Align histidinol-phosphatase (EC 3.1.3.15); inositol-phosphate phosphatase (EC 3.1.3.25) (characterized)
to candidate WP_028950187.1 Q385_RS0102695 inositol monophosphatase
Query= BRENDA::Q6NPM8 (346 letters) >NCBI__GCF_000619805.1:WP_028950187.1 Length = 258 Score = 107 bits (268), Expect = 3e-28 Identities = 75/233 (32%), Positives = 115/233 (49%), Gaps = 10/233 (4%) Query: 83 LDRFAAVGNALADASGEVIRKYFRK--KFDIVDKDDMSPVTIADQMAEEAMVSIIFQNLP 140 ++ F A G ++++ F+K K D+ +K VT D+++EE + S I P Sbjct: 1 MNNFVQTAKEAALIGGGILKENFKKVKKSDVENKGIKDFVTYVDKLSEERIRSYILSKYP 60 Query: 141 SHAIYGEEKGWRCKEESADYVWVLDPIDGTKSFITGKPVFGTLIALLYKGKPILGLIDQP 200 H+ GEE G K ++DYVWV+DP+DGTK++I G +F +AL++KG I G I P Sbjct: 61 DHSFLGEEDG---KFGNSDYVWVVDPLDGTKNYICGFEIFAVSVALIHKGDIIAGSIYVP 117 Query: 201 ILKERWIGMNGRRTKLNGEDISTRSCPKLSQAYLYTTSPHLFSEEAEKAYSRVRDKV--- 257 IL + + LNGE I P + A + T P +E + S +R+ + Sbjct: 118 ILDKLYWAGKSEGAYLNGEKIKVSDRP-IESAVVSTGFPFREIKELDSYLSMLREAMITF 176 Query: 258 -KVPLYGCDCYAYALLASGFVDLVIESGLKPYDFLALVPVIEGAGGTITDWTG 309 V G AL+A G D E L +D A + +I+ AGG T++ G Sbjct: 177 SGVRRPGAAAVDLALVAEGVFDGFFEMKLSIWDIAAGILLIKEAGGICTNFDG 229 Lambda K H 0.318 0.133 0.392 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: 198 Number of extensions: 8 Number of successful extensions: 2 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: 346 Length of database: 258 Length adjustment: 27 Effective length of query: 319 Effective length of database: 231 Effective search space: 73689 Effective search space used: 73689 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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