GapMind for catabolism of small carbon sources

 

Protein 642682979 in Chlorobium phaeobacteroides BS1

Annotation: IMG__ChlphaBS1_FD:642682979

Length: 227 amino acids

Source: ChlphaBS1_FD in IMG

Candidate for 37 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 40% 83% 149.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
L-aspartate catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 40% 83% 149.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
L-glutamate catabolism gltL med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 40% 83% 149.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 38% 75% 137.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 38% 75% 137.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
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) 37% 77% 136.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 38% 76% 134.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 38% 76% 134.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 82% 134.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 82% 134.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 37% 80% 133.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
putrescine catabolism potA lo Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 38% 56% 131.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 35% 62% 130.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 35% 51% 129.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 36% 55% 129.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 35% 81% 128.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 36% 51% 128.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 37% 58% 128.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 38% 72% 127.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 55% 126.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 55% 126.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 55% 126.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 55% 126.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 55% 126.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 55% 126.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 35% 62% 122.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 35% 62% 122.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 33% 55% 119.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 32% 57% 118.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
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) 35% 76% 115.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 33% 52% 115.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
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) 35% 76% 115.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 32% 54% 114 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 55% 113.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
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% 65% 112.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
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) 31% 51% 110.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 34% 61% 109.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 204.5

Sequence Analysis Tools

View 642682979 at IMG

Find papers: PaperBLAST

Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MSTTILKLVAVRKELELSRDIRQTIIPGLSLEVEEGEFISITGPSGSGKSTLLYIMGGLD
KPTFGEVWLDGVNISDKNEKEMSKIRNEKIGFIYQFHFLLPEFTAVENVSMPMMINSTRT
KAEIRQRAQMLLDKVGLSDRYDYRPSQLSGGQQQRVAVARSLANEPKLVLGDEPTGNLDS
KSGNQVYELFEQLNQEFNQTVIFVTHDEEFARRAKRRIHLVDGKIDK

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