Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate WP_004299867.1 C665_RS03125 inositol monophosphatase
Query= curated2:P56160 (259 letters) >NCBI__GCF_000310185.1:WP_004299867.1 Length = 269 Score = 83.6 bits (205), Expect = 4e-21 Identities = 71/228 (31%), Positives = 109/228 (47%), Gaps = 22/228 (9%) Query: 33 KRDDTPVTEADRNAEELIRQGISAKFPDDGLFGEEFDEHPSG----NGRR--WIIDPIDG 86 K D + TEAD +++ + + A P + GEE G R W IDPIDG Sbjct: 38 KADGSLFTEADMASQQRFSEALPAFLPG-AVLGEEMTAAEQAALWKEGARGLWCIDPIDG 96 Query: 87 TRSFIHGVPLYGVMIALEVEGAMQLGVINFPALGELYQAERGSGAFMNGSPVQVSAIAEN 146 T +F +G+PL+ V IA ++ +GV+ P E + A RG+GAF+NG+ + + A A Sbjct: 97 TTNFANGIPLFAVSIAYLIDHEPVIGVVYNPITDESFYAARGAGAFLNGTELPLRAGATE 156 Query: 147 SASTVVFTEKEYLLDPPSNHPVDQLRIDAGLV--RGWG-DCYGHMLVASGRAEVAVDKIM 203 V + + + S+H D+L + R +G VA+GR +V + Sbjct: 157 LRDAVAGVDFKRI----SHHLGDELAVRPPYYSQRNFGSSALEWCFVAAGRLDVYLHGGQ 212 Query: 204 SPWDCAAVIPIVEEAGGCCFDYRGRQSIIDGEGLVSANNAMGRNLIAA 251 WD AA I+ EAGG +DG G++ + A+ R +IAA Sbjct: 213 MLWDYAAGRLILAEAGGIA-------EALDG-GVLMSGPAIKRGVIAA 252 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: 173 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: 269 Length adjustment: 25 Effective length of query: 234 Effective length of database: 244 Effective search space: 57096 Effective search space used: 57096 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