GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruII-B in Escherichia coli BW25113

Align Phosphotransferase system IIB component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB) (characterized)
to candidate 17939 b3899 PTS system, fructose-like enzyme IIBC component (VIMSS)

Query= TCDB::Q5V5X1
         (143 letters)



>FitnessBrowser__Keio:17939
          Length = 483

 Score = 82.0 bits (201), Expect = 1e-20
 Identities = 41/98 (41%), Positives = 62/98 (63%), Gaps = 3/98 (3%)

Query: 1   MKLVAVTSCPTGIAHSQMAAENLEQTAEEQGHDIKVEVQGAMGAENELSDSDIEAADAAI 60
           +++VA+T+CP GIAH+ M AE LEQ A   GH IKVE QG+ G EN LS  +I AAD  I
Sbjct: 5   LRIVAITNCPAGIAHTYMVAEALEQKARSLGHTIKVETQGSSGVENRLSSEEIAAADYVI 64

Query: 61  IASDTSVSQD---RFSGVPLIDGTVKDAVNDAEGMIAD 95
           +A+   +S D   RF+G  + +  +  A+ + + + ++
Sbjct: 65  LATGRGLSGDDRARFAGKKVYEIAISQALKNIDQIFSE 102


Lambda     K      H
   0.308    0.124    0.328 

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: 99
Number of extensions: 2
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: 143
Length of database: 483
Length adjustment: 24
Effective length of query: 119
Effective length of database: 459
Effective search space:    54621
Effective search space used:    54621
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 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 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