GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cmtB in Pseudomonas putida KT2440

Align Mannitol-specific phosphotransferase enzyme IIA component (characterized, see rationale)
to candidate PP_0793 PP_0793 Phosphotransferase system, fructose-specific EI/HPr/EIIA components

Query= uniprot:Q45420
         (145 letters)



>FitnessBrowser__Putida:PP_0793
          Length = 950

 Score =  105 bits (262), Expect = 2e-27
 Identities = 52/136 (38%), Positives = 82/136 (60%)

Query: 6   LKKENIVLHARVENKTEAIRLAGQILVNNGYVEDSYIDKMFEREALTSTYMGNFIAIPHG 65
           L  E I +  +  +K EA+RL    LV +G V + Y+  +  REA  ST++G  IAIPHG
Sbjct: 4   LANEQIAMGQKAADKAEALRLLADRLVADGLVAEGYLQGLQAREAQGSTFLGQGIAIPHG 63

Query: 66  TEDAKQFVKHSGISIIQIPDGVDFGDGNIVKLLIGIAGKNNEHLEILSKIAIVCSEVENV 125
           T   +  V  +G+ ++Q P+GVD+GDG +V L IGIA +++EHL +L  +     E +  
Sbjct: 64  TPQTRDLVYATGVRLLQFPEGVDWGDGQMVYLAIGIAARSDEHLRLLQLLTRALGETDLA 123

Query: 126 ETMIKAATEEEILSIL 141
           E + +A++ E +L +L
Sbjct: 124 EALRRASSAEALLKLL 139


Lambda     K      H
   0.316    0.135    0.365 

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: 212
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: 145
Length of database: 950
Length adjustment: 29
Effective length of query: 116
Effective length of database: 921
Effective search space:   106836
Effective search space used:   106836
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 (21.6 bits)
S2: 49 (23.5 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