Align Phosphoserine phosphatase SerB1; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_015799305.1 AFER_RS09950 HAD-IB family hydrolase
Query= SwissProt::P9WGJ3 (308 letters) >NCBI__GCF_000023265.1:WP_015799305.1 Length = 273 Score = 126 bits (316), Expect = 7e-34 Identities = 86/254 (33%), Positives = 132/254 (51%), Gaps = 6/254 (2%) Query: 58 AAFFDVDNTLVQGSSAVHFGRGLAARHYFTYRDVLGFLYAQAKFQLLGKENSNDVAAGRR 117 AAFFD+D T++ +S + FG R V ++AQ ++ LG N + R Sbjct: 3 AAFFDLDKTVISRASLLAFGARFFQEGLINRRTVARSVWAQLVYRYLGA-NERRLRRLER 61 Query: 118 KALAFIEGRSVAELVALGEEIYDEIIADKIWDGTRELTQMHLDAGQQVWLITATPYELAA 177 L +G + + + E EI+ ++ EL ++H AG++V+L++A+P E+ Sbjct: 62 SVLDLTQGWHQSVVRRVVAEALTEIVTPLVYREAVELIKLHQLAGRKVFLVSASPEEIVE 121 Query: 178 TIARRLGLTGALGTVAE-SVDGIFTGRLVGEILHGTGKAHAVRSLAIREGLNLKRCTAYS 236 +A LG+ G + T +G +TG + +G KA A+ +A REG++L AYS Sbjct: 122 PMAAFLGVDGQIATKPRVDEEGTYTGEMAF-YNYGPYKAEAMAEVAQREGIDLAASYAYS 180 Query: 237 DSYNDVPMLSLVGTAVAINPDARLRSLARERGWEIRDFRIARKAAR---IGVPSALALGA 293 DSY D+PML VG VA+NPD L +ARE GWEI +FR K R + A+ LG Sbjct: 181 DSYTDLPMLEAVGHPVAVNPDRVLARVAREHGWEILEFRHHTKVGRHRVLRTVGAVGLGI 240 Query: 294 AGGALAALASRRQS 307 A A+ A R++ Sbjct: 241 AITAIPATPFLRRA 254 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: 194 Number of extensions: 10 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: 273 Length adjustment: 26 Effective length of query: 282 Effective length of database: 247 Effective search space: 69654 Effective search space used: 69654 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: 48 (23.1 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