GapMind for catabolism of small carbon sources

 

Protein WP_048060827.1 in Methanothermobacter thermautotrophicus str. Delta H

Annotation: NCBI__GCF_000008645.1:WP_048060827.1

Length: 347 amino acids

Source: GCF_000008645.1 in NCBI

Candidate for 58 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism malK lo Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 35% 86% 167.9 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 33% 97% 167.5 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 31% 98% 165.6 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 31% 98% 165.6 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 90% 162.5 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 90% 162.5 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 90% 162.5 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 32% 95% 162.2 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 32% 95% 162.2 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 32% 95% 162.2 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 32% 95% 162.2 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 32% 95% 162.2 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 34% 86% 162.2 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 32% 95% 162.2 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 32% 93% 160.2 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 32% 94% 159.1 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 32% 94% 159.1 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 31% 94% 157.9 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 31% 97% 157.9 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 32% 85% 155.6 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
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) 31% 92% 154.5 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 38% 70% 153.7 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 32% 84% 153.3 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
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) 37% 88% 152.5 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
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) 37% 88% 152.5 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
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) 30% 90% 151.8 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
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) 30% 90% 151.8 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
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) 30% 90% 151.8 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
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) 30% 90% 151.8 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
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) 30% 90% 151.8 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
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) 30% 90% 151.8 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
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) 30% 90% 151.8 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
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% 79% 150.6 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 36% 75% 146.7 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 33% 75% 145.6 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 31% 84% 145.6 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 36% 66% 144.8 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 36% 58% 144.4 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) 35% 99% 132.9 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 35% 88% 132.1 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
L-lysine catabolism hisP lo ABC transporter for L-Lysine, ATPase component (characterized) 32% 98% 130.6 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 33% 98% 125.2 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 33% 98% 125.2 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
L-glutamate catabolism gltL lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 33% 98% 125.2 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 34% 91% 111.7 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
L-isoleucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) 33% 94% 106.3 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
L-phenylalanine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) 33% 94% 106.3 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 31% 68% 103.6 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
L-leucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 30% 94% 103.2 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
L-valine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 30% 94% 103.2 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
L-alanine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 35% 92% 101.3 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 35% 92% 101.3 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
L-leucine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 35% 92% 101.3 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
L-proline catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 35% 92% 101.3 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
L-serine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 35% 92% 101.3 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
L-threonine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 35% 92% 101.3 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
L-isoleucine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 96% 99.4 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8
L-valine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 96% 99.4 ABC-type molybdate transporter (EC 7.3.2.5) 35% 201.8

Sequence Analysis Tools

View WP_048060827.1 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

MHVIELSGITKSYGDIKVLEDVNLKVREGETLGIIGPTGAGKSTLLRIMDLLERPDDGEI
LFMGENVDDLKPLEVRRRMGMVFQNTPVFRGTVAESILYGPRIRGERPHESEVKDVLETM
GLKGYGSRRTTELSGGERQRLALAQVLINRPEVVLLDEATSSLDPISRSRMEDVIAELDV
TVIFTTHDLLQGQKLADRIAILNRSILQTGEPREIFKKPASRFVAEFVGARNMLRGRAHI
TAEGISLIECDGISIYSSERATGDVSATIRPEDITVSWQRTDSSALNQLEGRVLAVRDAG
SVQQLEVRCGGETLTVHMTGKSLNDMGITTGSRVWIEFKASAVHVIR

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