GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_1821 in Dyella japonica UNC79MFTsu3.2

Annotation: FitnessBrowser__Dyella79:N515DRAFT_1821

Length: 238 amino acids

Source: Dyella79 in FitnessBrowser

Candidate for 23 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 42% 92% 169.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 40% 86% 154.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 40% 86% 154.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 87% 154.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 87% 154.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 39% 70% 154.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 37% 90% 153.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
L-asparagine catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 37% 90% 152.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
L-aspartate catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 37% 90% 152.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 38% 93% 146.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
putrescine catabolism potA lo Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 39% 59% 146.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 36% 52% 136 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
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) 38% 54% 136 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 35% 70% 135.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
D-maltose catabolism malK1 lo MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) 34% 61% 134 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 64% 132.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 64% 132.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
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) 37% 54% 130.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
D-mannose catabolism TT_C0211 lo Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) 37% 56% 122.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 61% 121.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 61% 121.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 61% 121.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
D-cellobiose catabolism TM0028 lo TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 32% 72% 94.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8

Sequence Analysis Tools

View N515DRAFT_1821 at FitnessBrowser

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MLKMTHLSKVYRTEVVETYALRDFNIDVKEGEFVAVTGPSGSGKTTFLTIAGLLETFTGG
EYHLDGVEVSNLNDNARSKIRNEKIGFIFQAFNLIPDLNVYDNVEVPLRYRGMKALERKQ
RIMDALERVGLASRAKHYPAELSGGQQQRVAIARALAGSPRLLLADEPTGNLDTQMARGV
MELLEEIHREGATIVMVTHDPELATRAQRNVHVIDGQVVDLAEDPRFHQQQARAGAPA

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:

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