Protein WP_099020204.1 in Marinicella litoralis KMM 3900
Annotation: NCBI__GCF_002591915.1:WP_099020204.1
Length: 228 amino acids
Source: GCF_002591915.1 in NCBI
Candidate for 28 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 34% | 56% | 134 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| putrescine catabolism | potA | lo | Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) | 34% | 56% | 132.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 32% | 89% | 130.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 32% | 89% | 130.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| L-glutamate catabolism | gltL | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 32% | 89% | 130.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) | 36% | 57% | 129.8 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 35% | 86% | 129.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 34% | 63% | 127.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| trehalose catabolism | thuK | lo | Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) | 31% | 54% | 126.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 34% | 64% | 125.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 34% | 64% | 125.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 32% | 53% | 123.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 32% | 55% | 122.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 60% | 122.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 60% | 122.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 60% | 122.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 60% | 122.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 60% | 122.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 60% | 122.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 33% | 54% | 119.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| D-maltose catabolism | malK | lo | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 32% | 55% | 115.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| 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% | 51% | 114 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| 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) | 33% | 66% | 108.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 32% | 56% | 107.8 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| D-cellobiose catabolism | TM0027 | lo | TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 31% | 88% | 105.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| 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) | 30% | 53% | 104 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| trehalose catabolism | malK | 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) | 30% | 53% | 104 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
| L-proline catabolism | HSERO_RS00900 | lo | ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) | 30% | 89% | 86.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 53% | 237.7 |
Sequence Analysis Tools
View WP_099020204.1 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
MSDSVVLKCENLSKFFTDGQRKIQIFEGLDFQVKAGESVAIMGASGSGKSTLLHLLGGLD
TANAGDINIQGQQLSKLSGRQRGLLRNQHLGFVYQFHHLLPEFSALENVMMPLLIGKTAK
AAAKQQATEILQQVGLSDRLTHRPAQLSGGERQRAAIARAMVTSPACILADEPTGNLDEK
TASSVMDLLINLKEQLNTSLVLVTHDQKVADKMQHQYLLQQGALIKLS
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