Protein WP_035130886.1 in Flavobacterium beibuense F44-8

GapMind for catabolism of small carbon sources

Protein WP_035130886.1 in Flavobacterium beibuense F44-8

Annotation: NCBI__GCF_000769915.1:WP_035130886.1

Length: 222 amino acids

Source: GCF_000769915.1 in NCBI

Candidate for 44 steps in catabolism of small carbon sources

Pathway	Step	Score	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
L-asparagine catabolism	aatP	lo	ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized)	38%	89%	146	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-aspartate catabolism	aatP	lo	ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized)	38%	89%	146	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-glutamate catabolism	gltL	lo	ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized)	38%	89%	146	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
D-glucosamine (chitosamine) catabolism	AO353_21725	lo	ABC transporter for D-glucosamine, ATPase component (characterized)	37%	85%	142.1	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
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)	35%	85%	140.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-citrulline catabolism	AO353_03040	lo	ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)	37%	86%	140.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
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)	35%	85%	140.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-lysine 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)	35%	85%	140.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-asparagine catabolism	bztD	lo	BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)	36%	82%	139.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-aspartate catabolism	bztD	lo	BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)	36%	82%	139.4	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-asparagine catabolism	peb1C	lo	PEB1C, component of Uptake system for glutamate and aspartate (characterized)	36%	89%	139	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-aspartate catabolism	peb1C	lo	PEB1C, component of Uptake system for glutamate and aspartate (characterized)	36%	89%	139	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
D-sorbitol (glucitol) catabolism	mtlK	lo	ABC transporter for D-Sorbitol, ATPase component (characterized)	35%	57%	135.6	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-histidine catabolism	aapP	lo	ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)	34%	83%	133.7	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
D-alanine catabolism	Pf6N2E2_5405	lo	ABC transporter for D-Alanine, ATPase component (characterized)	33%	85%	132.1	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
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)	34%	84%	132.1	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
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)	34%	84%	132.1	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
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)	34%	84%	132.1	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
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)	34%	84%	132.1	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
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)	34%	84%	132.1	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
D-mannitol catabolism	mtlK	lo	SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)	33%	63%	128.6	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-tryptophan catabolism	ecfA2	lo	Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)	38%	74%	124.8	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
D-glucosamine (chitosamine) catabolism	SM_b21216	lo	ABC transporter for D-Glucosamine, ATPase component (characterized)	32%	58%	123.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-arginine catabolism	braG	lo	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	31%	87%	113.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-glutamate catabolism	braG	lo	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	31%	87%	113.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-histidine catabolism	braG	lo	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	31%	87%	113.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-isoleucine catabolism	livF	lo	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	31%	87%	113.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-leucine catabolism	livF	lo	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	31%	87%	113.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-valine catabolism	livF	lo	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	31%	87%	113.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
D-alanine catabolism	AZOBR_RS08250	lo	Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)	31%	92%	110.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-proline catabolism	AZOBR_RS08250	lo	Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)	31%	92%	110.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-arabinose catabolism	xylGsa	lo	Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)	34%	86%	107.8	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-isoleucine catabolism	livG	lo	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)	30%	91%	107.8	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-leucine catabolism	livG	lo	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)	30%	91%	107.8	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-valine catabolism	livG	lo	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)	30%	91%	107.8	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-phenylalanine catabolism	livF	lo	high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)	31%	89%	105.5	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
glycerol catabolism	glpS	lo	GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)	30%	59%	104	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-proline catabolism	HSERO_RS00900	lo	ABC transporter ATP-binding protein (characterized, see rationale)	33%	88%	103.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-serine catabolism	Ac3H11_1692	lo	ABC transporter ATP-binding protein (characterized, see rationale)	33%	88%	103.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-tyrosine catabolism	Ac3H11_1692	lo	ABC transporter ATP-binding protein (characterized, see rationale)	33%	88%	103.2	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-phenylalanine catabolism	livG	lo	ABC transporter ATP-binding protein (characterized, see rationale)	30%	89%	97.8	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-proline catabolism	HSERO_RS00895	lo	ABC transporter ATP-binding protein (characterized, see rationale)	30%	89%	97.8	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-serine catabolism	Ac3H11_1693	lo	ABC transporter ATP-binding protein (characterized, see rationale)	30%	89%	97.8	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4
L-tyrosine catabolism	Ac3H11_1693	lo	ABC transporter ATP-binding protein (characterized, see rationale)	30%	89%	97.8	lipoprotein releasing system, ATP-binding protein; EC 3.6.3.-	44%	198.4

Sequence Analysis Tools

View WP_035130886.1 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

MIQAKNIHKYYDSLHVLKGVDLHIKKGEVVSIVGASGAGKTTLLQILGTLDKPKSEKGTS
LLIDGEDVLNMKDKALSKFRNLKLGFIFQFHQLFPEFTALENVCIPAFIAGKQKAETEAE
AKKLLEYLGLSHRINHKPGELSGGEQQRVAVARALINKPAVIFADEPSGNLDTHSAENLH
NLFFKLRDEMGQTFVIVTHNEELANMADRKLVMSDGQIISGH

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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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