Protein WP_009566877.1 in Acidithiobacillus ferrooxidans ATCC 23270

GapMind for catabolism of small carbon sources

Protein WP_009566877.1 in Acidithiobacillus ferrooxidans ATCC 23270

Annotation: NCBI__GCF_000021485.1:WP_009566877.1

Length: 231 amino acids

Source: GCF_000021485.1 in NCBI

Candidate for 42 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	lo	Arginine transport ATP-binding protein ArtM (characterized)	36%	89%	141	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
L-asparagine catabolism	bztD	lo	BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)	35%	87%	137.9	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
L-aspartate catabolism	bztD	lo	BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)	35%	87%	137.9	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
L-glutamate catabolism	gltL	lo	BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)	35%	87%	137.9	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
D-maltose catabolism	thuK	lo	Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)	34%	56%	135.6	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
trehalose catabolism	thuK	lo	Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)	34%	56%	135.6	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
D-cellobiose catabolism	gtsD	lo	Sugar ABC transporter ATP-binding protein (characterized, see rationale)	34%	61%	134	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
D-glucose catabolism	gtsD	lo	Sugar ABC transporter ATP-binding protein (characterized, see rationale)	34%	61%	134	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
lactose catabolism	gtsD	lo	Sugar ABC transporter ATP-binding protein (characterized, see rationale)	34%	61%	134	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
D-maltose catabolism	gtsD	lo	Sugar ABC transporter ATP-binding protein (characterized, see rationale)	34%	61%	134	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
sucrose catabolism	gtsD	lo	Sugar ABC transporter ATP-binding protein (characterized, see rationale)	34%	61%	134	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
trehalose catabolism	gtsD	lo	Sugar ABC transporter ATP-binding protein (characterized, see rationale)	34%	61%	134	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
L-histidine catabolism	BPHYT_RS24015	lo	ABC transporter related (characterized, see rationale)	37%	86%	131.3	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
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)	38%	78%	130.6	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
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)	38%	78%	130.6	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
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)	38%	78%	130.6	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
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)	38%	78%	130.6	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
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)	38%	78%	130.6	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
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)	38%	78%	130.6	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
D-xylose catabolism	gtsD	lo	ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)	33%	55%	128.3	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
L-arabinose catabolism	araV	lo	AraV, component of Arabinose, fructose, xylose porter (characterized)	34%	54%	127.5	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
D-fructose catabolism	araV	lo	AraV, component of Arabinose, fructose, xylose porter (characterized)	34%	54%	127.5	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
sucrose catabolism	araV	lo	AraV, component of Arabinose, fructose, xylose porter (characterized)	34%	54%	127.5	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
D-xylose catabolism	araV	lo	AraV, component of Arabinose, fructose, xylose porter (characterized)	34%	54%	127.5	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
D-cellobiose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	35%	57%	126.7	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
D-cellobiose catabolism	msiK	lo	MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)	35%	53%	126.7	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
D-galactose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	35%	57%	126.7	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
D-glucose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	35%	57%	126.7	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
lactose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	35%	57%	126.7	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
D-maltose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	35%	57%	126.7	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
D-mannose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	35%	57%	126.7	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
sucrose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	35%	57%	126.7	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
trehalose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	35%	57%	126.7	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
D-mannitol catabolism	mtlK	lo	ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)	34%	60%	125.6	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
lactose catabolism	lacK	lo	ABC transporter for Lactose, ATPase component (characterized)	36%	61%	124.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
N-acetyl-D-glucosamine catabolism	SMc02869	lo	N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)	35%	60%	122.9	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
D-glucosamine (chitosamine) catabolism	SMc02869	lo	N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)	35%	60%	122.9	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
D-sorbitol (glucitol) catabolism	mtlK	lo	ABC transporter for D-Sorbitol, ATPase component (characterized)	32%	64%	122.1	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
D-maltose catabolism	musK	lo	ABC-type maltose transporter (EC 7.5.2.1) (characterized)	35%	53%	118.6	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
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)	31%	57%	118.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
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)	31%	57%	118.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8
D-maltose catabolism	malK_Bb	lo	ABC-type maltose transport, ATP binding protein (characterized, see rationale)	30%	61%	116.3	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	50%	218.8

Sequence Analysis Tools

View WP_009566877.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MSEQIILSVEHLRQSFAIGRERLEVIRDVNLQVRPGERLAIVGASGQGKSTLMHLMGGLE
RPSGGVVRILGQEVYKLSESARSRLRNQSVGFVYQLHRLLPEFTALENVLLPLLIRRVPR
RSVEPWGKEILTRVGLSERLDHKPGMLSGGERQRVALARALVTRPALLLADEPTGNLDSE
SAESVHQLMLDLNQELGTALVIVTHEPALAAHMEHVLRLQDGVLQPLDAVH

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update 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