Align Phosphoserine phosphatase 1; PSP 1; PSPase 1; Metal-independent phosphoserine phosphatase 1; iPSP1; O-phosphoserine phosphohydrolase 1; EC 3.1.3.3 (characterized)
to candidate WP_012673440.1 SULAZ_RS02855 histidine phosphatase family protein
Query= SwissProt::D3DFG8 (211 letters) >NCBI__GCF_000021545.1:WP_012673440.1 Length = 211 Score = 252 bits (644), Expect = 3e-72 Identities = 121/211 (57%), Positives = 159/211 (75%) Query: 1 MVKLILVRHAESEWNPVGRYQGLLDPDLSERGKKQAKLLAQELSREHLDVIYSSPLKRTY 60 MV++I VRHAES WNP+GRYQG LDP+LSERG +QAKL+ + L + + +YSSPLKRTY Sbjct: 1 MVRIIFVRHAESLWNPIGRYQGRLDPELSERGHRQAKLIGKALKKYNPSALYSSPLKRTY 60 Query: 61 LTALEIAEAKNLEVIKEDRIIEIDHGMWSGMLVEEVMEKYPEDFRRWVEEPHKVEFQGGE 120 TA I++ NL +IK IIEIDHG WSG+LVEEV EKYP+ FR+W+ +PH+V+F GE Sbjct: 61 QTAEYISQELNLPIIKNQDIIEIDHGDWSGLLVEEVKEKYPDMFRQWIYQPHEVKFPKGE 120 Query: 121 SLASVYNRVKGFLEEVRKRHWNQTVVVVSHTVPMRAMYCALLGVDLSKFWSFGCDNASYS 180 SL V++RVK FL ++ +H +T+VVVSHTVP+RA A L +D+ KFWSFGCDNASYS Sbjct: 121 SLKDVFDRVKKFLSDMLSKHEGETIVVVSHTVPIRACLTAGLNLDMDKFWSFGCDNASYS 180 Query: 181 VIHMEERRNVILKLNITCHLGEFYVEAHKAI 211 ++ + R ++ KLN T +LGE +V A A+ Sbjct: 181 ILDYDPLRPILYKLNNTYYLGEEFVPALDAL 211 Lambda K H 0.320 0.136 0.408 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: 183 Number of extensions: 2 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: 211 Length of database: 211 Length adjustment: 21 Effective length of query: 190 Effective length of database: 190 Effective search space: 36100 Effective search space used: 36100 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: 45 (21.9 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