GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Pseudomonas fluorescens GW456-L13

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate PfGW456L13_3525 ABC transporter, ATP-binding protein

Query= uniprot:G8ALJ0
         (294 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3525
          Length = 243

 Score = 79.0 bits (193), Expect = 1e-19
 Identities = 78/241 (32%), Positives = 106/241 (43%), Gaps = 29/241 (12%)

Query: 12  LTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTLR 71
           L V  L   +G   A+  VSFS   G   A++GPNGAGK+TL   +T  Y    G +   
Sbjct: 4   LEVSDLGFAYGSREALRKVSFSLEPGRFAALLGPNGAGKSTLIALLTRLYDLQHGEI--- 60

Query: 72  HADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIAG 131
              G        P  R      +   FQ   L   +SV +NL    H           A 
Sbjct: 61  RVGGCSLRSAARPALR-----QLGVVFQQSTLDLDLSVEQNL--RYH-----------AA 102

Query: 132 LLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVMLC 191
           L GL       R  V+LA+  L   R     +   G+     +RR+EIARA+  EP +L 
Sbjct: 103 LHGLSRRQTDLRVDVELARQALTDRRRERVRELNGGH-----RRRVEIARALLHEPRLLL 157

Query: 192 LDEPAAGLNPRESGEL-ADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250
           LDE +AGL+P     L   + +  RDEH I VL   H +  V   SD +++L  GR ++ 
Sbjct: 158 LDEASAGLDPASRLALNQHIRSLCRDEH-ISVLWTTHLLDEVQP-SDDLLILHQGRLVAS 215

Query: 251 G 251
           G
Sbjct: 216 G 216


Lambda     K      H
   0.319    0.137    0.397 

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: 161
Number of extensions: 9
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: 294
Length of database: 243
Length adjustment: 25
Effective length of query: 269
Effective length of database: 218
Effective search space:    58642
Effective search space used:    58642
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 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