GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruII-B in Actinomyces timonensis 7400942

Align PTS system, fructose-specific, IIB subunnit, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized)
to candidate WP_017177510.1 A1QA_RS0103340 PTS transporter subunit EIIA

Query= TCDB::D2RXA4
         (150 letters)



>NCBI__GCF_000295095.1:WP_017177510.1
          Length = 700

 Score = 95.1 bits (235), Expect = 2e-24
 Identities = 53/116 (45%), Positives = 74/116 (63%), Gaps = 2/116 (1%)

Query: 4   VAVTSCPTGIAHSQMAAENLEQTATDRGHEIDVEVQGAMGQENELSSDAIAEADAVIIAA 63
           V  TSCPTGIAH+ MAAE LEQ   DRG  + +E QG+ G+ + L  + IA ADAV+ A 
Sbjct: 201 VGATSCPTGIAHTFMAAEALEQAGKDRGITVRIEGQGS-GKIDALDPEVIARADAVVFAH 259

Query: 64  DTSV-NQDRFEGKPVVTAPVKDAVNDVEDLLERAIAAADGETSTADSAQSEGAADA 118
           D  +  ++RF GKPV+   VK AVND   L+++A+AAAD  ++    A  E + ++
Sbjct: 260 DLPIKGRERFAGKPVIDVGVKAAVNDAGSLVDKALAAADDPSAARVPAGGESSEES 315


Lambda     K      H
   0.307    0.122    0.323 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 185
Number of extensions: 4
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 150
Length of database: 700
Length adjustment: 27
Effective length of query: 123
Effective length of database: 673
Effective search space:    82779
Effective search space used:    82779
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 48 (23.1 bits)

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