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_028950818.1 Q385_RS0106090 histidine phosphatase family protein
Query= SwissProt::D3DFP8 (203 letters) >NCBI__GCF_000619805.1:WP_028950818.1 Length = 206 Score = 189 bits (480), Expect = 3e-53 Identities = 97/202 (48%), Positives = 132/202 (65%), Gaps = 2/202 (0%) Query: 1 MKRLYLVRHAQSEYNEKGIFQGRLDSDLTPLGFVQARLLAREFLKKK-VDIIYSSPQRRA 59 MK +YL RH +SEYN K I QG +D+ LT G QA+ LA EFLK+K + I SS +RA Sbjct: 1 MKYIYLCRHGESEYNAKKIVQGHIDTQLTEKGINQAKALA-EFLKEKNIQKIVSSDLKRA 59 Query: 60 YKTALTISDMLGTQLVVDERLREMSFGEYEGKHFWSMLEAHKDVFLNWLSNPVKHPLPTQ 119 Y+TA T++D+L Q+ VDER+REM FG +EG + + + KD F NWLSNPVKHPLP Q Sbjct: 60 YQTAKTVADILNLQVNVDERIREMHFGTWEGLSYDWIYQNAKDHFYNWLSNPVKHPLPKQ 119 Query: 120 ESMEEFEKRVRSFLEDVKSSHYQNMLIVAHGGTLHAIVCLLTGIGLENLWNIHMDNAGIT 179 E FEKR+R F ED+K S N+LIV HGG++ ++C++ +G+E LW DN G++ Sbjct: 120 EDPYHFEKRLRLFWEDIKKSQEHNILIVGHGGSIQGLLCIVMNLGIECLWKFRHDNTGLS 179 Query: 180 EIHMEGEKSTLVYLNKLCHTRQ 201 I K + ++N HT + Sbjct: 180 LIVSNNSKDEVKFINLSFHTEK 201 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: 150 Number of extensions: 2 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: 203 Length of database: 206 Length adjustment: 21 Effective length of query: 182 Effective length of database: 185 Effective search space: 33670 Effective search space used: 33670 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