Protein GFF4342 in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Protein GFF4342 in Pseudomonas simiae WCS417

Annotation: FitnessBrowser__WCS417:GFF4342

Length: 473 amino acids

Source: WCS417 in FitnessBrowser

Candidate for 13 steps in catabolism of small carbon sources

Pathway	Step	Score	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
L-tyrosine catabolism	aroP	hi	L-tyrosine transporter (characterized)	92%	100%	869.8	Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs	57%	557.0
L-tryptophan catabolism	aroP	hi	Aromatic amino acid transport protein AroP (characterized, see rationale)	74%	99%	700.3	Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs	57%	557.0
L-phenylalanine catabolism	aroP	med	Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized)	68%	97%	622.1	L-tyrosine transporter	92%	869.8
phenylacetate catabolism	H281DRAFT_04042	med	Aromatic amino acid transporter AroP (characterized, see rationale)	66%	97%	619.8	L-tyrosine transporter	92%	869.8
L-threonine catabolism	RR42_RS28305	med	D-serine/D-alanine/glycine transporter (characterized, see rationale)	42%	94%	400.2	L-tyrosine transporter	92%	869.8
D-alanine catabolism	cycA	med	L-alanine and D-alanine permease (characterized)	44%	93%	397.1	L-tyrosine transporter	92%	869.8
L-alanine catabolism	cycA	med	L-alanine and D-alanine permease (characterized)	44%	93%	397.1	L-tyrosine transporter	92%	869.8
L-histidine catabolism	permease	med	histidine permease (characterized)	42%	97%	383.6	L-tyrosine transporter	92%	869.8
D-serine catabolism	cycA	lo	D-serine/D-alanine/glycine transporter (characterized)	39%	96%	352.8	L-tyrosine transporter	92%	869.8
L-asparagine catabolism	ansP	lo	Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)	37%	92%	330.5	L-tyrosine transporter	92%	869.8
L-arginine catabolism	rocE	lo	arginine permease (characterized)	33%	79%	254.2	L-tyrosine transporter	92%	869.8
L-lysine catabolism	lysP	lo	lysine-specific permease (characterized)	34%	71%	249.6	L-tyrosine transporter	92%	869.8
L-asparagine catabolism	AGP1	lo	general amino acid permease AGP1 (characterized)	30%	70%	209.1	L-tyrosine transporter	92%	869.8

Sequence Analysis Tools

View GFF4342 at FitnessBrowser

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

MSVSPSSSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAF
MIMRQLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYVHY
WWPEIPTWVSAAAFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGTG
GPQASVTNLWEHGGFFPHGVGGLVMAMAIIMFSFGGLEMLGFTAAEADKPRTVIPKAINQ
VIYRILIFYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSDTAAHILNFV
VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALAKIDKRGVPVRSILASAAITLVAVLMN
YLIPQHALELLMSLVVATLVINWAMISFSHFKFRQHMNRTGQVPLFKALWYPYGNYVCLA
FVVFILVIMLMIPGIQVSVFAIPVWVMFMAVCYGIKNKRSAQQALAPAASPVK

This GapMind analysis is from Sep 17 2021. 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 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