GapMind for catabolism of small carbon sources

 

Protein WP_041458893.1 in Ammonifex degensii KC4

Annotation: NCBI__GCF_000024605.1:WP_041458893.1

Length: 240 amino acids

Source: GCF_000024605.1 in NCBI

Candidate for 91 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 63% 100% 297.7 Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity 63% 294.3
L-asparagine catabolism glnQ med Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 63% 97% 294.3 Arginine transport ATP-binding protein ArtM 63% 297.7
L-glutamate catabolism gltL med Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 63% 97% 294.3 Arginine transport ATP-binding protein ArtM 63% 297.7
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 59% 94% 279.6 Arginine transport ATP-binding protein ArtM 63% 297.7
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 59% 92% 278.9 Arginine transport ATP-binding protein ArtM 63% 297.7
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 59% 92% 278.9 Arginine transport ATP-binding protein ArtM 63% 297.7
L-asparagine catabolism aapP med 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) 59% 93% 275 Arginine transport ATP-binding protein ArtM 63% 297.7
L-aspartate catabolism aapP med 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) 59% 93% 275 Arginine transport ATP-binding protein ArtM 63% 297.7
L-glutamate catabolism aapP med 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) 59% 93% 275 Arginine transport ATP-binding protein ArtM 63% 297.7
L-histidine catabolism aapP med 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) 59% 93% 275 Arginine transport ATP-binding protein ArtM 63% 297.7
L-leucine catabolism aapP med 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) 59% 93% 275 Arginine transport ATP-binding protein ArtM 63% 297.7
L-proline catabolism aapP med 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) 59% 93% 275 Arginine transport ATP-binding protein ArtM 63% 297.7
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 57% 96% 272.3 Arginine transport ATP-binding protein ArtM 63% 297.7
L-lysine catabolism hisP med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 57% 96% 272.3 Arginine transport ATP-binding protein ArtM 63% 297.7
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 58% 91% 271.9 Arginine transport ATP-binding protein ArtM 63% 297.7
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 58% 91% 271.9 Arginine transport ATP-binding protein ArtM 63% 297.7
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-Glucosamine, putative ATPase component (characterized) 53% 94% 264.2 Arginine transport ATP-binding protein ArtM 63% 297.7
L-histidine catabolism hisP med histidine transport ATP-binding protein hisP (characterized) 54% 98% 263.1 Arginine transport ATP-binding protein ArtM 63% 297.7
L-asparagine catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 55% 100% 258.8 Arginine transport ATP-binding protein ArtM 63% 297.7
L-aspartate catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 55% 100% 258.8 Arginine transport ATP-binding protein ArtM 63% 297.7
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 53% 94% 250.8 Arginine transport ATP-binding protein ArtM 63% 297.7
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 53% 99% 248.1 Arginine transport ATP-binding protein ArtM 63% 297.7
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 53% 99% 248.1 Arginine transport ATP-binding protein ArtM 63% 297.7
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 51% 98% 246.9 Arginine transport ATP-binding protein ArtM 63% 297.7
L-citrulline catabolism PS417_17605 med 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) 51% 90% 240.7 Arginine transport ATP-binding protein ArtM 63% 297.7
L-histidine catabolism PA5503 med Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 42% 72% 187.6 Arginine transport ATP-binding protein ArtM 63% 297.7
L-tryptophan catabolism ecfA2 med Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 40% 80% 142.9 Arginine transport ATP-binding protein ArtM 63% 297.7
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 41% 65% 177.6 Arginine transport ATP-binding protein ArtM 63% 297.7
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 38% 62% 164.5 Arginine transport ATP-binding protein ArtM 63% 297.7
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 39% 66% 164.1 Arginine transport ATP-binding protein ArtM 63% 297.7
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 39% 66% 164.1 Arginine transport ATP-binding protein ArtM 63% 297.7
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 38% 65% 161 Arginine transport ATP-binding protein ArtM 63% 297.7
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 38% 67% 160.2 Arginine transport ATP-binding protein ArtM 63% 297.7
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 38% 64% 159.8 Arginine transport ATP-binding protein ArtM 63% 297.7
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 38% 66% 159.8 Arginine transport ATP-binding protein ArtM 63% 297.7
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 38% 63% 159.5 Arginine transport ATP-binding protein ArtM 63% 297.7
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 37% 64% 158.7 Arginine transport ATP-binding protein ArtM 63% 297.7
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 37% 64% 158.7 Arginine transport ATP-binding protein ArtM 63% 297.7
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) 42% 53% 158.3 Arginine transport ATP-binding protein ArtM 63% 297.7
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 39% 57% 154.1 Arginine transport ATP-binding protein ArtM 63% 297.7
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 36% 68% 153.7 Arginine transport ATP-binding protein ArtM 63% 297.7
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 62% 152.9 Arginine transport ATP-binding protein ArtM 63% 297.7
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 62% 152.9 Arginine transport ATP-binding protein ArtM 63% 297.7
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 62% 152.9 Arginine transport ATP-binding protein ArtM 63% 297.7
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 62% 152.9 Arginine transport ATP-binding protein ArtM 63% 297.7
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 62% 152.9 Arginine transport ATP-binding protein ArtM 63% 297.7
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 62% 152.9 Arginine transport ATP-binding protein ArtM 63% 297.7
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 62% 152.9 Arginine transport ATP-binding protein ArtM 63% 297.7
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 62% 152.9 Arginine transport ATP-binding protein ArtM 63% 297.7
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 62% 152.9 Arginine transport ATP-binding protein ArtM 63% 297.7
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 67% 152.1 Arginine transport ATP-binding protein ArtM 63% 297.7
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 67% 152.1 Arginine transport ATP-binding protein ArtM 63% 297.7
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 67% 152.1 Arginine transport ATP-binding protein ArtM 63% 297.7
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 67% 152.1 Arginine transport ATP-binding protein ArtM 63% 297.7
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 67% 152.1 Arginine transport ATP-binding protein ArtM 63% 297.7
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 67% 152.1 Arginine transport ATP-binding protein ArtM 63% 297.7
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 34% 95% 151 Arginine transport ATP-binding protein ArtM 63% 297.7
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) 36% 62% 151 Arginine transport ATP-binding protein ArtM 63% 297.7
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 36% 63% 150.6 Arginine transport ATP-binding protein ArtM 63% 297.7
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) 35% 96% 148.7 Arginine transport ATP-binding protein ArtM 63% 297.7
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 38% 68% 145.6 Arginine transport ATP-binding protein ArtM 63% 297.7
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 34% 61% 144.8 Arginine transport ATP-binding protein ArtM 63% 297.7
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 35% 65% 144.1 Arginine transport ATP-binding protein ArtM 63% 297.7
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 35% 61% 142.5 Arginine transport ATP-binding protein ArtM 63% 297.7
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% 62% 141.7 Arginine transport ATP-binding protein ArtM 63% 297.7
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 61% 141.4 Arginine transport ATP-binding protein ArtM 63% 297.7
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 32% 72% 137.1 Arginine transport ATP-binding protein ArtM 63% 297.7
D-mannose catabolism TM1750 lo TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 34% 75% 135.6 Arginine transport ATP-binding protein ArtM 63% 297.7
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) 34% 79% 132.5 Arginine transport ATP-binding protein ArtM 63% 297.7
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) 32% 65% 132.1 Arginine transport ATP-binding protein ArtM 63% 297.7
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) 32% 65% 132.1 Arginine transport ATP-binding protein ArtM 63% 297.7
L-isoleucine catabolism livG lo High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 31% 95% 130.6 Arginine transport ATP-binding protein ArtM 63% 297.7
L-phenylalanine catabolism livG lo High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 31% 95% 130.6 Arginine transport ATP-binding protein ArtM 63% 297.7
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 34% 65% 129.4 Arginine transport ATP-binding protein ArtM 63% 297.7
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 33% 92% 125.6 Arginine transport ATP-binding protein ArtM 63% 297.7
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 77% 125.6 Arginine transport ATP-binding protein ArtM 63% 297.7
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 32% 75% 125.2 Arginine transport ATP-binding protein ArtM 63% 297.7
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 32% 85% 123.2 Arginine transport ATP-binding protein ArtM 63% 297.7
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) 32% 95% 121.7 Arginine transport ATP-binding protein ArtM 63% 297.7
L-phenylalanine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 93% 117.1 Arginine transport ATP-binding protein ArtM 63% 297.7
L-proline catabolism HSERO_RS00900 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 93% 117.1 Arginine transport ATP-binding protein ArtM 63% 297.7
L-serine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 93% 117.1 Arginine transport ATP-binding protein ArtM 63% 297.7
L-tyrosine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 93% 117.1 Arginine transport ATP-binding protein ArtM 63% 297.7
L-alanine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 95% 114.4 Arginine transport ATP-binding protein ArtM 63% 297.7
L-serine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 95% 114.4 Arginine transport ATP-binding protein ArtM 63% 297.7
L-threonine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 95% 114.4 Arginine transport ATP-binding protein ArtM 63% 297.7
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 32% 65% 112.8 Arginine transport ATP-binding protein ArtM 63% 297.7
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 86% 107.8 Arginine transport ATP-binding protein ArtM 63% 297.7
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 86% 107.8 Arginine transport ATP-binding protein ArtM 63% 297.7
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 86% 107.8 Arginine transport ATP-binding protein ArtM 63% 297.7
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 86% 107.8 Arginine transport ATP-binding protein ArtM 63% 297.7

Sequence Analysis Tools

View WP_041458893.1 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

MIEVRGLYKNFGKLEVLRGIDCQVAAGEVVVIIGPSGSGKSTFLRCLNFLEEPTAGTIVI
DGVKLNHSSTDINLVRQKVGMVFQSFNLFPHKTALENIILAPMVVKKVPRQQAERKAYEL
LRKVGLEEKAHSYPDQLSGGQQQRVAIARALAMEPKVMLFDEPTSALDPEMVGEVLAVMR
DLAREGMTMVVVTHEMRFARDVADRVIFMDEGRIVEEGPPEKIFREPENPRTRAFLSKFL

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