GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PS417_11895 in Pseudomonas simiae WCS417

Align Inositol transport system permease protein (characterized)
to candidate GFF2365 PS417_12060 sugar ABC transporter permease

Query= reanno::WCS417:GFF2333
         (340 letters)



>lcl|FitnessBrowser__WCS417:GFF2365 PS417_12060 sugar ABC
           transporter permease
          Length = 325

 Score =  270 bits (689), Expect = 5e-77
 Identities = 154/343 (44%), Positives = 218/343 (63%), Gaps = 24/343 (6%)

Query: 1   MNAITDNKPATVPTKSRRRLPTELSIFLVLIGIGLVFELFGWIVRDQS-FLMNSQRLVLM 59
           MNA T   P T   ++R RL  +        G+ LVF L   ++   S + M  +  + +
Sbjct: 1   MNAKTITAPVTAAPRNRLRLSLDR------FGLPLVFILLCVVMAFSSEYFMTWRNWMDI 54

Query: 60  ILQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFSRAVFPSLTDLPV 119
           + Q SI G+LA+G+T VI+T GIDLS GS+LA + + +A +A T  +            +
Sbjct: 55  LRQTSINGILAVGMTYVILTKGIDLSVGSILAFAGLCSAMVA-TQGYG-----------L 102

Query: 120 WIPVAMGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSY 179
              V+ G+  G + G +NG ++A   IPPF+ATLGM+  ARG+     +G P++ L D+Y
Sbjct: 103 LAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSIARGMTFILNDGSPITDLPDAY 162

Query: 180 TAIGHG-----AMPVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLI 234
            A+G G      +P+IIF VVA+IF + LRYT YG+Y YA+GGN ++ARTSGI V++ + 
Sbjct: 163 LALGIGKIGPIGVPIIIFAVVALIFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMF 222

Query: 235 IVYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIG 294
            VY ++GLLAGLAGVV SAR  +     G+SYELDAIAA VIGGTSL+GG G I GT+ G
Sbjct: 223 SVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFG 282

Query: 295 ALILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVIDQYRNKRK 337
           AL++GV+ +G   +GV +Y Q + KGLIIV AV+ID +R K++
Sbjct: 283 ALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAVLIDVWRKKKR 325


Lambda     K      H
   0.325    0.140    0.394 

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: 306
Number of extensions: 16
Number of successful extensions: 3
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: 340
Length of database: 325
Length adjustment: 28
Effective length of query: 312
Effective length of database: 297
Effective search space:    92664
Effective search space used:    92664
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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