GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmB in Burkholderia phytofirmans PsJN

Align Beta-phosphoglucomutase; Beta-PGM; EC 5.4.2.6 (characterized)
to candidate BPHYT_RS16100 BPHYT_RS16100 HAD family hydrolase

Query= SwissProt::P77366
         (219 letters)



>FitnessBrowser__BFirm:BPHYT_RS16100
          Length = 237

 Score = 64.7 bits (156), Expect = 1e-15
 Identities = 44/119 (36%), Positives = 63/119 (52%), Gaps = 10/119 (8%)

Query: 83  VHSLRELTVNAVL--PGIRSLLADLRAQQISVGLASVSLN--APTILAALELREFF---T 135
           + S+R+    A +  P +  + A L    +  G AS S      T+L    L  FF    
Sbjct: 80  IDSIRQAVEAAAMQAPTVEGIEAALAQVPLPKGCASNSFRPYVETVLTRTGLVRFFGDRL 139

Query: 136 FCADASQLKNSKPDPEIFLAACAGLGVPPQACIGIEDAQAGIDAINASGMRSVG-IGAG 193
           FCADA  + N KP P+++LAA  GLG+ P AC+ +ED+  G+ A  A+GM  +G IG G
Sbjct: 140 FCADA--VPNPKPAPDVYLAAAKGLGLAPSACLVVEDSVTGVTAATAAGMTVLGFIGGG 196


Lambda     K      H
   0.320    0.135    0.392 

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: 123
Number of extensions: 9
Number of successful extensions: 1
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: 219
Length of database: 237
Length adjustment: 23
Effective length of query: 196
Effective length of database: 214
Effective search space:    41944
Effective search space used:    41944
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: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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