GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroL in Burkholderia phytofirmans PsJN

Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate BPHYT_RS13350 BPHYT_RS13350 shikimate kinase

Query= curated2:Q7NH27
         (177 letters)



>FitnessBrowser__BFirm:BPHYT_RS13350
          Length = 324

 Score = 85.9 bits (211), Expect = 6e-22
 Identities = 63/170 (37%), Positives = 91/170 (53%), Gaps = 3/170 (1%)

Query: 9   LVGMMGSGKSTVGRLLAEKLGYGFVDLDALIEQVSGKRVGEIFEREGEAVFRDLESRVL- 67
           L+G+ G+GKST+GR+LA++    FV+L  +IEQ++G    EI    G A +R  E R L 
Sbjct: 148 LIGLRGAGKSTLGRMLAQERKVPFVELTRVIEQLAGCPPSEIHSLYGAAAYRRYEHRALE 207

Query: 68  AEVSAYTRLVVATGGGVVLARRNWG-YLHHGVVVWLDADIETLLGRVEHEPGTRPLLAGG 126
           A +  + R V+A+ GG+V     +   L H   VWL A  E  + RV  +   RP+    
Sbjct: 208 AVIQEHERAVIASPGGLVSESGTFNTLLSHCYTVWLQAAPEEHMRRVVAQGDLRPMSGNK 267

Query: 127 DRHLRLVELLGERARLYAQADVRVSAAGLPPAVAEETLR-CLAARLAEDS 175
           +    L  +L  R+ LYA+AD+    +    A A   LR  LAARLA +S
Sbjct: 268 EAMDDLKRILAGRSELYARADMTFDTSEKTLADAYLQLRDRLAARLAAES 317


Lambda     K      H
   0.320    0.139    0.401 

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: 143
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: 177
Length of database: 324
Length adjustment: 23
Effective length of query: 154
Effective length of database: 301
Effective search space:    46354
Effective search space used:    46354
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 Aug 03 2021. The underlying query database was built on Aug 03 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