Protein WP_108403064.1 in Limnohabitans curvus MWH-C5
Annotation: NCBI__GCF_003063475.1:WP_108403064.1
Length: 465 amino acids
Source: GCF_003063475.1 in NCBI
Candidate for 19 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-tryptophan catabolism | aroP | hi | Amino acid permease (characterized, see rationale) | 64% | 96% | 602.8 | L-alanine and D-alanine permease | 37% | 333.2 |
| L-threonine catabolism | RR42_RS28305 | med | D-serine/D-alanine/glycine transporter (characterized, see rationale) | 37% | 93% | 336.3 | L-alanine and D-alanine permease | 37% | 333.2 |
| D-alanine catabolism | cycA | med | L-alanine and D-alanine permease (characterized) | 37% | 97% | 333.2 | histidine permease | 36% | 323.9 |
| L-alanine catabolism | cycA | med | L-alanine and D-alanine permease (characterized) | 37% | 97% | 333.2 | histidine permease | 36% | 323.9 |
| L-histidine catabolism | permease | lo | histidine permease (characterized) | 36% | 95% | 323.9 | L-alanine and D-alanine permease | 37% | 333.2 |
| L-proline catabolism | proY | lo | GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized) | 36% | 96% | 321.6 | L-alanine and D-alanine permease | 37% | 333.2 |
| L-phenylalanine catabolism | aroP | lo | Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized) | 37% | 91% | 309.3 | L-alanine and D-alanine permease | 37% | 333.2 |
| L-tyrosine catabolism | aroP | lo | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized) | 35% | 98% | 302.8 | L-alanine and D-alanine permease | 37% | 333.2 |
| L-arginine catabolism | rocE | lo | Amino-acid permease RocE (characterized) | 34% | 99% | 302.4 | L-alanine and D-alanine permease | 37% | 333.2 |
| phenylacetate catabolism | H281DRAFT_04042 | lo | Aromatic amino acid transporter AroP (characterized, see rationale) | 33% | 97% | 288.9 | L-alanine and D-alanine permease | 37% | 333.2 |
| D-serine catabolism | cycA | lo | D-serine/D-alanine/glycine transporter (characterized) | 32% | 95% | 276.6 | L-alanine and D-alanine permease | 37% | 333.2 |
| L-lysine catabolism | lysP | lo | Lysine permease LysP (characterized) | 35% | 94% | 269.6 | L-alanine and D-alanine permease | 37% | 333.2 |
| L-asparagine catabolism | ansP | lo | L-asparagine permease; L-asparagine transport protein (characterized) | 30% | 91% | 262.3 | L-alanine and D-alanine permease | 37% | 333.2 |
| L-serine catabolism | serP | lo | Serine permease SerP1 (characterized) | 30% | 98% | 210.3 | L-alanine and D-alanine permease | 37% | 333.2 |
| L-threonine catabolism | serP1 | lo | Serine uptake transporter, SerP1, of 259 aas and 12 TMSs (Trip et al. 2013). L-serine is the highest affinity substrate (Km = 18 μM), but SerP1 also transports L-threonine and L-cysteine (Km values = 20 - 40 μM) (characterized) | 31% | 99% | 210.3 | L-alanine and D-alanine permease | 37% | 333.2 |
| L-isoleucine catabolism | Bap2 | lo | Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) | 31% | 80% | 196.1 | L-alanine and D-alanine permease | 37% | 333.2 |
| L-leucine catabolism | Bap2 | lo | Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) | 31% | 80% | 196.1 | L-alanine and D-alanine permease | 37% | 333.2 |
| L-valine catabolism | Bap2 | lo | Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) | 31% | 80% | 196.1 | L-alanine and D-alanine permease | 37% | 333.2 |
| L-tryptophan catabolism | TAT | lo | tryptophan permease (characterized) | 30% | 67% | 184.5 | L-alanine and D-alanine permease | 37% | 333.2 |
Sequence Analysis Tools
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
MDSFQQIVEQEQGLKKVLSAGQMGMIAIGGAIGTGLFLGSGLAIGFAGPSVIISYAIGAL
IALILMGCLAEMTIVHPTSGSFGAYAEHYMGPWAGFMVRYAYWACNVLAIGTEVTAIGIY
MKFWYPDIPSWFWISSFSLALVLINAFSVNIFGLVEYWFSVIKIVAIIAFIMIGSYVVFG
PATRVGDVVPGLHHYTEHGGFLPQGLWGMWIAVIVAIFGYLGIEMIAVAAGEAHEPEKAI
KSAVRTTLIRLALFYLLTMGLMLAIVPWTQAGHEESPFVKVMTAVNISGASGVVNFVVLI
AALSAMNSQLYITTRMMFSLSCAGYAPKQLGRLNKRGIPMLGLLLSTGGVALATILSIVA
PKQSFTLMMAVSMFGALFTWFMIFVTHFFFRKKWGNENSQALPFRMPGFPYLTFLGGALM
LAIMITTAFTKEFQMTLVFGIPALIFVSVVYFVWYAKKTDISQHM
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