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.
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