GapMind for catabolism of small carbon sources

 

Alignments for a candidate for levD in Klebsiella michiganensis M5al

Align PTS system fructose-specific EIIA component; EIIA-Fru; Fructose-specific phosphotransferase enzyme IIA component; lev-PTS; p16 (characterized)
to candidate BWI76_RS17890 BWI76_RS17890 PTS mannose transporter subunit EIIAB

Query= SwissProt::P26379
         (146 letters)



>FitnessBrowser__Koxy:BWI76_RS17890
          Length = 322

 Score = 80.9 bits (198), Expect = 2e-20
 Identities = 39/104 (37%), Positives = 65/104 (62%)

Query: 2   ISVIISGHGDFPIALKESSGMIFGEENNLIAVPFFKGEGIQTLQEKYHQALKDIPEEHEV 61
           I+++I  HG     L +++ M+ GE+ N+  + F  GE  +TL EKY+  L  +     V
Sbjct: 3   IAIVIGTHGWAAEQLLKTAEMLLGEQENVGWIDFVPGENAETLIEKYNAQLAKLDTAKGV 62

Query: 62  LFLVDIFGGTPYNAAASFIAEDQRMDMAAGVNLPILLEVLSLRE 105
           LFLVD +GG+P+NAA+  + + +  ++ AGVN+P+L+E L  R+
Sbjct: 63  LFLVDTWGGSPFNAASRIVVDKEHYEVIAGVNIPMLVETLMARD 106


Lambda     K      H
   0.318    0.135    0.375 

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: 94
Number of extensions: 5
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: 146
Length of database: 322
Length adjustment: 22
Effective length of query: 124
Effective length of database: 300
Effective search space:    37200
Effective search space used:    37200
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: 41 (21.7 bits)
S2: 45 (21.9 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