Align Histidinol-phosphatase; Hol-Pase; Histidinol-phosphate phosphatase; EC 3.1.3.15 (characterized)
to candidate WP_017600618.1 D471_RS0121990 HAD-IB family hydrolase
Query= SwissProt::P0DV34 (222 letters) >NCBI__GCF_000341125.1:WP_017600618.1 Length = 265 Score = 78.6 bits (192), Expect = 1e-19 Identities = 67/221 (30%), Positives = 100/221 (45%), Gaps = 7/221 (3%) Query: 5 AIFDLDNTLINTDSDHAWPQYLIKKGLVDAAETE--AQNEKFYRDYQNGCLD-IDAFLKF 61 A FD+DNTL+ S + + + L + L + A + +R D I+A + Sbjct: 16 AFFDVDNTLMRGASIYHFARGLASRDLFTTRDLLRFAWGQTVFRVTGAEQPDHINAAREA 75 Query: 62 HLAPLARYSKEELAEFHREFMAEYIIPHISPMQRMLVQSHQMAGDETLVISSTNEFIITP 121 LA +A + +L E + + I R LVQ H AG ++++T + Sbjct: 76 ALAFVAGHDVGDLVALCEEIYDDSMADRIWEGTRRLVQRHLDAGQPVWLVTATPVELAQI 135 Query: 122 VCHLFGITNIIGTQLETGSDGRYTGNYIGTPSLKEGKITRLNQWLAERGETLQSYGKTYF 181 + G+T +GT+ E+ DG YTG G K + G L + Sbjct: 136 IRRRLGLTGALGTEAES-VDGVYTGRLNGDLMHGPAKAVAVRALARREGWDLAACSA--- 191 Query: 182 YSDSKNDLPLLRLVSEPVAVNPDAELEKEAKEKGWPVLNFK 222 YSDS NDLPLL LV P AVNPD +L + A+ WPV +F+ Sbjct: 192 YSDSSNDLPLLSLVGHPHAVNPDGDLRRYARTHQWPVHDFR 232 Lambda K H 0.317 0.135 0.400 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: 124 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: 222 Length of database: 265 Length adjustment: 23 Effective length of query: 199 Effective length of database: 242 Effective search space: 48158 Effective search space used: 48158 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: 46 (22.3 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