Protein WP_101443438.1 in Pontibacter ramchanderi LP43

GapMind for catabolism of small carbon sources

Protein WP_101443438.1 in Pontibacter ramchanderi LP43

Annotation: NCBI__GCF_002846395.1:WP_101443438.1

Length: 221 amino acids

Source: GCF_002846395.1 in NCBI

Candidate for 49 steps in catabolism of small carbon sources

Pathway	Step	Score	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
lactose catabolism	lacK	lo	ABC transporter for Lactose, ATPase component (characterized)	38%	59%	150.6	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
putrescine catabolism	potA	lo	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)	36%	56%	150.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
D-maltose catabolism	malK_Bb	lo	ABC-type maltose transport, ATP binding protein (characterized, see rationale)	39%	61%	149.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
L-lysine catabolism	hisP	lo	ABC transporter for L-Lysine, ATPase component (characterized)	35%	88%	144.8	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
L-arginine catabolism	artP	lo	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)	35%	88%	144.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
L-histidine catabolism	hisP	lo	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)	35%	88%	144.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
L-fucose catabolism	SM_b21106	lo	ABC transporter for L-Fucose, ATPase component (characterized)	36%	56%	144.1	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
L-citrulline catabolism	AO353_03040	lo	ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)	36%	89%	139.8	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
D-glucosamine (chitosamine) catabolism	SM_b21216	lo	ABC transporter for D-Glucosamine, ATPase component (characterized)	34%	59%	139.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
N-acetyl-D-glucosamine catabolism	SMc02869	lo	N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)	35%	64%	138.7	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
D-glucosamine (chitosamine) catabolism	SMc02869	lo	N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)	35%	64%	138.7	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
D-sorbitol (glucitol) catabolism	mtlK	lo	ABC transporter for D-Sorbitol, ATPase component (characterized)	34%	60%	137.5	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
D-cellobiose catabolism	gtsD	lo	ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)	36%	55%	136	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
D-galactose catabolism	PfGW456L13_1897	lo	ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)	36%	55%	136	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
D-glucose catabolism	gtsD	lo	ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)	36%	55%	136	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
lactose catabolism	gtsD	lo	ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)	36%	55%	136	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
D-maltose catabolism	gtsD	lo	ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)	36%	55%	136	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
sucrose catabolism	gtsD	lo	ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)	36%	55%	136	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
trehalose catabolism	gtsD	lo	ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)	36%	55%	136	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
D-mannitol catabolism	mtlK	lo	ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)	33%	57%	134.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
D-cellobiose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	63%	134	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
D-galactose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	63%	134	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
D-glucose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	63%	134	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
lactose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	63%	134	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
D-maltose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	63%	134	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
D-mannose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	63%	134	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
sucrose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	63%	134	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
trehalose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	63%	134	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
D-maltose catabolism	malK	lo	ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)	34%	58%	133.7	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
D-xylose catabolism	gtsD	lo	ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)	34%	55%	133.3	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
xylitol catabolism	HSERO_RS17020	lo	ABC-type sugar transport system, ATPase component protein (characterized, see rationale)	37%	50%	128.6	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
D-maltose catabolism	thuK	lo	Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)	31%	58%	128.3	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
trehalose catabolism	thuK	lo	Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)	31%	58%	128.3	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
D-cellobiose catabolism	SMc04256	lo	ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)	35%	58%	127.1	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
D-mannose catabolism	TT_C0211	lo	Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)	32%	56%	124.8	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
sucrose catabolism	thuK	lo	Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)	32%	56%	124.8	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
trehalose catabolism	treV	lo	TreV, component of Trehalose porter (characterized)	31%	65%	122.9	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
L-isoleucine catabolism	livF	lo	high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)	32%	89%	114.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
L-leucine catabolism	livF	lo	high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)	32%	89%	114.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
L-phenylalanine catabolism	livF	lo	high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)	32%	89%	114.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
L-valine catabolism	livF	lo	high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)	32%	89%	114.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
D-alanine catabolism	AZOBR_RS08250	lo	Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)	33%	91%	114	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
L-proline catabolism	AZOBR_RS08250	lo	Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)	33%	91%	114	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
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)	31%	92%	112.1	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
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)	31%	92%	112.1	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
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)	31%	92%	112.1	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
L-arginine catabolism	braG	lo	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	31%	87%	106.3	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
L-glutamate catabolism	braG	lo	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	31%	87%	106.3	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2
L-histidine catabolism	braG	lo	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	31%	87%	106.3	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	45%	212.2

Sequence Analysis Tools

View WP_101443438.1 at NCBI

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

MLQVVNVHKKYGSLEVLKGIDLTIHAGEVVSIVGASGAGKSTLLHILGTLDSADTGDVLF
DDKNISRLNASELARFRNRHIGFIFQFHNLLPEFTAIENACLPGFLAGRPEMEVTERAAE
LLSMLNLGHRMHHKPSEMSGGEQQRTAVARALINSPRIIFADEPSGNLDSKNAQELHEIF
FKLRDEFNQTFVIVTHNEQLATMADRKLVMKDGLIVQEVKA

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)
Organisms (tab-delimited)
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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