Protein WP_013458990.1 in Sulfuricurvum kujiense DSM 16994

GapMind for catabolism of small carbon sources

Protein WP_013458990.1 in Sulfuricurvum kujiense DSM 16994

Annotation: NCBI__GCF_000183725.1:WP_013458990.1

Length: 258 amino acids

Source: GCF_000183725.1 in NCBI

Candidate for 45 steps in catabolism of small carbon sources

Pathway	Step	Score	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
L-histidine catabolism	Ac3H11_2560	med	ABC transporter for L-Histidine, ATPase component (characterized)	42%	81%	171	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
putrescine catabolism	potA	lo	PotG aka B0855, component of Putrescine porter (characterized)	38%	65%	165.6	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
L-arabinose catabolism	xacJ	lo	Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)	36%	55%	150.6	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
D-sorbitol (glucitol) catabolism	mtlK	lo	ABC transporter for D-Sorbitol, ATPase component (characterized)	36%	59%	149.4	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
D-maltose catabolism	malK	lo	Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized)	38%	57%	148.3	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
N-acetyl-D-glucosamine catabolism	SMc02869	lo	N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)	37%	63%	147.9	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
D-glucosamine (chitosamine) catabolism	SMc02869	lo	N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)	37%	63%	147.9	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
D-cellobiose catabolism	gtsD	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)	37%	55%	146.4	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
D-glucose catabolism	gtsD	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)	37%	55%	146.4	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
lactose catabolism	gtsD	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)	37%	55%	146.4	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
D-maltose catabolism	gtsD	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)	37%	55%	146.4	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
D-maltose 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)	37%	55%	146.4	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
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)	37%	55%	146.4	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
sucrose catabolism	gtsD	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)	37%	55%	146.4	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
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)	37%	55%	146.4	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
trehalose catabolism	gtsD	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)	37%	55%	146.4	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
trehalose 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)	37%	55%	146.4	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
L-arabinose catabolism	xacK	lo	Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)	38%	56%	145.2	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
D-maltose catabolism	malK1	lo	MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized)	34%	68%	140.2	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
D-alanine catabolism	Pf6N2E2_5405	lo	ABC transporter for D-Alanine, ATPase component (characterized)	36%	90%	139	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
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)	36%	85%	136	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
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)	36%	85%	136	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
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)	36%	85%	136	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
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)	36%	85%	136	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
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)	36%	85%	136	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
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)	36%	85%	136	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
D-maltose catabolism	malK_Bb	lo	ABC-type maltose transport, ATP binding protein (characterized, see rationale)	36%	60%	135.2	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
D-glucosamine (chitosamine) catabolism	SM_b21216	lo	ABC transporter for D-Glucosamine, ATPase component (characterized)	38%	57%	134	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
D-cellobiose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	35%	56%	133.3	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
D-glucose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	35%	56%	133.3	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
lactose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	35%	56%	133.3	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
D-maltose catabolism	aglK	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	35%	56%	133.3	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
D-maltose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	35%	56%	133.3	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
sucrose catabolism	aglK	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	35%	56%	133.3	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
sucrose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	35%	56%	133.3	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
trehalose catabolism	aglK	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	35%	56%	133.3	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
trehalose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	35%	56%	133.3	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
D-galactose catabolism	PfGW456L13_1897	lo	ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)	35%	54%	132.9	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
D-maltose catabolism	musK	lo	ABC-type maltose transporter (EC 7.5.2.1) (characterized)	37%	50%	132.1	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
D-glucosamine (chitosamine) catabolism	AO353_21725	lo	ABC transporter for D-glucosamine, ATPase component (characterized)	33%	87%	131	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
D-mannitol catabolism	mtlK	lo	ABC transporter for D-mannitol and D-mannose, ATPase component (characterized)	33%	57%	131	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
lactose catabolism	lacK	lo	LacK, component of Lactose porter (characterized)	34%	57%	129.4	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
trehalose catabolism	treV	lo	TreV, component of Trehalose porter (characterized)	32%	69%	129	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
L-isoleucine catabolism	livG	lo	High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)	30%	96%	121.7	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8
L-phenylalanine catabolism	livG	lo	High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)	30%	96%	121.7	CynD, component of Bispecific cyanate/nitrite transporter	44%	171.8

Sequence Analysis Tools

View WP_013458990.1 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

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Sequence

MSYLQIRNVWKTYDDNVILEKLNFTIEKGEFCTLIGPSGCGKSTFLRMLLGKESPTRGTI
LLEGEPLSNEPGSDRGVVFQKYTLFPHLRALENVMLGLEMEHSAFLGKAFGSARRRIKEE
AMEMIKAVGLEQSAHKYPSELSGGMQQRLSIAQALVKKPKILLLDEPFGALDPGSRSDMQ
ELVHGLWQTYGLTAFMVTHDVKEAFELGTRLLVFDKVRNDPHSPNAYGATVVNDIKLDKN
KRKNKGEGHVDHDETIIA

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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SQLite3 databases

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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