GapMind for catabolism of small carbon sources

 

Protein WP_011384976.1 in Magnetospirillum magneticum AMB-1

Annotation: NCBI__GCF_000009985.1:WP_011384976.1

Length: 398 amino acids

Source: GCF_000009985.1 in NCBI

Candidate for 22 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism paaJ2 hi 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized) 57% 100% 437.2 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 42% 309.3
4-hydroxybenzoate catabolism pcaF hi 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized) 57% 100% 437.2 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 55% 414.8
phenylacetate catabolism paaJ1 hi 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized) 57% 100% 437.2 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 42% 309.3
phenylacetate catabolism paaJ2 hi 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized) 57% 100% 437.2 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 42% 309.3
L-phenylalanine catabolism paaJ1 hi 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized) 57% 100% 437.2 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 42% 309.3
L-phenylalanine catabolism paaJ2 hi 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized) 57% 100% 437.2 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 42% 309.3
L-tryptophan catabolism pcaF hi 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized) 57% 100% 437.2 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 55% 414.8
L-isoleucine catabolism fadA med subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 56% 100% 427.9 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 57% 437.2
L-isoleucine catabolism fadA med acetyl-CoA C-acyltransferase (EC 2.3.1.16) (TIGR01930) 100% 427.5 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 57% 437.2
4-hydroxybenzoate catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 42% 99% 309.3 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 57% 437.2
L-arginine catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 42% 99% 309.3 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 57% 437.2
L-citrulline catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 42% 99% 309.3 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 57% 437.2
2-deoxy-D-ribonate catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 42% 99% 309.3 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 57% 437.2
2-deoxy-D-ribose catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 42% 99% 309.3 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 57% 437.2
L-leucine catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 42% 99% 309.3 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 57% 437.2
L-lysine catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 42% 99% 309.3 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 57% 437.2
phenylacetate catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 42% 99% 309.3 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 57% 437.2
L-phenylalanine catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 42% 99% 309.3 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 57% 437.2
L-proline catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 42% 99% 309.3 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 57% 437.2
L-tyrosine catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 42% 99% 309.3 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 57% 437.2
4-hydroxybenzoate catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 39% 100% 238.4 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 57% 437.2
phenylacetate catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 39% 100% 238.4 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 57% 437.2
L-phenylalanine catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 39% 100% 238.4 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 57% 437.2

Sequence Analysis Tools

View WP_011384976.1 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

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MLDAYIYDGLRSPIGRHGGGLAPVRSDDLAAEVIRALVARSSFKPEDVEDVILGCTNQAG
EDSRNVARHAALLAGLPVEVAGQTVNRLCASGLAAVLDAARSVTCGEGDLYLAGGVESMT
RAPFVLAKGDSAWSRDARIFDTTIGARFANPKVVKSFGGHSMPETADNIAHDLGLSREAS
DAFAAASQAKYAKAKAEGFYEGEIHPITIAGRKGDTIVAEDEHPRPQTDLAALTKLKPLF
EGGVVTAGNASGINDGAAALFIGSRAAGEKAGIAPIARIVAGAAAGVPPRVMGLGPVPAI
TKALARAKLSLKDLDLIEINEAFAVQVLGCVTQLGVAADDSRLNPNGGAIAIGHPLGCSG
ARLALTAARQLQRTGGRHAVVSLCIGVGHGLAAVIERV

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