Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate 352328 BT2801 inositol-1-monophosphatase (NCBI ptt file)
Query= curated2:P56160 (259 letters) >FitnessBrowser__Btheta:352328 Length = 267 Score = 99.4 bits (246), Expect = 7e-26 Identities = 70/224 (31%), Positives = 105/224 (46%), Gaps = 13/224 (5%) Query: 26 RSLQVFSKRDDTPVTEADRNAEELIRQGISAKFPDDGLFGEEFDEHPSGNGRRWIIDPID 85 R +V K V+ D+ +E + + +SA P+ G EE W+IDP+D Sbjct: 30 RRERVMEKHAHDYVSYVDKESEVRLVKALSALLPEAGFITEEGSATYQDEPYCWVIDPLD 89 Query: 86 GTRSFIHGVPLYGVMIALEVEGAMQLGVINFPALGELYQAERGSGAFMNGSPVQVSAIAE 145 GT ++IH Y V IAL + LGV+ E + A +G AFMNG + VS + Sbjct: 90 GTTNYIHDEAPYCVCIALRSRTELLLGVVYEVCRNECFYAWKGGKAFMNGEEIHVSDV-R 148 Query: 146 NSASTVVFTEKEYLLD---PPSNHPVDQLRIDAGLVRGWGD-----CYGHMLVASGRAEV 197 + + VFTE Y D P + H +D L G +R G CY +A+GR + Sbjct: 149 DIKNAFVFTELPYNYDQYKPTALHLIDNLYGAVGGIRMNGSAAAAICY----IANGRFDA 204 Query: 198 AVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQSIIDGEGLVSAN 241 + + WD +A IV EAGG ++ G I+G +++ N Sbjct: 205 WAEAFIGKWDYSAAALIVLEAGGRVTNFYGDDHFIEGHHIIATN 248 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: 161 Number of extensions: 12 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: 267 Length adjustment: 25 Effective length of query: 234 Effective length of database: 242 Effective search space: 56628 Effective search space used: 56628 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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