Protein NP_347515.1 in Clostridium acetobutylicum ATCC 824

GapMind for catabolism of small carbon sources

Protein NP_347515.1 in Clostridium acetobutylicum ATCC 824

Annotation: NCBI__GCF_000008765.1:NP_347515.1

Length: 243 amino acids

Source: GCF_000008765.1 in NCBI

Candidate for 10 steps in catabolism of small carbon sources

Pathway	Step	Score	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
L-lysine catabolism	hisP	med	ABC transporter for L-Lysine, ATPase component (characterized)	48%	97%	232.6	Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.-	58%	292.4
D-glucosamine (chitosamine) catabolism	AO353_21725	med	ABC transporter for D-glucosamine, ATPase component (characterized)	47%	94%	231.5	Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.-	58%	292.4
L-citrulline catabolism	PS417_17605	med	ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)	45%	89%	227.6	Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.-	58%	292.4
L-asparagine catabolism	peb1C	med	PEB1C, component of Uptake system for glutamate and aspartate (characterized)	47%	99%	226.5	Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.-	58%	292.4
L-aspartate catabolism	peb1C	med	PEB1C, component of Uptake system for glutamate and aspartate (characterized)	47%	99%	226.5	Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.-	58%	292.4
L-glutamate catabolism	gltL	med	PEB1C, component of Uptake system for glutamate and aspartate (characterized)	47%	99%	226.5	Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.-	58%	292.4
D-alanine catabolism	Pf6N2E2_5405	med	ABC transporter for D-Alanine, ATPase component (characterized)	46%	95%	225.7	Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.-	58%	292.4
L-proline catabolism	proV	lo	glycine betaine/l-proline transport atp-binding protein prov (characterized)	39%	60%	164.9	Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.-	58%	292.4
L-arabinose catabolism	xylGsa	lo	Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)	34%	90%	126.7	Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.-	58%	292.4
L-phenylalanine catabolism	livG	lo	High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)	31%	97%	125.6	Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.-	58%	292.4

Sequence Analysis Tools

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MIKIESLHKTYGDNEVLKGISLEIKAGEIVAVIGPSGTGKSTFLRCLNYLERPDSGTLLI
GDVRVDFENISKDEVYSLRKKTSMVFQNYNLFKNKTALENVMEALRVVKKMPKDEAEKVS
LEALKQVGLLDKANSYPSRLSGGQQQRIGIARAMVLKPEIILFDEPTSALDPEWVGEVLD
VIKGIASRHLTMIIVTHEMSFAREIADKIVFLDGGKIIQYGTPEEVFEKSNNDRVNQFIK
KLH

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources