GapMind for catabolism of small carbon sources

 

Protein WP_074201299.1 in Sulfurivirga caldicuralii DSM 17737

Annotation: NCBI__GCF_900141795.1:WP_074201299.1

Length: 545 amino acids

Source: GCF_900141795.1 in NCBI

Candidate for 64 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-mannose catabolism TM1750 med TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 51% 78% 267.7 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
D-mannose catabolism TM1749 med TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 44% 80% 208 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
D-cellobiose catabolism TM0027 med TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 41% 94% 188 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 39% 68% 156.4 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 35% 71% 154.8 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 40% 57% 151.8 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
D-cellobiose catabolism TM0028 lo TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 33% 83% 145.2 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 34% 95% 144.1 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 34% 95% 144.1 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
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) 39% 57% 143.7 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 37% 100% 140.6 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 35% 93% 136 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-lysine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 35% 93% 136 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 35% 93% 130.2 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-histidine catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 36% 82% 129.8 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
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) 36% 82% 129.8 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 35% 59% 128.3 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-asparagine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 36% 88% 127.1 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-aspartate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 36% 88% 127.1 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-citrulline catabolism PS417_17605 lo ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 35% 85% 127.1 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-glutamate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 36% 88% 127.1 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-histidine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 36% 88% 127.1 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-leucine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 36% 88% 127.1 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-proline catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 36% 88% 127.1 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-glutamate catabolism gltL lo GluA aka CGL1950, component of Glutamate porter (characterized) 34% 92% 126.7 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 37% 89% 126.3 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 33% 65% 125.9 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 33% 65% 125.9 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 33% 65% 125.9 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-asparagine catabolism aatP lo ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 34% 93% 125.2 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-aspartate catabolism aatP lo ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 34% 93% 125.2 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 32% 72% 124.8 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 34% 97% 122.9 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 32% 70% 122.5 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 32% 70% 122.5 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 32% 70% 122.5 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 32% 70% 122.5 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 32% 70% 122.5 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 32% 70% 122.5 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 86% 121.3 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 86% 121.3 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 33% 67% 119 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 33% 84% 118.2 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 34% 61% 117.9 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 31% 63% 116.7 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 33% 87% 116.7 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 32% 65% 116.3 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 57% 116.3 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
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) 31% 60% 115.2 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 34% 55% 114.8 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
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) 34% 55% 113.2 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
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) 34% 52% 112.5 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 30% 72% 110.5 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 30% 72% 110.5 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 32% 65% 110.2 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
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) 32% 58% 109 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 60% 108.6 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 60% 108.6 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 60% 108.6 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 60% 108.6 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 31% 62% 106.7 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
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) 32% 59% 105.5 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 33% 80% 97.1 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 30% 79% 91.7 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 488.4

Sequence Analysis Tools

View WP_074201299.1 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

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Sequence

MAQQDDTQSILKVERLAVSLPDGTPILKGIDFELRRGEVFALVGESGSGKSMTALAIMRL
LPEGLRYDRGCIYLQDTELLSLPEAAMQRIRGRRIAMIFQEPMSALNPVMTIGEQIGEAL
KLHLGLRGRKQRERVIQLLQEVGIPEPETRLDWYPHQLSGGQRQRVMIAMALACEPDVLI
ADEPTTALDVTIQAQILDLLKSLQRKRGLAVLFITHDMGVVAEIADRVAVMYHGEIVEQA
DTRHFLIDPEHPYTQQLLKNALPLRALKPAPKNQSLLEAKGIKVWFQQGGGWFSRKKRIT
RAVDGVDLTIRPGETLALVGESGSGKSTLGMALLRLNELTEGQILFDEQVDLATLNERAL
RPWRRHIQVIFQDPFAAFNPRMTVGESIREGMITLKVGPQDKASQRERVAELLQKVGLQP
EHMDRYPHEFSGGQRQRLGIARALAVEPRLIICDEPTSALDVTVRAQIIDLLNTLQEEQG
VSYLFITHDLSILPRIAHRVAVMQQGKIVEEGRVEQILRVPQHPYTQQLLEAAPKLVRTA
VSDLW

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