GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rhaP in Pseudomonas simiae WCS417

Align RhaP, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate GFF2365 PS417_12060 sugar ABC transporter permease

Query= TCDB::Q7BSH3
         (333 letters)



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

 Score =  204 bits (518), Expect = 3e-57
 Identities = 116/301 (38%), Positives = 175/301 (58%), Gaps = 4/301 (1%)

Query: 14  LIIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTKSIDLSVAANLAFT 73
           L+ +++ VV +  +  F T  N   I   TSI  ILA+    VILTK IDLSV + LAF 
Sbjct: 29  LVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSVGSILAFA 88

Query: 74  GMAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIVVTLGTLTIYRGMA 133
           G+  AM+  A     L+  +   +  GA LG +NGF+V  L IPP V TLG L+I RGM 
Sbjct: 89  GLCSAMV--ATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSIARGMT 146

Query: 134 FVLSGGAWVNAHQMTPIFLSVPRTPVLGLPVLSWVGIIIVILMYVLLRYTQFGRSAYATG 193
           F+L+ G+ +       + L + +   +G+P++ +   ++ ++ +++LRYT +GR  YA G
Sbjct: 147 FILNDGSPITDLPDAYLALGIGKIGPIGVPIIIFA--VVALIFWMVLRYTTYGRYVYAVG 204

Query: 194 GNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVDIANGFELDSVAACVI 253
           GN  +A  +GI      F  +V+SG LAGLA  +  +R   A       +ELD++AA VI
Sbjct: 205 GNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDAIAAVVI 264

Query: 254 GGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGTVIILAVAFNARRERN 313
           GG S++GG GS+ GT+ GAL +GVI N L ++G+S + Q    G +I+ AV  +  R++ 
Sbjct: 265 GGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAVLIDVWRKKK 324

Query: 314 R 314
           R
Sbjct: 325 R 325


Lambda     K      H
   0.328    0.141    0.413 

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: 303
Number of extensions: 19
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: 333
Length of database: 325
Length adjustment: 28
Effective length of query: 305
Effective length of database: 297
Effective search space:    90585
Effective search space used:    90585
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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