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_011603112.1 FRAAL_RS08410 histidine phosphatase family protein
Query= SwissProt::D3DFG8 (211 letters) >NCBI__GCF_000058485.1:WP_011603112.1 Length = 233 Score = 85.5 bits (210), Expect = 7e-22 Identities = 59/190 (31%), Positives = 91/190 (47%), Gaps = 10/190 (5%) Query: 2 VKLILVRHAESEWNPVGRYQGLLDPDLSERGKKQAKLLAQELSREHLDVIYSSPLKRTYL 61 ++L+L RH + WN VGR+QG DP L G+ Q +A + +++ SS L+R Sbjct: 1 MRLLLWRHGRTTWNDVGRFQGHADPPLDATGRAQVAAVAPIIRAMRPELVVSSDLQRCRD 60 Query: 62 TALEIAEAKNLEVIKEDRIIEIDHGMWSGMLVEEVMEKYPEDFRRWVEEPHKVEFQGGES 121 TA + +L + R+ EID G+WSG+ E +++PE+ R W V GGE+ Sbjct: 61 TAAGL----DLPFRSDARLREIDLGLWSGLTGAEAADRFPEEDRAW-RRGDDVRRGGGET 115 Query: 122 LASVYNRVKGFLEEVRKRHWNQ----TVVVVSHTVPMRAMYCALLGVDLSKFWSFG-CDN 176 V R +E+R VV V H R++ +LG+ +W FG N Sbjct: 116 YREVARRAGEVFDEIRAEGQPSGPAGLVVFVLHGGTARSLIGHVLGLPPELWWHFGPLAN 175 Query: 177 ASYSVIHMEE 186 +SV+ E Sbjct: 176 CRWSVLRQVE 185 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: 115 Number of extensions: 9 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: 211 Length of database: 233 Length adjustment: 22 Effective length of query: 189 Effective length of database: 211 Effective search space: 39879 Effective search space used: 39879 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