GapMind for catabolism of small carbon sources

 

Protein WP_017177065.1 in Actinomyces timonensis 7400942

Annotation: NCBI__GCF_000295095.1:WP_017177065.1

Length: 299 amino acids

Source: GCF_000295095.1 in NCBI

Candidate for 28 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 46% 83% 204.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
L-proline catabolism opuBA med 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) 43% 73% 195.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
L-proline catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 44% 83% 191.4 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 43% 59% 181.8 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 37% 84% 162.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 40% 63% 161 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 41% 62% 154.8 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 40% 56% 154.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
trehalose catabolism thuK lo Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) 37% 72% 152.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 38% 69% 151.8 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
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) 34% 72% 149.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 39% 57% 149.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
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% 72% 143.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
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) 33% 72% 143.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
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) 39% 58% 142.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
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) 39% 58% 142.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
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) 39% 58% 142.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
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) 39% 58% 142.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
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) 39% 58% 142.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
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) 39% 58% 142.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
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) 39% 58% 142.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 35% 63% 140.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
L-alanine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 90% 100.9 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 90% 100.9 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
L-leucine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 90% 100.9 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
L-proline catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 90% 100.9 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
L-serine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 90% 100.9 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6
L-threonine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 90% 100.9 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 52% 239.6

Sequence Analysis Tools

View WP_017177065.1 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

MSGEIEFDSVTKRYPVPRRAKRQGTGTAAGPAVDAFSATIAPGTTTVLLGSSGSGKTTLM
RMVNRMVEPSSGRVLIDGEDVAGRDPVALRRSIGYVMQNGGLLPHRRVIDNITLVPRLNG
TGRAQAAHRAHELMDILGLDPALAERYPHELSGGQAQRVGVARALAADPAILLMDEPFGA
VDPLVRRELQAETARLQRELGKTILFVTHDVDEALALGDEIIVLREGARIAQRGSGPQIL
HHPADAFVERFLGLDDDIRASRLRETAVRDSGASPALAPAAVPPAAAAPAPERAEVPRP

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