GapMind for catabolism of small carbon sources

 

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

Align PTS system fructose-specific EIIA component; EIIA-Fru; Fructose-specific phosphotransferase enzyme IIA component (characterized)
to candidate WP_017177510.1 A1QA_RS0103340 PTS transporter subunit EIIA

Query= SwissProt::D4GYE4
         (154 letters)



>NCBI__GCF_000295095.1:WP_017177510.1
          Length = 700

 Score = 95.5 bits (236), Expect = 1e-24
 Identities = 54/143 (37%), Positives = 79/143 (55%), Gaps = 1/143 (0%)

Query: 13  ELISLEEPPAT-KEGAIEFLLDLAVDAGRVDDRDAALDALLEREGEATTGVGFGIGIPHA 71
           EL++L+  P T K   I +L  +   AGR D  +      L RE  A TG+  GI IPH 
Sbjct: 17  ELVALDASPGTDKSDVITYLAGVVAGAGRADGPEGLATDALARESTAPTGIPGGIAIPHC 76

Query: 72  KTDAVSKPTVAFARSAEGIDFDAMDDKPAKLLFMILVPAAGGEDHLQILSALSRSLMHED 131
           +++ V   ++ FAR AE +DF A D + A L+FMI  PA   + HL++L+ L+R LM  D
Sbjct: 77  RSEHVLAASLGFARLAEPVDFGAADGQAADLIFMIAAPAGADDMHLKLLAKLARGLMRTD 136

Query: 132 VREKLLEAESKQTVQDVLAEVVE 154
             + L  A S + V  ++ E V+
Sbjct: 137 FTDALRSAGSAEEVVRMVTEQVQ 159


Lambda     K      H
   0.315    0.134    0.359 

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: 221
Number of extensions: 15
Number of successful extensions: 1
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: 154
Length of database: 700
Length adjustment: 28
Effective length of query: 126
Effective length of database: 672
Effective search space:    84672
Effective search space used:    84672
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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