Align Probable histidinol-phosphatase; HolPase; EC 3.1.3.15 (uncharacterized)
to candidate 8500182 DvMF_0940 histidinol phosphate phosphatase HisJ family (RefSeq)
Query= curated2:Q9RX45 (260 letters) >FitnessBrowser__Miya:8500182 Length = 274 Score = 118 bits (295), Expect = 1e-31 Identities = 83/263 (31%), Positives = 119/263 (45%), Gaps = 31/263 (11%) Query: 6 DSHLHTPLCGHATGTPREYAQAALDAGLSGLCFTDHMPMPRWYDAP--WRMKLEQ-LPEY 62 D H HT H T E A+D G+ F++H P P Y P +R KL P Y Sbjct: 5 DLHTHTSH-SHGQATVEEMFAIAMDRGMEVFGFSEHSPRPLAYSYPKDYREKLTAGFPRY 63 Query: 63 IAEIQAVQQEFAGRLD---VRLGLEADFHPGTEKFVEKVLGMFDWDYVIGSVHYLGAWGF 119 + E++A+ AGR D V LGLE D+ PG E F + + + +DY+IG +H+LG WGF Sbjct: 64 VDEVRALA---AGRQDGKTVLLGLEMDWLPGQEPFTAETIHRYPFDYIIGGIHFLGTWGF 120 Query: 120 D-NPEFVAEYEERDLGGLYRDYYALVEGAARSGLFDAIGHLDLPKKFGHLDPDPVYALH- 177 D + + + Y+ + SG+F+ H D+ K F V A H Sbjct: 121 DCTVDDWKDLAPEQANDAFERYFDSLRRMGASGMFNIAAHPDIIKIFA------VDAFHE 174 Query: 178 -------------ALDVVAGQGLALDFNTAGWRKPVAEAYPAPDLVRAAAERGIPFVLGS 224 AL + G+A++ ++AG RK E YP P ++ A E +P GS Sbjct: 175 WLDRPESRQRVRDALATLRAAGMAMEISSAGLRKLCKEIYPCPTIMEMARELELPITFGS 234 Query: 225 DAHQPGEVGFRFADAVKEIRDVG 247 DAH V + F + R G Sbjct: 235 DAHCTSTVAWGFDQLEEYARRFG 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: 232 Number of extensions: 18 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: 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 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