Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate WP_012505093.1 PAES_RS02495 inositol monophosphatase family protein
Query= curated2:P56160 (259 letters) >NCBI__GCF_000020625.1:WP_012505093.1 Length = 261 Score = 124 bits (312), Expect = 2e-33 Identities = 80/247 (32%), Positives = 127/247 (51%), Gaps = 7/247 (2%) Query: 1 MTPDLQLALELAEKAGKLTLDYFGRRSLQ-VFSKRDDTPVTEADRNAEELIRQGISAKFP 59 M +L+ A++ A +AG + L FG S Q + K VT AD+ +E+ I + ++A FP Sbjct: 1 MKRELEKAIQAAREAGSIILAKFGELSEQDIHPKEFKDFVTGADKESEKRIAEILTAAFP 60 Query: 60 DDGLFGEEFDEHPSGNGRRWIIDPIDGTRSFIHGVPLYGVMIAL-EVEGAMQLGVINFPA 118 +D L EE +GR+WI+DP+DGT +FIH P++ V IAL + + + V+ P Sbjct: 61 EDSLLCEEGSSANGTSGRKWIVDPLDGTLNFIHSFPVFCVSIALSDSNNELLVAVVYQPV 120 Query: 119 LGELYQAERGSGAFMNGSPVQVSAIAENS----ASTVVFTEKEYLLDPPSNHPVDQLRID 174 L EL+ AE+G G +NG PV++S + A+ + F E Y L+ + D + Sbjct: 121 LDELFTAEKGKGTKLNGKPVRISDRQDTRQLLIATGIPFKEYHY-LESYVSMLKDVIHDS 179 Query: 175 AGLVRGWGDCYGHMLVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQSIIDG 234 AG+ R A GR + + + PWD AA + +V EAGG + G + Sbjct: 180 AGIRRAGSAAIDLAYTACGRFDAFWEYKLYPWDYAAGVLLVREAGGIVTGFDGNPDVFAH 239 Query: 235 EGLVSAN 241 +++ N Sbjct: 240 HSIIAGN 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: 180 Number of extensions: 8 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: 261 Length adjustment: 24 Effective length of query: 235 Effective length of database: 237 Effective search space: 55695 Effective search space used: 55695 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