GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gtsA in Pseudomonas putida KT2440

Align GtsA (GLcE), component of Glucose porter, GtsABCD (characterized)
to candidate PP_1015 PP_1015 mannose/glucose ABC transporter, glucose-binding periplasmic protein

Query= TCDB::Q88P38
         (428 letters)



>lcl|FitnessBrowser__Putida:PP_1015 PP_1015 mannose/glucose ABC
           transporter, glucose-binding periplasmic protein
          Length = 428

 Score =  858 bits (2218), Expect = 0.0
 Identities = 428/428 (100%), Positives = 428/428 (100%)

Query: 1   MNSTLRLAAAISFASLIPLGAQAADAKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFIWK 60
           MNSTLRLAAAISFASLIPLGAQAADAKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFIWK
Sbjct: 1   MNSTLRLAAAISFASLIPLGAQAADAKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFIWK 60

Query: 61  DGAVAGGGGATAMTVLKSRAVAGNPPGVAQIKGPDIQDWAATGLLDADVLKDVAKEGKWD 120
           DGAVAGGGGATAMTVLKSRAVAGNPPGVAQIKGPDIQDWAATGLLDADVLKDVAKEGKWD
Sbjct: 61  DGAVAGGGGATAMTVLKSRAVAGNPPGVAQIKGPDIQDWAATGLLDADVLKDVAKEGKWD 120

Query: 121 SLLDKKVADTVKYDGDYVAVPVNIHRINWLWINPEVFKKAGIDKAPTTLDEFYAAADKLK 180
           SLLDKKVADTVKYDGDYVAVPVNIHRINWLWINPEVFKKAGIDKAPTTLDEFYAAADKLK
Sbjct: 121 SLLDKKVADTVKYDGDYVAVPVNIHRINWLWINPEVFKKAGIDKAPTTLDEFYAAADKLK 180

Query: 181 AAGFIPLAHGGQPWQDSTVFESVVLSVMGVDGYKKALVDLDSATLTGPQMVKALTELKKV 240
           AAGFIPLAHGGQPWQDSTVFESVVLSVMGVDGYKKALVDLDSATLTGPQMVKALTELKKV
Sbjct: 181 AAGFIPLAHGGQPWQDSTVFESVVLSVMGVDGYKKALVDLDSATLTGPQMVKALTELKKV 240

Query: 241 ATYMDPDGKGQDWNLEAAKVINGKAGMQIMGDWAKSEWTLAKKTAGKDYQCVPFPGTDKS 300
           ATYMDPDGKGQDWNLEAAKVINGKAGMQIMGDWAKSEWTLAKKTAGKDYQCVPFPGTDKS
Sbjct: 241 ATYMDPDGKGQDWNLEAAKVINGKAGMQIMGDWAKSEWTLAKKTAGKDYQCVPFPGTDKS 300

Query: 301 FLYNIDSLVVFKQNNAGTSAGQQDIARKVLGEDFQKVFSINKGSIPVRNDMLADMGKYGF 360
           FLYNIDSLVVFKQNNAGTSAGQQDIARKVLGEDFQKVFSINKGSIPVRNDMLADMGKYGF
Sbjct: 301 FLYNIDSLVVFKQNNAGTSAGQQDIARKVLGEDFQKVFSINKGSIPVRNDMLADMGKYGF 360

Query: 361 DACAQTSAKDFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADPADAAKKL 420
           DACAQTSAKDFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADPADAAKKL
Sbjct: 361 DACAQTSAKDFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADPADAAKKL 420

Query: 421 AAAIKAAQ 428
           AAAIKAAQ
Sbjct: 421 AAAIKAAQ 428


Lambda     K      H
   0.315    0.131    0.392 

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: 802
Number of extensions: 33
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: 428
Length of database: 428
Length adjustment: 32
Effective length of query: 396
Effective length of database: 396
Effective search space:   156816
Effective search space used:   156816
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: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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