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 WP_011766534.1 AZO_RS14115 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
Query= SwissProt::D3DFG8 (211 letters) >NCBI__GCF_000061505.1:WP_011766534.1 Length = 249 Score = 59.3 bits (142), Expect = 6e-14 Identities = 45/131 (34%), Positives = 64/131 (48%), Gaps = 9/131 (6%) Query: 1 MVKLILVRHAESEWNPVGRYQGLLDPDLSERGKKQAKLLAQELSRE--HLDVIYSSPLKR 58 M K++L+RH ES WN R+ G D DL+E G +A+ Q L RE D+ ++S LKR Sbjct: 1 MYKIVLLRHGESTWNKENRFTGWTDVDLTELGVGEARAAGQLLKREGYSFDLAFTSVLKR 60 Query: 59 TYLT---ALEIAEAKNLEVIKEDRIIEIDHGMWSGMLVEEVMEKYPED----FRRWVEEP 111 T LE +A L V R+ E +G G+ E K+ +D +RR + P Sbjct: 61 ANKTLNIVLEELDALWLPVEHSWRLNERHYGALQGLNKAETAAKFGDDQVLVWRRSYDIP 120 Query: 112 HKVEFQGGESL 122 +G E L Sbjct: 121 PPALEEGDERL 131 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: 125 Number of extensions: 9 Number of successful extensions: 1 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: 249 Length adjustment: 23 Effective length of query: 188 Effective length of database: 226 Effective search space: 42488 Effective search space used: 42488 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: 46 (22.3 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