GapMind for catabolism of small carbon sources

 

Protein WP_019386899.1 in Arenitalea lutea P7-3-5

Annotation: NCBI__GCF_000283015.1:WP_019386899.1

Length: 303 amino acids

Source: GCF_000283015.1 in NCBI

Candidate for 36 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 34% 67% 149.4 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 34% 63% 141.4 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 70% 138.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 70% 138.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 70% 138.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 70% 138.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 70% 138.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 70% 138.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 70% 138.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 70% 138.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
L-proline catabolism opuBA lo BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 35% 76% 138.3 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 74% 137.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 74% 137.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 74% 137.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 74% 137.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 35% 69% 136 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 36% 71% 133.3 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 32% 60% 132.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 36% 71% 132.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 31% 73% 130.6 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 32% 63% 130.6 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 32% 70% 129.8 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 32% 70% 129.8 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 32% 70% 129.8 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 32% 70% 129.8 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
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) 31% 60% 129.4 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
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) 31% 60% 129.4 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
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) 31% 60% 129.4 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
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) 31% 60% 129.4 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
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) 31% 60% 129.4 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
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) 31% 60% 129.4 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
sucrose catabolism thuK 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) 31% 60% 129.4 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
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) 31% 60% 129.4 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
trehalose catabolism thuK 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) 31% 60% 129.4 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 32% 62% 127.9 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 31% 81% 102.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 38% 159.1

Sequence Analysis Tools

View WP_019386899.1 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

Fitness BLAST: loading...

Sequence

MLIVKNLKFSYKKTAVLKNISFDANQGENVAIIGESGSGKSTLLKVLYGEYDLDEGHIFW
NDNEILGPKFNLVVGYDFMKYVAQEFDLMPFITVEENIGKFLSRFYPEEKHRRTQELIEV
VELTEFAKTKVKTLSGGQKQRVALARALAKQPEIILLDEPFSHIDNFKKQSLRRSVFKYL
KDNHITCIVATHDKEDVLGYADQMIVLNNNKIAVKDTPEQLYKHPKTPLVASFFGEFNVI
NNQIYYAHQLEVVNDSELKMTVTNAYYKGHYFLIEAELNGEHMFFEHPKSLKPGTEICLA
IKK

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