Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate WP_018125061.1 B149_RS0110035 3'(2'),5'-bisphosphate nucleotidase CysQ
Query= BRENDA::Q8NS80 (260 letters) >NCBI__GCF_000375485.1:WP_018125061.1 Length = 276 Score = 97.1 bits (240), Expect = 4e-25 Identities = 67/217 (30%), Positives = 99/217 (45%), Gaps = 17/217 (7%) Query: 28 ASDLEVSSKPDMTPVSDADLATEEALREKIATARPADSILGEEFGGDVEFSGRQW----I 83 A D EV +K D +P+++ADLA+ + + +A P +L EE G R W + Sbjct: 28 ARDFEVMTKQDQSPLTEADLASHQCIINALAEHFPDIPVLSEESKGIDYEQRRDWERFFL 87 Query: 84 IDPIDGTKNYVRGVPVWATLIALLDNGKPVAGVISAPALARRWWASEGAGAWRTFNGSSP 143 IDP+DGTK +V+ + IAL+++G+PVAGV+ AP W+A++ GAWR+ G Sbjct: 88 IDPLDGTKEFVKRNGEFTVNIALIEDGRPVAGVVFAPVPDTLWFAADELGAWRSQKGGEA 147 Query: 144 RKLSVSQVSKLDD----ASLSFSSLSGWAERDLRDQFVSLTDTTWRLRGYGDFFSYCLVA 199 + + L S S S S A D + L G C +A Sbjct: 148 EPIEAGRFESLSGLRIVGSRSHPSTSMQAFLDELPEH--------ELLAMGSSIKLCAIA 199 Query: 200 EGAVDIAAE-PEVSLWDLAPLSILVTEAGGKFTSLAG 235 + D+ S WD A +V +AGG L G Sbjct: 200 DSGADVYPRLGPTSEWDTAAAHCVVEQAGGSVVRLDG 236 Lambda K H 0.315 0.133 0.396 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: 168 Number of extensions: 6 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: 276 Length adjustment: 25 Effective length of query: 235 Effective length of database: 251 Effective search space: 58985 Effective search space used: 58985 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 (21.6 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