Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate Echvi_0848 Echvi_0848 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family
Query= curated2:P56160 (259 letters) >FitnessBrowser__Cola:Echvi_0848 Length = 262 Score = 107 bits (268), Expect = 2e-28 Identities = 82/266 (30%), Positives = 125/266 (46%), Gaps = 28/266 (10%) Query: 5 LQLALELAEKAGKLTLDYFGRRSLQVFS------KRDDTPVTEADRNAEELIRQGISAKF 58 L + +A +AG F RR Q F K + V+ D+ AE+++ G+ Sbjct: 7 LDKTIAIAREAGA-----FIRRERQSFDLNKVEHKGFNDLVSYVDKEAEKIVVSGLQEIL 61 Query: 59 PDDGLFGEEFDEHPSGNGRRWIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPA 118 P+ G EE + G WI+DP+DGT +F+HGVP++ V IAL +G + LGV+ Sbjct: 62 PEAGFITEEGTINKEGEVYNWIVDPLDGTTNFVHGVPVFSVSIALMKDGEIILGVVYEVN 121 Query: 119 LGELYQAERGSGAFMNGSPVQVSAIAENSASTV-------VFTEKEY---LLDPPSNHPV 168 E + A +G GAF N +P+ VS SA V F E + LL H Sbjct: 122 NNECFYATKGGGAFCNDTPIGVSPTPSLSAGLVATGFPYSAFEEVDKYLGLLKDIIQHSH 181 Query: 169 DQLRIDAGLVRGWGDCYGHMLVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGR 228 RI + V CY VA+GR + + ++ +D A + I++EAGG D+ G Sbjct: 182 GVRRIGSAAV---DLCY----VAAGRMDGYFEYNLNSYDVAGGVIILQEAGGKVTDFSGG 234 Query: 229 QSIIDGEGLVSANNAMGRNLIAAIGN 254 + G LV +N + + L+ + N Sbjct: 235 DDYVFGRELVGSNEKIHKELLGKVKN 260 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: 188 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: 262 Length adjustment: 25 Effective length of query: 234 Effective length of database: 237 Effective search space: 55458 Effective search space used: 55458 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