GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rbsC in Pseudomonas simiae WCS417

Align Ribose import permease protein RbsC (characterized)
to candidate GFF2365 PS417_12060 sugar ABC transporter permease

Query= SwissProt::P0AGI1
         (321 letters)



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

 Score =  276 bits (707), Expect = 4e-79
 Identities = 150/303 (49%), Positives = 203/303 (66%), Gaps = 9/303 (2%)

Query: 18  MEQKSLIALLVLIAIVSTLSPNFF-TINNLFNILQQTSVNAIMAVGMTLVILTSGIDLSV 76
           +++  L  + +L+ +V   S  +F T  N  +IL+QTS+N I+AVGMT VILT GIDLSV
Sbjct: 22  LDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSV 81

Query: 77  GSLLALTGAVAASIVGIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLL 136
           GS+LA  G  +A +       L AV+A +  GA +G V G +VA   +  F+ATL M+ +
Sbjct: 82  GSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSI 141

Query: 137 LRGVTMVYTNGSPVNTGFTENADLFGWFGIGR--PLGVPTPVWIMGIVFLAAWYMLHHTR 194
            RG+T +  +GSP+    T+  D +   GIG+  P+GVP  + I  +V L  W +L +T 
Sbjct: 142 ARGMTFILNDGSPI----TDLPDAYLALGIGKIGPIGVP--IIIFAVVALIFWMVLRYTT 195

Query: 195 LGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQPTAGTGYE 254
            GRY+YA+GGNE + R SGI V K+   VY + GLLA LAG++  AR +SA P AG  YE
Sbjct: 196 YGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYE 255

Query: 255 LDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLAV 314
           LDAIAAVV+GGTSL+GG G IVGTL GAL++G +NNGLNLLGVSSYYQ + K ++I+ AV
Sbjct: 256 LDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAV 315

Query: 315 LVD 317
           L+D
Sbjct: 316 LID 318


Lambda     K      H
   0.324    0.139    0.393 

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: 278
Number of extensions: 12
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: 321
Length of database: 325
Length adjustment: 28
Effective length of query: 293
Effective length of database: 297
Effective search space:    87021
Effective search space used:    87021
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: 48 (23.1 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