Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate WP_013706794.1 DESAC_RS09210 inositol monophosphatase family protein
Query= curated2:P56160 (259 letters) >NCBI__GCF_000195295.1:WP_013706794.1 Length = 260 Score = 122 bits (305), Expect = 1e-32 Identities = 80/254 (31%), Positives = 132/254 (51%), Gaps = 9/254 (3%) Query: 6 QLALELAEKAGKLTLDYFGRRSLQVFSKRDDTPVTEADRNAEELIRQGISAKFPDDGLFG 65 Q+A + A KAG L F + R D PVTE+D ++E+I Q + FP+ + Sbjct: 7 QIARQAALKAGALLRRNFAQPHKITLKGRHD-PVTESDLQSQEIIVQTLLQVFPNHHILA 65 Query: 66 EEFDEHPSGNGRR---WIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPALGEL 122 EE S + WIIDP+DGT +F HG P++ V IA + +GA+ GV+ P EL Sbjct: 66 EEQGAPNSAKSSQDNCWIIDPLDGTVNFAHGFPMFAVSIAFQQQGAVLYGVVYDPMREEL 125 Query: 123 YQAERGSGAFMNGSPVQVSAIAENSASTVVFTEKEYLLDPPSNHPVDQLR----IDAGLV 178 ++A RG GA++N P++VS + E +V T Y ++ + + + + + G+ Sbjct: 126 FEAARGRGAWLNRQPIRVSTVRELD-QALVATGFPYNVNERLENTIRRFKKLVALAEGVR 184 Query: 179 RGWGDCYGHMLVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQSIIDGEGLV 238 R +A+GR + ++ + PWD AA + IVEEAGG ++ G + + + Sbjct: 185 RPGSAALDLSCLAAGRFDGFWEEGLKPWDTAAAVLIVEEAGGRVSNFGGGPFDLASDNVA 244 Query: 239 SANNAMGRNLIAAI 252 ++N + R L+ A+ Sbjct: 245 ASNGLLHRQLLQAL 258 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: 9 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: 260 Length adjustment: 24 Effective length of query: 235 Effective length of database: 236 Effective search space: 55460 Effective search space used: 55460 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