Align Phosphoserine phosphatase SerB1; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_041590012.1 TERTU_RS01600 HAD-IB family hydrolase
Query= SwissProt::P9WGJ3 (308 letters) >NCBI__GCF_000023025.1:WP_041590012.1 Length = 236 Score = 90.9 bits (224), Expect = 3e-23 Identities = 69/221 (31%), Positives = 99/221 (44%), Gaps = 3/221 (1%) Query: 55 LTAAAFFDVDNTLVQGSSAVHFGRGLAARHYFTYRDVLGFLYAQAKFQLLGKENSNDVAA 114 L + A FD+DNTL+ G S +G L A D +F K + D+ A Sbjct: 19 LLSLAIFDLDNTLIGGDSDHAWGEFLVAEKIV---DADTHSRTNDRFYEDYKRGTLDIHA 75 Query: 115 GRRKALAFIEGRSVAELVALGEEIYDEIIADKIWDGTRELTQMHLDAGQQVWLITATPYE 174 R ALA ++ ++ EL L + + I L H G ++ +ITAT Sbjct: 76 YLRFALAPLKQYNMTELDELHQRFFAACIRPLWLPKAEALIASHRQQGHRLLVITATNRF 135 Query: 175 LAATIARRLGLTGALGTVAESVDGIFTGRLVGEILHGTGKAHAVRSLAIREGLNLKRCTA 234 + A I LG+ L + AE VD +TG G GK +++ G L Sbjct: 136 ITAPIVAALGIDDLLASDAEIVDNRYTGEPSGIPCFQQGKVARLKNWLAETGETLANSYF 195 Query: 235 YSDSYNDVPMLSLVGTAVAINPDARLRSLARERGWEIRDFR 275 YSDS ND+P+L +V VA++PD RLR+ A + W I R Sbjct: 196 YSDSANDLPLLQVVDQPVAVDPDERLRAFAEQHQWPILSLR 236 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: 138 Number of extensions: 4 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: 236 Length adjustment: 25 Effective length of query: 283 Effective length of database: 211 Effective search space: 59713 Effective search space used: 59713 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