GapMind for catabolism of small carbon sources

 

Protein WP_028485526.1 in Thiomicrorhabdus chilensis DSM 12352

Annotation: NCBI__GCF_000483485.1:WP_028485526.1

Length: 261 amino acids

Source: GCF_000483485.1 in NCBI

Candidate for 51 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 99% 164.9 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 43% 58% 164.5 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 43% 69% 160.6 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 43% 55% 155.2 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 37% 70% 152.9 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 38% 70% 151.4 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 68% 150.6 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 68% 150.6 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 40% 66% 149.8 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
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) 39% 60% 147.5 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
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) 39% 60% 147.5 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 38% 56% 144.8 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
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) 39% 64% 144.4 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
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) 39% 64% 144.4 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 40% 54% 144.1 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
D-cellobiose catabolism msiK lo MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 40% 51% 143.7 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 36% 64% 143.3 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 40% 64% 141 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 37% 72% 139.4 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 63% 139 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 63% 139 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 63% 139 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 63% 139 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 63% 139 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 63% 139 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 63% 139 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 63% 139 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 63% 139 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 35% 71% 138.7 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 38% 64% 138.3 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
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) 33% 57% 137.5 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 41% 54% 137.1 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
D-cellobiose catabolism gtsD 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% 61% 136.3 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
D-glucose catabolism gtsD 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% 61% 136.3 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
lactose catabolism gtsD 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% 61% 136.3 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
D-maltose catabolism gtsD 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% 61% 136.3 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
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) 37% 61% 136.3 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
sucrose catabolism gtsD 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% 61% 136.3 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
trehalose catabolism gtsD 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% 61% 136.3 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 41% 53% 133.7 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 33% 82% 125.6 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 33% 75% 125.6 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 34% 62% 120.6 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
L-proline catabolism HSERO_RS00895 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 30% 82% 104.4 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
L-alanine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 84% 100.1 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 84% 100.1 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
L-leucine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 84% 100.1 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
L-proline catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 84% 100.1 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
L-serine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 84% 100.1 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
L-threonine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 84% 100.1 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 33% 55% 98.6 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 45% 202.2

Sequence Analysis Tools

View WP_028485526.1 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

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Sequence

MGSANIWITDLFHFYNKKQVSPTLENINLTIPQGQLTALIGRSGCGKSTLLQMIAGLLMP
SEGSVRINAHTVTKPSAKWNMMFQKPSLYPWMTVRENAALGLVFSGTYKDKKDRVEELLD
MVGLKDHKDKNVQQLSGGQQQRVALARSLATEPDVLLLDEPFSALDAFTRAALQTEVAQI
CHDYGITMVLVTHDIDEAVAMADKVVIMNHNPGRIVGSMDVNLPYPRDRNEAPFIELKEY
LFSEFEKIDQAKESELEQMAS

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