Protein WP_055436456.1 in Lacinutrix algicola AKS293

GapMind for catabolism of small carbon sources

Protein WP_055436456.1 in Lacinutrix algicola AKS293

Annotation: NCBI__GCF_001418085.1:WP_055436456.1

Length: 303 amino acids

Source: GCF_001418085.1 in NCBI

Candidate for 50 steps in catabolism of small carbon sources

Pathway	Step	Score	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
putrescine catabolism	potA	lo	Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized)	33%	64%	150.6	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-maltose catabolism	malK_Bb	lo	ABC-type maltose transport, ATP binding protein (characterized, see rationale)	34%	70%	149.8	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-maltose catabolism	malK	lo	Maltose-transporting ATPase (EC 3.6.3.19) (characterized)	34%	63%	147.1	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-maltose catabolism	thuK	lo	ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)	31%	89%	145.6	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
sucrose catabolism	thuK	lo	ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)	31%	89%	145.6	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
trehalose catabolism	thuK	lo	ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)	31%	89%	145.6	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-mannitol catabolism	mtlK	lo	ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)	34%	63%	142.5	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
L-arabinose catabolism	araV	lo	AraV, component of Arabinose, fructose, xylose porter (characterized)	32%	74%	140.2	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-fructose catabolism	araV	lo	AraV, component of Arabinose, fructose, xylose porter (characterized)	32%	74%	140.2	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
sucrose catabolism	araV	lo	AraV, component of Arabinose, fructose, xylose porter (characterized)	32%	74%	140.2	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-xylose catabolism	araV	lo	AraV, component of Arabinose, fructose, xylose porter (characterized)	32%	74%	140.2	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
N-acetyl-D-glucosamine catabolism	SMc02869	lo	N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)	34%	70%	139.8	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-cellobiose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	33%	76%	139.8	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-cellobiose catabolism	gtsD	lo	GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)	32%	61%	139.8	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-galactose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	33%	76%	139.8	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-glucosamine (chitosamine) catabolism	SMc02869	lo	N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)	34%	70%	139.8	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-glucose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	33%	76%	139.8	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-glucose catabolism	gtsD	lo	GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)	32%	61%	139.8	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
lactose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	33%	76%	139.8	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
lactose catabolism	gtsD	lo	GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)	32%	61%	139.8	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-maltose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	33%	76%	139.8	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-maltose catabolism	gtsD	lo	GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)	32%	61%	139.8	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-mannose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	33%	76%	139.8	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
sucrose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	33%	76%	139.8	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
sucrose catabolism	gtsD	lo	GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)	32%	61%	139.8	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
trehalose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	33%	76%	139.8	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
trehalose catabolism	gtsD	lo	GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)	32%	61%	139.8	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-sorbitol (glucitol) catabolism	mtlK	lo	ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized)	33%	63%	139	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
xylitol catabolism	Dshi_0546	lo	ABC transporter for Xylitol, ATPase component (characterized)	33%	72%	138.7	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
L-fucose catabolism	SM_b21106	lo	ABC transporter for L-Fucose, ATPase component (characterized)	34%	64%	137.1	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-glucosamine (chitosamine) catabolism	SM_b21216	lo	ABC transporter for D-Glucosamine, ATPase component (characterized)	31%	69%	136.7	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-maltose catabolism	musK	lo	ABC-type maltose transporter (EC 7.5.2.1) (characterized)	31%	63%	136	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
L-proline catabolism	opuBA	lo	BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized)	33%	77%	136	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
trehalose catabolism	treV	lo	TreV, component of Trehalose porter (characterized)	32%	85%	134.8	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-maltose catabolism	aglK	lo	ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)	32%	72%	134.4	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
sucrose catabolism	aglK	lo	ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)	32%	72%	134.4	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
trehalose catabolism	aglK	lo	ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)	32%	72%	134.4	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
lactose catabolism	lacK	lo	LacK, component of Lactose porter (characterized)	32%	64%	133.3	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-xylose catabolism	gtsD	lo	ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)	31%	61%	133.3	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
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)	30%	60%	132.5	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-maltose catabolism	malK_Aa	lo	ABC-type maltose transporter (EC 7.5.2.1) (characterized)	31%	60%	132.1	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-galactose catabolism	PfGW456L13_1897	lo	ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)	32%	61%	131.3	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-cellobiose catabolism	SMc04256	lo	ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)	33%	65%	129.4	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
xylitol catabolism	HSERO_RS17020	lo	ABC-type sugar transport system, ATPase component protein (characterized, see rationale)	32%	57%	123.2	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-cellobiose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	30%	69%	114.4	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-glucose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	30%	69%	114.4	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
lactose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	30%	69%	114.4	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
D-maltose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	30%	69%	114.4	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
sucrose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	30%	69%	114.4	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9
trehalose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	30%	69%	114.4	Fe(3+)-transporting ATPase; EC 3.6.3.30	38%	164.9

Sequence Analysis Tools

View WP_055436456.1 at NCBI

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MLNVKNLSFSYKKTPVLKDLSFNVKPGEYLAVIGESGCGKSTLLKVLRGEYDLNNGTVFW
KKEEILGPKHNLVIGYDFMKYVAQEFELEPYISVAENIGQHLSNFYKEEKKERTAELLEV
VELTNLASTKVKLLSGGQKQRVALARALANAPKILLLDEPFSHIDNFKKQSLRRNIFKYL
KDKNITCIVASHDKEDVLGFADQMMVLNDNKIEAYNTPEQLYNTPETPLIASFFGEFNVI
NDTIVYAHQLKIVEKSDLKAIVKNSYFKGNHYLIEADLDGNKVFFENSKTLKKETTIFLE
IPL

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

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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 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