GapMind for catabolism of small carbon sources

 

Protein CCNA_01515 in Caulobacter crescentus NA1000

Annotation: CCNA_01515 C4-dicarboxylate transporter large subunit

Length: 426 amino acids

Source: Caulo in FitnessBrowser

Candidate for 8 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-glucuronate catabolism dctM hi Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale) 47% 100% 409.5 Sialic acid TRAP transporter large permease protein SiaM 41% 313.2
L-malate catabolism dctM lo C4-dicarboxylate TRAP transporter large permease protein DctM (characterized) 37% 100% 309.3 Sialic acid TRAP transporter large permease protein SiaM 41% 313.2
fumarate catabolism dctM lo C4-dicarboxylate TRAP transporter large permease protein DctM (characterized) 37% 100% 309.3 Sialic acid TRAP transporter large permease protein SiaM 41% 313.2
succinate catabolism dctM lo C4-dicarboxylate TRAP transporter large permease protein DctM (characterized) 37% 100% 309.3 Sialic acid TRAP transporter large permease protein SiaM 41% 313.2
D-gluconate catabolism gntB lo Large component of TRAP-type D-gluconate transporter (characterized) 38% 99% 304.3 Sialic acid TRAP transporter large permease protein SiaM 41% 313.2
2-oxoglutarate (alpha-ketoglutarate) catabolism dctM lo TRAP transporter, subunit DctM (characterized, see rationale) 38% 98% 295.4 Sialic acid TRAP transporter large permease protein SiaM 41% 313.2
4-hydroxybenzoate catabolism fcbT3 lo FcbT3, component of Tripartite 4-chlorobenzoate symporter (also binds and may transport 4-bromo-, 4-iodo-, and 4-fluorobenzoate and with a lower affinity, 3-chlorobenzoate, 2-chlorobenzoate, 4-hydroxybenzoate, 3-hydroxybenzoate, and benzoate) (characterized) 31% 97% 211.5 Sialic acid TRAP transporter large permease protein SiaM 41% 313.2
L-glutamate catabolism gtrB lo GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized) 31% 97% 192.6 Sialic acid TRAP transporter large permease protein SiaM 41% 313.2

Sequence Analysis Tools

View CCNA_01515 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MELTLLLGLLALLLIIGVPVAFALGLASLVTFIFMDIAPVVAFQRIATGVNVFSLMAIPF
FIFAGDLMQQAGIAERLVRVADAAMGRIRGGLGVVDVGASMMFGGVSGSAVASVSALGST
LIPLMKEKGYDADYAVNVTSTSAILGILIPPSHNMIIYAAAAGVSVSVADLFLAGVLPGI
LTGIFLAAAAWIIAVRRGYPKGEFPGWPAFAAAFASALPGLLTAVIIFGGVLGGVFTPTE
SSAVAVIYTLVIAVIVYRTLGFRGFTTAAQNAVKTTAMVMLIIGSAAAFGWLLALLEAPE
QLATLLQTLTDNPILILLLINLILLILGTFMDMAPLIVITSPIFLPVAMATGMDPVQFGI
MMMLNLGIGLVTPPVGSVLFVGCAVGKIKVEQAVRTIWPFYLALFAALMAITFVPALTLT
LPGLAG

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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