GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gtrA in Pseudomonas stutzeri RCH2

Align GtrA aka SLL1102, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate GFF3942 Psest_4012 TRAP-type mannitol/chloroaromatic compound transport system, small permease component

Query= TCDB::P74225
         (179 letters)



>lcl|FitnessBrowser__psRCH2:GFF3942 Psest_4012 TRAP-type
           mannitol/chloroaromatic compound transport system, small
           permease component
          Length = 181

 Score = 99.8 bits (247), Expect = 2e-26
 Identities = 65/162 (40%), Positives = 92/162 (56%), Gaps = 6/162 (3%)

Query: 4   LLKIAQLIDQFTAWIGKFTAWLVLAMVLTGGWNVVGRYLGRLVGQNLASNGLLEAQWYLF 63
           LL++A LID     +G+  AW+ L +V+     VV RY     G  + +  L EA  Y  
Sbjct: 8   LLRVAGLIDACNMRLGQLCAWITLFLVIGTTIVVVLRY-----GFGIGAIALQEAVMYGH 62

Query: 64  DLVFLLGAAYTLQTNDHVRVDIFYKSLGDRQRAWVNLLGTCLFLFPFCGLVIFYSWESVI 123
            LVF+  AA+TLQ N HVRVDIFY+    R++A V+ LG  LFL P C  + + SW+ V 
Sbjct: 63  ALVFMGAAAWTLQRNGHVRVDIFYQKFSGRRQATVDGLGHLLFLLPVCLFLGWNSWDYVS 122

Query: 124 NSWHIWETSPDPGGLP-RYPIKTMIIVGFVLLIFQGIAEVIK 164
           NSW   E S + GGL   Y  K++I++    L  Q ++++IK
Sbjct: 123 NSWSTLEGSNESGGLKFVYLQKSIILLLVGSLALQAVSDLIK 164


Lambda     K      H
   0.328    0.145    0.476 

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: 150
Number of extensions: 11
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: 179
Length of database: 181
Length adjustment: 19
Effective length of query: 160
Effective length of database: 162
Effective search space:    25920
Effective search space used:    25920
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 (21.7 bits)
S2: 44 (21.6 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, 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