Protein 5208455 in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Protein 5208455 in Shewanella loihica PV-4

Annotation: FitnessBrowser__PV4:5208455

Length: 498 amino acids

Source: PV4 in FitnessBrowser

Candidate for 42 steps in catabolism of small carbon sources

Pathway	Step	Score	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
L-arginine catabolism	kauB	hi	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)	73%	100%	745.7	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99)	57%	575.9
L-arginine catabolism	puuC	hi	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)	73%	100%	745.7	aldehyde dehydrogenase	55%	542.0
L-citrulline catabolism	puuC	hi	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)	73%	100%	745.7	aldehyde dehydrogenase	55%	542.0
putrescine catabolism	puuC	hi	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)	73%	100%	745.7	aldehyde dehydrogenase	55%	542.0
L-arginine catabolism	gabD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	57%	98%	575.9	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-arginine catabolism	patD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	57%	98%	575.9	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-citrulline catabolism	gabD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	57%	98%	575.9	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-citrulline catabolism	patD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	57%	98%	575.9	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
putrescine catabolism	gabD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	57%	98%	575.9	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
putrescine catabolism	patD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	57%	98%	575.9	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
4-hydroxybenzoate catabolism	adh	med	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)	44%	97%	413.3	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
2'-deoxyinosine catabolism	adh	med	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)	44%	97%	413.3	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
2-deoxy-D-ribose catabolism	adh	med	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)	44%	97%	413.3	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
ethanol catabolism	adh	med	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)	44%	97%	413.3	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-threonine catabolism	adh	med	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)	44%	97%	413.3	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
thymidine catabolism	adh	med	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)	44%	97%	413.3	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-tryptophan catabolism	adh	med	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)	44%	97%	413.3	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-phenylalanine catabolism	pad-dh	med	aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)	44%	93%	400.6	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-fucose catabolism	aldA	med	NAD(P)⁺ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)	41%	95%	359.4	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-rhamnose catabolism	aldA	med	NAD(P)⁺ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)	41%	95%	359.4	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-threonine catabolism	aldA	med	NAD(P)⁺ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)	41%	95%	359.4	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
4-hydroxybenzoate catabolism	praB	lo	2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)	38%	97%	337.8	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-tryptophan catabolism	praB	lo	2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)	38%	97%	337.8	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-tryptophan catabolism	nbaE	lo	2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)	36%	98%	306.2	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-arginine catabolism	davD	lo	Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)	35%	99%	290.8	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-citrulline catabolism	davD	lo	Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)	35%	99%	290.8	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-lysine catabolism	davD	lo	Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)	35%	99%	290.8	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-proline catabolism	davD	lo	Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)	35%	99%	290.8	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-arabinose catabolism	xacF	lo	Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)	36%	99%	283.9	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
D-galacturonate catabolism	dopDH	lo	Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)	36%	99%	283.9	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
D-glucuronate catabolism	dopDH	lo	Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)	36%	99%	283.9	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
D-xylose catabolism	dopDH	lo	Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)	36%	99%	283.9	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-arabinose catabolism	aldA	lo	lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)	32%	99%	256.9	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
D-xylose catabolism	aldA	lo	lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)	32%	99%	256.9	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-isoleucine catabolism	iolA	lo	methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)	33%	96%	238.8	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
myo-inositol catabolism	mmsA	lo	methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)	33%	96%	238.8	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
propionate catabolism	iolA	lo	methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)	33%	96%	238.8	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-threonine catabolism	iolA	lo	methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)	33%	96%	238.8	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-valine catabolism	iolA	lo	methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)	33%	96%	238.8	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-valine catabolism	mmsA	lo	methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)	33%	96%	238.8	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-arginine catabolism	astD	lo	N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)	32%	94%	199.5	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7
L-citrulline catabolism	astD	lo	N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)	32%	94%	199.5	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)	73%	745.7

Sequence Analysis Tools

View 5208455 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MSTPQNREQWQEMADSLVIQGQAFINGEYCAADSNDTFDCISPIDGRVLTQVASCDLLDA
NRAVANAREVFERGDWSQLPPVKRKQVMIRFADLLEANRDELALLETLDMGKPIRYSGAV
DVAGAARALRWSGEAVDKIYDEIAPTAHNEIGMITREPVGVVAAIVPWNFPLLMACWKLG
PALATGNSVVLKPSEKSPLTAIRMAQLAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDT
LVFTGSTKIAKQLMIYAGESNMKRVWLEAGGKSPNIVFNDAPNLKEAAIAAASAIAFNQG
EVCTAGSRLLVESGVKEELINLIEAEMQAWQPGHPLDPATTCGAVVDQQQLENVLRYIRA
GVAEGAQLRQGGQQVLAETGGVYVAPTIFANVKNEMTIAKEEIFGPVLSVITFDGMEEAI
RIGNDTIYGLAAGVWTSDISKAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDK
SLHAFDKYTEIKATWIAL

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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