GapMind for catabolism of small carbon sources

 

L-proline catabolism in Streptomyces kebangsaanensis SUK12

Best path

proY, put1, putA

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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
proY proline:H+ symporter RH94_RS16615 RH94_RS03380
put1 proline dehydrogenase
putA L-glutamate 5-semialdeyde dehydrogenase RH94_RS12920 RH94_RS00205
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) RH94_RS35175
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP RH94_RS07765 RH94_RS35170
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase RH94_RS19075 RH94_RS13405
AZOBR_RS08235 proline ABC transporter, permease component 1 RH94_RS35945
AZOBR_RS08240 proline ABC transporter, permease component 2 RH94_RS35950 RH94_RS13305
AZOBR_RS08245 proline ABC transporter, ATPase component 1 RH94_RS35955 RH94_RS13295
AZOBR_RS08250 proline ABC transporter, ATPase component 2 RH94_RS35960 RH94_RS13290
AZOBR_RS08260 proline ABC transporter, substrate-binding component
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS RH94_RS15170
CCNA_00435 proline transporter RH94_RS18530 RH94_RS20930
davD glutarate semialdehyde dehydrogenase RH94_RS37005 RH94_RS01805
davT 5-aminovalerate aminotransferase RH94_RS25670 RH94_RS36945
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase RH94_RS12595 RH94_RS13400
ectP proline transporter EctP RH94_RS15170
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase RH94_RS11175 RH94_RS19145
gcdG succinyl-CoA:glutarate CoA-transferase RH94_RS20585 RH94_RS04285
gcdH glutaryl-CoA dehydrogenase RH94_RS20440 RH94_RS20675
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component RH94_RS35940
HSERO_RS00885 proline ABC transporter, permease component 1 RH94_RS35945 RH94_RS13300
HSERO_RS00890 proline ABC transporter, permease component 2 RH94_RS35950
HSERO_RS00895 proline ABC transporter, ATPase component 1 RH94_RS35955 RH94_RS13295
HSERO_RS00900 proline ABC transporter, ATPase component 2 RH94_RS35960 RH94_RS13290
hutV proline ABC transporter, ATPase component HutV RH94_RS11290 RH94_RS22045
hutW proline ABC transporter, permease component HutW RH94_RS22050 RH94_RS29515
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) RH94_RS33870
N515DRAFT_2924 proline transporter RH94_RS18530 RH94_RS20930
natA proline ABC transporter, ATPase component 1 (NatA) RH94_RS35955 RH94_RS13295
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) RH94_RS35950
natD proline ABC transporter, permease component 2 (NatD) RH94_RS35945
natE proline ABC transporter, ATPase component 2 (NatE) RH94_RS35960 RH94_RS13290
opuBA proline ABC transporter, ATPase component OpuBA/BusAA RH94_RS22045 RH94_RS29525
opuBB proline ABC transporter, fused permease and substrate-binding components OpuBB/BusAB RH94_RS22050
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 RH94_RS13185 RH94_RS11695
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV RH94_RS11290 RH94_RS22045
proW proline ABC transporter, permease component ProW RH94_RS22050 RH94_RS29515
proX proline ABC transporter, substrate-binding component ProX
putP proline:Na+ symporter
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 24 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