GapMind for catabolism of small carbon sources

 

Protein 8501197 in Desulfovibrio vulgaris Miyazaki F

Annotation: DvMF_1931 TRAP dicarboxylate transporter, DctM subunit (RefSeq)

Length: 640 amino acids

Source: Miya 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
L-malate catabolism dctM hi C4-dicarboxylate TRAP transporter large permease protein DctM (characterized) 46% 98% 372.9 Sialic acid TRAP transporter permease protein SiaT; N-acetylneuraminic acid permease; N-acetylneuraminic acid transporter; Neu5Ac permease 31% 330.1
fumarate catabolism dctM hi C4-dicarboxylate TRAP transporter large permease protein DctM (characterized) 46% 98% 372.9 Sialic acid TRAP transporter permease protein SiaT; N-acetylneuraminic acid permease; N-acetylneuraminic acid transporter; Neu5Ac permease 31% 330.1
succinate catabolism dctM hi C4-dicarboxylate TRAP transporter large permease protein DctM (characterized) 46% 98% 372.9 Sialic acid TRAP transporter permease protein SiaT; N-acetylneuraminic acid permease; N-acetylneuraminic acid transporter; Neu5Ac permease 31% 330.1
D-glucuronate catabolism dctM med Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale) 43% 98% 348.6 C4-dicarboxylate TRAP transporter large permease protein DctM 46% 372.9
D-gluconate catabolism gntB lo TRAP-type large permease component (characterized, see rationale) 38% 97% 300.4 C4-dicarboxylate TRAP transporter large permease protein DctM 46% 372.9
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) 30% 98% 210.3 C4-dicarboxylate TRAP transporter large permease protein DctM 46% 372.9
2-oxoglutarate (alpha-ketoglutarate) catabolism dctM lo dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized) 35% 81% 208.4 Sialic acid TRAP transporter permease protein SiaT; N-acetylneuraminic acid permease; N-acetylneuraminic acid transporter; Neu5Ac permease 31% 330.1
4-hydroxybenzoate catabolism fcbT2 lo FcbT2, 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) 30% 65% 45.8 Sialic acid TRAP transporter permease protein SiaT; N-acetylneuraminic acid permease; N-acetylneuraminic acid transporter; Neu5Ac permease 31% 330.1

Sequence Analysis Tools

View 8501197 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

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

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSERNTFSWATANEWLEKPFLVAGLMVMILAITYQTGFRYSMATINEMLNDAGTVAFLAR
FVDVEGLKAGLQRIIGWSVWSEELSRYLFIWISYLAVPLAIMKRSNIRVDVLCAKLPPRA
QGMAWVVVDVCTLVLTGALCYMGFGHVQMQIAMPQTTPAMGIKYFIPYMILPVGFFLMTL
RTVQDLVRQARTMPALDVVGGVACGLLLFLPVLLSDQWSAVWLLFGYFVLFLLVGVPIAF
SLGLATIATVLGAGTLPLEYLAQIAFVSIDSFPILAIPFFIAAGVFMGAGGLSRRLLALG
DELVGALPGGMALATIVTCMFFAAISGSGPATVAAIGSITIPAMVERGYDKFFAAAVVAS
AGCIGVMIPPSNPFVVYGVAAQASVGKLFLAGIVPGVLCGLALMAVAYYISLKKGWRGEA
RHRDFRSVMQAMWEAKWALLVPVIVLGGIYGGIMTPTEAAAVSALYGMIVGLFIYREITW
RRMWDCMVESAQTSSVIIVLMAMATLFGNIMTIEQVPDHIAAMILGVTSNKIAILLLINV
FLLWVGTFMEALAAIVIITPILLPLVTQVGVDPIHFGVIMVVNLAIGFITPPVGVNLFVA
SSISKVSIGDVVRAAWPFLLVMIALLMAITYIPAISLCLL

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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