Protein WP_011187451.1 in Desulfotalea psychrophila LSv54
Annotation: NCBI__GCF_000025945.1:WP_011187451.1
Length: 421 amino acids
Source: GCF_000025945.1 in NCBI
Candidate for 14 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-proline catabolism | proV | hi | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 59% | 99% | 448 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 378.6 |
| L-proline catabolism | opuBA | med | 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) | 47% | 95% | 350.9 | glycine betaine/l-proline transport atp-binding protein prov | 59% | 448.0 |
| L-histidine catabolism | hutV | med | ABC transporter for L-Histidine, ATPase component (characterized) | 61% | 96% | 314.7 | glycine betaine/l-proline transport atp-binding protein prov | 59% | 448.0 |
| L-proline catabolism | hutV | med | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 59% | 96% | 309.3 | glycine betaine/l-proline transport atp-binding protein prov | 59% | 448.0 |
| L-histidine catabolism | Ac3H11_2560 | med | ABC transporter for L-Histidine, ATPase component (characterized) | 43% | 77% | 162.9 | glycine betaine/l-proline transport atp-binding protein prov | 59% | 448.0 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 36% | 86% | 173.3 | glycine betaine/l-proline transport atp-binding protein prov | 59% | 448.0 |
| putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 41% | 58% | 163.3 | glycine betaine/l-proline transport atp-binding protein prov | 59% | 448.0 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 64% | 160.2 | glycine betaine/l-proline transport atp-binding protein prov | 59% | 448.0 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 64% | 160.2 | glycine betaine/l-proline transport atp-binding protein prov | 59% | 448.0 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 64% | 160.2 | glycine betaine/l-proline transport atp-binding protein prov | 59% | 448.0 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 64% | 160.2 | glycine betaine/l-proline transport atp-binding protein prov | 59% | 448.0 |
| D-maltose catabolism | malK | lo | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 37% | 62% | 156.8 | glycine betaine/l-proline transport atp-binding protein prov | 59% | 448.0 |
| L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 39% | 81% | 147.9 | glycine betaine/l-proline transport atp-binding protein prov | 59% | 448.0 |
| glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 32% | 62% | 124.8 | glycine betaine/l-proline transport atp-binding protein prov | 59% | 448.0 |
Sequence Analysis Tools
View WP_011187451.1 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
Find homologs in fast.genomics
Fitness BLAST: loading...
Sequence
MKKIEVRNLYKIFGPDPDKGMKLLAQGMDKQDIHEKTGMTVGVQDASFTINQGEIFVIMG
LSGSGKSTLVRTLNRLIEPTSGEILVDGENILKMDKAELVTFRRAKTGMVFQSFALMPQL
TVIENVAFGLDLDGMEKEQRLERAQDALNQVGLNGWENSYPKELSGGMQQRVGLARGLAV
DPDILLMDEAFSALDPLIRTEMQDELLKLQDQQERTIVFISHDLDEALRIGDRIAIMEGG
RVVQVGTPEEILQNPADDYVRAFFRGVDPTGVISAGDIVRDTQPTVIWHTPAGSLRATLE
LLNNRDREYAYVIGSKRTFFGVVSTDSLCDTIEADGQGKNKPKIEDAFIPEAKAVQDDES
LQDILKKVASHPWPIPVVDEDGKYRGVVSKNSFLRTLYRAENGSHFGNNPTDGTHEGEDK
C
This GapMind analysis is from Sep 24 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:
- 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