Align Metal-independent phosphoserine phosphatase; iPSP; Phosphoglycerate mutase-like protein 3; EC 3.1.3.3 (characterized)
to candidate Dsui_2994 Dsui_2994 fructose-2,6-bisphosphatase
Query= SwissProt::F4KI56 (238 letters) >FitnessBrowser__PS:Dsui_2994 Length = 233 Score = 89.0 bits (219), Expect = 7e-23 Identities = 64/196 (32%), Positives = 99/196 (50%), Gaps = 12/196 (6%) Query: 19 KVESEVTEIVLVRHGETTWNAAGRIQGQIESDLNEVGLKQAVAIAERLGKEERPVAVYSS 78 + E V ++ L RHG+T WN R+QG ++ LN+ G QA + E+L E AVYSS Sbjct: 24 RAEEAVLDLYLARHGQTAWNLEKRLQGSTDNPLNDTGRSQARQLGEKLAGENF-AAVYSS 82 Query: 79 DLKRAKDTALMIAKTCFCPEVIEVPDLKERHVGSLQGLYWKEGAEKEPEAYSAFFSSQND 138 L RA+++A + V +P+L ER G +G+ ++G E + A F +++ Sbjct: 83 SLARARESAALARPGM---TVQALPELAERSFGKFEGMA-EDGREGQEATLLAEFKARSG 138 Query: 139 L--EIPGGGESFDQLADRSMDALEQIAKKHKGERVIVVTHGGVLRAIYLRITQASSAGKL 196 + GGES A R A+E+I ++ +V+VV+HGGV I + Q A + Sbjct: 139 KLEDSLDGGESLASQARRVAQAVERIRREQPRGQVLVVSHGGVTPLILAHLLQLPVAEAV 198 Query: 197 L-----NASVNVVHLR 207 N V +V LR Sbjct: 199 ARIRQGNDEVYLVRLR 214 Lambda K H 0.315 0.132 0.387 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: 134 Number of extensions: 10 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: 238 Length of database: 233 Length adjustment: 23 Effective length of query: 215 Effective length of database: 210 Effective search space: 45150 Effective search space used: 45150 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Apr 09 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