GapMind for catabolism of small carbon sources

 

Protein Ga0059261_2703 in Sphingomonas koreensis DSMZ 15582

Annotation: Ga0059261_2703 ABC-type multidrug transport system, ATPase component

Length: 313 amino acids

Source: Korea in FitnessBrowser

Candidate for 22 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 32% 72% 129 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9
2'-deoxyinosine catabolism nupA lo RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized) 32% 51% 119 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 33% 90% 118.2 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 31% 75% 107.1 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9
L-alanine catabolism braG lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 33% 96% 106.3 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9
L-isoleucine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 33% 96% 106.3 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9
L-leucine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 33% 96% 106.3 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9
L-proline catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 33% 96% 106.3 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9
L-serine catabolism braG lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 33% 96% 106.3 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9
L-threonine catabolism braG lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 33% 96% 106.3 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 32% 97% 106.3 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9
L-valine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 33% 96% 106.3 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 33% 88% 104 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 33% 88% 104 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 33% 88% 104 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 33% 88% 104 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9
D-ribose catabolism rbsA lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 31% 50% 102.8 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9
L-isoleucine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 33% 95% 101.3 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9
L-leucine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 33% 95% 101.3 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9
L-phenylalanine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 33% 95% 101.3 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9
L-valine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 33% 95% 101.3 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9
D-lactate catabolism PGA1_c12640 lo D-lactate transporter, ATP-binding component (characterized) 30% 94% 100.5 uncharacterized ABC transporter ATP-binding protein yadG 42% 229.9

Sequence Analysis Tools

View Ga0059261_2703 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

MQPILSVRGVSKTYASGHKALGSVDLDINKGEIFALLGPNGAGKTTLISIICGIVTPSSG
TIVVDGHDAISEPRAARMKIGLVPQELSVDMFETVQATTRYSRRLFGRPANDAYIDQVLK
DLSLYDKRNSKVMELSGGMKRRVLIAKALAHEPDILFLDEPTAGVDVSLRRDMWKLIGSL
RERGTTIILTTHYIEEAEEMADRVGVINKGELLLVEGKAELMKKLGKREMDIALVEPMTA
IPGELEEWHLALEDEGHRLRYTFDAQAERTGIPSLLRKLGDLGIQFKDLDTSKSSLEDIF
VDLVETRNEEKAA

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