Align Phosphoserine phosphatase SerB1; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_020562319.1 A3OW_RS0104935 HAD-IB family hydrolase
Query= SwissProt::P9WGJ3 (308 letters) >NCBI__GCF_000372865.1:WP_020562319.1 Length = 228 Score = 95.9 bits (237), Expect = 8e-25 Identities = 68/222 (30%), Positives = 104/222 (46%), Gaps = 13/222 (5%) Query: 59 AFFDVDNTLVQGSSAVHFGR-----GLAARHYFTYRDVLGFLYAQAKFQLLGKENSNDVA 113 A FD+DNTL+ S +G+ G+ +H + A A+F K+ D+ Sbjct: 4 AIFDLDNTLIADDSDYLWGQFLVDQGIVDKHQYEA--------ANARFYEDYKQGRLDIV 55 Query: 114 AGRRKALAFIEGRSVAELVALGEEIYDEIIADKIWDGTRELTQMHLDAGQQVWLITATPY 173 R +L + + +L A + EII + + REL H G + +ITAT Sbjct: 56 EFLRFSLRPLTLHAPRQLFAWRDRFVSEIITPILLEPARELIAKHKSRGDTLLVITATNR 115 Query: 174 ELAATIARRLGLTGALGTVAESVDGIFTGRLVGEILHGTGKAHAVRSLAIREGLNLKRCT 233 + I + G+ L T E VDG +TG VGE GK ++ + Sbjct: 116 FVTEPIVKLYGIDHLLATPPEFVDGRYTGNFVGEPCFQEGKVRLLQQWLEDNRETMNDSW 175 Query: 234 AYSDSYNDVPMLSLVGTAVAINPDARLRSLARERGWEIRDFR 275 YSDS+ND+P+L+ V AVA++PD +L++ AR+ GW I R Sbjct: 176 FYSDSHNDLPLLNRVDHAVAVDPDEKLKAHARKAGWPIISLR 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: 132 Number of extensions: 5 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: 308 Length of database: 228 Length adjustment: 25 Effective length of query: 283 Effective length of database: 203 Effective search space: 57449 Effective search space used: 57449 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