Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate WP_012474000.1 CPHAMN1_RS02765 inositol monophosphatase
Query= curated2:P56160 (259 letters) >NCBI__GCF_000020545.1:WP_012474000.1 Length = 266 Score = 131 bits (329), Expect = 2e-35 Identities = 79/242 (32%), Positives = 126/242 (52%), Gaps = 7/242 (2%) Query: 4 DLQLALELAEKAGKLTLDYFGRRSL-QVFSKRDDTPVTEADRNAEELIRQGISAKFPDDG 62 +L+ A++ A++AG + L FG L ++ K VTE D+ E I ISA FPDDG Sbjct: 5 ELETAVKAAKEAGAIALRKFGELDLTEIHPKEYKDFVTEVDKACERNIASAISAAFPDDG 64 Query: 63 LFGEEFDEHPSGNGRRWIIDPIDGTRSFIHGVPLYGVMIAL-EVEGAMQLGVINFPALGE 121 + EE +GR+WI+DP+DGT +FIH P++ + IAL + + GV+ P L E Sbjct: 65 MLCEEGSAAKGASGRKWIVDPLDGTLNFIHSFPVFAISIALSDARNNLVAGVVYQPVLDE 124 Query: 122 LYQAERGSGAFMNGSPVQVSAIAENS----ASTVVFTEKEYLLDPPSNHPVDQLRIDAGL 177 L+ AE+G GA++N SP+ VS+ A+ + F E Y L+ + + + AG+ Sbjct: 125 LFTAEKGKGAYLNDSPIHVSSRNNPEQFLIATGIPFKEYHY-LESYVSMLKEVIHGSAGI 183 Query: 178 VRGWGDCYGHMLVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQSIIDGEGL 237 R A GR + + + PWD +A + +V EAGG + G + + + Sbjct: 184 RRAGSAAIDLAYTACGRFDAFWEYKLFPWDFSAGVLLVREAGGIVTSFSGNSDVTEHHSI 243 Query: 238 VS 239 ++ Sbjct: 244 IA 245 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: 188 Number of extensions: 9 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: 259 Length of database: 266 Length adjustment: 25 Effective length of query: 234 Effective length of database: 241 Effective search space: 56394 Effective search space used: 56394 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