GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Lentibacillus jeotgali Grbi

Align Phosphoserine phosphatase RsbX; EC 3.1.3.3; Sigma-B negative effector (uncharacterized)
to candidate WP_010529418.1 ON01_RS02385 SpoIIE family protein phosphatase

Query= curated2:P17906
         (199 letters)



>NCBI__GCF_000224785.1:WP_010529418.1
          Length = 199

 Score =  132 bits (333), Expect = 3e-36
 Identities = 68/193 (35%), Positives = 109/193 (56%), Gaps = 2/193 (1%)

Query: 4   VEENEHIQTLVYQLNKEGKSICGDSFFMKADDKELICAVADGLGSGSLANESSAAIKDLV 63
           + E+  ++T V+Q  K+ +  CGDS+F    + E ICA+ADGLGSG LA ESS  +  ++
Sbjct: 1   MREHNKVETAVFQKAKKNRYYCGDSYFYTETENEYICALADGLGSGELAKESSEVVIGVI 60

Query: 64  ENYASEDVESIIERCNQAMKNKRGATASILKINFEQRQFTYCSVGNVRFILHSPSGESFY 123
           ++     VE +I+ CNQ +  KRGA   IL+I+F   Q+T+ S+GN+  +  + +G    
Sbjct: 61  KDNIDATVEQLIKECNQKLSGKRGAVIGILRIDFRAHQYTFSSIGNIGVLAINENGRKKR 120

Query: 124 PLPISGYLSGKPQKYKTHTATYEKGSKFIIHTDGLNVPDIRSHLKKGQSVEEISNSLKMY 183
            +P +GYL+G  + +K  T   E  ++FI+ +DG+   D+       + V ++      Y
Sbjct: 121 NIPNTGYLAGYHRPFKVVTDGLEHAARFILFSDGVTDKDLSQWFLLNKDVYQVVQMFADY 180

Query: 184 TTS--RKDDLTYI 194
           T S  R DD T I
Sbjct: 181 TDSVTRTDDTTLI 193


Lambda     K      H
   0.314    0.131    0.366 

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: 120
Number of extensions: 2
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: 199
Length of database: 199
Length adjustment: 21
Effective length of query: 178
Effective length of database: 178
Effective search space:    31684
Effective search space used:    31684
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: 45 (21.9 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