GapMind for catabolism of small carbon sources

 

Protein WP_054559834.1 in Croceitalea dokdonensis DOKDO 023

Annotation: NCBI__GCF_001306415.1:WP_054559834.1

Length: 231 amino acids

Source: GCF_001306415.1 in NCBI

Candidate for 86 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 40% 78% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 40% 78% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-glutamate catabolism gltL med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 40% 78% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 41% 78% 140.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 41% 78% 140.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
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) 40% 81% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
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) 40% 81% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
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) 40% 81% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
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) 40% 81% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
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) 40% 81% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
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) 40% 81% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 38% 87% 152.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 61% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 61% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 61% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 61% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 61% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 61% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 61% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 61% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 56% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 56% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 56% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 56% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 56% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 56% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-arginine catabolism artP lo histidine transport ATP-binding protein hisP (characterized) 38% 89% 139 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-histidine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 38% 89% 139 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-lysine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 38% 89% 139 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 38% 83% 136.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
trehalose catabolism thuK lo Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) 36% 55% 136.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 37% 90% 136 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 37% 82% 135.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 37% 63% 134.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 37% 63% 134.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 39% 58% 134 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
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% 57% 132.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 55% 132.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 59% 132.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 59% 132.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 36% 63% 132.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 37% 62% 131.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
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% 130.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 36% 58% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 36% 58% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 36% 58% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 36% 55% 129 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 36% 61% 128.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 36% 58% 128.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 35% 55% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 33% 55% 125.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 36% 57% 125.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 35% 58% 124.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 54% 123.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 54% 123.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 54% 123.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 54% 123.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 54% 123.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 54% 123.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
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% 68% 122.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 33% 56% 119 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 35% 58% 117.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
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) 33% 52% 115.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
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% 55% 109.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
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% 55% 109.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 33% 61% 109 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-alanine catabolism braG lo NatE, 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) 32% 80% 107.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-isoleucine catabolism natE lo NatE, 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) 32% 80% 107.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-leucine catabolism natE lo NatE, 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) 32% 80% 107.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-proline catabolism natE lo NatE, 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) 32% 80% 107.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-serine catabolism braG lo NatE, 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) 32% 80% 107.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-threonine catabolism braG lo NatE, 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) 32% 80% 107.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-valine catabolism natE lo NatE, 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) 32% 80% 107.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 33% 55% 104 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 33% 61% 103.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 31% 86% 102.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 31% 85% 100.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-leucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 30% 88% 96.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-valine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 30% 88% 96.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-isoleucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 31% 76% 90.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-leucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 31% 76% 90.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-phenylalanine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 31% 76% 90.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-valine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 31% 76% 90.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-arginine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 85% 88.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-glutamate catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 85% 88.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1
L-histidine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 85% 88.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 216.1

Sequence Analysis Tools

View WP_054559834.1 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

Fitness BLAST: loading...

Sequence

MITIKDLRKSFRTEEVETLALNNVNLHVENGEFVAIMGPSGCGKSTLLNIIGMLDNPTEG
SYNFAGHEVAGLKESQRTQLRKGNLGFVFQSFNLIDELTVYENVELPLIYLKMGKAERKE
KVMQVLERMKIAHREKHFPQQLSGGQQQRVAISRAVVTNPKLILADEPTGNLDSKNGIEV
MNLLTELNQEGTTIVMVTHSDRDSHYAHRVVNLFDGQIATESQNRAIGATV

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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