GapMind for catabolism of small carbon sources

 

Protein WP_085219373.1 in Sphingomonas indica Dd16

Annotation: NCBI__GCF_900177405.1:WP_085219373.1

Length: 233 amino acids

Source: GCF_900177405.1 in NCBI

Candidate for 61 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 40% 88% 144.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 40% 83% 143.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 41% 85% 140.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 41% 85% 140.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-arginine catabolism artP med ABC transporter for L-Arginine, putative ATPase component (characterized) 40% 81% 134 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 40% 88% 143.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 88% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 88% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-histidine catabolism hisP lo Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 39% 90% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 39% 82% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 37% 88% 136.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 36% 58% 132.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 38% 82% 130.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 38% 82% 130.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 35% 60% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 36% 78% 126.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 37% 62% 126.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 35% 64% 123.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 35% 64% 123.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
D-cellobiose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 34% 55% 122.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
D-glucose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 34% 55% 122.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
lactose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 34% 55% 122.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
D-maltose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 34% 55% 122.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
sucrose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 34% 55% 122.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
trehalose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 34% 55% 122.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 34% 55% 122.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 34% 58% 121.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
putrescine catabolism potA lo Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 36% 55% 121.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 59% 120.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 59% 120.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 59% 120.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 59% 120.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 52% 119 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 34% 55% 118.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
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) 34% 58% 118.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
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) 34% 58% 118.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 54% 116.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 54% 116.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 54% 116.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 54% 116.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
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) 34% 57% 115.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
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) 35% 53% 114.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 33% 57% 113.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 33% 76% 110.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
trehalose catabolism malK lo MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) 32% 60% 108.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 33% 57% 107.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 33% 59% 99.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-alanine catabolism braF lo NatA, 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% 82% 98.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-isoleucine catabolism natA lo NatA, 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% 82% 98.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-leucine catabolism natA lo NatA, 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% 82% 98.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-proline catabolism natA lo NatA, 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% 82% 98.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-serine catabolism braF lo NatA, 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% 82% 98.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-threonine catabolism braF lo NatA, 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% 82% 98.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-valine catabolism natA lo NatA, 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% 82% 98.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
D-cellobiose catabolism TM0027 lo TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 31% 87% 96.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-isoleucine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 88% 89.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-leucine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 88% 89.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-phenylalanine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 88% 89.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-proline catabolism HSERO_RS00900 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 88% 89.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-serine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 88% 89.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2
L-tyrosine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 88% 89.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 219.2

Sequence Analysis Tools

View WP_085219373.1 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

MAADPLIRLKGVTKTYGTGATAFQALKGVDLDVAQGEFLAVMGPSGSGKSTAMNILGCLD
VPTGGNYLFRGVPVETLDRDQRALLRRKYLGFVFQGFNLLARTSALENVELPLLYRGETK
EERHKAGMAALEKVGLADWWDHTPAELSGGQQQRVAIARAIVTHPDVLLADEPTGNLDSE
RSVEIMELLTDLNRNAGITVLMVTHEPEMAAFARSIVHFKDGLVERFERGGGG

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