Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate WP_086511370.1 BZY95_RS18535 inositol monophosphatase
Query= curated2:P56160 (259 letters) >NCBI__GCF_002151265.1:WP_086511370.1 Length = 273 Score = 92.4 bits (228), Expect = 9e-24 Identities = 74/221 (33%), Positives = 104/221 (47%), Gaps = 8/221 (3%) Query: 5 LQLALELAEKAGKLTLDYFGRRSLQVFSKRDDTPVTEADRNAEELIRQGISAKFPDDGLF 64 L+LA+++A +AG+ + ++ K VT+ D + LI + + A P + Sbjct: 7 LELAIDIAREAGEKIVAARHGQAFNQRLKNGQELVTDVDVAVDTLISERLEASLPGEQRL 66 Query: 65 GEEFD---EHPSGNGRRWIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPALGE 121 EE E S W+IDPIDGT +F HG+ V IA EG +LGV++ P LGE Sbjct: 67 SEELTPDREVMSTAESLWVIDPIDGTVNFAHGLRHVAVSIAWVSEGKTRLGVVHAPFLGE 126 Query: 122 LYQAERGSGAFMNGSPVQVSAIAENSASTVVFTEKEYLLD--PPSNHPVDQLRIDAGLVR 179 Y A G GA+ NG P+ S N +V T Y D PP + + VR Sbjct: 127 TYTALYGQGAWCNGKPIHASRTG-NLQRCLVATGFPYRRDSRPPLMRRLMAVLEHCQDVR 185 Query: 180 GWGDCYGHML-VASGRAEVAVDKIMSPWDCAAVIPIVEEAG 219 G + VA GR + + + SPWD AA + I EAG Sbjct: 186 RNGSAALDLCDVACGRLDAYYESV-SPWDFAAGVLIAREAG 225 Lambda K H 0.319 0.138 0.415 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: 172 Number of extensions: 8 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: 259 Length of database: 273 Length adjustment: 25 Effective length of query: 234 Effective length of database: 248 Effective search space: 58032 Effective search space used: 58032 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 (21.7 bits) S2: 47 (22.7 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