GapMind for catabolism of small carbon sources

 

Protein WP_009490041.1 in Catellicoccus marimammalium M35/04/3

Annotation: NCBI__GCF_000313915.1:WP_009490041.1

Length: 479 amino acids

Source: GCF_000313915.1 in NCBI

Candidate for 21 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-lysine catabolism lysP hi lysine-specific permease (characterized) 57% 98% 578.6 Histidine permease HisP 54% 544.3
L-histidine catabolism permease med Histidine permease HisP (characterized) 54% 99% 544.3 lysine-specific permease 57% 578.6
L-arginine catabolism rocE lo Amino-acid permease RocE (characterized) 39% 96% 369.8 lysine-specific permease 57% 578.6
L-alanine catabolism cycA lo General amino-acid permease GAP2 (characterized) 40% 82% 362.5 lysine-specific permease 57% 578.6
L-proline catabolism proY lo GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized) 39% 96% 342.4 lysine-specific permease 57% 578.6
L-phenylalanine catabolism aroP lo Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized) 38% 96% 327.4 lysine-specific permease 57% 578.6
L-threonine catabolism RR42_RS28305 lo D-serine/D-alanine/glycine transporter (characterized, see rationale) 36% 96% 324.7 lysine-specific permease 57% 578.6
D-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 36% 93% 306.6 lysine-specific permease 57% 578.6
L-tryptophan catabolism TAT lo tryptophan permease (characterized) 37% 82% 305.8 lysine-specific permease 57% 578.6
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 39% 75% 305.4 lysine-specific permease 57% 578.6
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 39% 75% 305.4 lysine-specific permease 57% 578.6
L-tryptophan catabolism aroP lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 39% 75% 305.4 lysine-specific permease 57% 578.6
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 39% 75% 305.4 lysine-specific permease 57% 578.6
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% 304.3 lysine-specific permease 57% 578.6
L-asparagine catabolism AGP1 lo general amino acid permease AGP1 (characterized) 34% 77% 300.4 lysine-specific permease 57% 578.6
phenylacetate catabolism H281DRAFT_04042 lo Aromatic amino acid transporter AroP (characterized, see rationale) 37% 95% 296.6 lysine-specific permease 57% 578.6
L-tyrosine catabolism TAT1 lo valine/tyrosine/tryptophan amino-acid permease (characterized) 32% 79% 287.7 lysine-specific permease 57% 578.6
L-asparagine catabolism ansP lo Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized) 36% 89% 282.7 lysine-specific permease 57% 578.6
D-serine catabolism cycA lo D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA (characterized) 36% 79% 279.3 lysine-specific permease 57% 578.6
L-serine catabolism serP 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) 32% 99% 239.2 lysine-specific permease 57% 578.6
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) 32% 99% 239.2 lysine-specific permease 57% 578.6

Sequence Analysis Tools

View WP_009490041.1 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

MSENDHSMQRGLKTRHLSMIAIGGSIGTGLFVASGSAISTAGPGGALVAYGLIGLLVFFM
MTSLGEMATYMPVSGSFSTYATKFVDPAFGFALGWNYWFNWAITLAVDISTSAIIMEYWF
PDVPGWIFSIIFFVLIFLMNLASVELFGEAEFWFSMIKVITVICFIGVGLLTVTGILGGH
ADGLMNFTKGDAPFVGGLPTIVSVFVVAGFSFQGVEMIGITAGESANPEKSIPKAIKQVF
WRILLFYLVSIFIIGLIIPYTSPNLLGSDATDIAISPFTLVFQRAGLAAAASVMNAVILT
SVLSAGNSGLYAGARMLCAMAQSGQAPKAFQKINRRGIPVNALLLTAAVGGLAFITSFMG
DKIYNFLLSASGLTGFIAWFGVAVSHYRFRRAFIKQGHDISELKYKSKWFPFGPIFAIIM
CIAVIVGQDIPGFINGNWDELIVTYMSLPLFFILFFYYKWKHKTHLIPLDEVDLTYHEE

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