GapMind for catabolism of small carbon sources

 

Protein WP_147568230.1 in Collinsella tanakaei YIT 12063

Annotation: NCBI__GCF_000225705.1:WP_147568230.1

Length: 246 amino acids

Source: GCF_000225705.1 in NCBI

Candidate for 9 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-gluconate catabolism gntEIIC lo PTS system, IIC component, component of The gluconate PTS uptake system. IIAGnt and IIBGnt form a high affinity 2:2 heterotetrameric complex (characterized) 35% 79% 154.5 Putative phosphotransferase system enzyme IIC, component of D-glucosaminate group translocating uptake porter, DgaABCD (IIA-141 aas, IIB-161 aas, IIC-249 aas, and IID-285 aas, respectively) 66% 330.1
D-cellobiose catabolism manY lo ManM, component of The glucose/mannose/2-deoxyglucose/fructose phosphotransferase systems (phosphorylates without transport), ManLMN (characterized) 31% 79% 103.2 Putative phosphotransferase system enzyme IIC, component of D-glucosaminate group translocating uptake porter, DgaABCD (IIA-141 aas, IIB-161 aas, IIC-249 aas, and IID-285 aas, respectively) 66% 330.1
D-fructose catabolism levF lo ManM, component of The glucose/mannose/2-deoxyglucose/fructose phosphotransferase systems (phosphorylates without transport), ManLMN (characterized) 31% 79% 103.2 Putative phosphotransferase system enzyme IIC, component of D-glucosaminate group translocating uptake porter, DgaABCD (IIA-141 aas, IIB-161 aas, IIC-249 aas, and IID-285 aas, respectively) 66% 330.1
D-glucose catabolism manY lo ManM, component of The glucose/mannose/2-deoxyglucose/fructose phosphotransferase systems (phosphorylates without transport), ManLMN (characterized) 31% 79% 103.2 Putative phosphotransferase system enzyme IIC, component of D-glucosaminate group translocating uptake porter, DgaABCD (IIA-141 aas, IIB-161 aas, IIC-249 aas, and IID-285 aas, respectively) 66% 330.1
lactose catabolism manY lo ManM, component of The glucose/mannose/2-deoxyglucose/fructose phosphotransferase systems (phosphorylates without transport), ManLMN (characterized) 31% 79% 103.2 Putative phosphotransferase system enzyme IIC, component of D-glucosaminate group translocating uptake porter, DgaABCD (IIA-141 aas, IIB-161 aas, IIC-249 aas, and IID-285 aas, respectively) 66% 330.1
D-maltose catabolism manY lo ManM, component of The glucose/mannose/2-deoxyglucose/fructose phosphotransferase systems (phosphorylates without transport), ManLMN (characterized) 31% 79% 103.2 Putative phosphotransferase system enzyme IIC, component of D-glucosaminate group translocating uptake porter, DgaABCD (IIA-141 aas, IIB-161 aas, IIC-249 aas, and IID-285 aas, respectively) 66% 330.1
sucrose catabolism levF lo ManM, component of The glucose/mannose/2-deoxyglucose/fructose phosphotransferase systems (phosphorylates without transport), ManLMN (characterized) 31% 79% 103.2 Putative phosphotransferase system enzyme IIC, component of D-glucosaminate group translocating uptake porter, DgaABCD (IIA-141 aas, IIB-161 aas, IIC-249 aas, and IID-285 aas, respectively) 66% 330.1
sucrose catabolism manY lo ManM, component of The glucose/mannose/2-deoxyglucose/fructose phosphotransferase systems (phosphorylates without transport), ManLMN (characterized) 31% 79% 103.2 Putative phosphotransferase system enzyme IIC, component of D-glucosaminate group translocating uptake porter, DgaABCD (IIA-141 aas, IIB-161 aas, IIC-249 aas, and IID-285 aas, respectively) 66% 330.1
trehalose catabolism manY lo ManM, component of The glucose/mannose/2-deoxyglucose/fructose phosphotransferase systems (phosphorylates without transport), ManLMN (characterized) 31% 79% 103.2 Putative phosphotransferase system enzyme IIC, component of D-glucosaminate group translocating uptake porter, DgaABCD (IIA-141 aas, IIB-161 aas, IIC-249 aas, and IID-285 aas, respectively) 66% 330.1

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Sequence

MGVYYWFCRLRFGYTFSSALLQPTVIAVFVGLITGEMVLSMQIGAALQLVYLGVTSTPGG
NVPSDPALAGCIAIPLGVMANMSPEVAVALAIPFGVAGVFVDQLRRSTNSIWVHLADKYA
EDANCNGIMRCAFLYPALMGFLIRFPLVFAINYLGASAAADLLAVIPDWLMHSFEIMGGI
LPALGFAITIMVIGKKSMIPFFLIGYFAMVYFGDAGLTTMAMAIFGTCFALILRMIMFRK
EGVLNE

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