GapMind for catabolism of small carbon sources

 

Protein Ga0059261_1321 in Sphingomonas koreensis DSMZ 15582

Annotation: Ga0059261_1321 ABC-type antimicrobial peptide transport system, ATPase component

Length: 238 amino acids

Source: Korea in FitnessBrowser

Candidate for 45 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) 41% 90% 140.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
L-lysine catabolism hisP lo ABC transporter for L-Lysine, ATPase component (characterized) 38% 92% 143.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
L-arginine catabolism artP 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) 37% 91% 141.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
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) 37% 91% 141.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 40% 88% 138.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 38% 81% 134.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 88% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 88% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 37% 61% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
putrescine catabolism potA lo Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 37% 58% 126.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 76% 125.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 36% 85% 124.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 36% 85% 124.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 36% 63% 123.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 36% 84% 123.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
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) 35% 88% 122.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
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) 35% 88% 122.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
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) 35% 88% 122.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
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) 35% 88% 122.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
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) 35% 88% 122.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 62% 120.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 62% 120.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 62% 120.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 62% 120.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 62% 120.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 62% 120.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 62% 120.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 62% 120.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 37% 57% 120.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 34% 64% 120.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 56% 119.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 56% 119.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 56% 119.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 56% 119.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
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% 57% 115.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
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) 33% 57% 115.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 32% 58% 112.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
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) 33% 86% 112.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
L-histidine catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 33% 89% 109.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 33% 89% 109.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
D-maltose 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% 57% 107.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
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% 57% 107.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
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% 57% 107.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
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% 58% 107.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
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% 52% 103.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5

Sequence Analysis Tools

View Ga0059261_1321 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

VADADPIIRLRNITKVFGEGATAFQALKGVDLDIAERDFVAVMGPSGSGKSTTMNILGCL
DVPTSGEFLFKGVYIETLDRDQRALVRRKYLGFVFQGFNLLSRTNALENVELPLLYRGED
KKVRHELGMAALEKVGLADWWDHTPAELSGGQPQRVAIARAIVTSPAVLLADEPTGNLDS
ARSVEIMELLTSLNKDSGITVLMVTHEPDMAAFARTIVHFKDGLVERTEAGNGAGVPA

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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