GapMind for catabolism of small carbon sources

 

Protein CCNA_00647 in Caulobacter crescentus NA1000

Annotation: CCNA_00647 nitrate transport ATP-binding protein nrtD

Length: 261 amino acids

Source: Caulo in FitnessBrowser

Candidate for 31 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 lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 97% 174.5 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
D-cellobiose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 40% 55% 160.2 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
D-glucose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 40% 55% 160.2 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
lactose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 40% 55% 160.2 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
D-maltose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 40% 55% 160.2 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
sucrose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 40% 55% 160.2 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
trehalose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 40% 55% 160.2 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 39% 55% 159.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 42% 57% 159.5 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 38% 60% 158.7 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 41% 61% 156.4 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 41% 61% 156.4 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 39% 62% 156.4 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 38% 55% 155.2 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 38% 60% 154.5 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 39% 65% 153.3 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 37% 59% 151 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 37% 60% 148.3 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 40% 57% 147.1 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 37% 62% 147.1 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 38% 60% 143.3 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 38% 60% 143.3 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 40% 52% 142.5 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 37% 64% 142.5 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
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) 35% 59% 140.2 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 38% 51% 138.7 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
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) 39% 55% 136.3 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
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) 36% 58% 136 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
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) 36% 56% 135.6 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
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) 36% 56% 135.6 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 60% 131.3 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 55% 277.3

Sequence Analysis Tools

View CCNA_00647 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MAKAYLSIENVGVTFAKGSVRSEVLTGVDLKIDKGEFVSIIGHSGCGKSTLLNVVAGLVP
VTTGAVILDRQEVNAPGPDRAVVFQNHSLLPWLSVRENVSLAVDKVFGGVKSAAERKEWV
LHNLELVKMTHALDKRPAEISGGMKQRVGIARALSMEPKVLLLDEPFGALDALTRAHLQD
SVMEIHSALKNTVLMITHDVDEATLLSDRIVMMTNGPRACVGQVLDVPLARPRDRLAVAE
HPTYVHARAAVIEFLYARRAA

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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