Protein YP_425589.1 in Rhodospirillum rubrum ATCC 11170

GapMind for catabolism of small carbon sources

Protein YP_425589.1 in Rhodospirillum rubrum ATCC 11170

Annotation: NCBI__GCF_000013085.1:YP_425589.1

Length: 366 amino acids

Source: GCF_000013085.1 in NCBI

Candidate for 56 steps in catabolism of small carbon sources

Pathway	Step	Score	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
putrescine catabolism	potA	med	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)	49%	75%	267.7	Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter	44%	264.2
D-cellobiose catabolism	gtsD	med	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)	44%	91%	257.7	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-glucose catabolism	gtsD	med	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)	44%	91%	257.7	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
lactose catabolism	gtsD	med	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)	44%	91%	257.7	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-maltose catabolism	gtsD	med	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)	44%	91%	257.7	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-maltose catabolism	thuK	med	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)	44%	91%	257.7	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-mannose catabolism	TT_C0211	med	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)	44%	91%	257.7	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
sucrose catabolism	gtsD	med	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)	44%	91%	257.7	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
sucrose catabolism	thuK	med	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)	44%	91%	257.7	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
trehalose catabolism	gtsD	med	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)	44%	91%	257.7	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
trehalose catabolism	thuK	med	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)	44%	91%	257.7	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-maltose catabolism	malK	med	Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized)	43%	89%	255.8	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-sorbitol (glucitol) catabolism	mtlK	med	ABC transporter for D-Sorbitol, ATPase component (characterized)	43%	87%	246.9	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-mannitol catabolism	mtlK	med	MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)	44%	83%	246.5	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
lactose catabolism	lacK	med	ABC transporter for Lactose, ATPase component (characterized)	41%	99%	244.2	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
xylitol catabolism	Dshi_0546	med	ABC transporter for Xylitol, ATPase component (characterized)	41%	87%	244.2	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
N-acetyl-D-glucosamine catabolism	SMc02869	med	N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)	41%	99%	243	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
L-fucose catabolism	SM_b21106	med	ABC transporter for L-Fucose, ATPase component (characterized)	41%	95%	243	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-glucosamine (chitosamine) catabolism	SM_b21216	med	ABC transporter for D-Glucosamine, ATPase component (characterized)	41%	89%	243	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-glucosamine (chitosamine) catabolism	SMc02869	med	N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)	41%	99%	243	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-galactose catabolism	PfGW456L13_1897	med	ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)	40%	92%	240.7	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-maltose catabolism	musK	med	ABC-type maltose transporter (EC 7.5.2.1) (characterized)	40%	93%	236.1	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-maltose catabolism	malK1	med	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)	42%	88%	234.6	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-cellobiose catabolism	aglK'	med	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	41%	88%	234.2	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-glucose catabolism	aglK'	med	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	41%	88%	234.2	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
lactose catabolism	aglK'	med	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	41%	88%	234.2	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-maltose catabolism	aglK	med	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	41%	88%	234.2	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-maltose catabolism	aglK'	med	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	41%	88%	234.2	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
sucrose catabolism	aglK	med	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	41%	88%	234.2	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
sucrose catabolism	aglK'	med	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	41%	88%	234.2	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
trehalose catabolism	aglK	med	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	41%	88%	234.2	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
trehalose catabolism	aglK'	med	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	41%	88%	234.2	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-maltose catabolism	malK_Bb	med	ABC-type maltose transport, ATP binding protein (characterized, see rationale)	46%	71%	232.6	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
xylitol catabolism	HSERO_RS17020	med	ABC-type sugar transport system, ATPase component protein (characterized, see rationale)	41%	85%	229.2	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
trehalose catabolism	treV	med	TreV, component of Trehalose porter (characterized)	45%	74%	220.7	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
L-histidine catabolism	hutV	med	ABC transporter for L-Histidine, ATPase component (characterized)	41%	82%	171.4	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-xylose catabolism	gtsD	lo	ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)	40%	92%	243.8	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
L-arabinose catabolism	xacK	lo	Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)	39%	94%	240.7	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-maltose catabolism	malK_Sm	lo	MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)	37%	95%	229.2	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
trehalose catabolism	malK	lo	MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)	37%	95%	229.2	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
L-arabinose catabolism	xacJ	lo	Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)	47%	64%	228	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-cellobiose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	37%	90%	205.3	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-galactose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	37%	90%	205.3	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-glucose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	37%	90%	205.3	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
lactose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	37%	90%	205.3	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-maltose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	37%	90%	205.3	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-mannose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	37%	90%	205.3	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
sucrose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	37%	90%	205.3	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
trehalose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	37%	90%	205.3	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
L-arabinose catabolism	araV	lo	AraV, component of Arabinose, fructose, xylose porter (characterized)	36%	83%	201.4	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-fructose catabolism	araV	lo	AraV, component of Arabinose, fructose, xylose porter (characterized)	36%	83%	201.4	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
sucrose catabolism	araV	lo	AraV, component of Arabinose, fructose, xylose porter (characterized)	36%	83%	201.4	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
D-xylose catabolism	araV	lo	AraV, component of Arabinose, fructose, xylose porter (characterized)	36%	83%	201.4	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
L-proline catabolism	proV	lo	Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)	40%	59%	181	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
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)	35%	72%	178.7	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7
L-tryptophan catabolism	ecfA2	lo	Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)	34%	90%	136	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31	49%	267.7

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Sequence

MLGICSSGASTNSMAYLDLKDLHKAFGAARVVSDFTLAVERGEFVSFLGPSGCGKTTVLR
MIGGFETPSSGRILIDGQDVTALTPARRKVGMVFQAYALFPNLTVAENVAFGLKVAREPA
SQTARRVDEMLELIKLPQLKDRYPYQLSGGQQQRVALARALAVRPKILLLDEPLSALDAK
IRVSLREEIRAVQRELGITTVFVTHDQEEALSMSDRVVVMHNGRADQVGAPFEIYNAPKT
RFVASFVGTLNLLEGVALAPDRLTIEGQGITTTRGLAGAAVGATVSLALRPEAIGPLPTP
ERTNKLEATVVDVGFQGALVRVKVAVGRQSLTYVTFNAPNSPPPERGTALTLWFGPDDVL
VLADEA

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

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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