Align Metal-independent phosphoserine phosphatase; iPSP; Phosphoglycerate mutase-like protein 3; EC 3.1.3.3 (characterized)
to candidate Dsui_1264 Dsui_1264 fructose-2,6-bisphosphatase
Query= SwissProt::F4KI56 (238 letters) >FitnessBrowser__PS:Dsui_1264 Length = 216 Score = 129 bits (324), Expect = 5e-35 Identities = 84/203 (41%), Positives = 110/203 (54%), Gaps = 7/203 (3%) Query: 25 TEIVLVRHGETTWNAAGRIQGQIESDLNEVGLKQAVAIAERLGKEERPV-AVYSSDLKRA 83 T I ++RHGET WNA RIQG ++ LN GL+QA A A RL E V AVYSSDL RA Sbjct: 6 TRICVIRHGETFWNADRRIQGHLDIGLNPTGLRQARAAARRLAAEAGTVTAVYSSDLARA 65 Query: 84 KDTALMIAKTCFCPEVIEVPDLKERHVGSLQGLYWKEGAEKEPEAYSAFFSSQNDLEIPG 143 + TA IA P + P L+ER G +GL + E ++ P AY+AF + Q +L IP Sbjct: 66 RVTAEAIAAHLGRPVCLR-PALRERSYGIFEGLTYDEARQQHPGAYAAFEARQPELPIP- 123 Query: 144 GGESFDQLADRSMDALEQIAKKHKGERVIVVTHGGVLRAIYLRITQASSAG----KLLNA 199 GES + + R LE +A +H+GE V++V HGGVL I + A + NA Sbjct: 124 QGESLEDFSARVSRCLEALAAEHRGETVVLVCHGGVLDVINRHVRGRPLAAPRDFTIPNA 183 Query: 200 SVNVVHLRDQKWIIDSWSDVSHL 222 + + W I WS HL Sbjct: 184 GITWLERDGAGWRIVQWSCTRHL 206 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: 162 Number of extensions: 11 Number of successful extensions: 4 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: 216 Length adjustment: 22 Effective length of query: 216 Effective length of database: 194 Effective search space: 41904 Effective search space used: 41904 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