GapMind for catabolism of small carbon sources

 

Alignments for a candidate for levD in Cronobacter condimenti 1330

Align PTS system fructose-specific EIIA component; EIIA-Fru; Fructose-specific phosphotransferase enzyme IIA component; lev-PTS; p16 (characterized)
to candidate WP_007668613.1 BN137_RS13775 PTS mannose transporter subunit IIAB

Query= SwissProt::P26379
         (146 letters)



>NCBI__GCF_000319285.1:WP_007668613.1
          Length = 320

 Score = 78.6 bits (192), Expect = 8e-20
 Identities = 37/104 (35%), Positives = 64/104 (61%)

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

Query: 62  LFLVDIFGGTPYNAAASFIAEDQRMDMAAGVNLPILLEVLSLRE 105
           +FLVD +GG+P+NAA+  + +    ++ AGVN+P+L+E    R+
Sbjct: 63  VFLVDTWGGSPFNAASRIVVDKPNYEVVAGVNIPMLVETFMARD 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: 84
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: 146
Length of database: 320
Length adjustment: 22
Effective length of query: 124
Effective length of database: 298
Effective search space:    36952
Effective search space used:    36952
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 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