GapMind for catabolism of small carbon sources

 

Protein HSERO_RS22810 in Herbaspirillum seropedicae SmR1

Annotation: FitnessBrowser__HerbieS:HSERO_RS22810

Length: 423 amino acids

Source: HerbieS in FitnessBrowser

Candidate for 10 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism gadh2 hi gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized) 44% 96% 361.3 Alcohol dehydrogenase (quinone), cytochrome c subunit; ADH; Alcohol dehydrogenase (quinone), subunit II; Cytochrome c-553; Cytochrome c553; Ethanol:Q2 reductase; G3-ADH subunit II; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 45% 347.4
D-gluconate catabolism gadh2 hi gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized) 44% 96% 361.3 Alcohol dehydrogenase (quinone), cytochrome c subunit; ADH; Alcohol dehydrogenase (quinone), subunit II; Cytochrome c-553; Cytochrome c553; Ethanol:Q2 reductase; G3-ADH subunit II; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 45% 347.4
D-glucose catabolism gadh2 hi gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized) 44% 96% 361.3 Alcohol dehydrogenase (quinone), cytochrome c subunit; ADH; Alcohol dehydrogenase (quinone), subunit II; Cytochrome c-553; Cytochrome c553; Ethanol:Q2 reductase; G3-ADH subunit II; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 45% 347.4
lactose catabolism gadh2 hi gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized) 44% 96% 361.3 Alcohol dehydrogenase (quinone), cytochrome c subunit; ADH; Alcohol dehydrogenase (quinone), subunit II; Cytochrome c-553; Cytochrome c553; Ethanol:Q2 reductase; G3-ADH subunit II; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 45% 347.4
D-maltose catabolism gadh2 hi gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized) 44% 96% 361.3 Alcohol dehydrogenase (quinone), cytochrome c subunit; ADH; Alcohol dehydrogenase (quinone), subunit II; Cytochrome c-553; Cytochrome c553; Ethanol:Q2 reductase; G3-ADH subunit II; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 45% 347.4
sucrose catabolism gadh2 hi gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized) 44% 96% 361.3 Alcohol dehydrogenase (quinone), cytochrome c subunit; ADH; Alcohol dehydrogenase (quinone), subunit II; Cytochrome c-553; Cytochrome c553; Ethanol:Q2 reductase; G3-ADH subunit II; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 45% 347.4
trehalose catabolism gadh2 hi gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized) 44% 96% 361.3 Alcohol dehydrogenase (quinone), cytochrome c subunit; ADH; Alcohol dehydrogenase (quinone), subunit II; Cytochrome c-553; Cytochrome c553; Ethanol:Q2 reductase; G3-ADH subunit II; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 45% 347.4
ethanol catabolism adhBqn med Alcohol dehydrogenase (quinone), cytochrome c subunit; ADH; Alcohol dehydrogenase (quinone), subunit II; Cytochrome c-553; Cytochrome c553; Ethanol:Q2 reductase; G3-ADH subunit II; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 (characterized) 45% 90% 347.4 gluconate 2-dehydrogenase (EC 1.1.1.215) 44% 361.3
ethanol catabolism etoh-dh-c med alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized) 42% 90% 344.7 gluconate 2-dehydrogenase (EC 1.1.1.215) 44% 361.3
2-deoxy-D-ribose catabolism drdehyd-cytc med cytochrome c component of deoxyribose dehydrogenase (characterized) 45% 87% 336.3 gluconate 2-dehydrogenase (EC 1.1.1.215) 44% 361.3

Sequence Analysis Tools

View HSERO_RS22810 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

Fitness BLAST: loading...

Sequence

MKKLTSLFAALAWSLGALGTLTTAQAADQDLVARGQYLARAGDCMACHSAAGKPAYSGGL
AIDSGHGIIYSTNITPDKEHGIGNYSEAQFSAAVRHGVRADGTQLYPAMPYPSYAKVSDE
DIHALYTYFMQGVQPVASTPPASSMSFPFNIRWGMKLWNVFFANDKPFREQDGWSAEIKR
GAYLVEGLGHCGSCHTPRGVAMNEKASDSSQAQFLSGGDLNGWAVPSLRGMPHWSAQDIV
DYLQTGRNKTASVAGEMSLVVEHSTSHLKREDLQAMAAYLKTLSPVASSGSGRVIPQGVD
ATVSKLTAAKDLTLGERLYLDNCAACHFVTGRGAPGIFPVLDGATVVNAENPSALLHVIL
AGARTPSTEKAPSILVMPGFAHRLSDEEAAALATFVRQGWGNHAGKVSEREVGKLRAGMD
KQH

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:

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