Align Putative phosphoserine phosphatase 2; PSP 2; PSPase 2; Metal-independent phosphoserine phosphatase 2; iPSP2; O-phosphoserine phosphohydrolase 2; EC 3.1.3.3 (characterized)
to candidate WP_089301794.1 CHB84_RS12115 histidine phosphatase family protein
Query= SwissProt::D3DFP8 (203 letters) >NCBI__GCF_900188115.1:WP_089301794.1 Length = 198 Score = 99.0 bits (245), Expect = 5e-26 Identities = 58/171 (33%), Positives = 94/171 (54%), Gaps = 2/171 (1%) Query: 1 MKRLYLVRHAQSEYNEKGIFQGRLDSDLTPLGFVQARLLAREFLKKKVDIIYSSPQRRAY 60 M+RL L RH ++EYN G QG++D++LTP+G+ QAR + + +++ SS RRA Sbjct: 1 MRRLVLWRHGETEYNAAGRMQGQIDTELTPVGWDQARFVVPRLARFAPELVVSSDLRRAN 60 Query: 61 KTALTISDMLGTQLVVDERLREMSFGEYEGKHFWSMLEAHKDVFLNWLSNPVKHPLPTQE 120 TA ++ +G L VD+RLRE G+++G + E W ++ P P E Sbjct: 61 DTATVFTEAIGVGLQVDKRLRETHLGQWQGLTSAEVDEGWPGERQRWRADASWSP-PGGE 119 Query: 121 SMEEFEKRVRSFLEDVKSSHYQNMLIVAHGGTLHAIVCLLTGIGLENLWNI 171 S + +R + +++ S Y +++VAHGG + A+ L G+ L LW I Sbjct: 120 SRVDVSERAYEVVAELQDSTYAAVMLVAHGGLIVALTARLLGLPLA-LWPI 169 Lambda K H 0.321 0.136 0.402 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: 110 Number of extensions: 6 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: 203 Length of database: 198 Length adjustment: 21 Effective length of query: 182 Effective length of database: 177 Effective search space: 32214 Effective search space used: 32214 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 (21.9 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