GapMind for catabolism of small carbon sources

 

Protein WP_047092763.1 in Erythrobacter marinus HWDM-33

Annotation: NCBI__GCF_001013305.1:WP_047092763.1

Length: 459 amino acids

Source: GCF_001013305.1 in NCBI

Candidate for 35 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism gabD hi Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 (characterized) 40% 99% 349.4
L-citrulline catabolism gabD hi Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 (characterized) 40% 99% 349.4
putrescine catabolism gabD hi Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 (characterized) 40% 99% 349.4
4-hydroxybenzoate catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 40% 98% 333.2 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 40% 98% 333.2 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 40% 98% 333.2 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
ethanol catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 40% 98% 333.2 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
L-threonine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 40% 98% 333.2 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
thymidine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 40% 98% 333.2 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
L-tryptophan catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 40% 98% 333.2 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
L-arginine catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 30% 91% 246.5 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
L-citrulline catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 30% 91% 246.5 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
putrescine catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 30% 91% 246.5 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
L-arabinose catabolism xacF lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 32% 95% 245.4 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
D-galacturonate catabolism dopDH lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 32% 95% 245.4 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
D-glucuronate catabolism dopDH lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 32% 95% 245.4 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
D-xylose catabolism dopDH lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 32% 95% 245.4 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 34% 94% 243.4 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 89% 236.5 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 89% 236.5 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 89% 236.5 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 89% 236.5 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 89% 236.5 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
L-fucose catabolism aldA lo NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 33% 95% 235.7 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
L-rhamnose catabolism aldA lo NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 33% 95% 235.7 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
L-threonine catabolism aldA lo NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 33% 95% 235.7 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 32% 95% 233.8 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 32% 95% 233.8 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 32% 95% 229.6 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 30% 92% 205.7 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 31% 91% 200.3 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 31% 91% 200.3 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 31% 91% 200.3 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 31% 91% 200.3 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 31% 91% 200.3 Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 40% 349.4

Sequence Analysis Tools

View WP_047092763.1 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

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Sequence

MTKIQTCNPATGETLATYDLMSEQEAFGKIEHAQSAFLDWREKSHEERAEYLRQIAKVLR
GNSDRISQLMTREMGKLLRDGATEVELCAGIFEYTAENGPAELADQEREYSGGEKRGIVS
FAPIGIIYSVQPWNFPLYQPARVLAANLMAGNAVILKHASICTGSGLLLRDLCLEAGLPA
GLFDVVLVGHDLSDKIIEHKLIRAVTMTGSDGAGSHIGELAAKNLKKTVLELGSNDAYLV
LADADIELAVKTCVQGRLYNNGETCVSAKRFVVVDAVYDAFVSAFVDQMKATKMGDPNDE
DTQLGPVSSKEQFDTLVEQVGKSVDGGATLLCGGDPEEGREGFYYPATVLADCKPGTPAY
DDELFGPVASVIRAKDDEDAMRIANDSRYGLGGGIFSKDEDKAIKLARDHFDTGMVRINS
FGAADPNMPFGGVKDSGYGREHGGFGMKEFVNTKAIFLP

This GapMind analysis is from Sep 24 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:

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:

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:

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:

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