Align Phosphoserine phosphatase; PSP; EC 3.1.3.3 (characterized)
to candidate 5207809 Shew_0326 HAD family hydrolase (RefSeq)
Query= SwissProt::Q72H00 (249 letters) >FitnessBrowser__PV4:5207809 Length = 240 Score = 50.1 bits (118), Expect = 4e-11 Identities = 39/121 (32%), Positives = 54/121 (44%), Gaps = 6/121 (4%) Query: 101 APERARELAEAFFRERRRYPLYPEAEAFLAEARRRGLALALLTNGVPDLQREKLVGAGLA 160 A E A++ F +R + + PE A L R L +TNG D QR GL Sbjct: 95 AGEAAQQALAYFVEQRSDFTVAPEVIAKLTRLARH-YPLIGITNGNVDAQR-----IGLG 148 Query: 161 HHFSLVLISGEVGIGKPDPRLFRMALCAFGVAPEEAAMVGDNPQKDVRGARLAGVRAVWV 220 VL G KP P +F A + E +GD+ + DV+GAR AG +A W+ Sbjct: 149 EVLEFVLHPGNGTRMKPYPDMFYQACQRLDIGCHELLHLGDSFKADVQGARRAGCQAAWL 208 Query: 221 D 221 + Sbjct: 209 N 209 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: 109 Number of extensions: 9 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: 240 Length adjustment: 24 Effective length of query: 225 Effective length of database: 216 Effective search space: 48600 Effective search space used: 48600 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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