Align Phosphoserine phosphatase SerB1; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate Ac3H11_1314 Phosphoserine phosphatase (EC 3.1.3.3)
Query= SwissProt::P9WGJ3 (308 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1314 Length = 236 Score = 81.3 bits (199), Expect = 2e-20 Identities = 68/222 (30%), Positives = 98/222 (44%), Gaps = 14/222 (6%) Query: 59 AFFDVDNTLVQGSSAVHFGRGLAARHYFTYR----DVLGFLYAQAKFQLLGKENSNDVAA 114 A FD+D+TL+ S +G FT R D + F +F + + +V Sbjct: 11 ALFDLDHTLLPLDSDYEWGE-------FTIRIGWNDPVEFARRNDEFYAHYQAGTLNVHD 63 Query: 115 GRRKALAFIEGRSVAELVALGEEIYDEIIADKIWDGTRELTQMHLDAGQQVWLITATPYE 174 R A + R A ++ E+I I +L + H AG +V ++TAT Sbjct: 64 YVRFATEAVRLRGPEAAAAAHQQFMREVITPAIKPQALDLIRQHQAAGDEVLIVTATNEF 123 Query: 175 LAATIARRLGLTGALGT-VAESVDGIFTGRLVGEILHGTGKAHAVRSLAIREGLNLKRC- 232 + IA+ LG+ L + G +TG + G GK + L+ Sbjct: 124 VTGPIAQALGVPQLLAVQLVRDASGWYTGEIDGVPTMREGKVTRMEQWLAARQLSWADVD 183 Query: 233 -TAYSDSYNDVPMLSLVGTAVAINPDARLRSLARERGWEIRD 273 T YSDS NDVP+L V VA NPD RLR+LA++RGW I D Sbjct: 184 STFYSDSMNDVPLLEKVNRPVATNPDPRLRALAQQRGWRILD 225 Lambda K H 0.319 0.134 0.388 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: 150 Number of extensions: 8 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: 308 Length of database: 236 Length adjustment: 25 Effective length of query: 283 Effective length of database: 211 Effective search space: 59713 Effective search space used: 59713 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: 47 (22.7 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