Protein WP_061533926.1 in Collimonas arenae Ter10
Annotation: NCBI__GCF_001584165.1:WP_061533926.1
Length: 242 amino acids
Source: GCF_001584165.1 in NCBI
Candidate for 16 steps in catabolism of small carbon sources
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
L-arginine catabolism | artP | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 56% | 96% | 254.2 | Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC | 56% | 257.7 |
L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 56% | 96% | 254.2 | Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC | 56% | 257.7 |
L-lysine catabolism | hisP | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 56% | 96% | 254.2 | Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC | 56% | 257.7 |
D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 51% | 94% | 248.1 | Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC | 56% | 257.7 |
L-histidine catabolism | BPHYT_RS24015 | med | ABC transporter related (characterized, see rationale) | 53% | 95% | 247.3 | Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC | 56% | 257.7 |
L-histidine catabolism | hisP | med | 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) | 51% | 98% | 244.6 | Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC | 56% | 257.7 |
L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 53% | 91% | 237.7 | Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC | 56% | 257.7 |
L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 53% | 91% | 237.7 | Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC | 56% | 257.7 |
L-citrulline catabolism | AO353_03040 | med | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 48% | 99% | 232.3 | Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC | 56% | 257.7 |
L-citrulline catabolism | PS417_17605 | med | 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) | 50% | 89% | 223.8 | Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC | 56% | 257.7 |
L-asparagine catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 47% | 98% | 211.1 | Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC | 56% | 257.7 |
L-aspartate catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 47% | 98% | 211.1 | Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC | 56% | 257.7 |
L-glutamate catabolism | gltL | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 47% | 98% | 211.1 | Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC | 56% | 257.7 |
L-histidine catabolism | PA5503 | med | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 42% | 72% | 174.9 | Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC | 56% | 257.7 |
L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 36% | 89% | 144.4 | Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC | 56% | 257.7 |
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% | 82% | 142.5 | Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC | 56% | 257.7 |
Sequence Analysis Tools
View WP_061533926.1 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
MPLIAIDNVKKSFGDNQVLKGIRLDVEPGEVIAIIGKSGSGKSTLLRCINGLESIDEGNI
SVAGSHLGKTELELRALRLKVGMIFQQFNLFPHLTVGRNVMLSPMIVKGTSESEARKSAQ
ENLARVGLAEKFDAYPDQLSGGQQQRVAIARALTMQPQALLCDEITSALDPELVNEVLTV
VRGLAEEGMTLLMVTHEMRFAREVCDRVVFMHQGKVHEIGPPEDIFANPKTLELQQFLGA
SH
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