GapMind for catabolism of small carbon sources

 

Protein WP_169331911.1 in Nafulsella turpanensis ZLM-10

Annotation: NCBI__GCF_000346615.1:WP_169331911.1

Length: 234 amino acids

Source: GCF_000346615.1 in NCBI

Candidate for 52 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% 83% 145.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 40% 83% 145.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
L-glutamate catabolism gltL med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 40% 83% 145.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 38% 66% 151.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 40% 90% 151 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
L-asparagine catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 39% 94% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
L-aspartate catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 39% 94% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 38% 88% 146.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 38% 88% 146.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 39% 92% 145.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 39% 92% 145.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
L-histidine catabolism hisP lo Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 37% 87% 145.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
L-lysine catabolism hisP lo Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 37% 87% 145.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 40% 50% 144.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 38% 56% 138.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 37% 59% 137.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 38% 52% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 37% 56% 135.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 36% 85% 134.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
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% 57% 133.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 34% 58% 133.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 34% 58% 133.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 60% 132.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 60% 132.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 34% 55% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 36% 58% 130.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 37% 56% 129.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 34% 87% 129 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 37% 75% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 76% 127.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
D-cellobiose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 55% 127.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
D-glucose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 55% 127.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
lactose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 55% 127.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
D-maltose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 55% 127.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
sucrose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 55% 127.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
trehalose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 55% 127.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 55% 127.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 35% 59% 126.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 32% 55% 125.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
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) 33% 56% 125.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 37% 55% 124 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 35% 52% 124 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 32% 56% 122.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 34% 64% 121.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
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% 55% 120.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
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) 33% 55% 120.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 59% 120.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 32% 55% 120.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 59% 120.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 59% 120.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
D-mannose catabolism TM1749 lo TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 35% 69% 117.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 35% 66% 112.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 260.0

Sequence Analysis Tools

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

MIQTSQISKIYRMGSEIVEALKSISITVNKGEYVAFMGPSGSGKSTLMNIIGCLDTPTKG
QYILNNNDVSDLSENELAEIRNKEIGFVFQTFNLLPRASSLENVALPLVYAGYSRSEREE
RAYQALENVGLGDRAKHKPNELSGGQRQRVAIARALVNNPSIILADEPTGNLDSKTSYDI
MNLFQQLHDAGNTIIMVTHEDDIAHYAHRIVRMRDGLVETDVRNENITAIEALK

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