GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtrA in Azospirillum brasilense Sp245

Align GtrA aka SLL1102, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate AZOBR_RS20020 AZOBR_RS20020 C4-dicarboxylate ABC transporter substrate-binding protein

Query= TCDB::P74225
         (179 letters)



>FitnessBrowser__azobra:AZOBR_RS20020
          Length = 179

 Score =  125 bits (314), Expect = 4e-34
 Identities = 68/171 (39%), Positives = 94/171 (54%), Gaps = 5/171 (2%)

Query: 4   LLKIAQLIDQFTAWIGKFTAWLVLAMVLTGGWNVVGRYLGRLVGQNLASNGLLEAQWYLF 63
           LL+I+ LID     IGK   WLVL  V+    N V RY       + +SN  LE QWYLF
Sbjct: 4   LLRISGLIDAVNDGIGKLVYWLVLVAVIVSSGNAVIRY-----SLHYSSNAWLELQWYLF 58

Query: 64  DLVFLLGAAYTLQTNDHVRVDIFYKSLGDRQRAWVNLLGTCLFLFPFCGLVIFYSWESVI 123
             +FLL + YT   N+H+R+DI       R +  V++ G   FLFP   L+++ SW    
Sbjct: 59  SAIFLLCSGYTFLRNEHIRIDIVLGRFSRRVQCMVDIFGILFFLFPMAILIMWLSWPMFW 118

Query: 124 NSWHIWETSPDPGGLPRYPIKTMIIVGFVLLIFQGIAEVIKNLAIALGHVD 174
           +S+   E S D GGL R+P K ++  GF LL  Q ++E+IK +A   G +D
Sbjct: 119 DSFITKEMSSDAGGLIRWPAKILVPAGFFLLTMQAVSELIKRIAFLAGLID 169


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: 124
Number of extensions: 7
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: 179
Length adjustment: 19
Effective length of query: 160
Effective length of database: 160
Effective search space:    25600
Effective search space used:    25600
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 (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