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 YP_001312627.1 Smed_3882 phosphoglycerate mutase
Query= SwissProt::D3DFG8 (211 letters) >NCBI__GCF_000017145.1:YP_001312627.1 Length = 198 Score = 92.4 bits (228), Expect = 5e-24 Identities = 66/194 (34%), Positives = 103/194 (53%), Gaps = 7/194 (3%) Query: 5 ILVRHAESEWNPVGRYQG--LLDPDLSERGKKQAKLLAQELSREHLDVIYSSPLKRTYLT 62 +LVRHA + VG Y D L G++QA+ L+ LS + + IY+SP KRT T Sbjct: 6 LLVRHAAHD--NVGCYLAGRTGDVPLGAAGREQAQRLSARLSGQGIRAIYASPRKRTQQT 63 Query: 63 ALEIAEAKNL-EVIKEDRIIEIDHGMWSGMLVEEVMEKYPEDFRRWVEEPHKVEFQGGES 121 A IA ++ EV+ + + E+D G WSG + V+++ P +RRW V GGE+ Sbjct: 64 AEAIAAVSDVSEVLTTEALDEVDFGEWSGKTFD-VLDEDPH-WRRWNAVRSLVRAPGGET 121 Query: 122 LASVYNRVKGFLEEVRKRHWNQTVVVVSHTVPMRAMYCALLGVDLSKFWSFGCDNASYSV 181 + V +R G + + +RH + +V+VSH ++ + C +LG+ + F AS SV Sbjct: 122 MLDVQSRAVGLVAALAQRHGQEKIVLVSHADVIKTVVCHVLGLSADAWPRFDIAPASISV 181 Query: 182 IHMEERRNVILKLN 195 + M + IL LN Sbjct: 182 VAMGDWGAKILTLN 195 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: 114 Number of extensions: 8 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: 211 Length of database: 198 Length adjustment: 21 Effective length of query: 190 Effective length of database: 177 Effective search space: 33630 Effective search space used: 33630 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