Align Probable histidinol-phosphatase; HolPase; EC 3.1.3.15 (uncharacterized)
to candidate WP_092486701.1 BM299_RS15995 histidinol-phosphatase HisJ family protein
Query= curated2:Q9RX45 (260 letters) >NCBI__GCF_900115975.1:WP_092486701.1 Length = 258 Score = 203 bits (517), Expect = 3e-57 Identities = 105/250 (42%), Positives = 152/250 (60%), Gaps = 7/250 (2%) Query: 4 LCDSHLHTPLCGHATGTPREYAQAALDAGLSGLCFTDHMPM----PRWYDAPWRMKLEQL 59 L D H+HT CGHATG +EY + A++ GL + F DH+PM + D M EQL Sbjct: 3 LPDYHIHTCRCGHATGEMKEYVERAIELGLPEIGFADHLPMYWLAEKERDPGIAMTSEQL 62 Query: 60 PEYIAEIQAVQQEFAGRLDVRLGLEADFHPGTEKFVEKVLGMFDWDYVIGSVHYLGAWGF 119 PEY+AE++ ++ + +RLG+EAD+ PG E +EK+L + +DYV+GS+H++ WGF Sbjct: 63 PEYVAEVEKLRAANP-EIPIRLGIEADYIPGREAELEKILKAYPFDYVLGSIHFIDGWGF 121 Query: 120 DNPEFVAEYEERDLGGLYRDYYALVEGAARSGLFDAIGHLDLPKKFGHLDPDPVYALH-- 177 DNP ++ Y DL LYR Y+ L++ AA+S LFD + H DL KKFG+ V ++ Sbjct: 122 DNPAYIDRYRHCDLDALYRRYFQLLQQAAQSRLFDIMAHPDLIKKFGYKPQGDVQGVYEE 181 Query: 178 ALDVVAGQGLALDFNTAGWRKPVAEAYPAPDLVRAAAERGIPFVLGSDAHQPGEVGFRFA 237 V A G+ ++ NTAG R PV E YP+ ++A G+ GSDAH P +VG++F Sbjct: 182 TARVFAETGVCVEINTAGLRAPVEEMYPSFGFLQACRNHGVSVTTGSDAHTPEQVGYQFD 241 Query: 238 DAVKEIRDVG 247 A++ I VG Sbjct: 242 KALELITKVG 251 Lambda K H 0.322 0.142 0.455 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: 265 Number of extensions: 15 Number of successful extensions: 4 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: 260 Length of database: 258 Length adjustment: 24 Effective length of query: 236 Effective length of database: 234 Effective search space: 55224 Effective search space used: 55224 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 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 10 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