Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate WP_011318778.1 AVA_RS10020 3'(2'),5'-bisphosphate nucleotidase CysQ
Query= curated2:P56160 (259 letters) >NCBI__GCF_000204075.1:WP_011318778.1 Length = 290 Score = 50.4 bits (119), Expect = 4e-11 Identities = 40/120 (33%), Positives = 54/120 (45%), Gaps = 12/120 (10%) Query: 34 RDDTPVTEADRNAEELIRQGISAKF--PDDGLFGEEFDEHPSGNGRR------WIIDPID 85 + + PVT AD + I Q + A D EE + + WIIDP+D Sbjct: 40 KQNEPVTIADITVSQYILQKLQAALGQEDFAYVSEETYKSELSEDTKTKTDWVWIIDPLD 99 Query: 86 GTRSFIHGVPLYGVMIALEVEGAMQLGVINFPALGELYQAERGSGAFM----NGSPVQVS 141 GTR FI Y V IAL E L V+ P +LY A + SG F+ N + +Q+S Sbjct: 100 GTRGFIEKTGDYAVHIALVKEHRPVLAVVAIPEAEKLYFAIKDSGTFVETRNNSNVLQLS 159 Lambda K H 0.319 0.138 0.415 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: 144 Number of extensions: 6 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 259 Length of database: 290 Length adjustment: 25 Effective length of query: 234 Effective length of database: 265 Effective search space: 62010 Effective search space used: 62010 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 (21.7 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