GapMind for catabolism of small carbon sources

 

Protein 7024902 in Shewanella sp. ANA-3

Annotation: Shewana3_2076 inner membrane ABC transporter permease protein YjfF (RefSeq)

Length: 320 amino acids

Source: ANA3 in FitnessBrowser

Candidate for 28 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arabinose catabolism araZsh hi Inner-membrane translocator (characterized, see rationale) 100% 100% 614.8 Inner membrane ABC transporter permease protein YjfF 56% 337.0
D-galactose catabolism yjtF hi Inner membrane ABC transporter permease protein YjfF (characterized) 56% 94% 337 Fructose import permease protein FruG 38% 216.5
D-fructose catabolism fruG lo Fructose import permease protein FruG (characterized) 38% 93% 216.5 Inner membrane ABC transporter permease protein YjfF 56% 337.0
sucrose catabolism fruG lo Fructose import permease protein FruG (characterized) 38% 93% 216.5 Inner membrane ABC transporter permease protein YjfF 56% 337.0
xylitol catabolism PS417_12060 lo ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) 36% 91% 179.1 Inner membrane ABC transporter permease protein YjfF 56% 337.0
D-cellobiose catabolism mglC lo Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 34% 96% 168.3 Inner membrane ABC transporter permease protein YjfF 56% 337.0
D-glucose catabolism mglC lo Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 34% 96% 168.3 Inner membrane ABC transporter permease protein YjfF 56% 337.0
lactose catabolism mglC lo Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 34% 96% 168.3 Inner membrane ABC transporter permease protein YjfF 56% 337.0
D-maltose catabolism mglC lo Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 34% 96% 168.3 Inner membrane ABC transporter permease protein YjfF 56% 337.0
sucrose catabolism mglC lo Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 34% 96% 168.3 Inner membrane ABC transporter permease protein YjfF 56% 337.0
trehalose catabolism mglC lo Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 34% 96% 168.3 Inner membrane ABC transporter permease protein YjfF 56% 337.0
D-xylose catabolism xylH lo Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 34% 96% 168.3 Inner membrane ABC transporter permease protein YjfF 56% 337.0
D-ribose catabolism rbsC lo Ribose import permease protein RbsC (characterized) 34% 97% 165.2 Inner membrane ABC transporter permease protein YjfF 56% 337.0
D-fructose catabolism frcC lo Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 35% 85% 161.8 Inner membrane ABC transporter permease protein YjfF 56% 337.0
sucrose catabolism frcC lo Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 35% 85% 161.8 Inner membrane ABC transporter permease protein YjfF 56% 337.0
D-mannose catabolism HSERO_RS03645 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 34% 88% 157.9 Inner membrane ABC transporter permease protein YjfF 56% 337.0
myo-inositol catabolism iatP lo Inositol ABC transport system, permease protein IatP, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized) 35% 87% 153.3 Inner membrane ABC transporter permease protein YjfF 56% 337.0
L-fucose catabolism HSERO_RS05255 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 32% 93% 150.6 Inner membrane ABC transporter permease protein YjfF 56% 337.0
D-galactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 31% 94% 144.4 Inner membrane ABC transporter permease protein YjfF 56% 337.0
D-mannose catabolism frcC lo Fructose import permease protein FrcC (characterized) 30% 85% 140.6 Inner membrane ABC transporter permease protein YjfF 56% 337.0
D-ribose catabolism frcC lo Fructose import permease protein FrcC (characterized) 30% 85% 140.6 Inner membrane ABC transporter permease protein YjfF 56% 337.0
2'-deoxyinosine catabolism H281DRAFT_01112 lo deoxynucleoside transporter, permease component 2 (characterized) 31% 86% 139.8 Inner membrane ABC transporter permease protein YjfF 56% 337.0
D-fructose catabolism fruF lo Fructose import permease protein FruF (characterized) 30% 80% 130.6 Inner membrane ABC transporter permease protein YjfF 56% 337.0
sucrose catabolism fruF lo Fructose import permease protein FruF (characterized) 30% 80% 130.6 Inner membrane ABC transporter permease protein YjfF 56% 337.0
D-xylose catabolism xylF_Tm lo ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized) 31% 92% 121.7 Inner membrane ABC transporter permease protein YjfF 56% 337.0
D-galactose catabolism ytfT lo Galactofuranose transporter permease protein YtfT (characterized) 31% 75% 110.9 Inner membrane ABC transporter permease protein YjfF 56% 337.0
L-arabinose catabolism gguB lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 31% 54% 97.4 Inner membrane ABC transporter permease protein YjfF 56% 337.0
D-galactose catabolism gguB lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 31% 54% 97.4 Inner membrane ABC transporter permease protein YjfF 56% 337.0

Sequence Analysis Tools

View 7024902 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MIARRFIPLWITASLLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISG
GIDLSVGAVIALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIV
TLAGMFLARGLATTLSEESIAIDHPFYDAVAEMSIALPGNGALDLSSLIFILFFVIIAVV
MHYTRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALG
AIGVELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGL
LLFFFILLQKLLNGRKTQHG

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, 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