Protein 209035 in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Protein 209035 in Desulfovibrio vulgaris Hildenborough

Annotation: MicrobesOnline__882:209035

Length: 244 amino acids

Source: 882 in MicrobesOnline

Candidate for 51 steps in catabolism of small carbon sources

Pathway	Step	Score	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
L-asparagine catabolism	glnQ	med	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)	60%	99%	298.1	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-glutamate catabolism	gltL	med	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)	60%	99%	298.1	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-histidine catabolism	aapP	med	ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)	60%	93%	289.7	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-arginine catabolism	artP	med	Arginine transport ATP-binding protein ArtM (characterized)	58%	100%	282	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-asparagine catabolism	aapP	med	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)	57%	93%	282	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-aspartate catabolism	aapP	med	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)	57%	93%	282	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-glutamate catabolism	aapP	med	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)	57%	93%	282	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-leucine catabolism	aapP	med	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)	57%	93%	282	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-proline catabolism	aapP	med	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)	57%	93%	282	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-asparagine catabolism	bztD	med	BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)	57%	91%	281.6	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-aspartate catabolism	bztD	med	BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)	57%	91%	281.6	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
D-alanine catabolism	Pf6N2E2_5405	med	ABC transporter for D-Alanine, ATPase component (characterized)	55%	95%	280	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-asparagine catabolism	aatP	med	ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized)	58%	100%	279.3	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-aspartate catabolism	aatP	med	ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized)	58%	100%	279.3	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-histidine catabolism	bgtA	med	BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)	59%	97%	279.3	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-lysine catabolism	hisP	med	BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)	59%	97%	279.3	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
D-glucosamine (chitosamine) catabolism	AO353_21725	med	ABC transporter for D-Glucosamine, putative ATPase component (characterized)	55%	94%	271.6	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-histidine catabolism	hisP	med	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)	54%	98%	270	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-asparagine catabolism	peb1C	med	PEB1C, component of Uptake system for glutamate and aspartate (characterized)	55%	99%	269.6	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-aspartate catabolism	peb1C	med	PEB1C, component of Uptake system for glutamate and aspartate (characterized)	55%	99%	269.6	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-asparagine catabolism	bgtA	med	ATPase (characterized, see rationale)	56%	92%	268.1	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-aspartate catabolism	bgtA	med	ATPase (characterized, see rationale)	56%	92%	268.1	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-histidine catabolism	BPHYT_RS24015	med	ABC transporter related (characterized, see rationale)	53%	94%	265	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-citrulline catabolism	AO353_03040	med	ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)	50%	97%	250	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-citrulline catabolism	PS417_17605	med	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)	50%	89%	240	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-histidine catabolism	PA5503	med	Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)	42%	72%	183	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
D-sorbitol (glucitol) catabolism	mtlK	med	ABC transporter for D-Sorbitol, ATPase component (characterized)	40%	70%	166	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-proline catabolism	proV	lo	Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)	37%	67%	175.6	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
D-mannitol catabolism	mtlK	lo	ABC transporter for D-mannitol and D-mannose, ATPase component (characterized)	40%	63%	167.2	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
D-maltose catabolism	aglK	lo	ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)	40%	65%	166.8	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
D-maltose catabolism	thuK	lo	ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)	40%	65%	166.8	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
sucrose catabolism	aglK	lo	ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)	40%	65%	166.8	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
trehalose catabolism	aglK	lo	ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)	40%	65%	166.8	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
N-acetyl-D-glucosamine catabolism	SMc02869	lo	N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)	39%	66%	166.4	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
D-glucosamine (chitosamine) catabolism	SMc02869	lo	N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)	39%	66%	166.4	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
D-cellobiose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	41%	63%	166	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
D-glucose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	41%	63%	166	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
lactose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	41%	63%	166	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
D-maltose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	41%	63%	166	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
sucrose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	41%	63%	166	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
trehalose catabolism	aglK'	lo	Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)	41%	63%	166	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
D-maltose catabolism	malK	lo	Maltose-transporting ATPase (EC 3.6.3.19) (characterized)	41%	63%	162.9	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
lactose catabolism	lacK	lo	ABC transporter for Lactose, ATPase component (characterized)	39%	65%	161.8	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
sucrose catabolism	thuK	lo	ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)	39%	68%	161.4	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-alanine catabolism	braG	lo	NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)	35%	96%	136	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-isoleucine catabolism	natE	lo	NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)	35%	96%	136	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-leucine catabolism	natE	lo	NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)	35%	96%	136	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-proline catabolism	natE	lo	NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)	35%	96%	136	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-serine catabolism	braG	lo	NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)	35%	96%	136	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-threonine catabolism	braG	lo	NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)	35%	96%	136	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1
L-valine catabolism	natE	lo	NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)	35%	96%	136	Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.-	63%	310.1

Sequence Analysis Tools

View 209035 at MicrobesOnline

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

MTPMIEIRNLHKSYGDHHVLRGIDLTVRTGEVVVVIGPSGSGKSTALRCINRLEEITSGT
IIVDGYDLYDPKTDINHVRTEAGMVFQQFNLFPHMSVLENVTIGPVKVRRMARQEAQALG
LALLEKVGLADKAHAYPDQLSGGQKQRVAIARSLAMQPKVLLFDEPTSALDPELVGEVLE
VMKQLAREGMTMVVVTHEMGFAREVADRVIFIDYGKIQEEGPPNELFADPKNPRLREFLG
KVIH

This GapMind analysis is from Sep 17 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