Align Phosphoserine phosphatase; PSP; EC 3.1.3.3 (characterized)
to candidate WP_011868510.1 MMARC5_RS03765 TIGR02253 family HAD-type hydrolase
Query= SwissProt::P94512 (260 letters) >NCBI__GCF_000016125.1:WP_011868510.1 Length = 225 Score = 67.4 bits (163), Expect = 2e-16 Identities = 41/128 (32%), Positives = 70/128 (54%), Gaps = 2/128 (1%) Query: 133 YDETFAVLDQLKG-KYELLLLTNGDPSLQKEKLAGVPELAPYFNEIVISGAFGKGKPDVS 191 Y +T L L+ L +LT+G Q EKL + + P+F+E++ S +G GKP++ Sbjct: 96 YSDTIKTLMDLRSIGLSLGILTDGITIKQWEKLIRLG-IHPFFDEVITSEEYGLGKPNIE 154 Query: 192 IFEHCLKLMNIEKDDAIMVGDNLNTDILGASRAGIKTVWINRTDKKNETDVKPDYIISSL 251 F + LK +N++ ++ I VGD + D++ A G+ TV I R +D DY I ++ Sbjct: 155 FFNYGLKKINLKAEEVIYVGDRADKDMVPAKTVGMTTVRILRGKYSEISDDVSDYTIKNI 214 Query: 252 HDLFPILE 259 +L I++ Sbjct: 215 SELSKIIK 222 Lambda K H 0.318 0.138 0.409 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: 154 Number of extensions: 11 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 260 Length of database: 225 Length adjustment: 23 Effective length of query: 237 Effective length of database: 202 Effective search space: 47874 Effective search space used: 47874 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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