Protein WP_011868438.1 in Methanococcus maripaludis C5
Annotation: NCBI__GCF_000016125.1:WP_011868438.1
Length: 389 amino acids
Source: GCF_000016125.1 in NCBI
Candidate for 24 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 | med | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 45% | 95% | 325.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| 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) | 45% | 93% | 313.9 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| L-histidine catabolism | hutV | med | ABC transporter for L-Histidine, ATPase component (characterized) | 51% | 95% | 259.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| 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) | 47% | 96% | 245 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 39% | 93% | 154.8 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 39% | 93% | 154.8 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| L-glutamate catabolism | gltL | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 39% | 93% | 154.8 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 34% | 72% | 153.7 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 35% | 96% | 152.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| L-arginine catabolism | artP | lo | AotP aka PA0892, component of Arginine/ornithine (but not lysine) porter (characterized) | 38% | 91% | 148.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| L-histidine catabolism | hisP | lo | histidine transport ATP-binding protein hisP (characterized) | 38% | 91% | 147.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| L-lysine catabolism | hisP | lo | histidine transport ATP-binding protein hisP (characterized) | 38% | 91% | 147.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 38% | 86% | 147.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 36% | 85% | 144.8 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 36% | 85% | 144.8 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 35% | 96% | 142.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| L-asparagine catabolism | aatP | lo | ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) | 36% | 92% | 142.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| L-aspartate catabolism | aatP | lo | ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) | 36% | 92% | 142.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 35% | 91% | 138.7 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| 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) | 34% | 77% | 131.7 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| 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) | 33% | 84% | 126.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| D-cellobiose catabolism | cbtD | lo | CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) | 32% | 85% | 123.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| 2'-deoxyinosine catabolism | nupA | lo | RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized) | 31% | 59% | 117.9 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
| D-cellobiose catabolism | TM0028 | lo | TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 32% | 82% | 110.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 359.0 |
Sequence Analysis Tools
View WP_011868438.1 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
MNDPIIQVTELYKIFGKKPEKAYPLIKEGFSRKEIKEKTKQVVGLKDINFDVKKGEIFVI
MGLSGSGKSTLIRCINRLIKPTYGKIVLENGVDISQMREKDLLEIRRKYFGMVFQKFGLL
PNRSVLENVALGLEIQGVGLEERIEKSEKALSLVGLKGWEKSKISELSGGMQQRVGLARG
LAVEPEILLMDEPFSALDPLIRLEMQELLLKIQKKMKKTIIFITHDLNEAIKLGDRIMIL
NEEGSLVQLSHPEEILLNPQNDFVESFVKEVDKTTVIRAESLVKKPEFTLNTRMEKEHAV
KILGDLSLEYAYVLDDSGKYLGVVSAEELQNSEQIMNCIQKIKPLEDVKTINQGLPQFIS
SDYPVPVVDDENNFLGYVEFEEVINLIKN
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