permease component 1 BWI76_RS07280 BWI76_RS26345
HSERO_RS00890 proline ABC transporter, permease component 2 BWI76_RS07275 BWI76_RS26340
HSERO_RS00895 proline ABC transporter, ATPase component 1 BWI76_RS07270 BWI76_RS05980
HSERO_RS00900 proline ABC transporter, ATPase component 2 BWI76_RS07265 BWI76_RS05975
put1 proline dehydrogenase BWI76_RS10795
putA L-glutamate 5-semialdeyde dehydrogenase BWI76_RS10795 BWI76_RS07615
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) BWI76_RS18355 BWI76_RS07580
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BWI76_RS08095 BWI76_RS08965
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase BWI76_RS23445 BWI76_RS01360
AZOBR_RS08235 proline ABC transporter, permease component 1 BWI76_RS26345 BWI76_RS07280
AZOBR_RS08240 proline ABC transporter, permease component 2 BWI76_RS26340 BWI76_RS07275
AZOBR_RS08245 proline ABC transporter, ATPase component 1 BWI76_RS26335 BWI76_RS05980
AZOBR_RS08250 proline ABC transporter, ATPase component 2 BWI76_RS26330 BWI76_RS05975
AZOBR_RS08260 proline ABC transporter, substrate-binding component BWI76_RS26365 BWI76_RS26350
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS BWI76_RS07630
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase BWI76_RS05620 BWI76_RS03865
davT 5-aminovalerate aminotransferase BWI76_RS26375 BWI76_RS14020
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BWI76_RS13115 BWI76_RS20455
ectP proline transporter EctP BWI76_RS07630
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BWI76_RS01365 BWI76_RS20455
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hutV proline ABC transporter, ATPase component HutV BWI76_RS22065 BWI76_RS17620
hutW proline ABC transporter, permease component HutW BWI76_RS22070
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) BWI76_RS26335 BWI76_RS05980
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) BWI76_RS05985
natD proline ABC transporter, permease component 2 (NatD) BWI76_RS05990 BWI76_RS26345
natE proline ABC transporter, ATPase component 2 (NatE) BWI76_RS26330 BWI76_RS05975
opuBA proline ABC transporter, ATPase component OpuBA/BusAA BWI76_RS22065 BWI76_RS17620
opuBB proline ABC transporter, fused permease and substrate-binding components OpuBB/BusAB BWI76_RS22070
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase
proP proline:H+ symporter ProP BWI76_RS02250 BWI76_RS03450
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV BWI76_RS22065 BWI76_RS17620
proW proline ABC transporter, permease component ProW BWI76_RS22070 BWI76_RS15035
proX proline ABC transporter, substrate-binding component ProX BWI76_RS22075
proY proline:H+ symporter BWI76_RS06245 BWI76_RS08745
putP proline:Na+ symporter BWI76_RS10800 BWI76_RS25550
SLC6A7 proline:Na+ symporter

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