Protein CA265_RS13715 in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Protein CA265_RS13715 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: FitnessBrowser__Pedo557:CA265_RS13715

Length: 248 amino acids

Source: Pedo557 in FitnessBrowser

Candidate for 16 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	L-rhamnose-1-dehydrogenase; EC 1.1.1.173 (characterized)	38%	95%	144.8	3-oxoacyl-[acyl-carrier-protein] reductase, chloroplastic (EC 1.1.1.100)	35%	142.1
L-fucose catabolism	fucDH	lo	SDR family oxidoreductase (characterized, see rationale)	36%	94%	129	L-rhamnose-1-dehydrogenase; EC 1.1.1.173	38%	144.8
D-xylose catabolism	DKDP-dehydrog	lo	SDR family oxidoreductase (characterized, see rationale)	36%	94%	129	L-rhamnose-1-dehydrogenase; EC 1.1.1.173	38%	144.8
D-galactose catabolism	galdh	lo	Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)	33%	93%	112.8	L-rhamnose-1-dehydrogenase; EC 1.1.1.173	38%	144.8
lactose catabolism	galdh	lo	Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)	33%	93%	112.8	L-rhamnose-1-dehydrogenase; EC 1.1.1.173	38%	144.8
D-xylose catabolism	xdh	lo	NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale)	32%	90%	98.2	L-rhamnose-1-dehydrogenase; EC 1.1.1.173	38%	144.8
4-hydroxybenzoate catabolism	fadB	lo	3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)	31%	57%	75.1	L-rhamnose-1-dehydrogenase; EC 1.1.1.173	38%	144.8
4-hydroxybenzoate catabolism	paaH	lo	3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)	31%	57%	75.1	L-rhamnose-1-dehydrogenase; EC 1.1.1.173	38%	144.8
L-arginine catabolism	fadB	lo	3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)	31%	57%	75.1	L-rhamnose-1-dehydrogenase; EC 1.1.1.173	38%	144.8
L-citrulline catabolism	fadB	lo	3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)	31%	57%	75.1	L-rhamnose-1-dehydrogenase; EC 1.1.1.173	38%	144.8
L-lysine catabolism	fadB	lo	3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)	31%	57%	75.1	L-rhamnose-1-dehydrogenase; EC 1.1.1.173	38%	144.8
phenylacetate catabolism	fadB	lo	3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)	31%	57%	75.1	L-rhamnose-1-dehydrogenase; EC 1.1.1.173	38%	144.8
phenylacetate catabolism	paaH	lo	3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)	31%	57%	75.1	L-rhamnose-1-dehydrogenase; EC 1.1.1.173	38%	144.8
L-phenylalanine catabolism	fadB	lo	3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)	31%	57%	75.1	L-rhamnose-1-dehydrogenase; EC 1.1.1.173	38%	144.8
L-phenylalanine catabolism	paaH	lo	3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)	31%	57%	75.1	L-rhamnose-1-dehydrogenase; EC 1.1.1.173	38%	144.8
L-proline catabolism	fadB	lo	3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)	31%	57%	75.1	L-rhamnose-1-dehydrogenase; EC 1.1.1.173	38%	144.8

Sequence Analysis Tools

View CA265_RS13715 at FitnessBrowser

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MKTLTIIITGASTGIGRAIAALFLKQGHNVVINSANESNLIRAFNELGAQHQLAMVAGDI
SKATTGQLLVETAVARFGTVDVLVNNAGIFEPKAFLEVDEAHLDSFLNINLKGTFFTSQA
AIAQMLKQDGGSIINIGTVLVDHAIGGFPATAPISSKGGIHALTKQLAAEFGKNNIRVNG
IAPGIIRSPLQEKNGISNADDLAGLHLLNRIGETQDVAQLALYLAESNFVTGEIINLDGG
HVAGHHMG

This GapMind analysis is from Sep 17 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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SQLite3 databases

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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