Protein WP_015739570.1 in Ammonifex degensii KC4

GapMind for catabolism of small carbon sources

Protein WP_015739570.1 in Ammonifex degensii KC4

Annotation: NCBI__GCF_000024605.1:WP_015739570.1

Length: 260 amino acids

Source: GCF_000024605.1 in NCBI

Candidate for 52 steps in catabolism of small carbon sources

Pathway	Step	Score	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
L-isoleucine catabolism	livG	hi	High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)	44%	99%	234.2	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	44%	208.4
L-phenylalanine catabolism	livG	hi	High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)	44%	99%	234.2	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-leucine catabolism	livG	hi	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)	42%	99%	224.2	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	44%	208.4
L-valine catabolism	livG	hi	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)	42%	99%	224.2	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	44%	208.4
L-proline catabolism	HSERO_RS00895	med	ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)	45%	99%	232.3	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-serine catabolism	Ac3H11_1693	med	ABC transporter ATP-binding protein (characterized, see rationale)	45%	97%	220.3	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-tyrosine catabolism	Ac3H11_1693	med	ABC transporter ATP-binding protein (characterized, see rationale)	45%	97%	220.3	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-alanine catabolism	braF	med	High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)	42%	99%	219.5	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-serine catabolism	braF	med	High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)	42%	99%	219.5	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-threonine catabolism	braF	med	High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)	42%	99%	219.5	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
D-alanine catabolism	AZOBR_RS08245	med	Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)	42%	90%	201.8	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-proline catabolism	AZOBR_RS08245	med	Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)	42%	90%	201.8	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-arginine catabolism	braF	med	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	42%	88%	198.7	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-glutamate catabolism	braF	med	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	42%	88%	198.7	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-histidine catabolism	braF	med	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	42%	88%	198.7	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-histidine catabolism	natA	lo	NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	39%	94%	179.1	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-leucine catabolism	natA	lo	NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	39%	94%	179.1	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-proline catabolism	natA	lo	NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	39%	94%	179.1	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-isoleucine catabolism	natA	lo	NatA, 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)	38%	96%	169.9	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-valine catabolism	natA	lo	NatA, 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)	38%	96%	169.9	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
D-lactate catabolism	PGA1_c12640	lo	D-lactate transporter, ATP-binding component (characterized)	36%	98%	168.7	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-isoleucine catabolism	livF	lo	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)	33%	100%	145.2	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-leucine catabolism	livF	lo	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)	33%	100%	145.2	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-valine catabolism	livF	lo	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)	33%	100%	145.2	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
D-cellobiose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	69%	144.8	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
D-galactose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	69%	144.8	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
D-glucose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	69%	144.8	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
lactose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	69%	144.8	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
D-maltose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	69%	144.8	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
D-mannose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	69%	144.8	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
sucrose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	69%	144.8	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
trehalose catabolism	glcV	lo	monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)	34%	69%	144.8	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-arginine catabolism	braG	lo	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	35%	96%	136.3	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-glutamate catabolism	braG	lo	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	35%	96%	136.3	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-histidine catabolism	braG	lo	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	35%	96%	136.3	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
D-fructose catabolism	frcA	lo	Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)	34%	95%	132.9	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
D-mannose catabolism	frcA	lo	Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)	34%	95%	132.9	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
D-ribose catabolism	frcA	lo	Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)	34%	95%	132.9	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
sucrose catabolism	frcA	lo	Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)	34%	95%	132.9	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-arginine catabolism	artP	lo	Histidine transport ATP-binding protein HisP (characterized)	33%	99%	131.7	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-histidine catabolism	hisP	lo	Histidine transport ATP-binding protein HisP (characterized)	33%	99%	131.7	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-lysine catabolism	hisP	lo	Histidine transport ATP-binding protein HisP (characterized)	33%	99%	131.7	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
D-alanine catabolism	AZOBR_RS08250	lo	Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)	32%	99%	122.1	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-proline catabolism	AZOBR_RS08250	lo	Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)	32%	99%	122.1	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-phenylalanine catabolism	livF	lo	high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)	31%	100%	117.1	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-alanine catabolism	braG	lo	NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	31%	98%	110.5	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-histidine catabolism	natE	lo	NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	31%	98%	110.5	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-leucine catabolism	natE	lo	NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	31%	98%	110.5	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-proline catabolism	natE	lo	NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	31%	98%	110.5	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-serine catabolism	braG	lo	NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	31%	98%	110.5	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
L-threonine catabolism	braG	lo	NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	31%	98%	110.5	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2
glycerol catabolism	glpT	lo	GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)	31%	59%	104	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	42%	224.2

Sequence Analysis Tools

View WP_015739570.1 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

Fitness BLAST: loading...

Sequence

MQQELLVVENLSLHFGGVAALTNIDLTVRKGEILAIIGPNGAGKTSFLNCISGLYRPSSG
RIFFEGRDITRLPPHRRAALGIARTFQNIELFKHMTVLDNIMLGRHVHLRSGILAGGIYW
GLAQKEEVRHRRRVEEIIDFLEIEFIRNKVVGSLSYGLQKRVELARALALEPKLLLLDEP
MAGMNVEEKEDMARFILDIAEEWGVTLVLIEHDMGVVMDLSDRVVVFDFGRKIAEGLPEE
IKQNPRVVEAYLGGQLAEED

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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