Protein WP_012589114.1 in Methylocella silvestris BL2

GapMind for catabolism of small carbon sources

Protein WP_012589114.1 in Methylocella silvestris BL2

Annotation: NCBI__GCF_000021745.1:WP_012589114.1

Length: 249 amino acids

Source: GCF_000021745.1 in NCBI

Candidate for 18 steps in catabolism of small carbon sources

Pathway	Step	Score	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
L-rhamnose catabolism	LRA1	med	NAD(P)⁺-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)	40%	98%	166	Short chain dehydrogenase AgnL6; Agnestins biosynthesis cluster protein L6; EC 1.1.1.-	43%	192.2
D-sorbitol (glucitol) catabolism	sdh	lo	Sorbitol dehydrogenase (EC 1.1.1.14) (characterized)	39%	98%	151.8	Short chain dehydrogenase AgnL6; Agnestins biosynthesis cluster protein L6; EC 1.1.1.-	43%	192.2
glycerol catabolism	dhaD	lo	NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)	36%	94%	149.1	Short chain dehydrogenase AgnL6; Agnestins biosynthesis cluster protein L6; EC 1.1.1.-	43%	192.2
L-fucose catabolism	fucDH	lo	Short-chain dehydrogenase/reductase SDR (characterized, see rationale)	35%	98%	139	Short chain dehydrogenase AgnL6; Agnestins biosynthesis cluster protein L6; EC 1.1.1.-	43%	192.2
4-hydroxybenzoate catabolism	badH	lo	BadH (characterized)	35%	98%	136.3	Short chain dehydrogenase AgnL6; Agnestins biosynthesis cluster protein L6; EC 1.1.1.-	43%	192.2
phenylacetate catabolism	badH	lo	BadH (characterized)	35%	98%	136.3	Short chain dehydrogenase AgnL6; Agnestins biosynthesis cluster protein L6; EC 1.1.1.-	43%	192.2
L-phenylalanine catabolism	badH	lo	BadH (characterized)	35%	98%	136.3	Short chain dehydrogenase AgnL6; Agnestins biosynthesis cluster protein L6; EC 1.1.1.-	43%	192.2
L-arabinose catabolism	xacB	lo	L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)	35%	92%	132.5	Short chain dehydrogenase AgnL6; Agnestins biosynthesis cluster protein L6; EC 1.1.1.-	43%	192.2
D-galactose catabolism	galdh	lo	L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)	34%	92%	129.4	Short chain dehydrogenase AgnL6; Agnestins biosynthesis cluster protein L6; EC 1.1.1.-	43%	192.2
lactose catabolism	galdh	lo	L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)	34%	92%	129.4	Short chain dehydrogenase AgnL6; Agnestins biosynthesis cluster protein L6; EC 1.1.1.-	43%	192.2
D-xylose catabolism	DKDP-dehydrog	lo	SDR family oxidoreductase (characterized, see rationale)	33%	97%	123.2	Short chain dehydrogenase AgnL6; Agnestins biosynthesis cluster protein L6; EC 1.1.1.-	43%	192.2
D-xylose catabolism	xdh	lo	D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)	33%	94%	122.1	Short chain dehydrogenase AgnL6; Agnestins biosynthesis cluster protein L6; EC 1.1.1.-	43%	192.2
2-deoxy-D-ribonate catabolism	deoxyribonate-dehyd	lo	2-deoxy-D-ribonate dehydrogenase (characterized)	33%	95%	120.2	Short chain dehydrogenase AgnL6; Agnestins biosynthesis cluster protein L6; EC 1.1.1.-	43%	192.2
2-deoxy-D-ribose catabolism	deoxyribonate-dehyd	lo	2-deoxy-D-ribonate dehydrogenase (characterized)	33%	95%	120.2	Short chain dehydrogenase AgnL6; Agnestins biosynthesis cluster protein L6; EC 1.1.1.-	43%	192.2
xylitol catabolism	xdhA	lo	D-xylulose reductase (EC 1.1.1.9) (characterized)	31%	99%	117.9	Short chain dehydrogenase AgnL6; Agnestins biosynthesis cluster protein L6; EC 1.1.1.-	43%	192.2
D-xylose catabolism	xdhA	lo	D-xylulose reductase (EC 1.1.1.9) (characterized)	31%	99%	117.9	Short chain dehydrogenase AgnL6; Agnestins biosynthesis cluster protein L6; EC 1.1.1.-	43%	192.2
D-mannitol catabolism	mt2d	lo	NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)	32%	95%	116.3	Short chain dehydrogenase AgnL6; Agnestins biosynthesis cluster protein L6; EC 1.1.1.-	43%	192.2
D-sorbitol (glucitol) catabolism	srlD	lo	Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)	31%	97%	99.4	Short chain dehydrogenase AgnL6; Agnestins biosynthesis cluster protein L6; EC 1.1.1.-	43%	192.2

Sequence Analysis Tools

View WP_012589114.1 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

MSRLSGKTAIVTGASKGIGAAIAKSLAAEGAAVVVNYASSKEGAQAVVADIKAKGGKAIA
VQGDVAKEADVLKIFAEAKNVFGPTDILVNNAGVYQFGAIDDLAEAEFHRHFNINVLGLL
LATREAVKQFKPEGGSIINISSAVTSMNIPQSVVYTATKGAVDSATRVLSKELGPRKIRV
NAINPGIVETEGTQAVGIAGSDMEAQFVAQTPLGRVGQPDDIAAVAVFLASDESRWVTGE
TIVVSGGLK

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