Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate HSERO_RS08580 HSERO_RS08580 inositol monophosphatase
Query= curated2:P56160 (259 letters) >FitnessBrowser__HerbieS:HSERO_RS08580 Length = 265 Score = 102 bits (255), Expect = 6e-27 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 9/247 (3%) Query: 3 PDLQLALELAEKAGKL-TLDYFGRRSLQVFSKRDDTPVTEADRNAEELIRQGISAKFPDD 61 P L A++ A +A + F L+V K + VTE D+ AE+ I + +PD Sbjct: 5 PMLNTAIKAARRAATIINRASFDVSLLKVSKKSHNDFVTEVDKAAEDAIIDVLKNAYPDH 64 Query: 62 GLFGEEF---DEHPSGNGRRWIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPA 118 + EE D N WIIDP+DGT +FIHG P Y V IAL+ G + V+ P Sbjct: 65 AILAEESGASDNLHDENENVWIIDPLDGTTNFIHGFPQYCVSIALQQRGIITQAVVYDPT 124 Query: 119 LGELYQAERGSGAFMNGSPVQVSAIAENSASTVVFTEKEYLLDPPSNHPVDQLRI----D 174 +L+ A +G+GA++N ++V + A ++ T + N V ++ Sbjct: 125 RNDLFTASKGAGAYLNEKRIRVGK-RDKIADALIGTGFPFRDLDGLNEYVKMFKVMTEHS 183 Query: 175 AGLVRGWGDCYGHMLVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQSIIDG 234 AGL R VA+GR + +K + PWD AA +V EAGG ++G + Sbjct: 184 AGLRRPGAAALDLAYVAAGRLDGFFEKGLKPWDIAAGSLLVTEAGGIVGTFKGDSDYLYK 243 Query: 235 EGLVSAN 241 +++A+ Sbjct: 244 GDVIAAS 250 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: 157 Number of extensions: 3 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: 265 Length adjustment: 25 Effective length of query: 234 Effective length of database: 240 Effective search space: 56160 Effective search space used: 56160 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 09 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