GapMind for catabolism of small carbon sources

 

Protein 8502259 in Desulfovibrio vulgaris Miyazaki F

Annotation: DvMF_2969 ABC transporter related (RefSeq)

Length: 418 amino acids

Source: Miya in FitnessBrowser

Candidate for 17 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA med PotG aka B0855, component of Putrescine porter (characterized) 42% 83% 251.1 Uncharacterized ABC transporter ATP-binding protein YdcT 56% 258.1
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 43% 75% 222.2 Uncharacterized ABC transporter ATP-binding protein YdcT 56% 258.1
D-cellobiose catabolism msiK med MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 41% 80% 219.2 Uncharacterized ABC transporter ATP-binding protein YdcT 56% 258.1
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 46% 71% 217.6 Uncharacterized ABC transporter ATP-binding protein YdcT 56% 258.1
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 47% 70% 210.7 Uncharacterized ABC transporter ATP-binding protein YdcT 56% 258.1
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 41% 72% 206.8 Uncharacterized ABC transporter ATP-binding protein YdcT 56% 258.1
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 41% 72% 206.8 Uncharacterized ABC transporter ATP-binding protein YdcT 56% 258.1
D-maltose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 43% 73% 204.9 Uncharacterized ABC transporter ATP-binding protein YdcT 56% 258.1
sucrose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 43% 73% 204.9 Uncharacterized ABC transporter ATP-binding protein YdcT 56% 258.1
trehalose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 43% 73% 204.9 Uncharacterized ABC transporter ATP-binding protein YdcT 56% 258.1
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 42% 71% 202.6 Uncharacterized ABC transporter ATP-binding protein YdcT 56% 258.1
D-sorbitol (glucitol) catabolism mtlK lo MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 40% 84% 221.1 Uncharacterized ABC transporter ATP-binding protein YdcT 56% 258.1
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 37% 93% 220.3 Uncharacterized ABC transporter ATP-binding protein YdcT 56% 258.1
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 38% 94% 218.8 Uncharacterized ABC transporter ATP-binding protein YdcT 56% 258.1
D-maltose catabolism malK_Sm lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 38% 80% 201.8 Uncharacterized ABC transporter ATP-binding protein YdcT 56% 258.1
trehalose catabolism malK lo MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) 37% 79% 201.8 Uncharacterized ABC transporter ATP-binding protein YdcT 56% 258.1
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 38% 81% 155.6 Uncharacterized ABC transporter ATP-binding protein YdcT 56% 258.1

Sequence Analysis Tools

View 8502259 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

MPTDISPVASSDAFPNASPVASPSASADLSVTRLVKRFEKFTAVNDVSFEVEQGRFFSIL
GPSGCGKTTLLRMIAGFESPDSGVIAIRGRDMAGIAPNRRPVNLIFQHLALFPMMSVAEN
VAFGLKRRGMAGGEISRRVQDVLERVGLPGYGVKMPAQLSGGQKQRVAIARCLVLEPAVL
LLDEPLGALDLKLREQMKVELKTLQAEVGTTFVYITHDQSEALVMSDHVAVMNAGRFEQV
DTPRNLYRRPASAFVAGFVGETNVWSGTLEEATGDAGLVRTDEGAVFRARVAAGLAKGTR
VDMFIRPEAVLIDPDGASCATDGATDGATDGAAGDGAGGGDAPLPVRGACANRVQVQVQA
ILFDGAASRLLTHLEGSRREVMVALPQNRLYDHIKPGDRITVGWDDRAGICFAAGSGR

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 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