GapMind for catabolism of small carbon sources

 

Protein WP_012466652.1 in Chlorobium limicola DSM 245

Annotation: NCBI__GCF_000020465.1:WP_012466652.1

Length: 244 amino acids

Source: GCF_000020465.1 in NCBI

Candidate for 49 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 39% 63% 147.1 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 63% 144.4 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 63% 144.4 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 59% 141 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 59% 141 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 59% 141 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 59% 141 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 35% 58% 137.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
putrescine catabolism potA lo Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 36% 55% 137.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
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) 35% 57% 137.5 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
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) 35% 57% 137.5 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 32% 63% 137.1 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 37% 50% 136.7 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 33% 100% 135.2 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 33% 100% 135.2 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 35% 67% 134.4 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 37% 62% 133.3 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 34% 58% 132.5 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 36% 60% 132.5 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 35% 62% 131.3 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
D-cellobiose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 33% 61% 131 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
D-glucose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 33% 61% 131 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
lactose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 33% 61% 131 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
D-maltose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 33% 61% 131 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
sucrose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 33% 61% 131 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
trehalose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 33% 61% 131 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 33% 57% 130.6 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 36% 55% 130.2 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 61% 127.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 35% 58% 127.5 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 57% 127.5 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 33% 63% 127.5 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 57% 127.5 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 57% 127.5 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 64% 124.8 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
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) 31% 60% 124.8 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 64% 124.8 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 64% 124.8 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 64% 124.8 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 64% 124.8 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 64% 124.8 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 35% 56% 124.4 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 33% 91% 121.3 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
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) 30% 92% 109 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
L-isoleucine 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% 92% 109 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
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% 92% 109 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
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) 30% 92% 109 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
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) 30% 92% 109 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8
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% 92% 109 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 181.8

Sequence Analysis Tools

View WP_012466652.1 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

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Sequence

MIELRNITLKYGEREILKNVSLTIKDNTIKAILGPSGVGKSTILKLMLGLIKPNSGQVFV
DGTDITSLREPELYPIRRKMGMVFQGNALFDSMSISENLGFFLRENLKLPETEVQERVAE
QIKFSGLEGYEDQLPENLSGGMRKRVAIGRALIFKPHMILFDEPTAGLDPVSSKRILHLI
RTLQQSSNLGAVIVTHIIDDVFSIADHAAVLYQGEIIFDDETEKLHQSEHPFICSILSDK
ILEL

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