GapMind for catabolism of small carbon sources

 

Protein WP_017550026.1 in Salinicoccus carnicancri Crm

Annotation: NCBI__GCF_000330705.1:WP_017550026.1

Length: 280 amino acids

Source: GCF_000330705.1 in NCBI

Candidate for 47 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism Ac3H11_2560 hi ABC transporter for L-Histidine, ATPase component (characterized) 44% 97% 229.9 CynD, component of Bispecific cyanate/nitrite transporter 48% 214.5
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 44% 57% 180.6 ABC transporter for L-Histidine, ATPase component 44% 229.9
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 59% 168.7 ABC transporter for L-Histidine, ATPase component 44% 229.9
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 59% 168.7 ABC transporter for L-Histidine, ATPase component 44% 229.9
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 59% 168.7 ABC transporter for L-Histidine, ATPase component 44% 229.9
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 59% 168.7 ABC transporter for L-Histidine, ATPase component 44% 229.9
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 59% 168.7 ABC transporter for L-Histidine, ATPase component 44% 229.9
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 59% 168.7 ABC transporter for L-Histidine, ATPase component 44% 229.9
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 36% 67% 161 ABC transporter for L-Histidine, ATPase component 44% 229.9
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 38% 57% 159.5 ABC transporter for L-Histidine, ATPase component 44% 229.9
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 39% 61% 158.7 ABC transporter for L-Histidine, ATPase component 44% 229.9
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 39% 65% 157.9 ABC transporter for L-Histidine, ATPase component 44% 229.9
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 39% 65% 157.9 ABC transporter for L-Histidine, ATPase component 44% 229.9
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 37% 62% 157.9 ABC transporter for L-Histidine, ATPase component 44% 229.9
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 35% 59% 157.1 ABC transporter for L-Histidine, ATPase component 44% 229.9
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) 38% 56% 156 ABC transporter for L-Histidine, ATPase component 44% 229.9
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% 75% 154.8 ABC transporter for L-Histidine, ATPase component 44% 229.9
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 37% 61% 154.8 ABC transporter for L-Histidine, ATPase component 44% 229.9
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 38% 62% 154.1 ABC transporter for L-Histidine, ATPase component 44% 229.9
trehalose catabolism thuK lo Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) 39% 52% 154.1 ABC transporter for L-Histidine, ATPase component 44% 229.9
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 35% 63% 153.7 ABC transporter for L-Histidine, ATPase component 44% 229.9
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 36% 58% 152.9 ABC transporter for L-Histidine, ATPase component 44% 229.9
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 38% 56% 152.9 ABC transporter for L-Histidine, ATPase component 44% 229.9
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 57% 151.8 ABC transporter for L-Histidine, ATPase component 44% 229.9
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 57% 151.8 ABC transporter for L-Histidine, ATPase component 44% 229.9
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 57% 151.8 ABC transporter for L-Histidine, ATPase component 44% 229.9
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 57% 151.8 ABC transporter for L-Histidine, ATPase component 44% 229.9
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) 37% 57% 151 ABC transporter for L-Histidine, ATPase component 44% 229.9
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 37% 59% 149.8 ABC transporter for L-Histidine, ATPase component 44% 229.9
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) 34% 58% 149.1 ABC transporter for L-Histidine, ATPase component 44% 229.9
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 39% 50% 147.9 ABC transporter for L-Histidine, ATPase component 44% 229.9
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 35% 57% 146.4 ABC transporter for L-Histidine, ATPase component 44% 229.9
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 39% 57% 145.2 ABC transporter for L-Histidine, ATPase component 44% 229.9
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) 37% 56% 143.7 ABC transporter for L-Histidine, ATPase component 44% 229.9
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 60% 143.7 ABC transporter for L-Histidine, ATPase component 44% 229.9
L-alanine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 35% 83% 114.4 ABC transporter for L-Histidine, ATPase component 44% 229.9
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 35% 83% 114.4 ABC transporter for L-Histidine, ATPase component 44% 229.9
L-leucine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 35% 83% 114.4 ABC transporter for L-Histidine, ATPase component 44% 229.9
L-proline catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 35% 83% 114.4 ABC transporter for L-Histidine, ATPase component 44% 229.9
L-serine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 35% 83% 114.4 ABC transporter for L-Histidine, ATPase component 44% 229.9
L-threonine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 35% 83% 114.4 ABC transporter for L-Histidine, ATPase component 44% 229.9
L-alanine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 79% 92.4 ABC transporter for L-Histidine, ATPase component 44% 229.9
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 79% 92.4 ABC transporter for L-Histidine, ATPase component 44% 229.9
L-leucine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 79% 92.4 ABC transporter for L-Histidine, ATPase component 44% 229.9
L-proline catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 79% 92.4 ABC transporter for L-Histidine, ATPase component 44% 229.9
L-serine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 79% 92.4 ABC transporter for L-Histidine, ATPase component 44% 229.9
L-threonine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 79% 92.4 ABC transporter for L-Histidine, ATPase component 44% 229.9

Sequence Analysis Tools

View WP_017550026.1 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

MKVSLKEVNKSFQKGKGETLEVLDDIDFNISEGEFVSLIGPSGCGKSTILKLVAGLDAPT
SGEVLMNGRTVTGPGTDRVVVFQEGGLFPWMTVIENVTYGLLRKKMSKEEAHEKAMEGLR
MVHLANFTGSYPHELSGGMKQRVAIARALVMDPDVLLMDEPFAALDEQTRLVLHKELQRI
WQDTGKTILFITHNIREALTLSDRVLLMSTRPGSLKREFTVQAARPRDPSDSNVVDLERR
VMEDLEEEMEKVLKEEFGDDYHLEKSRVRDSDHSNMGSHI

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