GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__SynE:Synpcc7942_2078
          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 (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