Protein WP_040362879.1 in Collinsella tanakaei YIT 12063

GapMind for catabolism of small carbon sources

Protein WP_040362879.1 in Collinsella tanakaei YIT 12063

Annotation: NCBI__GCF_000225705.1:WP_040362879.1

Length: 248 amino acids

Source: GCF_000225705.1 in NCBI

Candidate for 53 steps in catabolism of small carbon sources

Pathway	Step	Score	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
L-asparagine catabolism	aapP	med	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)	56%	93%	271.9	uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ	54%	265.4
L-aspartate catabolism	aapP	med	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)	56%	93%	271.9	uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ	54%	265.4
L-glutamate catabolism	aapP	med	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)	56%	93%	271.9	uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ	54%	265.4
L-histidine catabolism	aapP	med	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)	56%	93%	271.9	uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ	54%	265.4
L-leucine catabolism	aapP	med	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)	56%	93%	271.9	uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ	54%	265.4
L-proline catabolism	aapP	med	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)	56%	93%	271.9	uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ	54%	265.4
D-alanine catabolism	Pf6N2E2_5405	med	ABC transporter for D-Alanine, ATPase component (characterized)	54%	94%	264.6	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-asparagine catabolism	glnQ	med	Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized)	56%	98%	263.8	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-glutamate catabolism	gltL	med	Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized)	56%	98%	263.8	uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ	54%	265.4
L-asparagine catabolism	bztD	med	BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)	54%	91%	259.6	uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ	54%	265.4
L-aspartate catabolism	bztD	med	BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)	54%	91%	259.6	uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ	54%	265.4
L-arginine catabolism	artP	med	Arginine transport ATP-binding protein ArtM (characterized)	54%	100%	255.4	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-lysine catabolism	hisP	med	Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale)	52%	92%	248.1	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-histidine catabolism	bgtA	med	BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)	53%	96%	242.3	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-histidine catabolism	hisP	med	Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)	50%	97%	241.9	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-histidine catabolism	BPHYT_RS24015	med	ABC transporter related (characterized, see rationale)	50%	95%	238	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-asparagine catabolism	bgtA	med	ATPase (characterized, see rationale)	52%	92%	235.7	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-aspartate catabolism	bgtA	med	ATPase (characterized, see rationale)	52%	92%	235.7	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
D-glucosamine (chitosamine) catabolism	AO353_21725	med	ABC transporter for D-Glucosamine, putative ATPase component (characterized)	51%	94%	235.7	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-citrulline catabolism	AO353_03040	med	ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)	49%	98%	235.3	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
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)	50%	90%	226.9	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-asparagine catabolism	aatP	med	ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)	49%	100%	226.5	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-aspartate catabolism	aatP	med	ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)	49%	100%	226.5	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-asparagine catabolism	peb1C	med	PEB1C, component of Uptake system for glutamate and aspartate (characterized)	48%	100%	221.5	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-aspartate catabolism	peb1C	med	PEB1C, component of Uptake system for glutamate and aspartate (characterized)	48%	100%	221.5	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-histidine catabolism	PA5503	med	Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)	42%	72%	179.5	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
D-maltose catabolism	thuK	lo	Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)	35%	64%	153.7	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
trehalose catabolism	thuK	lo	Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)	35%	64%	153.7	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
myo-inositol catabolism	PGA1_c07320	lo	Inositol transport system ATP-binding protein (characterized)	32%	84%	114.8	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
D-cellobiose catabolism	mglA	lo	glucose transporter, ATPase component (characterized)	32%	84%	114	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
D-glucose catabolism	mglA	lo	glucose transporter, ATPase component (characterized)	32%	84%	114	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
lactose catabolism	mglA	lo	glucose transporter, ATPase component (characterized)	32%	84%	114	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
D-maltose catabolism	mglA	lo	glucose transporter, ATPase component (characterized)	32%	84%	114	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
sucrose catabolism	mglA	lo	glucose transporter, ATPase component (characterized)	32%	84%	114	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
trehalose catabolism	mglA	lo	glucose transporter, ATPase component (characterized)	32%	84%	114	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-isoleucine catabolism	livG	lo	ABC transporter ATP-binding protein (characterized, see rationale)	30%	93%	111.3	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-leucine catabolism	livG	lo	ABC transporter ATP-binding protein (characterized, see rationale)	30%	93%	111.3	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-phenylalanine catabolism	livG	lo	ABC transporter ATP-binding protein (characterized, see rationale)	30%	93%	111.3	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-proline catabolism	HSERO_RS00895	lo	ABC transporter ATP-binding protein (characterized, see rationale)	30%	93%	111.3	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-serine catabolism	Ac3H11_1693	lo	ABC transporter ATP-binding protein (characterized, see rationale)	30%	93%	111.3	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-tyrosine catabolism	Ac3H11_1693	lo	ABC transporter ATP-binding protein (characterized, see rationale)	30%	93%	111.3	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-arginine catabolism	braG	lo	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	33%	91%	109.8	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-glutamate catabolism	braG	lo	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	33%	91%	109.8	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-histidine catabolism	braG	lo	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	33%	91%	109.8	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-isoleucine catabolism	livF	lo	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	33%	91%	109.8	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-leucine catabolism	livF	lo	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	33%	91%	109.8	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-valine catabolism	livF	lo	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	33%	91%	109.8	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-alanine catabolism	braG	lo	NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	30%	88%	107.8	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-histidine catabolism	natE	lo	NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	30%	88%	107.8	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-leucine catabolism	natE	lo	NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	30%	88%	107.8	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-proline catabolism	natE	lo	NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	30%	88%	107.8	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-serine catabolism	braG	lo	NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	30%	88%	107.8	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9
L-threonine catabolism	braG	lo	NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	30%	88%	107.8	AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)	56%	271.9

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Sequence

MVRIEGLRKSFGDLEVLRDVNLDIMPGEVVTIIGASGSGKSTLLRCINLLETPDAGHVWF
QGSDLTADHVDVNKLREDIGMVFQGFNLFNNMDVLDNCTLAPVTLKKATKQEAEQTAMHH
LESVGLADFADAAVAKLSGGQKQRVAIARALCMNPKIMLFDEPTSALDPEIVGEVLEAMR
KLAAEGMTMVVVTHEMAFARTVSDRVVFMDKGVIAEQGAPAQIFGNPQHARTREFLKRYL
DDADAVRA

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