GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Pseudomonas simiae WCS417

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate GFF3453 PS417_17675 ABC transporter

Query= uniprot:G8ALJ0
         (294 letters)



>FitnessBrowser__WCS417:GFF3453
          Length = 249

 Score =  157 bits (397), Expect = 2e-43
 Identities = 100/259 (38%), Positives = 148/259 (57%), Gaps = 15/259 (5%)

Query: 11  LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70
           LL  + L + +G   AVN V+     G I  IIGPNGAGKT+LF+C+TG    T G +  
Sbjct: 4   LLETKDLELAYGAFHAVNGVNLKVEAGTIHTIIGPNGAGKTSLFHCLTGERQATAGAI-- 61

Query: 71  RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130
            H DGK  + +   G R+     +AR+FQ   LF  +SV ENL +A       A G   A
Sbjct: 62  -HFDGKNLMRKPAHG-RVG--LGMARSFQLTSLFQNLSVRENLRLA-------AQGRDGA 110

Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190
             L       ++RE +++A   L+R++L   AD  AG L +G QR LE+  ++C++P +L
Sbjct: 111 RALNFWRRVDSKREHLEMADQVLERLQLTARADTLAGELSHGQQRVLEVGMSICSKPKLL 170

Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250
            LDEP +G+   +   +  L++ +  +H   VLLIEH+MS+VM+IS  + V+ +G+ + +
Sbjct: 171 MLDEPTSGMGIDDIPIMTQLISDLGRDHT--VLLIEHNMSIVMSISQRITVMSHGQILVE 228

Query: 251 GDPAFVKNDPAVIRAYLGE 269
           G P FV+ D  V  AYLGE
Sbjct: 229 GTPEFVRADERVRTAYLGE 247


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: 193
Number of extensions: 7
Number of successful extensions: 4
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: 249
Length adjustment: 25
Effective length of query: 269
Effective length of database: 224
Effective search space:    60256
Effective search space used:    60256
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