Protein WP_074201472.1 in Sulfurivirga caldicuralii DSM 17737

GapMind for catabolism of small carbon sources

Protein WP_074201472.1 in Sulfurivirga caldicuralii DSM 17737

Annotation: NCBI__GCF_900141795.1:WP_074201472.1

Length: 264 amino acids

Source: GCF_900141795.1 in NCBI

Candidate for 57 steps in catabolism of small carbon sources

Pathway	Step	Score	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
L-arabinose catabolism	araV	lo	AraV, component of Arabinose, fructose, xylose porter (characterized)	38%	62%	148.7	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
D-fructose catabolism	araV	lo	AraV, component of Arabinose, fructose, xylose porter (characterized)	38%	62%	148.7	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
sucrose catabolism	araV	lo	AraV, component of Arabinose, fructose, xylose porter (characterized)	38%	62%	148.7	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
D-xylose catabolism	araV	lo	AraV, component of Arabinose, fructose, xylose porter (characterized)	38%	62%	148.7	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
L-asparagine catabolism	glnQ	lo	Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized)	33%	97%	139.8	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
L-glutamate catabolism	gltL	lo	Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized)	33%	97%	139.8	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
L-proline catabolism	proV	lo	glycine betaine/l-proline transport atp-binding protein prov (characterized)	37%	55%	138.3	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
L-histidine catabolism	PA5503	lo	Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)	37%	65%	137.1	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
L-histidine catabolism	hutV	lo	ABC transporter for L-Histidine, ATPase component (characterized)	35%	80%	135.2	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
sucrose catabolism	thuK	lo	ABC transporter (characterized, see rationale)	36%	61%	135.2	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
D-cellobiose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	64%	132.1	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
D-galactose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	64%	132.1	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
D-glucose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	64%	132.1	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
lactose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	64%	132.1	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
D-maltose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	64%	132.1	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
D-mannose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	64%	132.1	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
sucrose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	64%	132.1	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
trehalose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	64%	132.1	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
putrescine catabolism	potA	lo	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)	35%	61%	131.7	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
L-histidine catabolism	BPHYT_RS24015	lo	ABC transporter related (characterized, see rationale)	32%	95%	131.3	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
L-citrulline catabolism	PS417_17605	lo	ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)	34%	89%	131	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
L-lysine catabolism	hisP	lo	ABC transporter for L-Lysine, ATPase component (characterized)	34%	98%	131	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
D-sorbitol (glucitol) catabolism	mtlK	lo	ABC transporter for D-Sorbitol, ATPase component (characterized)	34%	70%	129.4	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
L-alanine catabolism	braF	lo	NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	31%	93%	128.3	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
L-histidine catabolism	natA	lo	NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	31%	93%	128.3	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
L-leucine catabolism	natA	lo	NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	31%	93%	128.3	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
L-proline catabolism	natA	lo	NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	31%	93%	128.3	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
L-serine catabolism	braF	lo	NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	31%	93%	128.3	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
L-threonine catabolism	braF	lo	NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	31%	93%	128.3	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
L-proline catabolism	opuBA	lo	BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized)	33%	57%	126.3	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
D-glucosamine (chitosamine) catabolism	AO353_21725	lo	ABC transporter for D-Glucosamine, putative ATPase component (characterized)	32%	95%	125.2	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
L-arginine catabolism	artP	lo	ABC transporter for L-Arginine, putative ATPase component (characterized)	34%	91%	124.4	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
L-proline catabolism	hutV	lo	HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)	33%	89%	124.4	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
D-maltose catabolism	thuK	lo	Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)	35%	60%	123.6	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
trehalose catabolism	thuK	lo	Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)	35%	60%	123.6	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
D-mannose catabolism	TM1750	lo	TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)	30%	78%	122.1	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
L-histidine catabolism	bgtA	lo	BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)	32%	96%	121.3	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
D-mannitol catabolism	mtlK	lo	SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)	35%	64%	119	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
trehalose catabolism	treV	lo	TreV, component of Trehalose porter (characterized)	30%	78%	118.6	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
D-cellobiose catabolism	cbtD	lo	CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)	31%	71%	118.2	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
L-histidine catabolism	Ac3H11_2560	lo	ABC transporter for L-Histidine, ATPase component (characterized)	35%	80%	117.9	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
glycerol catabolism	glpT	lo	GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)	33%	60%	116.3	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
xylitol catabolism	HSERO_RS17020	lo	ABC-type sugar transport system, ATPase component protein (characterized, see rationale)	34%	51%	115.5	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
N-acetyl-D-glucosamine catabolism	SMc02869	lo	N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)	32%	71%	115.2	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
D-glucosamine (chitosamine) catabolism	SMc02869	lo	N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)	32%	71%	115.2	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
D-maltose catabolism	aglK	lo	ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)	33%	64%	115.2	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
sucrose catabolism	aglK	lo	ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)	33%	64%	115.2	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
trehalose catabolism	aglK	lo	ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)	33%	64%	115.2	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
L-asparagine catabolism	aatP	lo	ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)	31%	91%	114	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
L-aspartate catabolism	aatP	lo	ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)	31%	91%	114	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
lactose catabolism	lacK	lo	ABC transporter for Lactose, ATPase component (characterized)	33%	60%	108.6	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
D-cellobiose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	32%	60%	105.9	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
D-glucose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	32%	60%	105.9	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
lactose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	32%	60%	105.9	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
D-maltose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	32%	60%	105.9	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
sucrose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	32%	60%	105.9	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0
trehalose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	32%	60%	105.9	Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.-	61%	334.0

Sequence Analysis Tools

View WP_074201472.1 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

MRTLIDVDNLTFSRGARRIFDGLSLTIREGQITAIMGPSGTGKTTLLKLIAGQLTPDSGR
ILFDGQDVHALRRGELFRLRQRMGMLFQSGALLTDLNVFDNVAFPLREHTKLPEVLIEKL
VLMKLQAVGLRGARHLMASELSGGMARRVALARAIAMDPEVVMYDEPFVGQDPITMGVLL
KLIQRLNESLGLTSIVVSHDVQEVMSIAHYVYVISEGRVVAEGAAEEVAQSEQPYVRQFL
NGLPDGPVPFHYPAPAYAEELGLC

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)
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