Protein WP_050654665.1 in Rhodococcus qingshengii djl-6-2

GapMind for catabolism of small carbon sources

Protein WP_050654665.1 in Rhodococcus qingshengii djl-6-2

Annotation: NCBI__GCF_002893965.1:WP_050654665.1

Length: 487 amino acids

Source: GCF_002893965.1 in NCBI

Candidate for 12 steps in catabolism of small carbon sources

Pathway	Step	Score	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
D-alanine catabolism	cycA	hi	D-serine/D-alanine/glycine transporter (characterized)	70%	97%	659.1	Proline-specific permease (ProY)	42%	371.3
D-serine catabolism	cycA	hi	D-serine/D-alanine/glycine transporter (characterized)	70%	97%	659.1	L-alanine and D-alanine permease	41%	372.1
L-alanine catabolism	cycA	hi	D-serine/D-alanine/glycine transporter (characterized)	70%	97%	656.4	Proline-specific permease (ProY)	42%	371.3
L-threonine catabolism	RR42_RS28305	med	D-serine/D-alanine/glycine transporter (characterized, see rationale)	46%	95%	415.6	D-serine/D-alanine/glycine transporter	70%	659.1
L-proline catabolism	proY	med	Proline-specific permease (ProY) (characterized)	42%	98%	371.3	D-serine/D-alanine/glycine transporter	70%	659.1
phenylacetate catabolism	H281DRAFT_04042	med	Aromatic amino acid transporter AroP (characterized, see rationale)	41%	96%	367.1	D-serine/D-alanine/glycine transporter	70%	659.1
L-phenylalanine catabolism	aroP	med	Aromatic amino acid transport protein AroP (characterized, see rationale)	40%	98%	357.8	D-serine/D-alanine/glycine transporter	70%	659.1
L-serine catabolism	serP	med	Serine permease SerP1 (characterized)	41%	98%	337	D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA	62%	611.3
L-threonine catabolism	serP1	med	Serine uptake transporter, SerP1, of 259 aas and 12 TMSs (Trip et al. 2013). L-serine is the highest affinity substrate (Km = 18 μM), but SerP1 also transports L-threonine and L-cysteine (Km values = 20 - 40 μM) (characterized)	41%	98%	336.7	D-serine/D-alanine/glycine transporter	70%	659.1
L-histidine catabolism	permease	lo	histidine permease (characterized)	39%	100%	347.8	D-serine/D-alanine/glycine transporter	70%	659.1
L-tyrosine catabolism	aroP	lo	Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized)	39%	95%	346.7	D-serine/D-alanine/glycine transporter	70%	659.1
L-asparagine catabolism	ansP	lo	L-asparagine permease; L-asparagine transport protein (characterized)	38%	90%	313.2	D-serine/D-alanine/glycine transporter	70%	659.1

Sequence Analysis Tools

View WP_050654665.1 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

MSDHANTPDLTKPSREDPHLSRQLSNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSVIFV
YMIIGFMLFFVMRAMGELLLSNMAYKSFSDFAADLLGPWAGFFTGWTYWFCWIVTGIADV
IAISGYFKYWWPGLAAWIPALLTIAALLLLNLPTVRAFGETEFWFALIKIIAIVSLIVVG
IVMVVSGFTAPNGATSGIDNLWNDGGMFPTGFMGFVAGFQIAVFAFVGIELVGTTAAEAK
DPEKNLPKAINSIPIRVLLFYVVALTVIIAVTPWREISADKSPFVAMFTLAGLGIAASVI
NFVVLTSAASSANSGIYSTSRMVFGLAQEGDAPRALGKLNSRKVPANALMFSCIFLLASL
ILLFSGDSVIEAFTVVTTISALLFMFVWTIILASYMVYRKRRPHLHEASKFKMPGGIVMC
WVVLAFFVFILWALTTKDDTLQALLVTPIWFVVLGIAWAIIRRRPAHRARYDAFKSELDA
SRQNGDK

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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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