Align Phosphoserine phosphatase SerB1; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_019556519.1 F612_RS0104285 HAD-IB family hydrolase
Query= SwissProt::P9WGJ3 (308 letters) >NCBI__GCF_000381085.1:WP_019556519.1 Length = 217 Score = 92.4 bits (228), Expect = 8e-24 Identities = 65/213 (30%), Positives = 97/213 (45%), Gaps = 3/213 (1%) Query: 57 AAAFFDVDNTLVQGSSAVHFGRGLAARHYFTYRDVLGFLYAQAKFQLLGKENSNDVAAGR 116 A FD+DNTL+ G S +G L Y D F +F K + D+ A + Sbjct: 2 ALVIFDLDNTLIGGDSDYLWGAFLVENQYV---DATEFAAQNEQFYEDYKAGTLDIMAYQ 58 Query: 117 RKALAFIEGRSVAELVALGEEIYDEIIADKIWDGTRELTQMHLDAGQQVWLITATPYELA 176 R AL + S+ L + I + L H + G +V +ITAT + Sbjct: 59 RFALKPLSQHSMETLNEWHAQFMQTFIEPIVLPKALALVNDHKNKGDRVIIITATNTFIT 118 Query: 177 ATIARRLGLTGALGTVAESVDGIFTGRLVGEILHGTGKAHAVRSLAIREGLNLKRCTAYS 236 I R G+T LGT E V+ +TG + G GK + RE ++L YS Sbjct: 119 RRIGLRYGITELLGTNGEIVNKRYTGEVEGIPTFQAGKVTRLNEWLERENVSLAGSVFYS 178 Query: 237 DSYNDVPMLSLVGTAVAINPDARLRSLARERGW 269 DS+ND+P+L +V V ++ D +L ++A+ RGW Sbjct: 179 DSFNDLPLLDIVDNPVVVDGDDKLLNIAKTRGW 211 Lambda K H 0.319 0.134 0.388 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: 119 Number of extensions: 8 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: 308 Length of database: 217 Length adjustment: 24 Effective length of query: 284 Effective length of database: 193 Effective search space: 54812 Effective search space used: 54812 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: 47 (22.7 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