Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate WP_036261099.1 DL86_RS10760 inositol monophosphatase
Query= curated2:P56160 (259 letters) >NCBI__GCF_000746085.1:WP_036261099.1 Length = 263 Score = 103 bits (256), Expect = 5e-27 Identities = 76/250 (30%), Positives = 126/250 (50%), Gaps = 12/250 (4%) Query: 12 AEKAGK-LTLDYFGRRSLQVFSKRDDTPVTEADRNAEELIRQGISAKFPDDGLFGEEFDE 70 A KAG+ L D+ +LQV K V+ ADR AE+++ + ++ P G EE Sbjct: 14 ALKAGRGLKRDFGEVENLQVSVKGPGDFVSAADRKAEKILFEELTKARPGYGFVLEEGGA 73 Query: 71 -HPSGNGRRWIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPALGELYQAERGS 129 + W IDP+DGT +F+HG+P++ + I L EG + G++ PA +++ AE+G Sbjct: 74 VEGADKSHTWFIDPLDGTTNFLHGLPIFAISIGLAREGQIVAGLVYNPANDDMFIAEKGQ 133 Query: 130 GAFMNGSPVQVSAIAENSASTV------VFTEKEYLLDPPSNHPVDQLRIDAGLVRGWGD 183 GA+ N ++V+A + + + + + KE+ P + AG +R G Sbjct: 134 GAYYNNRRLRVAARRDMADALIGCGIPHIGKAKEH---PRFKAEFASVMARAGNIRRLGA 190 Query: 184 CYGHM-LVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQSIIDGEGLVSANN 242 + VASG + ++ + WD AA I I++EAGG D G Q ++ + + N+ Sbjct: 191 AALDLCFVASGSYDGFWERNLQAWDIAAGIVIIKEAGGFVTDADGGQDMLAKGSICAGND 250 Query: 243 AMGRNLIAAI 252 M RNL+ I Sbjct: 251 VMHRNLLDLI 260 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: 167 Number of extensions: 10 Number of successful extensions: 3 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: 263 Length adjustment: 25 Effective length of query: 234 Effective length of database: 238 Effective search space: 55692 Effective search space used: 55692 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