GapMind for catabolism of small carbon sources

 

Protein WP_021333985.1 in Rhodococcus qingshengii djl-6-2

Annotation: NCBI__GCF_002893965.1:WP_021333985.1

Length: 463 amino acids

Source: GCF_002893965.1 in NCBI

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism permease hi histidine permease (characterized) 64% 96% 605.1 Proline-specific permease (ProY) 61% 549.7
L-proline catabolism proY med Proline-specific permease (ProY) (characterized) 61% 96% 549.7 histidine permease 64% 605.1
D-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 51% 98% 486.1 histidine permease 64% 605.1
L-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 51% 98% 486.1 histidine permease 64% 605.1
L-phenylalanine catabolism aroP med Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized) 45% 97% 407.5 histidine permease 64% 605.1
phenylacetate catabolism H281DRAFT_04042 med Aromatic amino acid transporter AroP (characterized, see rationale) 44% 99% 404.4 histidine permease 64% 605.1
L-threonine catabolism RR42_RS28305 med D-serine/D-alanine/glycine transporter (characterized, see rationale) 43% 96% 401.7 histidine permease 64% 605.1
L-tryptophan catabolism aroP med Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized) 44% 95% 387.5 histidine permease 64% 605.1
L-tyrosine catabolism aroP med Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized) 44% 95% 387.5 histidine permease 64% 605.1
D-serine catabolism cycA med D-serine/D-alanine/glycine transporter (characterized) 42% 96% 372.1 histidine permease 64% 605.1
L-asparagine catabolism ansP lo Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized) 36% 90% 323.2 histidine permease 64% 605.1
L-lysine catabolism lysP lo The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized) 40% 91% 303.1 histidine permease 64% 605.1
L-arginine catabolism rocE lo Amino-acid permease RocE (characterized) 34% 99% 294.3 histidine permease 64% 605.1
L-serine catabolism serP lo Serine transporter, SerP2 or YdgB, of 459 aas and 12 TMSs (Trip et al. 2013). Transports L-alanine (Km = 20 μM), D-alanine (Km = 38 μM), L-serine, D-serine (Km = 356 μM) and glycine (Noens and Lolkema 2015). The encoding gene is adjacent to the one encoding SerP1 (TC# 2.A.3.1.21) (characterized) 35% 97% 285 histidine permease 64% 605.1
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) 36% 98% 282.7 histidine permease 64% 605.1
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 33% 81% 229.2 histidine permease 64% 605.1
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 33% 81% 229.2 histidine permease 64% 605.1
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 33% 81% 229.2 histidine permease 64% 605.1

Sequence Analysis Tools

View WP_021333985.1 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

MNSDAATQDGLKRGLTARHIRFIALGSAIGTGLFYGSAEAIKRAGPSVLLAYLIGGIAVY
LVLRALGEMAVRNPVSGSFSEYANKHLGPLAGFMTGWTYTFEMVIVCLADVTAFGLYMQF
WFPDVPRWIWVLAVVFFIGAINLLSVKVFGELEFWFTLVKITAIIAMIAGGIAIIVFGFG
VHDTDAGISHLWSDGGFFATGFGGFVACFAIVMFAFGGTEIIGITAGEAEDPAQTIRKAV
NTVPVRIILFYICTLAVIMAIIPWQTINSDNSPFVQIFENLGLGTAASILNIVVITAALS
AINSDVFGAGRMMFGMSHAGQAPQVMKRVSANGVPWMTVVIMTVALLVGVVLNYLIPDQV
FLVIASLATFATIFVWIMILLSQFRSRAQMSADETAALKFPVPLWPYGQIFAIVFLAFVI
VLLGVIADTRVALLVGAGWLVLLTGAYYKWVKPAVSAADRSDS

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:

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:

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:

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