Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate WP_078429653.1 BK574_RS18935 inositol monophosphatase
Query= curated2:P56160 (259 letters) >NCBI__GCF_002019605.1:WP_078429653.1 Length = 257 Score = 101 bits (251), Expect = 2e-26 Identities = 67/203 (33%), Positives = 103/203 (50%), Gaps = 6/203 (2%) Query: 29 QVFSKRDDTP-VTEADRNAEELIRQGISAKFPDDGLFGEEFDEHPSGNGRRWIIDPIDGT 87 Q+ SK D VTE D +E+ + I +++P + EE H W+IDPIDGT Sbjct: 31 QMKSKSSDIDLVTEVDEWSEQYLMDKIKSQYPHHAIMTEESGWHEGQAEYEWVIDPIDGT 90 Query: 88 RSFIHGVPLYGVMIALEVEGAMQLGVINFPALGELYQAERGSGAFMNGSPVQVSAIAENS 147 +F H P + + I ++ +G +GV+ P + E+Y+A +GSGA +NG P+ VS E Sbjct: 91 VNFAHRFPFFCISIGVKFQGETVIGVVYVPKIDEMYEAIKGSGATLNGKPITVSR-TERL 149 Query: 148 ASTVVFTEKEY--LLDPPSN-HPVDQLRIDAGLVRGWGDCYGHML-VASGRAEVAVDKIM 203 VV T Y DP +N + + + G +R G + VA+GR + + + Sbjct: 150 NQAVVATGFPYDRATDPNNNVNHFNAIITKVGGIRRTGSAAIDLCQVAAGRFDGYWELKL 209 Query: 204 SPWDCAAVIPIVEEAGGCCFDYR 226 WD A + I+EEA G F Y+ Sbjct: 210 QEWDICAGLLIIEEANGKTFSYK 232 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: 172 Number of extensions: 14 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: 259 Length of database: 257 Length adjustment: 24 Effective length of query: 235 Effective length of database: 233 Effective search space: 54755 Effective search space used: 54755 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 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