Align phosphoserine phosphatase (EC 3.1.3.3) (characterized)
to candidate Synpcc7942_2078 Synpcc7942_2078 phosphoglycerate mutase
Query= BRENDA::D3DFG8 (211 letters) >FitnessBrowser__SynE:Synpcc7942_2078 Length = 212 Score = 104 bits (259), Expect = 1e-27 Identities = 62/201 (30%), Positives = 103/201 (51%), Gaps = 1/201 (0%) Query: 1 MVKLILVRHAESEWNPVGRYQGLLDPDLSERGKKQAKLLAQELSREHLDVIYSSPLKRTY 60 +++L LVRH E+ + G Y G +P L+E G++ A+ LA + + Y SP+ R Sbjct: 2 VLRLYLVRHGETTASREGGYSGSGNPPLTEAGQQMAQALADTYADLNWQAAYVSPMLRAQ 61 Query: 61 LTALEIAEAKNLEVIKEDRIIEIDHGMWSGMLVEEVMEKYPEDFRRWVEEPHKVEFQGGE 120 TA + + L++ D + EID G+W +EVM + +D+ W+ EP GGE Sbjct: 62 ETAQPLCQQAKLDMRIRDGLREIDFGIWENRTPDEVMASHQQDYLHWLAEPAWNPPTGGE 121 Query: 121 SLASVYNRVKGFLEEVRKRHWNQTVVVVSHTVPMRAMYCALLGVDLSKFWS-FGCDNASY 179 S V +RV ++E+ + + V+VVSH +R + C LLG+DL ++ AS Sbjct: 122 SAVVVASRVSLVIQEITETIADGNVLVVSHKATLRILLCNLLGIDLGRYRDRIAMPVASL 181 Query: 180 SVIHMEERRNVILKLNITCHL 200 S++ + + +L HL Sbjct: 182 SILSFNQHGPCLERLGDRSHL 202 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: 117 Number of extensions: 3 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: 212 Length adjustment: 21 Effective length of query: 190 Effective length of database: 191 Effective search space: 36290 Effective search space used: 36290 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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