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_011988773.1 CKL_RS00935 histidine phosphatase family protein
Query= SwissProt::D3DFG8 (211 letters) >NCBI__GCF_000016505.1:WP_011988773.1 Length = 211 Score = 126 bits (316), Expect = 3e-34 Identities = 73/204 (35%), Positives = 111/204 (54%), Gaps = 2/204 (0%) Query: 1 MVKLILVRHAESEWNPVGRYQG-LLDPDLSERGKKQAKLLAQELSREHLDVIYSSPLKRT 59 MVKL LVRH E+ WN + QG + D L+++G +QA LL + + D+IYSSPL+R Sbjct: 1 MVKLYLVRHGETIWNIERKMQGGMKDSPLTKKGIEQANLLKNRMENINFDIIYSSPLERA 60 Query: 60 YLTALEIAEAKNLEVIKEDRIIEIDHGMWSGMLVEEVMEKYPEDFRRWVEEPHKVEFQGG 119 T+ +A +N+ +IK+DR++EID G W G+ E+ E+ PE + P G Sbjct: 61 VKTSRIVAAQRNIPIIKDDRLMEIDIGEWGGLTKEQARERNPEQLNNFWTNPKIYVPDTG 120 Query: 120 ESLASVYNRVKGFLEEVRKRHWNQTVVVVSHTVPMRAMYCALLGVDLSKFWSFG-CDNAS 178 ES A V RV ++E+ ++ +++++V+HTV +R M L + W AS Sbjct: 121 ESFAQVKTRVVSLIKEIISKYEGKSILIVTHTVILRIMMAYFENRPLDELWEGSYIHQAS 180 Query: 179 YSVIHMEERRNVILKLNITCHLGE 202 S + +E IL T HLGE Sbjct: 181 LSEVEIENGCYNILLYGDTSHLGE 204 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: 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: 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