Align Metal-independent phosphoserine phosphatase; iPSP; Phosphoglycerate mutase-like protein 3; EC 3.1.3.3 (characterized)
to candidate GFF2008 PGA1_c20420 phosphoglycerate mutase-like protein
Query= SwissProt::F4KI56 (238 letters) >FitnessBrowser__Phaeo:GFF2008 Length = 193 Score = 67.4 bits (163), Expect = 2e-16 Identities = 58/173 (33%), Positives = 84/173 (48%), Gaps = 14/173 (8%) Query: 26 EIVLVRHGETTWNAAGRIQGQIESDLNEVGLKQAVAIAERLGK-EERPVAVYSSDLKRAK 84 +I +RHG+T WNA GRIQGQ+ES L+ +G++ A A + + A Y S L RA+ Sbjct: 9 KIWFLRHGQTEWNAEGRIQGQLESRLSPLGIEHAQQQAGLMAPILAQGPACYVSPLGRAQ 68 Query: 85 DTA-LMIAKTCFCPEVIEVPDLKERHVGSLQGLYWKEGAEKEPEAYSAFFSSQNDLEIPG 143 TA + + F + L E G QGL +E A + PE Y+A + + Sbjct: 69 QTARIALGDQPFITDA----RLAEAQAGVFQGLTRQEVAAEYPEIYAANPLNLDLFCAAP 124 Query: 144 GGESFDQLADRSMDALEQIAKKHKGERVIVVTH---GGVLRAIYLRITQASSA 193 GE FD R D L ++ E +VV H G VLR + +++A A Sbjct: 125 QGEGFDAFQARITDFLTGLS-----EPTVVVAHGLWGQVLRGVICGLSRAEMA 172 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: 99 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: 238 Length of database: 193 Length adjustment: 22 Effective length of query: 216 Effective length of database: 171 Effective search space: 36936 Effective search space used: 36936 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: 45 (21.9 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