GapMind for catabolism of small carbon sources

 

Protein WP_011373656.1 in Sulfurimonas denitrificans DSM 1251

Annotation: NCBI__GCF_000012965.1:WP_011373656.1

Length: 236 amino acids

Source: GCF_000012965.1 in NCBI

Candidate for 52 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% 90% 141 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 39% 87% 145.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 39% 82% 144.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 39% 82% 144.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-asparagine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 86% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 40% 85% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-aspartate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 86% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 40% 85% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-glutamate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 86% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-histidine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 86% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-leucine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 86% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-proline catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 86% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 39% 65% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 39% 88% 138.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 39% 88% 138.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 39% 63% 137.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 39% 51% 137.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-asparagine catabolism aatP lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 36% 91% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-aspartate catabolism aatP lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 36% 91% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 36% 84% 136.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-arginine catabolism artP lo Histidine transport ATP-binding protein HisP (characterized) 37% 90% 135.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 37% 90% 135.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 37% 87% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 36% 85% 132.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 35% 90% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 38% 59% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 34% 59% 130.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 34% 61% 130.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 36% 55% 130.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 34% 89% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 35% 60% 125.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 35% 60% 125.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 36% 63% 125.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 36% 63% 125.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 36% 63% 125.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 33% 59% 123.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-citrulline catabolism PS417_17605 lo ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 35% 82% 122.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 34% 56% 121.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
D-cellobiose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 56% 120.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 34% 90% 120.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
D-glucose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 56% 120.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
lactose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 56% 120.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
D-maltose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 56% 120.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
sucrose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 56% 120.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
trehalose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 56% 120.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
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) 33% 59% 119.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 56% 118.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 32% 64% 115.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 34% 78% 111.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
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) 31% 56% 111.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 31% 61% 109.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6
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) 34% 55% 108.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 207.6

Sequence Analysis Tools

View WP_011373656.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MTLDEKEAVISLHKVVKSYGSAEATTYALRGVNLEIKRGEFVAIMGPSGSGKSTAMNIIG
CLDTLSSGDYLFGGVDIQKLSLDQRTLLRRNYIGFIFQGFNLLGKTTAIENVELPLLYRG
FPARQRSEMAMNALRSVGLEQVAHHTPAELSGGQQQRVAIARAIVTDPFILLADEPTGNL
DTAKSREIMELLSSFNKEKGLTIVMVTHENEMASYASRIIRFRDGKIDDTLHVEKA

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