Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate WP_026608218.1 METAC_RS0118930 inositol monophosphatase
Query= curated2:P56160 (259 letters) >NCBI__GCF_000427445.1:WP_026608218.1 Length = 263 Score = 108 bits (269), Expect = 1e-28 Identities = 76/249 (30%), Positives = 130/249 (52%), Gaps = 10/249 (4%) Query: 12 AEKAGK-LTLDYFGRRSLQVFSKRDDTPVTEADRNAEELIRQGISAKFPDDGLFGEEFDE 70 A KAG+ L D+ +LQV K V+ AD+ AE+++++ ++ P G EE E Sbjct: 14 ALKAGRGLKRDFGEVENLQVSVKGPGDFVSAADKKAEKILQEELAKARPGYGFVLEESGE 73 Query: 71 -HPSGNGRRWIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPALGELYQAERGS 129 S W IDP+DGT +F+HG+P++ + I L EG + G++ PA +++ AE+G Sbjct: 74 IEGSDKSHTWFIDPLDGTTNFLHGLPIFAISIGLAREGQIVAGLVYNPATDDMFVAEKGQ 133 Query: 130 GAFMNGSPVQVSAIAENSASTVVFTEKEYLLDPPSNHP-----VDQLRIDAGLVRGWGDC 184 GA+ N ++V+A ++ A T++ + L HP + ++ AG +R G Sbjct: 134 GAYYNNRRLRVAA-RKDMADTLIGCGVPH-LGKAKEHPRFKAELAEVMARAGNIRRLGAA 191 Query: 185 YGHM-LVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQSIIDGEGLVSANNA 243 + VA+G + ++ + PWD AA I ++ EAGG D G ++ + + N+A Sbjct: 192 ALDLCFVAAGNYDGFWERNLQPWDMAAGIIMIREAGGFVTDADGGHDMLAKGSICAGNDA 251 Query: 244 MGRNLIAAI 252 + R L+ I Sbjct: 252 IHRALLGLI 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: 169 Number of extensions: 9 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