GapMind for Amino acid biosynthesis

 

Aligments for a candidate for serB in Synechococcus elongatus PCC 7942

Align phosphoserine phosphatase (EC 3.1.3.3) (characterized)
to candidate Synpcc7942_2078 Synpcc7942_2078 phosphoglycerate mutase

Query= BRENDA::D3DFG8
         (211 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_2078 Synpcc7942_2078
           phosphoglycerate mutase
          Length = 212

 Score =  104 bits (259), Expect = 1e-27
 Identities = 62/201 (30%), Positives = 103/201 (51%), Gaps = 1/201 (0%)

Query: 1   MVKLILVRHAESEWNPVGRYQGLLDPDLSERGKKQAKLLAQELSREHLDVIYSSPLKRTY 60
           +++L LVRH E+  +  G Y G  +P L+E G++ A+ LA   +  +    Y SP+ R  
Sbjct: 2   VLRLYLVRHGETTASREGGYSGSGNPPLTEAGQQMAQALADTYADLNWQAAYVSPMLRAQ 61

Query: 61  LTALEIAEAKNLEVIKEDRIIEIDHGMWSGMLVEEVMEKYPEDFRRWVEEPHKVEFQGGE 120
            TA  + +   L++   D + EID G+W     +EVM  + +D+  W+ EP      GGE
Sbjct: 62  ETAQPLCQQAKLDMRIRDGLREIDFGIWENRTPDEVMASHQQDYLHWLAEPAWNPPTGGE 121

Query: 121 SLASVYNRVKGFLEEVRKRHWNQTVVVVSHTVPMRAMYCALLGVDLSKFWS-FGCDNASY 179
           S   V +RV   ++E+ +   +  V+VVSH   +R + C LLG+DL ++        AS 
Sbjct: 122 SAVVVASRVSLVIQEITETIADGNVLVVSHKATLRILLCNLLGIDLGRYRDRIAMPVASL 181

Query: 180 SVIHMEERRNVILKLNITCHL 200
           S++   +    + +L    HL
Sbjct: 182 SILSFNQHGPCLERLGDRSHL 202


Lambda     K      H
   0.320    0.136    0.408 

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: 117
Number of extensions: 3
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: 211
Length of database: 212
Length adjustment: 21
Effective length of query: 190
Effective length of database: 191
Effective search space:    36290
Effective search space used:    36290
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: 45 (21.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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