GapMind for catabolism of small carbon sources

 

Protein WP_077276746.1 in Vagococcus penaei CD276

Annotation: NCBI__GCF_001998885.1:WP_077276746.1

Length: 401 amino acids

Source: GCF_001998885.1 in NCBI

Candidate for 42 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
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) 51% 74% 229.2 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
L-histidine catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 43% 83% 198.4 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
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) 43% 83% 198.4 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 36% 89% 217.2 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 92% 181.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 92% 181.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 92% 181.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 92% 181.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 92% 181.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 92% 181.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 92% 181.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 92% 181.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 38% 69% 181.4 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
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) 41% 64% 173.3 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
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) 41% 64% 173.3 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
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) 35% 83% 169.9 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 33% 88% 166.4 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 37% 66% 165.6 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 40% 64% 163.7 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
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) 35% 78% 161.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
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) 35% 78% 161.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
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) 35% 78% 161.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
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) 35% 78% 161.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
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) 35% 78% 161.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
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) 35% 78% 161.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
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) 35% 78% 161.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
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) 35% 78% 161.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 33% 68% 160.6 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 70% 158.3 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 70% 158.3 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 38% 61% 158.3 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 38% 61% 157.5 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 37% 70% 156.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 35% 65% 154.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
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) 36% 65% 154.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
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) 36% 65% 154.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 35% 71% 153.7 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 36% 72% 153.7 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 37% 64% 153.3 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 37% 62% 147.5 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 36% 57% 146.7 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 35% 62% 146.4 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 63% 506.9

Sequence Analysis Tools

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MKRMIEFQSVSKIYKGNKIAVDNVNLSFEKGEFICFIGTSGSGKTTCMRMINRMTDPSKG
KILIDGDDILSFNPIELRRKIGYVIQNIGLMPHMTIRENIVLVPKLLKVDQEERNRIADK
MIDLVELPREMLDRYPSELSGGQQQRIGVVRALAANQDIILMDEPFGALDPITRDSLQDL
VKDLQERLGKTIVFVTHDMDEALKLASRIAIMSEGKLIQFDTPDNILRNPANNFVEELIG
ENRLIQGKTDTTTVGEVMLNEAVTITPEKSLSQAIRLMREKRVDTLLVVDGAGILKGFID
IETLDRKRHTATSVSDLLNPNVFFVKKTSLLRDTLQRILKRGLKYVPVVDEQKKVVGILT
RASLVDIVYDVIWGEEEDLAAASSQQSDDVVTPVSKSQTEV

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