GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Haloglycomyces albus DSM 45210

Align Phosphoserine phosphatase; PSP; EC 3.1.3.3 (characterized)
to candidate WP_025274439.1 HALAL_RS17780 HAD family hydrolase

Query= SwissProt::Q72H00
         (249 letters)



>NCBI__GCF_000527155.1:WP_025274439.1
          Length = 229

 Score = 87.8 bits (216), Expect = 2e-22
 Identities = 51/157 (32%), Positives = 78/157 (49%), Gaps = 5/157 (3%)

Query: 87  RERVFREALEEAGGAPERARELAEAFFRERRRYPLYPEAEAFLAEARRRGLALALLTNGV 146
           R   FREA+ + GG  E A  L + +F +R       +      E+     +LAL+TNG 
Sbjct: 75  RRAAFREAVAQCGGDIESADRLCDRYFDDRLSGQRLYDRTIETLESLAHNYSLALVTNG- 133

Query: 147 PDLQREKLVGAGLAHHFSLVLISGEVGIGKPDPRLFRMALCAFGVAPEEAAMVGDNPQKD 206
                 +    GL   F +V+ + E G  KPD R+F +A+    VAPE    +GD+P +D
Sbjct: 134 ----NTRPESMGLGERFDVVVTAAESGFVKPDSRIFGVAIERLDVAPENCVHIGDHPVED 189

Query: 207 VRGARLAGVRAVWVDRGLRPEDPEASPDLRVGDLREV 243
           V  A+ AG+R +W++R     D    PD  +G L ++
Sbjct: 190 VAAAQNAGLRTIWLNRSGGESDVNIKPDAEIGRLPDL 226


Lambda     K      H
   0.322    0.140    0.417 

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: 132
Number of extensions: 6
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: 249
Length of database: 229
Length adjustment: 23
Effective length of query: 226
Effective length of database: 206
Effective search space:    46556
Effective search space used:    46556
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 (21.9 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Jul 25 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