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_013538091.1 THEAM_RS06760 alpha-ribazole phosphatase
Query= SwissProt::D3DFG8 (211 letters) >NCBI__GCF_000185805.1:WP_013538091.1 Length = 215 Score = 162 bits (410), Expect = 4e-45 Identities = 90/205 (43%), Positives = 124/205 (60%), Gaps = 3/205 (1%) Query: 1 MVKLILVRHAESEWNPVGRYQGLLDPDLSERGKKQAKLLAQELSREHLDVIYSSPLKRTY 60 M ++ILVRH ++ WN GRYQG +D L+E GK+QA+ + + L + +YSSPL R Sbjct: 1 MPRIILVRHGKTVWNAEGRYQGKMDIPLNEEGKEQARRVGEALKGFPVKAVYSSPLSRCR 60 Query: 61 LTALEIAEAKNLEVIKEDRIIEIDHGMWSGMLVEEVMEKYPEDFRRWVEEPHKVEFQGGE 120 TA EIA+ NLEV ++ EIDHG W G+L EV +KYPE + W P +V+ GGE Sbjct: 61 DTAAEIAKHHNLEVQVKEGFKEIDHGEWEGLLASEVEKKYPELLKLWRTRPAEVKMPGGE 120 Query: 121 SLASVYNR-VKGFLEEVRKRHWNQTVVVVSHTVPMRAMYCALLGVDLSKFWSFGCDNASY 179 SL VY+R VK F E V +V+V H + + C LLGVDL+KFW+F N Sbjct: 121 SLRDVYDRAVKAFNEVVSSHSDEDLIVIVGHDATNKVLMCHLLGVDLNKFWAFKQANCGI 180 Query: 180 SVI-HMEERRNVILKL-NITCHLGE 202 +V+ + E NV++ + N T HLG+ Sbjct: 181 TVLEYSPETGNVVVHVANATGHLGK 205 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: 141 Number of extensions: 5 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: 211 Length of database: 215 Length adjustment: 22 Effective length of query: 189 Effective length of database: 193 Effective search space: 36477 Effective search space used: 36477 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: 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