Protein WP_023433080.1 in Lutibaculum baratangense AMV1

GapMind for catabolism of small carbon sources

Protein WP_023433080.1 in Lutibaculum baratangense AMV1

Annotation: NCBI__GCF_000496075.1:WP_023433080.1

Length: 831 amino acids

Source: GCF_000496075.1 in NCBI

Candidate for 50 steps in catabolism of small carbon sources

Pathway	Step	Score	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
L-isoleucine catabolism	livF	hi	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)	48%	100%	229.2	Branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	49%	210.7
L-leucine catabolism	livF	hi	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)	48%	100%	229.2	Branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	49%	210.7
L-valine catabolism	livF	hi	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)	48%	100%	229.2	Branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	49%	210.7
L-alanine catabolism	braG	med	High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)	48%	100%	219.5	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	48%	229.2
L-serine catabolism	braG	med	High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)	48%	100%	219.5	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	48%	229.2
L-threonine catabolism	braG	med	High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)	48%	100%	219.5	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	48%	229.2
D-alanine catabolism	AZOBR_RS08250	med	Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)	46%	99%	219.2	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	48%	229.2
L-proline catabolism	AZOBR_RS08250	med	Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)	46%	99%	219.2	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	48%	229.2
L-phenylalanine catabolism	livF	med	High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)	46%	100%	217.6	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	48%	229.2
L-proline catabolism	HSERO_RS00900	med	ABC transporter ATP-binding protein (characterized, see rationale)	45%	100%	215.3	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	48%	229.2
L-serine catabolism	Ac3H11_1692	med	ABC transporter ATP-binding protein (characterized, see rationale)	45%	100%	215.3	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	48%	229.2
L-tyrosine catabolism	Ac3H11_1692	med	ABC transporter ATP-binding protein (characterized, see rationale)	45%	100%	215.3	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	48%	229.2
L-arginine catabolism	braG	med	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	44%	96%	205.3	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	48%	229.2
L-glutamate catabolism	braG	med	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	44%	96%	205.3	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	48%	229.2
L-histidine catabolism	braG	med	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	44%	96%	205.3	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	48%	229.2
L-proline catabolism	HSERO_RS00895	med	ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)	44%	98%	199.5	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-isoleucine catabolism	livG	med	ABC transporter ATP-binding protein (characterized, see rationale)	44%	96%	199.1	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-leucine catabolism	livG	med	ABC transporter ATP-binding protein (characterized, see rationale)	44%	96%	199.1	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-phenylalanine catabolism	livG	med	ABC transporter ATP-binding protein (characterized, see rationale)	44%	96%	199.1	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-serine catabolism	Ac3H11_1693	med	ABC transporter ATP-binding protein (characterized, see rationale)	44%	96%	199.1	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-tyrosine catabolism	Ac3H11_1693	med	ABC transporter ATP-binding protein (characterized, see rationale)	44%	96%	199.1	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
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%	100%	195.7	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
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%	100%	195.7	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
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%	100%	195.7	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-valine catabolism	livG	med	High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)	42%	100%	195.7	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-arginine catabolism	braF	med	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	41%	88%	186	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-glutamate catabolism	braF	med	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	41%	88%	186	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-histidine catabolism	braF	med	ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)	41%	88%	186	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-isoleucine catabolism	natE	med	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)	42%	94%	181.8	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	48%	229.2
L-leucine catabolism	natE	med	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)	42%	94%	181.8	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	48%	229.2
L-proline catabolism	natE	med	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)	42%	94%	181.8	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	48%	229.2
L-valine catabolism	natE	med	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)	42%	94%	181.8	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	48%	229.2
D-alanine catabolism	AZOBR_RS08245	med	Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)	42%	88%	178.3	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-proline catabolism	AZOBR_RS08245	med	Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)	42%	88%	178.3	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-histidine catabolism	natE	med	NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)	40%	97%	169.9	ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM	48%	229.2
D-alanine catabolism	AZOBR_RS08240	lo	Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)	38%	67%	218.4	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-proline catabolism	AZOBR_RS08240	lo	Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)	38%	67%	218.4	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-alanine catabolism	braE	lo	High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)	38%	75%	213.8	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-isoleucine catabolism	livM	lo	High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)	38%	75%	213.8	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-leucine catabolism	livM	lo	High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)	38%	75%	213.8	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-serine catabolism	braE	lo	High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)	38%	75%	213.8	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-threonine catabolism	braE	lo	High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)	38%	75%	213.8	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-valine catabolism	livM	lo	High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)	38%	75%	213.8	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-arginine catabolism	braE	lo	Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)	37%	71%	194.5	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-glutamate catabolism	braE	lo	Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)	37%	71%	194.5	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-histidine catabolism	braE	lo	Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)	37%	71%	194.5	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-phenylalanine catabolism	livM	lo	ABC transporter ATP-binding protein (characterized, see rationale)	31%	94%	167.5	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-proline catabolism	HSERO_RS00890	lo	ABC transporter ATP-binding protein (characterized, see rationale)	31%	94%	167.5	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-serine catabolism	Ac3H11_1694	lo	ABC transporter ATP-binding protein (characterized, see rationale)	31%	94%	167.5	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4
L-tyrosine catabolism	Ac3H11_1694	lo	ABC transporter ATP-binding protein (characterized, see rationale)	31%	94%	167.5	Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW	37%	337.4

Sequence Analysis Tools

View WP_023433080.1 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

MRYGNLLALGALVALAAAGIAVGNGYQLFVLSLMGLTAIVGIGLNVLVGMTGQISLGHVG
FYAIGAYTVAILTVGHGWSFWIALPLAGLLAGIAGAVLSVPALRVRGPYLAMITIAFGFI
VEQSAAELGWLTGGWNGIMGIMPPVLFGTMLGPQEIAVLVLVLMLAALGFYALFSESPWG
KALRALRDSEVAAQSIGLNPVLLRCVAFALSAVFAGVAGGVYAAMSGFISPESFPFFESI
LFLLVVMIGGADTLLGPVVGAIVVVLLPELFSSLAEYRLLFVGLLLLVVLRVAPRGIVGG
LSGLAARFARPPQGQRQPGGPAALPLDGREGRPLEVENLSISFGGVRAVQELGFRAEPGR
VTSIIGPNGAGKTTALNLVAGFYRPGSGRISLGDRDLTGLASHRVARAGISRTYQTTQLF
QQMSVIDNVMVAMILGRTRAGDVVRRLETGERRRRAEALLGFVGYRGRPEARAGELAHID
RRLVEIARALAFDPSVMLLDEPAAGLGEEDTAALSRLLRRIADSGVTIILIEHDMGLVMG
ISDHVLVLDAGRKIAEGRPEEVRENPVVLKAYLGEGAPVVARGRQAGEAGRTALKVSGLS
ASYGASEVLQGLDLEVGEGELVAVLGANGAGKSTLMRALAGLHRPVGGAIGFAGEDVAAW
PANRIARAGLVLVPEGRQVFPELTVVQNIRLGAYGRPPADLSREVERLLDRFPRLRERKG
QRAGFLSGGEQQMLAIARGLVARPKVLLLDEPSLGLAPTLIHELYTILAELRDEGVTILL
VDQMAEMALAVADRAYVLSSGVIVAGGTAAEIRRDGTLEDAYLGGTATAAS

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)
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Protein sequences (fasta format)
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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