Protein WP_048079924.1 in Methanobacterium veterum MK4
Annotation: NCBI__GCF_000745485.1:WP_048079924.1
Length: 279 amino acids
Source: GCF_000745485.1 in NCBI
Candidate for 30 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-tryptophan catabolism | ecfA2 | med | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 42% | 95% | 205.7 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-tryptophan catabolism | ecfA1 | med | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 40% | 93% | 189.9 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtM (characterized) | 38% | 90% | 162.2 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-asparagine catabolism | glnQ | lo | Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) | 38% | 93% | 159.8 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-glutamate catabolism | gltL | lo | Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) | 38% | 93% | 159.8 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-asparagine catabolism | aatP | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 36% | 100% | 148.3 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-aspartate catabolism | aatP | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 36% | 100% | 148.3 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 34% | 96% | 147.5 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-histidine catabolism | hisP | lo | Histidine transport ATP-binding protein HisP (characterized) | 35% | 95% | 147.1 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-lysine catabolism | hisP | lo | Histidine transport ATP-binding protein HisP (characterized) | 35% | 95% | 147.1 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 35% | 92% | 144.4 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 35% | 86% | 138.3 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 35% | 86% | 138.3 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 34% | 96% | 137.9 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| D-mannose catabolism | TM1750 | lo | TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 32% | 77% | 134.8 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| 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) | 34% | 82% | 124 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| D-cellobiose catabolism | cbtF | lo | CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) | 32% | 77% | 121.3 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-alanine catabolism | braF | lo | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 30% | 88% | 117.9 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-histidine catabolism | natA | lo | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 30% | 88% | 117.9 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-leucine catabolism | natA | lo | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 30% | 88% | 117.9 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-proline catabolism | natA | lo | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 30% | 88% | 117.9 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-serine catabolism | braF | lo | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 30% | 88% | 117.9 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-threonine catabolism | braF | lo | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 30% | 88% | 117.9 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-isoleucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 90% | 110.2 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-leucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 90% | 110.2 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-phenylalanine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 90% | 110.2 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-proline catabolism | HSERO_RS00895 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 90% | 110.2 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-serine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 90% | 110.2 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| L-tyrosine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 90% | 110.2 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
| 2'-deoxyinosine catabolism | nupA | lo | Purine/cytidine ABC transporter ATP-binding protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized) | 33% | 53% | 107.8 | Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- | 46% | 234.2 |
Sequence Analysis Tools
View WP_048079924.1 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
MNIIETKDIAYSYPDGTKALDKVNFKAEEGKIIALLGPNGAGKSTLFLHFNGILRPTSGK
VLLNGDEIKYDKKALMHVRQNVGIVFQNPDDQLFAPTVVEDVAFGPMNLGLSKEEVEKRV
DESLKRVGMEEFKKKAPHHLSGGQKKRVAIAGILAMNPRIMVLDEPTSGLDPKGASQILK
ILYELNKEGMTIIISTHDVDLVPLYAYSVYIISKGKIIKEGNPQEVFGDVKTIREANLRL
PRIAHLMEILEKEDKLPFDKPYPLTIGEARKKLRDHFDD
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