GapMind for catabolism of small carbon sources

 

Protein WP_085219448.1 in Sphingomonas indica Dd16

Annotation: NCBI__GCF_900177405.1:WP_085219448.1

Length: 226 amino acids

Source: GCF_900177405.1 in NCBI

Candidate for 84 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% 148.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 61% 151 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 61% 151 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 61% 151 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 61% 151 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 61% 151 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 61% 151 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 40% 55% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 41% 64% 146.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 41% 64% 146.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 38% 68% 145.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-asparagine catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 38% 85% 143.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-aspartate catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 38% 85% 143.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 39% 55% 143.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 39% 78% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 39% 78% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 37% 56% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 38% 84% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 38% 84% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 36% 90% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 40% 53% 139.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-maltose catabolism malK lo Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 36% 57% 139 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 39% 56% 138.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
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) 39% 81% 136.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
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) 39% 81% 136.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
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) 39% 81% 136.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
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) 39% 81% 136.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
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) 39% 81% 136.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
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) 39% 81% 136.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 36% 83% 135.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 39% 59% 134.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 38% 57% 134 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 57% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 57% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 57% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 57% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 57% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 57% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 57% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 57% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 57% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 38% 51% 132.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 62% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 34% 89% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 62% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 62% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 62% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 62% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 34% 64% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 62% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 37% 59% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 62% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 62% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-proline catabolism opuBA lo BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) 37% 51% 131.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-histidine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 39% 84% 130.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-lysine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 39% 84% 130.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 34% 55% 130.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 34% 55% 130.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 55% 130.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 36% 62% 130.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 35% 61% 129.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 32% 59% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 32% 59% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 32% 59% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 32% 59% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 36% 87% 129 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 35% 59% 127.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
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% 53% 126.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
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) 37% 57% 125.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 35% 58% 124.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
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) 36% 53% 124.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 33% 55% 121.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 51% 119.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 35% 78% 119 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
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) 34% 55% 114.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 32% 85% 114 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
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) 36% 75% 113.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
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) 36% 75% 113.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-mannose catabolism TM1749 lo TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 32% 72% 113.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
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) 33% 55% 111.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 31% 61% 107.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 34% 59% 104.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 33% 59% 103.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 31% 66% 91.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9

Sequence Analysis Tools

View WP_085219448.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MLSMRNIQRTYRTDTIETTALDDIQLDIADGEFVAIMGPSGCGKSTLLNVVGMLDSPTGG
SYVFNGTEVANLPEAKLADFRKENIGFIFQSFNLVDELSVRENVELALLYHNVPAAERRA
RVDAVMDKVGIAHRAKHRPSQLSGGQQQRVAVARALVGEPKLILADEPTGNLDTSHGEEV
MKMLQQLNREGSTIVMVTHSPSHADYAGRVVNMLDGRILQERRRAA

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