GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Lentibacillus jeotgali Grbi

Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_010531689.1 ON01_RS13975 Cof-type HAD-IIB family hydrolase

Query= SwissProt::Q58989
         (211 letters)



>NCBI__GCF_000224785.1:WP_010531689.1
          Length = 283

 Score = 43.9 bits (102), Expect = 3e-09
 Identities = 26/48 (54%), Positives = 30/48 (62%), Gaps = 1/48 (2%)

Query: 137 EVLKENA-KGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLKIA 183
           E+   NA KG  L+ IA    + LEDTVA+GD  NDISMFK A   IA
Sbjct: 200 EIAHGNASKGNGLKSIAAYFKVPLEDTVAIGDNLNDISMFKTAATGIA 247


Lambda     K      H
   0.314    0.136    0.358 

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: 138
Number of extensions: 5
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: 283
Length adjustment: 24
Effective length of query: 187
Effective length of database: 259
Effective search space:    48433
Effective search space used:    48433
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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