Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate WP_092482990.1 BM299_RS08205 inositol monophosphatase family protein
Query= curated2:P56160 (259 letters) >NCBI__GCF_900115975.1:WP_092482990.1 Length = 269 Score = 109 bits (272), Expect = 7e-29 Identities = 83/257 (32%), Positives = 120/257 (46%), Gaps = 8/257 (3%) Query: 4 DLQLALELAEKAGKLTLDYFGRRSLQVFSKRDDTPVTEADRNAEELIRQGISAKFPDDGL 63 +L LA+ A +AG+L + R + VTE DR AEE+ I +FP+ + Sbjct: 7 ELALAVRAAREAGRLIREKINRHRVTETKSCLSDLVTEVDRLAEEVTLHMIRDRFPEHTV 66 Query: 64 FGEEFDEH---PSGNGRRWIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPALG 120 GEE +G W +DP+DGT +F+ G+P V IAL G LGVI+ P Sbjct: 67 VGEEEQAGRAWETGKNLTWFVDPLDGTTNFVFGLPFCAVSIALAHRGRPVLGVIHDPFRE 126 Query: 121 ELYQAERGSGAFMNGSPVQVS-AIAENSASTVVFTEKEYLLDPPSNHPVDQLRI--DAGL 177 E + A RG GA +NG+PV V AI S +V P H VD + Sbjct: 127 ETFTAVRGGGAHLNGAPVSVDRAICTLDRSLLVTGYPGNAAMRPRMHRVDYKEVIDRCSN 186 Query: 178 VRGWGDCYGHM-LVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQ-SIIDGE 235 +R G + VA GR + + PWD AA + +VEEAGG D G+ + + Sbjct: 187 LRALGSAALELAYVACGRLTGFWEVALRPWDVAAGMVLVEEAGGTVSDLAGQPLEMTEYV 246 Query: 236 GLVSANNAMGRNLIAAI 252 + ++N + R +A + Sbjct: 247 DIAASNGLIHREFLACL 263 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: 172 Number of extensions: 7 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: 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 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