GapMind for catabolism of small carbon sources

 

Protein WP_047094318.1 in Erythrobacter marinus HWDM-33

Annotation: NCBI__GCF_001013305.1:WP_047094318.1

Length: 240 amino acids

Source: GCF_001013305.1 in NCBI

Candidate for 42 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 41% 81% 154.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 41% 83% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 41% 83% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 41% 83% 146.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-asparagine catabolism glnQ med Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 41% 87% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-glutamate catabolism gltL med Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 41% 87% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-citrulline catabolism PS417_17605 med ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 41% 79% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-arginine catabolism artP med Histidine transport ATP-binding protein HisP (characterized) 40% 87% 136.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-histidine catabolism hisP med Histidine transport ATP-binding protein HisP (characterized) 40% 87% 136.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 38% 85% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 38% 87% 141 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 39% 64% 138.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 39% 64% 138.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 39% 64% 138.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 84% 137.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 84% 137.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 37% 91% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-asparagine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 39% 81% 136.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-aspartate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 39% 81% 136.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-glutamate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 39% 81% 136.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-histidine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 39% 81% 136.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-leucine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 39% 81% 136.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-proline catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 39% 81% 136.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 89% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 89% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 38% 87% 131.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 38% 87% 131.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 61% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 61% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 61% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 61% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 61% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 61% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-proline catabolism opuBA lo BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) 34% 61% 126.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 35% 62% 124 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 38% 76% 123.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-histidine catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 35% 74% 107.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 35% 74% 107.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 34% 76% 107.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
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) 33% 57% 107.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 31% 62% 92.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2
L-proline catabolism HSERO_RS00900 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 31% 91% 90.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 217.2

Sequence Analysis Tools

View WP_047094318.1 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

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Sequence

MTQHKLIELEGITKTFGKGPAAFQALKGVDMKIDRGDFVAIMGPSGSGKSTTMNILGCLD
VPTDGIFRFRGIEVQALTRDQRSLLRRRYLGFVFQGFNLLARTTALENVELPLLYRGETK
KQRRIAAERSLDKVGLLPWASHTPAELSGGQQQRVAIARALVTDPDVLLADEPTGNLDTE
RSLEIMELLTDLSDTGITVLMVTHEEEMAEYARTIVHFRDGLVARIDRGHKSGAPLKEKV

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