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_028996411.1 H537_RS0100940 2,3-diphosphoglycerate-dependent phosphoglycerate mutase
Query= SwissProt::D3DFG8 (211 letters) >NCBI__GCF_000430725.1:WP_028996411.1 Length = 247 Score = 52.8 bits (125), Expect = 6e-12 Identities = 36/109 (33%), Positives = 58/109 (53%), Gaps = 7/109 (6%) Query: 1 MVKLILVRHAESEWNPVGRYQGLLDPDLSERGKKQAKLLAQELSRE---HLDVIYSSPLK 57 M KL+L+RH ES WN R+ G D L++ G QA+ A +L +E DV Y+S LK Sbjct: 1 MYKLVLIRHGESTWNLENRFTGWTDVPLTDTGVAQAR-QAGKLLKEGGWEFDVAYTSVLK 59 Query: 58 RTYLT---ALEIAEAKNLEVIKEDRIIEIDHGMWSGMLVEEVMEKYPED 103 R T L+ + L V+K+ + E +G G+ ++ ++Y ++ Sbjct: 60 RAIWTLWHCLDEMDRTWLPVVKDWHLNERHYGSLQGLNKADMAKQYGDE 108 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: 139 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: 211 Length of database: 247 Length adjustment: 23 Effective length of query: 188 Effective length of database: 224 Effective search space: 42112 Effective search space used: 42112 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: 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