Align Phosphoserine phosphatase; PSP; EC 3.1.3.3 (characterized)
to candidate WP_025367425.1 THITH_RS09165 HAD-IA family hydrolase
Query= SwissProt::Q72H00 (249 letters) >NCBI__GCF_000227685.2:WP_025367425.1 Length = 254 Score = 73.2 bits (178), Expect = 5e-18 Identities = 46/122 (37%), Positives = 61/122 (50%), Gaps = 1/122 (0%) Query: 113 FRERRRYPLYPEAEAFLAEARRRGLALALLTNGVPDLQREKLVGAGLAHHFSLVLISGEV 172 F E + YPE +A L RR GL LA+++N L G GL V+ + EV Sbjct: 109 FAEPSAWQKYPEIDALLQGLRRSGLRLAIVSNFDARLV-PVCRGLGLEPRVDTVVFAAEV 167 Query: 173 GIGKPDPRLFRMALCAFGVAPEEAAMVGDNPQKDVRGARLAGVRAVWVDRGLRPEDPEAS 232 G KP +F A+ GVAP VGD+ +DV GAR AG+RAV++ R P Sbjct: 168 GAAKPRAGIFHEAVARLGVAPANTLHVGDSFAEDVAGARAAGLRAVYLQRDQADHRPMGD 227 Query: 233 PD 234 P+ Sbjct: 228 PE 229 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: 159 Number of extensions: 8 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: 254 Length adjustment: 24 Effective length of query: 225 Effective length of database: 230 Effective search space: 51750 Effective search space used: 51750 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