Align Phosphoserine phosphatase 1; PSP 1; PSPase 1; Metal-independent phosphoserine phosphatase 1; iPSP1; O-phosphoserine phosphohydrolase 1; EC 3.1.3.3 (characterized)
to candidate WP_012384411.1 BIND_RS07185 histidine phosphatase family protein
Query= SwissProt::D3DFG8 (211 letters) >NCBI__GCF_000019845.1:WP_012384411.1 Length = 195 Score = 76.6 bits (187), Expect = 3e-19 Identities = 50/160 (31%), Positives = 84/160 (52%), Gaps = 8/160 (5%) Query: 4 LILVRHAESEWNPVGRYQGLLDPDLSERGKKQAKLLAQELSR----EHLDVIYSSPLKRT 59 + LVRH ++E+N GR+QG +D L+ RGK QA+ + L R +H ++++SPL RT Sbjct: 2 IYLVRHGQTEFNAQGRFQGQVDSPLTARGKDQARQIGGMLRRLIEPDHA-IVFASPLGRT 60 Query: 60 YLTALEIAEAKNL--EVIKEDRIIEIDHGMWSGMLVEEVMEKYPEDFRRWVEEPHKVEFQ 117 TA +AEA + E++ + ++EI G W G+ E+ +P+ + Sbjct: 61 KQTAHILAEAAGIRQEIVFDPGLMEIGMGCWEGLTNSEIEANWPDARSGFSRNEWYFHSP 120 Query: 118 GGESLASVYNRVKGFLEEVRKRHWNQTVVVVSHTVPMRAM 157 GE + +R++G L V H + ++VSH V R + Sbjct: 121 DGERYEAFSDRLEGALHRVTS-HSCTSRIIVSHGVASRVL 159 Lambda K H 0.320 0.136 0.408 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: 102 Number of extensions: 7 Number of successful extensions: 3 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: 211 Length of database: 195 Length adjustment: 21 Effective length of query: 190 Effective length of database: 174 Effective search space: 33060 Effective search space used: 33060 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 (21.8 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