Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate Pf1N1B4_1668 3'(2'),5'-bisphosphate nucleotidase (EC 3.1.3.7)
Query= curated2:P56160 (259 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1668 Length = 277 Score = 92.4 bits (228), Expect = 9e-24 Identities = 86/279 (30%), Positives = 126/279 (45%), Gaps = 35/279 (12%) Query: 3 PDLQLALELAEKAGKLTLDYFGRRSLQVFSKRDDTPVTEADRNAEELIRQGISAKFPDDG 62 P + +ELA KAG+ L ++ R ++ V +K DD+PVT AD A +I G++A P Sbjct: 8 PLMAPVVELALKAGEAILPFW-RVNVGVTAKADDSPVTAADMAAHHVILAGLTALDPSIP 66 Query: 63 LFGEEFDEHP----SGNGRRWIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPA 118 + EE P +G R W++DP+DGT+ FI G + V IAL +G + GV++ P Sbjct: 67 VLSEEDANIPQSVRTGWQRWWLVDPLDGTKEFISGSEEFTVNIALIEQGRVVFGVVSMPT 126 Query: 119 LGELYQAERGSGAFMNGS-----PVQVSAI-AENSASTVVFTEKEYLLDPPSNHPVDQLR 172 G Y G GA+ P+QV + TVV + + + +Q R Sbjct: 127 NGRFYVGGAGLGAWRGDKGAEPLPIQVREVPVAGELFTVVASRR--------HSSPEQER 178 Query: 173 IDAGLVRGWGDC----YGHMLVASGRAEVAVD-----KIMSPWDCAAVIPIVEEAGGCCF 223 + AGL G+ G L AE A D S WD AA ++E AGG Sbjct: 179 LLAGLSDSLGELQLANIGSSLKFCLLAEGAADCYPRLAPTSQWDTAAAQGVLEGAGGEVL 238 Query: 224 D-------YRGRQSIIDGEGLVSANNAMGRNLIAAIGNG 255 D Y R+S+++ L A R + A+ G Sbjct: 239 DLSGEPFCYPARESLLNEFFLALPAKAAWREKLLALARG 277 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: 186 Number of extensions: 10 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: 277 Length adjustment: 25 Effective length of query: 234 Effective length of database: 252 Effective search space: 58968 Effective search space used: 58968 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