GapMind for catabolism of small carbon sources

 

Protein WP_110207539.1 in Nocardioides daejeonensis MJ31

Annotation: NCBI__GCF_003194585.1:WP_110207539.1

Length: 330 amino acids

Source: GCF_003194585.1 in NCBI

Candidate for 60 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA med PotG aka B0855, component of Putrescine porter (characterized) 43% 81% 228.4 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 47% 224.9
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 40% 85% 151.4 PotG aka B0855, component of Putrescine porter 43% 228.4
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 40% 85% 151.4 PotG aka B0855, component of Putrescine porter 43% 228.4
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 42% 78% 140.2 PotG aka B0855, component of Putrescine porter 43% 228.4
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 38% 88% 194.1 PotG aka B0855, component of Putrescine porter 43% 228.4
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 38% 88% 194.1 PotG aka B0855, component of Putrescine porter 43% 228.4
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 82% 192.2 PotG aka B0855, component of Putrescine porter 43% 228.4
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 82% 192.2 PotG aka B0855, component of Putrescine porter 43% 228.4
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 77% 191 PotG aka B0855, component of Putrescine porter 43% 228.4
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 77% 191 PotG aka B0855, component of Putrescine porter 43% 228.4
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 77% 191 PotG aka B0855, component of Putrescine porter 43% 228.4
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 77% 191 PotG aka B0855, component of Putrescine porter 43% 228.4
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 77% 191 PotG aka B0855, component of Putrescine porter 43% 228.4
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 77% 191 PotG aka B0855, component of Putrescine porter 43% 228.4
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 36% 82% 189.5 PotG aka B0855, component of Putrescine porter 43% 228.4
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 41% 64% 188 PotG aka B0855, component of Putrescine porter 43% 228.4
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 36% 97% 187.6 PotG aka B0855, component of Putrescine porter 43% 228.4
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 95% 187.2 PotG aka B0855, component of Putrescine porter 43% 228.4
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 95% 187.2 PotG aka B0855, component of Putrescine porter 43% 228.4
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 95% 187.2 PotG aka B0855, component of Putrescine porter 43% 228.4
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 44% 53% 182.2 PotG aka B0855, component of Putrescine porter 43% 228.4
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 34% 92% 180.6 PotG aka B0855, component of Putrescine porter 43% 228.4
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 41% 63% 177.9 PotG aka B0855, component of Putrescine porter 43% 228.4
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 35% 81% 177.9 PotG aka B0855, component of Putrescine porter 43% 228.4
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 38% 76% 177.9 PotG aka B0855, component of Putrescine porter 43% 228.4
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 39% 72% 176.4 PotG aka B0855, component of Putrescine porter 43% 228.4
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) 38% 69% 175.3 PotG aka B0855, component of Putrescine porter 43% 228.4
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 38% 72% 173.7 PotG aka B0855, component of Putrescine porter 43% 228.4
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 36% 68% 173.3 PotG aka B0855, component of Putrescine porter 43% 228.4
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 31% 94% 170.6 PotG aka B0855, component of Putrescine porter 43% 228.4
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 31% 94% 170.6 PotG aka B0855, component of Putrescine porter 43% 228.4
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 31% 94% 170.6 PotG aka B0855, component of Putrescine porter 43% 228.4
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 31% 94% 170.6 PotG aka B0855, component of Putrescine porter 43% 228.4
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 31% 94% 170.6 PotG aka B0855, component of Putrescine porter 43% 228.4
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 31% 94% 170.6 PotG aka B0855, component of Putrescine porter 43% 228.4
D-maltose catabolism malK lo Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 38% 64% 169.9 PotG aka B0855, component of Putrescine porter 43% 228.4
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 34% 83% 169.1 PotG aka B0855, component of Putrescine porter 43% 228.4
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 65% 166.8 PotG aka B0855, component of Putrescine porter 43% 228.4
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 65% 166.8 PotG aka B0855, component of Putrescine porter 43% 228.4
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 65% 166.8 PotG aka B0855, component of Putrescine porter 43% 228.4
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 65% 166.8 PotG aka B0855, component of Putrescine porter 43% 228.4
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 65% 166.8 PotG aka B0855, component of Putrescine porter 43% 228.4
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 65% 166.8 PotG aka B0855, component of Putrescine porter 43% 228.4
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 65% 166.8 PotG aka B0855, component of Putrescine porter 43% 228.4
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 65% 166.8 PotG aka B0855, component of Putrescine porter 43% 228.4
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 63% 166 PotG aka B0855, component of Putrescine porter 43% 228.4
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 63% 166 PotG aka B0855, component of Putrescine porter 43% 228.4
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 63% 166 PotG aka B0855, component of Putrescine porter 43% 228.4
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 63% 166 PotG aka B0855, component of Putrescine porter 43% 228.4
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 38% 64% 164.5 PotG aka B0855, component of Putrescine porter 43% 228.4
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) 34% 85% 164.5 PotG aka B0855, component of Putrescine porter 43% 228.4
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) 35% 72% 164.1 PotG aka B0855, component of Putrescine porter 43% 228.4
trehalose catabolism malK 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) 35% 72% 164.1 PotG aka B0855, component of Putrescine porter 43% 228.4
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 36% 71% 163.3 PotG aka B0855, component of Putrescine porter 43% 228.4
L-arginine catabolism artP lo ABC transporter for L-Arginine, putative ATPase component (characterized) 38% 94% 146 PotG aka B0855, component of Putrescine porter 43% 228.4
L-proline catabolism HSERO_RS00895 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 34% 97% 140.2 PotG aka B0855, component of Putrescine porter 43% 228.4
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 34% 97% 137.1 PotG aka B0855, component of Putrescine porter 43% 228.4
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 97% 111.7 PotG aka B0855, component of Putrescine porter 43% 228.4
L-leucine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 97% 111.7 PotG aka B0855, component of Putrescine porter 43% 228.4
L-proline catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 97% 111.7 PotG aka B0855, component of Putrescine porter 43% 228.4

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Sequence

MLEIDDLTVRYDDTSAVDGVSLRVERGEILAVLGPSGCGKSTLLRAVAGLEPPAAGCVRA
DGEDLARVPTHRRGFALMFQDGQLFNQKTVAGNVGYPLRIRRRPRAEVRDRVAELLELVG
LSAYAERRPDSLSGGERQRVALARALAVEPRLLLLDEPLSALDAALRDRLAGELREILTA
AGTTALLVTHDHEEAFAVADRMALMRAGRVVQSGTPADVWAAPVDAEAADFLGYDRVVRG
DAAALLLRAAGRSGGGAVALRRSALEVDEHGPLAGRIVAFRSAPELLRLTVAVPGIGEIA
AVARQAGVWAEVGAEVSLRVVPDRLAVLSH

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