GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__WCS417:GFF2365
          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.

Links

Downloads

Related tools

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