GapMind for catabolism of small carbon sources

 

Protein WP_108358912.1 in Limnohabitans curvus MWH-C5

Annotation: NCBI__GCF_003063475.1:WP_108358912.1

Length: 677 amino acids

Source: GCF_003063475.1 in NCBI

Candidate for 25 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism fadB hi 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 45% 94% 552.7 6-carboxyhex-2-enoyl-CoA hydratase 43% 521.5
4-hydroxybenzoate catabolism paaH hi 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 45% 94% 552.7 6-carboxyhex-2-enoyl-CoA hydratase 43% 521.5
L-arginine catabolism fadB hi 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 45% 94% 552.7 6-carboxyhex-2-enoyl-CoA hydratase 43% 521.5
L-citrulline catabolism fadB hi 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 45% 94% 552.7 6-carboxyhex-2-enoyl-CoA hydratase 43% 521.5
L-lysine catabolism fadB hi 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 45% 94% 552.7 6-carboxyhex-2-enoyl-CoA hydratase 43% 521.5
phenylacetate catabolism fadB hi 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 45% 94% 552.7 6-carboxyhex-2-enoyl-CoA hydratase 43% 521.5
phenylacetate catabolism paaH hi 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 45% 94% 552.7 6-carboxyhex-2-enoyl-CoA hydratase 43% 521.5
L-phenylalanine catabolism fadB hi 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 45% 94% 552.7 6-carboxyhex-2-enoyl-CoA hydratase 43% 521.5
L-phenylalanine catabolism paaH hi 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 45% 94% 552.7 6-carboxyhex-2-enoyl-CoA hydratase 43% 521.5
L-proline catabolism fadB hi 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 45% 94% 552.7 6-carboxyhex-2-enoyl-CoA hydratase 43% 521.5
4-hydroxybenzoate catabolism pimF med 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 43% 95% 521.5 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 45% 552.7
phenylacetate catabolism pimF med 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 43% 95% 521.5 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 45% 552.7
L-phenylalanine catabolism pimF med 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 43% 95% 521.5 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 45% 552.7
L-isoleucine catabolism ech med Probable enoyl-CoA hydratase; EC 4.2.1.17 (characterized) 42% 74% 137.5 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 45% 552.7
4-hydroxybenzoate catabolism badK med BadK (characterized) 40% 72% 117.9 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 45% 552.7
phenylacetate catabolism badK med BadK (characterized) 40% 72% 117.9 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 45% 552.7
L-phenylalanine catabolism badK med BadK (characterized) 40% 72% 117.9 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 45% 552.7
4-hydroxybenzoate catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 33% 96% 132.1 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 45% 552.7
L-arginine catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 33% 96% 132.1 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 45% 552.7
L-citrulline catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 33% 96% 132.1 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 45% 552.7
L-lysine catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 33% 96% 132.1 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 45% 552.7
phenylacetate catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 33% 96% 132.1 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 45% 552.7
L-phenylalanine catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 33% 96% 132.1 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 45% 552.7
L-proline catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 33% 96% 132.1 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 45% 552.7
L-valine catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 33% 96% 132.1 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 45% 552.7

Sequence Analysis Tools

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

MEARGDVCVITIDNPPINATSLAVRQGLMAAIFDFKTNSDFQAAVIVGAGSTFVAGADIR
EFGKPMQEPILPEVIRAIEDCGKPVVAALHGAALGGGFELALACDARVADAKTVVGLPEV
SLGIIPGAGGTQMLPRRVGVSRAIRMICGAQRISAKEAKSLNLLDEVVASDVLDAAVALA
RRMQGKKCRIRDEAVPAEGPALIQQAAEDAMRAGKRRPAVEAAMEAIKSAAVLSIDDGLA
DERAVFLQLRLSREAYALRHVFFAERDSAKLPSELSATPIPVETVCVIGAGTMGTGIAIS
VLDAGMQVILLEQDAAALQRGQDRVIAHYRDRVAAQKMKADVAQAREACLHSTLDWADMA
KADLVIEAVFEDLAVKQEVFKKIDQFARAGAVLATNTSYLDVDAIAQATSRPQDVLGLHF
FSPANVMKLLEVVRGKDSRPDVLATGMALGKRLRKLPVLAGNHFGFIGNRIYNAYRNQCE
FMLEDGAWPEDVDASLKQFGMAMGPFAVADLSGLDIAWRMRQAQAASRAPGVRYVDILDR
LCEAGHLGRKTGAGYYTYVDGKQQPTTDEAVRHIIEDASQRRGIQRQPLNSATIQRRALL
TIVNEAARLMGEGVASRATDIDVVLVHGYGFPRWEGGPVFWARQQNREALTQEIKDLASQ
CGDGFVLADLSVLFEDQ

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