Align Phosphoserine phosphatase; PSP; EC 3.1.3.3 (characterized)
to candidate WP_041939246.1 FRAAL_RS12690 HAD family hydrolase
Query= SwissProt::Q72H00 (249 letters) >NCBI__GCF_000058485.1:WP_041939246.1 Length = 239 Score = 53.5 bits (127), Expect = 4e-12 Identities = 61/187 (32%), Positives = 76/187 (40%), Gaps = 34/187 (18%) Query: 80 AAWAGP-------FRERVFREALEEAGGAPERARELAEAFFRERRRYPLYPEAEAFLAEA 132 AA AGP R RE + G + L+ F RR L P A AFLAE Sbjct: 57 AAAAGPAFATQRELERRSLRETIRHFGSDADE-ESLSRRLFDYWRRPALLPGAAAFLAEI 115 Query: 133 RRRGLALALLTNGVPDLQREKLVGAGLAHHFSL-VLISGEVGIGKPDPRLFRMALCAFG- 190 L + L V D+ R L A AH + +++ E KP P FR+AL Sbjct: 116 E---LPVCL----VSDIDRVDLDAALDAHGLRVDAIVTSEY---KPRPEPFRLALDHLAP 165 Query: 191 --------------VAPEEAAMVGDNPQKDVRGARLAGVRAVWVDRGLRPEDPEASPDLR 236 +AP E VGD+ DV GA G+ AVW++R R AS Sbjct: 166 GQHGPGQHGPGQHSLAPGEVWHVGDSLACDVAGANALGIPAVWMNRTHRQRPAGASLVAE 225 Query: 237 VGDLREV 243 VGDL V Sbjct: 226 VGDLTAV 232 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: 111 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: 239 Length adjustment: 24 Effective length of query: 225 Effective length of database: 215 Effective search space: 48375 Effective search space used: 48375 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 10 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