Protein Ga0059261_1321 in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Protein Ga0059261_1321 in Sphingomonas koreensis DSMZ 15582

Annotation: FitnessBrowser__Korea:Ga0059261_1321

Length: 238 amino acids

Source: Korea in FitnessBrowser

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-glutamate catabolism	gltL	med	GluA aka CGL1950, component of Glutamate porter (characterized)	41%	90%	140.6	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
L-lysine catabolism	hisP	lo	ABC transporter for L-Lysine, ATPase component (characterized)	38%	92%	143.7	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
L-arginine catabolism	artP	lo	Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)	37%	91%	141.7	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
L-histidine catabolism	hisP	lo	Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)	37%	91%	141.7	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
L-histidine catabolism	BPHYT_RS24015	lo	ABC transporter related (characterized, see rationale)	40%	88%	138.3	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
D-alanine catabolism	Pf6N2E2_5405	lo	ABC transporter for D-Alanine, ATPase component (characterized)	38%	81%	134.4	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
L-asparagine catabolism	peb1C	lo	PEB1C, component of Uptake system for glutamate and aspartate (characterized)	36%	88%	133.7	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
L-aspartate catabolism	peb1C	lo	PEB1C, component of Uptake system for glutamate and aspartate (characterized)	36%	88%	133.7	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
D-sorbitol (glucitol) catabolism	mtlK	lo	ABC transporter for D-Sorbitol, ATPase component (characterized)	37%	61%	131.7	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
putrescine catabolism	potA	lo	Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized)	37%	58%	126.3	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
L-histidine catabolism	Ac3H11_2560	lo	ABC transporter for L-Histidine, ATPase component (characterized)	37%	76%	125.9	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
L-asparagine catabolism	bztD	lo	BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)	36%	85%	124.8	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
L-aspartate catabolism	bztD	lo	BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)	36%	85%	124.8	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
xylitol catabolism	Dshi_0546	lo	ABC transporter for Xylitol, ATPase component (characterized)	36%	63%	123.6	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
L-histidine catabolism	aapP	lo	ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)	36%	84%	123.2	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
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)	35%	88%	122.9	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
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)	35%	88%	122.9	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
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)	35%	88%	122.9	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
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)	35%	88%	122.9	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
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)	35%	88%	122.9	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
D-cellobiose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	36%	62%	120.9	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
D-galactose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	36%	62%	120.9	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
D-glucose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	36%	62%	120.9	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
lactose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	36%	62%	120.9	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
D-maltose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	36%	62%	120.9	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
D-mannose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	36%	62%	120.9	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
sucrose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	36%	62%	120.9	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
trehalose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	36%	62%	120.9	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
D-maltose catabolism	malK	lo	ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)	37%	57%	120.6	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
D-mannitol catabolism	mtlK	lo	SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)	34%	64%	120.6	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
L-arabinose catabolism	araV	lo	AraV, component of Arabinose, fructose, xylose porter (characterized)	34%	56%	119.4	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
D-fructose catabolism	araV	lo	AraV, component of Arabinose, fructose, xylose porter (characterized)	34%	56%	119.4	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
sucrose catabolism	araV	lo	AraV, component of Arabinose, fructose, xylose porter (characterized)	34%	56%	119.4	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
D-xylose catabolism	araV	lo	AraV, component of Arabinose, fructose, xylose porter (characterized)	34%	56%	119.4	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
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)	33%	57%	115.2	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
trehalose catabolism	thuK	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)	33%	57%	115.2	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
L-fucose catabolism	SM_b21106	lo	ABC transporter for L-Fucose, ATPase component (characterized)	32%	58%	112.5	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
D-cellobiose catabolism	TM0027	lo	TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)	33%	86%	112.1	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
L-histidine 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%	109.4	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
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%	109.4	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
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)	31%	57%	107.5	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
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%	107.5	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
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%	107.5	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
trehalose catabolism	malK	lo	MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized)	31%	58%	107.1	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5
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)	34%	52%	103.2	Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.-	51%	216.5

Sequence Analysis Tools

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

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Sequence

VADADPIIRLRNITKVFGEGATAFQALKGVDLDIAERDFVAVMGPSGSGKSTTMNILGCL
DVPTSGEFLFKGVYIETLDRDQRALVRRKYLGFVFQGFNLLSRTNALENVELPLLYRGED
KKVRHELGMAALEKVGLADWWDHTPAELSGGQPQRVAIARAIVTSPAVLLADEPTGNLDS
ARSVEIMELLTSLNKDSGITVLMVTHEPDMAAFARTIVHFKDGLVERTEAGNGAGVPA

This GapMind analysis is from Sep 17 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 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