Align Phosphoserine phosphatase SerB1; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_028312930.1 H566_RS0120660 HAD-IB family hydrolase
Query= SwissProt::P9WGJ3 (308 letters) >NCBI__GCF_000482785.1:WP_028312930.1 Length = 224 Score = 77.8 bits (190), Expect = 2e-19 Identities = 67/222 (30%), Positives = 97/222 (43%), Gaps = 12/222 (5%) Query: 59 AFFDVDNTLVQGSSAVHFGRGLAARHYFTYRDVLGFLYAQAKFQLLGKENSNDVAAGRRK 118 A FD+D+TL+ S R L AR GF+ + + D+ R+ Sbjct: 6 ALFDLDHTLISYDSGADLLRFLVARELVD----AGFVDRYTEHCIEYVAGRVDLRQLNRE 61 Query: 119 ALAFIEGRSVAELVALGEEIYDEIIADKIWDGTRELTQMHLDAGQQVWLITATPYELAAT 178 A + V L A E +E + L H +G L+TAT +A+ Sbjct: 62 YYALLMRYPVESLTAWRNEWREES-GKHVSAAAMRLVHSHHASGDLCCLVTATSEFIASA 120 Query: 179 IARRLGLTGALGT---VAESVDGIF-TGRLVGEILHGTGKAHAVRSLAIREGLN---LKR 231 G + T +AE G F +G + G + + GK VR + +GL+ Sbjct: 121 YREIFGFEHMVATRIAMAEGPQGSFISGEVEGLLNYREGKIANVRDWLLAQGLDWSSFDE 180 Query: 232 CTAYSDSYNDVPMLSLVGTAVAINPDARLRSLARERGWEIRD 273 YSDS+ND+P+L V VA+ PDARLR++A ERGW I D Sbjct: 181 SVFYSDSFNDLPLLEYVSHPVAVTPDARLRAVAIERGWRILD 222 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: 126 Number of extensions: 9 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: 224 Length adjustment: 25 Effective length of query: 283 Effective length of database: 199 Effective search space: 56317 Effective search space used: 56317 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 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