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_013841974.1 DESRU_RS09935 alpha-ribazole phosphatase
Query= SwissProt::D3DFG8 (211 letters) >NCBI__GCF_000215085.1:WP_013841974.1 Length = 204 Score = 119 bits (298), Expect = 4e-32 Identities = 66/199 (33%), Positives = 108/199 (54%), Gaps = 1/199 (0%) Query: 3 KLILVRHAESEWNPVGRYQGLLDPDLSERGKKQAKLLAQELSREHLDVIYSSPLKRTYLT 62 ++ LVRH E++WN G++QG D LS++G++QAK LA+ L + IYSS L R T Sbjct: 4 RIYLVRHGETDWNSGGKFQGHSDIPLSDKGREQAKRLAKRLKNVDIHGIYSSDLCRARET 63 Query: 63 ALEIAEAKNLEVIKEDRIIEIDHGMWSGMLVEEVMEKYPEDFRRWVEEPHKVEFQGGESL 122 A A+ L V + EI+ G W G+ +E+ EK+ E + W E P GESL Sbjct: 64 AEIAAKPHQLTVQTMTDLREINFGGWEGLTYQEITEKFGESYSCWSENPLMTRIPFGESL 123 Query: 123 ASVYNRVKGFLEEVRKRHWNQTVVVVSHTVPMRAMYCALLGVDLSKFWSFGCDNASYSVI 182 + +R ++ + H +T+++V+H +R + LG++++ +W D+ S S++ Sbjct: 124 QDMVDRCSRAMQALILEHPGETLLIVAHGGVIRTIVGTSLGINMNLYWKLKVDHVSLSIL 183 Query: 183 HMEERRNVILKL-NITCHL 200 IL+L N TCH+ Sbjct: 184 EYHGWDKAILELYNETCHI 202 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: 5 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: 204 Length adjustment: 21 Effective length of query: 190 Effective length of database: 183 Effective search space: 34770 Effective search space used: 34770 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