Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_015739200.1 ADEG_RS06135 phosphoserine phosphatase
Query= SwissProt::Q5M3B3 (215 letters) >NCBI__GCF_000024605.1:WP_015739200.1 Length = 225 Score = 89.4 bits (220), Expect = 5e-23 Identities = 63/205 (30%), Positives = 100/205 (48%), Gaps = 16/205 (7%) Query: 4 VKGLLVMDVDSTL-----VQEEVIDLLGEEAGVGREVAEITERAMRGELDFRQALNERVA 58 +KG+ + D+D TL + + + + LG GR+ E + G +D+ + V Sbjct: 5 IKGV-IFDLDGTLTPVTSIWQYIHECLGTWETYGRKHLE---DFLAGRIDYEEFARRDVG 60 Query: 59 TLKGLPDSIFEKVYARIHFNKGAKELVDELHSRGFKVGLVSGGFHETVDRLAKEAGIDYV 118 +G+P S E++ +RI + KGAKEL+ L RG + L+S G R+A+E G D Sbjct: 61 AWRGVPKSYLEELVSRIPYRKGAKELIAALKERGVRTFLLSSGLDLLASRVAEELGFDCW 120 Query: 119 KANHLEVIDGFLTGKVYGEI---VTKDVKVAKLKDWAAENGLKLSQTIAMGDGANDLPMI 175 AN L GF G+V G + V K L + + L+ + A+GD D+P+ Sbjct: 121 VANGL----GFTRGRVDGRVFIRVPWHGKPQHLPSFCSRFNLRPEELAAVGDSCGDVPLF 176 Query: 176 KTAGIGIAFCAKPIVRVQAPYQITE 200 G+ +A A P VR QA Q+ + Sbjct: 177 GQVGLAVAISAPPEVREQAHVQVED 201 Lambda K H 0.317 0.138 0.384 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: 108 Number of extensions: 6 Number of successful extensions: 2 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: 215 Length of database: 225 Length adjustment: 22 Effective length of query: 193 Effective length of database: 203 Effective search space: 39179 Effective search space used: 39179 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 45 (21.9 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