GapMind for catabolism of small carbon sources

 

Protein WP_013258465.1 in Desulfarculus baarsii DSM 2075

Annotation: NCBI__GCF_000143965.1:WP_013258465.1

Length: 233 amino acids

Source: GCF_000143965.1 in NCBI

Candidate for 65 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism artP med ABC transporter for L-Arginine, putative ATPase component (characterized) 41% 89% 149.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-Glucosamine, putative ATPase component (characterized) 40% 88% 148.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
L-glutamate catabolism gltL med Amino acid ABC transporter ATP binding protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized) 41% 91% 146 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
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% 83% 145.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
L-asparagine catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 43% 91% 143.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 42% 79% 143.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
L-aspartate catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 43% 91% 143.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 42% 79% 143.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 41% 83% 142.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
L-histidine catabolism hisP med Histidine transport ATP-binding protein HisP (characterized) 41% 83% 134.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
L-lysine catabolism hisP med Histidine transport ATP-binding protein HisP (characterized) 41% 83% 134.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 42% 67% 175.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 40% 87% 148.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 60% 145.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 60% 145.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 60% 145.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 60% 145.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 60% 145.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 60% 145.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 37% 93% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 39% 58% 141.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 38% 52% 140.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 63% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 63% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 63% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 63% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 63% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 63% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 63% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 63% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 39% 86% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 38% 90% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 81% 138.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 81% 138.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 38% 61% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 35% 58% 136.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
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) 38% 83% 136 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
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) 38% 83% 136 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
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) 38% 83% 136 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
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) 38% 83% 136 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
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) 38% 83% 136 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 38% 63% 136 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 58% 135.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 34% 92% 132.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 34% 92% 132.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 36% 57% 131 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
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) 37% 55% 130.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 62% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 62% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 62% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 62% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 35% 80% 126.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
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) 35% 60% 126.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
trehalose catabolism thuK 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) 35% 60% 126.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 35% 61% 125.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 36% 65% 125.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 36% 65% 125.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 32% 58% 123.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 37% 54% 123.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 36% 53% 122.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 38% 60% 122.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 34% 63% 119.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 33% 55% 113.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
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) 31% 57% 108.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3
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) 33% 56% 107.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 237.3

Sequence Analysis Tools

View WP_013258465.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MQLIELREITKTYNLGEVQVPVLKGVSLGVAQGELVALMGASGSGKSTLMNIMGCLDRPS
AGQYLLDGRDVAGFSADQRARLRNRKIGFVFQNFSLLPRTSALENVAMPLAYAADQPGDR
QARKRAAEMLERVGLAQRMHHEPNQLSGGQQQRVAIARALINRPELLLADEPTGNLDSKT
SQEVLQMFAKLNEEDGITIILVTHDAEVARHAKRTIAISDGVIVADGAEGEAS

This GapMind analysis is from Apr 09 2024. 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