Align Probable histidinol-phosphatase; HolPase; EC 3.1.3.15 (uncharacterized)
to candidate 207987 DVU2490 Histidinol phosphatase
Query= curated2:Q9RX45 (260 letters) >MicrobesOnline__882:207987 Length = 274 Score = 149 bits (377), Expect = 5e-41 Identities = 87/254 (34%), Positives = 128/254 (50%), Gaps = 13/254 (5%) Query: 6 DSHLHTPLCGHATGTPREYAQAALDAGLSGLCFTDHMPMPRWYDAP--WRMKLEQ-LPEY 62 D H HT H T +E +A GL F++H P P YD P +R KL + P+Y Sbjct: 5 DLHTHTSH-SHGQATVQEMFEAGCARGLLVHGFSEHSPRPSGYDYPKDYRDKLTRSFPDY 63 Query: 63 IAEIQAVQQEFAGRLDVRLGLEADFHPGTEKFVEKVLGMFDWDYVIGSVHYLGAWGFD-N 121 + +++ + +A V LGLE D+ PG E F++ + +D+DYVIG +H+LG WGFD Sbjct: 64 VEQVRTLAATYAPERTVLLGLEMDWLPGQEPFIDATIHRYDYDYVIGGIHFLGTWGFDYT 123 Query: 122 PEFVAEYEERDLGGLYRDYYALVEGAARSGLFDAIGHLDLPKKFG--------HLDPDPV 173 P+ + +Y Y+ + A SG+FD H D+ K F D Sbjct: 124 PDDWQGFSPEQTADIYVRYFESLRRMAASGMFDIAAHPDIIKIFSAAAFHDWLATDKAKA 183 Query: 174 YALHALDVVAGQGLALDFNTAGWRKPVAEAYPAPDLVRAAAERGIPFVLGSDAHQPGEVG 233 AL+ + G+A++ ++AG RKP E YP PD++R AA+ G+P GSDAH +G Sbjct: 184 VVRDALETMHTAGMAMEISSAGLRKPCKEIYPCPDIMRMAADIGLPVTFGSDAHCVNTIG 243 Query: 234 FRFADAVKEIRDVG 247 + F R G Sbjct: 244 WGFDTLADYARGFG 257 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: 237 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: 274 Length adjustment: 25 Effective length of query: 235 Effective length of database: 249 Effective search space: 58515 Effective search space used: 58515 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 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