Protein CA265_RS04345 in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Protein CA265_RS04345 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: FitnessBrowser__Pedo557:CA265_RS04345

Length: 216 amino acids

Source: Pedo557 in FitnessBrowser

Candidate for 61 steps in catabolism of small carbon sources

Pathway	Step	Score	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
L-arginine catabolism	artP	med	Arginine transport ATP-binding protein ArtM (characterized)	43%	90%	163.7	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-glutamate catabolism	gltL	lo	GluA aka CGL1950, component of Glutamate porter (characterized)	40%	89%	153.7	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
lactose catabolism	lacK	lo	LacK, component of Lactose porter (characterized)	39%	58%	147.1	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-asparagine catabolism	aatP	lo	Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)	39%	89%	143.3	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-aspartate catabolism	aatP	lo	Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)	39%	89%	143.3	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-asparagine catabolism	bgtA	lo	ATPase (characterized, see rationale)	40%	83%	141.7	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-aspartate catabolism	bgtA	lo	ATPase (characterized, see rationale)	40%	83%	141.7	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
sucrose catabolism	thuK	lo	ABC transporter (characterized, see rationale)	35%	55%	137.9	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-lysine catabolism	hisP	lo	ABC transporter for L-Lysine, ATPase component (characterized)	37%	89%	137.1	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
D-maltose catabolism	malK_Bb	lo	ABC-type maltose transport, ATP binding protein (characterized, see rationale)	34%	60%	137.1	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-asparagine catabolism	aapP	lo	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)	37%	83%	136	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-aspartate catabolism	aapP	lo	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)	37%	83%	136	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
D-glucosamine (chitosamine) catabolism	AO353_21725	lo	ABC transporter for D-Glucosamine, putative ATPase component (characterized)	37%	85%	136	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-glutamate catabolism	aapP	lo	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)	37%	83%	136	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-histidine catabolism	aapP	lo	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)	37%	83%	136	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-leucine catabolism	aapP	lo	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)	37%	83%	136	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-proline catabolism	aapP	lo	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)	37%	83%	136	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
D-alanine catabolism	Pf6N2E2_5405	lo	ABC transporter for D-Alanine, ATPase component (characterized)	36%	85%	134.8	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
D-sorbitol (glucitol) catabolism	mtlK	lo	ABC transporter for D-Sorbitol, ATPase component (characterized)	36%	60%	132.9	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
D-cellobiose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	37%	57%	131.3	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
D-glucose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	37%	57%	131.3	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
lactose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	37%	57%	131.3	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
D-maltose catabolism	aglK	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	37%	57%	131.3	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
D-maltose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	37%	57%	131.3	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
sucrose catabolism	aglK	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	37%	57%	131.3	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
sucrose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	37%	57%	131.3	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
trehalose catabolism	aglK	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	37%	57%	131.3	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
trehalose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	37%	57%	131.3	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-histidine catabolism	bgtA	lo	BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)	36%	84%	131	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
N-acetyl-D-glucosamine catabolism	SMc02869	lo	N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)	33%	63%	127.5	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
D-glucosamine (chitosamine) catabolism	SMc02869	lo	N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)	33%	63%	127.5	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
D-mannitol catabolism	mtlK	lo	SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)	30%	62%	122.1	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-tryptophan catabolism	ecfA2	lo	Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)	36%	73%	115.5	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-isoleucine catabolism	livG	lo	ABC transporter ATP-binding protein (characterized, see rationale)	32%	87%	109.8	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-leucine catabolism	livG	lo	ABC transporter ATP-binding protein (characterized, see rationale)	32%	87%	109.8	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-phenylalanine catabolism	livG	lo	ABC transporter ATP-binding protein (characterized, see rationale)	32%	87%	109.8	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-proline catabolism	HSERO_RS00895	lo	ABC transporter ATP-binding protein (characterized, see rationale)	32%	87%	109.8	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-serine catabolism	Ac3H11_1693	lo	ABC transporter ATP-binding protein (characterized, see rationale)	32%	87%	109.8	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-tyrosine catabolism	Ac3H11_1693	lo	ABC transporter ATP-binding protein (characterized, see rationale)	32%	87%	109.8	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-alanine catabolism	braG	lo	High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)	33%	91%	109.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-isoleucine catabolism	livF	lo	High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)	33%	91%	109.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-leucine catabolism	livF	lo	High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)	33%	91%	109.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-serine catabolism	braG	lo	High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)	33%	91%	109.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-threonine catabolism	braG	lo	High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)	33%	91%	109.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-valine catabolism	livF	lo	High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)	33%	91%	109.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-phenylalanine catabolism	livF	lo	High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)	32%	91%	105.5	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
D-alanine catabolism	AZOBR_RS08250	lo	Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)	33%	90%	103.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-proline catabolism	AZOBR_RS08250	lo	Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)	33%	90%	103.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-proline catabolism	HSERO_RS00900	lo	ABC transporter ATP-binding protein (characterized, see rationale)	33%	88%	102.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-serine catabolism	Ac3H11_1692	lo	ABC transporter ATP-binding protein (characterized, see rationale)	33%	88%	102.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-tyrosine catabolism	Ac3H11_1692	lo	ABC transporter ATP-binding protein (characterized, see rationale)	33%	88%	102.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-arabinose catabolism	xylGsa	lo	Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)	31%	86%	100.1	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-arginine catabolism	braG	lo	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	32%	86%	99	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-glutamate catabolism	braG	lo	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	32%	86%	99	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-histidine catabolism	braG	lo	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	32%	86%	99	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-isoleucine catabolism	natE	lo	NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)	31%	85%	98.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-leucine catabolism	natE	lo	NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)	31%	85%	98.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-proline catabolism	natE	lo	NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)	31%	85%	98.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-valine catabolism	natE	lo	NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)	31%	85%	98.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
L-histidine catabolism	natE	lo	NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	33%	64%	89.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2
glycerol catabolism	glpS	lo	GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)	31%	50%	88.6	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	47%	207.2

Sequence Analysis Tools

View CA265_RS04345 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MLKATGIRKSYGNLQILKGVNFEVQKGEIVSIIGPSGAGKSTLLHILGTLDKPDDGSVQL
KGTVINKLNGDLLSTFRNQNIGFVFQFHHLLPEFSAIENICIPAFIAKTNKKQAETRAFE
LLDLFGLKDRAQHKPNQLSGGEQQRVAIARALINNPSIILADEPSGNLDSENAAGLHQLF
VSLRDNFHQTFVIVTHNEHLAKTSDRVVSMKDGLIV

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:

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