GapMind for catabolism of small carbon sources

 

Protein WP_111608342.1 in Marinomonas arctica 328

Annotation: NCBI__GCF_003259225.1:WP_111608342.1

Length: 355 amino acids

Source: GCF_003259225.1 in NCBI

Candidate for 21 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
trehalose catabolism thuK med Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) 57% 83% 357.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 54% 367.5
trehalose catabolism malK med 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) 50% 100% 340.9 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 54% 367.5
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) 48% 99% 334.7 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 54% 367.5
D-maltose catabolism malK_Sm med 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) 49% 100% 328.9 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 54% 367.5
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 47% 100% 316.2 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 54% 367.5
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 47% 96% 309.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 54% 367.5
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 45% 93% 292 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 54% 367.5
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 44% 84% 245.7 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 54% 367.5
D-cellobiose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 43% 81% 225.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 54% 367.5
D-galactose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 43% 81% 225.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 54% 367.5
D-glucose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 43% 81% 225.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 54% 367.5
lactose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 43% 81% 225.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 54% 367.5
D-maltose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 43% 81% 225.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 54% 367.5
D-mannose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 43% 81% 225.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 54% 367.5
sucrose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 43% 81% 225.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 54% 367.5
trehalose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 43% 81% 225.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 54% 367.5
L-arabinose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 42% 78% 221.5 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 54% 367.5
D-fructose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 42% 78% 221.5 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 54% 367.5
sucrose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 42% 78% 221.5 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 54% 367.5
D-xylose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 42% 78% 221.5 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 54% 367.5
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 32% 91% 130.2 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 54% 367.5

Sequence Analysis Tools

View WP_111608342.1 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

MTDVILEKVGKTYPNGYHAIPSVDLSIEEGEFIVLVGPSGCGKSTLLRMVAGLESISTGE
LRIRGERMNEKEPADRDIAMVFQNYALYPHMTVYDNMAYGLKNRGMAKDLIAEKVSDVAA
MLGLTELLQRKPRQLSGGQRQRVAMGRAMVRDPKVFLFDEPLSNLDAKLRVQMRVEIRQL
QRKLGTTTLYVTHDQVEAMTLADRLVVLNKGKAEQIGTPMDLYNKPATPFVAAFIGSPSM
NLLDAHLTEQGITVSDELTLPLSHPHRGAIVWGIRPEHLDVSDEHNADFALRIQAVESLG
AETLIHGKVETTSGQGDAMVVRLSGPHLPDINSLMWLKAPAQYWHLFDAVTQQRL

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