Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate WP_028316352.1 G491_RS0123975 inositol monophosphatase
Query= curated2:P56160 (259 letters) >NCBI__GCF_000429905.1:WP_028316352.1 Length = 258 Score = 107 bits (267), Expect = 2e-28 Identities = 77/242 (31%), Positives = 118/242 (48%), Gaps = 14/242 (5%) Query: 8 ALELAEKAGKLTLDYFGRRSLQVFSKRDDTPVTEADRNAEELIRQGISAKFPDDGLFGEE 67 AL A A K+ L Y+GR + V K + +T+AD+ +EE+I + I+ FPD + EE Sbjct: 11 ALAAAHGAAKVLLKYYGRARV-VKKKGEIDLLTQADKASEEIIVEAIARAFPDHAILAEE 69 Query: 68 FDEHPSGNGRRWIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPALGELYQAER 127 + + WI+DP+DGT ++ HG+PL+ + I L G++ P EL+ A+ Sbjct: 70 GSGKEADSEYTWIVDPLDGTTNYAHGLPLFSISIGLARAEKTIFGLVLNPVTQELFVAKE 129 Query: 128 GSGAFMNGSPVQVSAIAENSASTVVFTEKEYLLDPPSNHPVDQLRIDAGLVRG------- 180 G GA +N P+ VS + S VV T Y L +D+ V+G Sbjct: 130 GQGATLNSRPISVSDQTDLQDSLVV-TGFPYGLKTMMPELMDRFSAVLPKVQGVRRLGSA 188 Query: 181 -WGDCYGHMLVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQSIIDGEGLVS 239 CY VA GR + ++ ++PWD AA IV EAGG D+ + G +++ Sbjct: 189 ALDLCY----VACGRFDGFWEQNLAPWDTAAGECIVREAGGKVTDFAENEFSPGGSQILA 244 Query: 240 AN 241 N Sbjct: 245 TN 246 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: 158 Number of extensions: 9 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: 258 Length adjustment: 24 Effective length of query: 235 Effective length of database: 234 Effective search space: 54990 Effective search space used: 54990 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