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
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
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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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