Align Phosphoserine phosphatase; PSP; EC 3.1.3.3 (characterized)
to candidate BPHYT_RS25610 BPHYT_RS25610 HAD family hydrolase
Query= SwissProt::Q72H00 (249 letters) >FitnessBrowser__BFirm:BPHYT_RS25610 Length = 228 Score = 60.5 bits (145), Expect = 3e-14 Identities = 46/139 (33%), Positives = 66/139 (47%), Gaps = 6/139 (4%) Query: 106 RELAEAFFRERRRYPLYPEAEAFLAEARRRGLALALLTNGVPDLQREKLVGAGLAHHFSL 165 ++L +A+ R + YP EA L R RGL LA+L+NG + +GL H F Sbjct: 85 KDLCDAYLRLQP----YPGVEATLTSLRERGLPLAILSNGSSFSIGSVVKNSGLDHLFDH 140 Query: 166 VLISGEVGIGKPDPRLFRMALCAFGVAPEEAAMVGDNPQKDVRGARLAGVRAVWVDRGLR 225 ++ + KP ++R+A A G + +E V N D GAR G + WV+R Sbjct: 141 LISVESTKVFKPHDAVYRLAENALGWSRDEILFVSSNGW-DACGARHFGYQVCWVNRNGN 199 Query: 226 PEDP-EASPDLRVGDLREV 243 D PD V DLRE+ Sbjct: 200 TLDVLGQKPDFAVTDLREL 218 Lambda K H 0.322 0.140 0.417 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: 112 Number of extensions: 7 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: 249 Length of database: 228 Length adjustment: 23 Effective length of query: 226 Effective length of database: 205 Effective search space: 46330 Effective search space used: 46330 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 (21.9 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Apr 09 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