GapMind for catabolism of small carbon sources

 

Protein WP_012568983.1 in Rhodospirillum centenum SW SW; ATCC 51521

Annotation: NCBI__GCF_000016185.1:WP_012568983.1

Length: 348 amino acids

Source: GCF_000016185.1 in NCBI

Candidate for 72 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
sucrose catabolism thuK med ABC transporter (characterized, see rationale) 41% 87% 233.4 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 43% 83% 224.9 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 42% 80% 221.1 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-maltose catabolism thuK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 42% 80% 221.1 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 42% 80% 221.1 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 42% 80% 221.1 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
trehalose catabolism thuK med Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) 40% 76% 218.4 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 40% 83% 203.8 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 43% 72% 198 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 42% 82% 167.9 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 45% 75% 154.8 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 52% 61% 238.8 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 97% 231.9 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 97% 231.9 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 97% 231.9 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 97% 231.9 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 97% 231.9 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 97% 231.9 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 40% 96% 230.7 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 49% 67% 225.7 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 38% 93% 221.9 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
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) 38% 91% 221.5 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 38% 91% 218 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 38% 94% 216.5 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
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) 37% 88% 215.3 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 87% 213.4 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 87% 213.4 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 40% 84% 212.2 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 40% 85% 211.8 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 39% 82% 211.5 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 37% 94% 209.5 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
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) 38% 87% 208.8 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 38% 90% 208 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 84% 206.1 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 38% 94% 203.8 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
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) 38% 87% 203.4 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 36% 84% 203 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
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) 35% 94% 201.8 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 39% 84% 199.5 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 63% 190.7 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 63% 190.7 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 63% 190.7 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 63% 190.7 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 63% 190.7 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 63% 190.7 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 39% 66% 184.5 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 39% 66% 184.5 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 39% 66% 184.5 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 39% 66% 184.5 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 41% 59% 174.9 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
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% 77% 173.7 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 35% 80% 171.4 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
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) 38% 89% 161 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 39% 98% 159.5 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 39% 91% 159.1 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 39% 91% 159.1 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 38% 92% 157.1 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-glutamate catabolism gltL lo GluA aka CGL1950, component of Glutamate porter (characterized) 39% 98% 156 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 36% 89% 154.5 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 35% 92% 154.5 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 37% 88% 153.3 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 90% 149.4 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 90% 149.4 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 35% 98% 145.6 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 35% 98% 145.6 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 34% 98% 142.1 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 34% 98% 142.1 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-proline catabolism HSERO_RS00895 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 35% 98% 139.8 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 35% 96% 137.9 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-leucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 35% 96% 137.9 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
L-valine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 35% 96% 137.9 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3
D-ribose catabolism rbsA lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 31% 54% 104 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 51% 309.3

Sequence Analysis Tools

View WP_012568983.1 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

MSIVLSGITKRFGVFTAVDHVDLTIAPGELVALLGPSGSGKTTLLRIMGGLDFADSGQLL
IDGQDATATEPHARRVGFVFQHYALFRHMTVFENVAFGLRVARRRPKLAEAEIRRRVLEL
LDLVQLAQLADRYPNQLSGGQRQRVALARALATEPRVLLLDEPFGALDAKVRKELRRWLR
EIHKGMGVITVFVTHDQEEALELADRVAILHRGRLEQVGTPAEIYDRPATAFVCDFLGGG
TRLACTIQGDHAEIAGLSLALPAGAWTRGPGIAFVRPHDVEVLPAAGPGSLSARVRAVQP
VGPELRLDLDLDGQVMEALLDRRTADAGALTPGAAVGVRLRHVNIFPA

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