GapMind for catabolism of small carbon sources

 

Protein WP_007679744.1 in Cronobacter condimenti 1330

Annotation: NCBI__GCF_000319285.1:WP_007679744.1

Length: 619 amino acids

Source: GCF_000319285.1 in NCBI

Candidate for 15 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism bglF hi β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 56% 99% 693.7 PTS beta-glucoside transporter, EIIBCA of 672 aas and 12 predicted TMSs 41% 506.1
D-cellobiose catabolism bglG hi β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 56% 99% 693.7 Aryl β-glucoside porter, IIBCA (BglP; SytA) (35% identical to 4.A.1.2.2) 40% 459.1
D-glucose catabolism bglF hi β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 56% 99% 693.7 PTS beta-glucoside transporter, EIIBCA of 672 aas and 12 predicted TMSs 41% 506.1
lactose catabolism bglF hi β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 56% 99% 693.7 PTS beta-glucoside transporter, EIIBCA of 672 aas and 12 predicted TMSs 41% 506.1
D-maltose catabolism bglF hi β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 56% 99% 693.7 PTS beta-glucoside transporter, EIIBCA of 672 aas and 12 predicted TMSs 41% 506.1
sucrose catabolism bglF hi β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 56% 99% 693.7 PTS beta-glucoside transporter, EIIBCA of 672 aas and 12 predicted TMSs 41% 506.1
trehalose catabolism bglF hi β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 56% 99% 693.7 PTS beta-glucoside transporter, EIIBCA of 672 aas and 12 predicted TMSs 41% 506.1
sucrose catabolism ptsS lo The sucrose porter, PtsS (regulated by SugR which also regulates other enzymes II) (characterized) 33% 98% 332.4 β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF 56% 693.7
sucrose catabolism sacP lo protein-Npi-phosphohistidine-sucrose phosphotransferase (EC 2.7.1.211) (characterized) 33% 98% 250 β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF 56% 693.7
D-cellobiose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 33% 99% 114 β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF 56% 693.7
D-glucose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 33% 99% 114 β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF 56% 693.7
lactose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 33% 99% 114 β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF 56% 693.7
D-maltose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 33% 99% 114 β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF 56% 693.7
sucrose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 33% 99% 114 β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF 56% 693.7
trehalose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 33% 99% 114 β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF 56% 693.7

Sequence Analysis Tools

View WP_007679744.1 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

MDYQALAQDILARVGGKENISSVIHCATRLRFRLKDDRKADAPGLKAHPGVIMVVVSGGQ
FQVVIGNHVHDVWLAVRREAGITDDGAQAEDDGPRGNLLARLIDIVSGIFTPFIGVLAAS
GILKGLLALAVVCRWIDPASGTYKIWFAASDALFFFFPLVLGYTAGKKFGGNPFITMTIG
GALTHPVMISAFEASQQAGALADSFLGVPVIWFNYSSSVIPIILAAWVSCWLEKQGNRLL
PCAMKNFFTPLLCLGVTVPLTFLVIGPVATWLSQMLANGYQFIYTFAPWLAGAATGALWQ
VCVIFGLHWGLVPLMVNNIAVLGHDSLLPMLLPAVMGQVGAALAVFLRSRDARQKMLAGS
SVTAGIFGITEPAVYGVNLPLRRPFIFGCAAGAVGGAIVGLSSTQVYSFGFANIFTIAQM
IPPDGVNATLWGGLFGTLSALVLACGLTLIAGLPAGAKEANTGSQNVPQNAALAPLSGTV
LALDNVPDPTFASGLLGQGAAIIPSDNQVRAPFAGVVASLFETRHAIGLAGDNGMELLIH
VGIDTVKLEGQLFTAHVRVGDRVNPGDLLIEFDRQAIIDAGYDLTTPIIISNSDSYGAVT
TVAATAVSAGMPLLTVEPA

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