Align Phosphoserine phosphatase SerB1; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_086509463.1 BZY95_RS08235 HAD-IB family hydrolase
Query= SwissProt::P9WGJ3 (308 letters) >NCBI__GCF_002151265.1:WP_086509463.1 Length = 218 Score = 93.2 bits (230), Expect = 5e-24 Identities = 68/217 (31%), Positives = 98/217 (45%), Gaps = 3/217 (1%) Query: 59 AFFDVDNTLVQGSSAVHFGRGLAARHYFTYRDVLGFLYAQAKFQLLGKENSNDVAAGRRK 118 A FD+DNTL+ S +G L + D + A +F + + D+ A Sbjct: 4 AIFDLDNTLLAIDSDHAWGEFLLEQGAV---DAKAYREANDRFMADYEAGTLDIHAFLAV 60 Query: 119 ALAFIEGRSVAELVALGEEIYDEIIADKIWDGTRELTQMHLDAGQQVWLITATPYELAAT 178 AL + S +L A ++ I I EL H G + +ITAT + Sbjct: 61 ALKPLADNSPEQLAAWHQQFMASKIEPNILAKGEELLARHRSRGDTLLIITATNRFITGP 120 Query: 179 IARRLGLTGALGTVAESVDGIFTGRLVGEILHGTGKAHAVRSLAIREGLNLKRCTAYSDS 238 IA RLG+ + E DG +TG++ G + GK + + L L YSDS Sbjct: 121 IAERLGVDHLIAVEPEVRDGRYTGQVSGTPSYREGKVKRLEEWLADKDLTLDDAWFYSDS 180 Query: 239 YNDVPMLSLVGTAVAINPDARLRSLARERGWEIRDFR 275 +ND+P+L LV VA++PDA LR +A RGW I R Sbjct: 181 HNDLPLLELVEHPVAVDPDATLREVAERRGWRIMSLR 217 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: 154 Number of extensions: 9 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: 308 Length of database: 218 Length adjustment: 24 Effective length of query: 284 Effective length of database: 194 Effective search space: 55096 Effective search space used: 55096 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