GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tctB in Pseudomonas fluorescens FW300-N2E2

Align TctB aka STM2787, component of The tricarboxylate transporter, TctABC (characterized)
to candidate Pf6N2E2_2769 Tricarboxylate transport protein TctB

Query= TCDB::Q9FA45
         (144 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2769
          Length = 153

 Score =  103 bits (256), Expect = 1e-27
 Identities = 58/141 (41%), Positives = 85/141 (60%), Gaps = 5/141 (3%)

Query: 5   RIFAGIWLLLCIAGLFIAWQIQSEYSYEPVGPRPFPLGIIGLMALCALALLLR-----HP 59
           RIFA + LL CI    +AW  Q+ +SYEPVGPR FPL ++GLM L  L +L R     H 
Sbjct: 6   RIFAAVLLLACIGLALMAWPYQAAFSYEPVGPRAFPLLMLGLMGLALLYMLFRPTPIVHS 65

Query: 60  DTVSWPRRHVLQKLITMIIILLMYAWGFEWLGFPIATALLTMVIGMLFGATIPAAGISGA 119
           D      R  LQK+   +++LL++A  FE LGF +A+ L+ + +  L+G     + +  +
Sbjct: 66  DEDPHLDRETLQKIGICVVLLLVFAGTFEPLGFILASILIGVPMARLYGGRWVPSVVIIS 125

Query: 120 VLGILLWYAFDRLLDVTLPLG 140
           ++ I L+  FD+L+DV LPLG
Sbjct: 126 LMAIGLYLLFDKLMDVPLPLG 146


Lambda     K      H
   0.332    0.147    0.498 

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: 97
Number of extensions: 6
Number of successful extensions: 2
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: 144
Length of database: 153
Length adjustment: 16
Effective length of query: 128
Effective length of database: 137
Effective search space:    17536
Effective search space used:    17536
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 42 (20.8 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