Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate Ga0059261_0715 Ga0059261_0715 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family
Query= curated2:P56160 (259 letters) >FitnessBrowser__Korea:Ga0059261_0715 Length = 271 Score = 97.8 bits (242), Expect = 2e-25 Identities = 83/254 (32%), Positives = 130/254 (51%), Gaps = 23/254 (9%) Query: 12 AEKAG-KLTLDYFGRRSLQVFSKRDDTPVTEADRNAEELIRQGISAKFPDDGLFGEE--- 67 A KAG +L D+ + LQV K V+ ADR AE+ + + + PD G EE Sbjct: 15 ARKAGPRLRRDFNEVQHLQVSRKGPADFVSIADRRAEDTLIEELQRARPDWGFLVEERGV 74 Query: 68 FDEHPSGNGRRWIIDPIDGTRSFIHGVPLYGVMIALE----VEGAMQL--GVINFPALGE 121 + P N RWIIDP+DGT +F+HG+P + + IA+E +G ++ G I P E Sbjct: 75 IEGDP--NKPRWIIDPLDGTSNFLHGIPHFCMSIAVEDPFGAQGKPEITHGYIYQPVTDE 132 Query: 122 LYQAERGSGAFMNGSPVQVSAIAENSASTVVFTEKEYLLDPPSNHPVDQLRID------- 174 + AE+G GA++ ++VSA ++ A +++ T ++ + + RI Sbjct: 133 SFWAEKGRGAWLQDQRLRVSA-RKDLADSLIGTGIPFM---GHGNFAEWSRIFGAIAPEV 188 Query: 175 AGLVRGWGDCYGHMLVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQSIIDG 234 AG+ R VA+GR + + + PWD AA I IV+EAGG DYRG+ + Sbjct: 189 AGIRRFGSAALDLAWVAAGRFDGFWESELKPWDVAAGILIVKEAGGFVTDYRGQDNAFAK 248 Query: 235 EGLVSANNAMGRNL 248 +++AN+A+ L Sbjct: 249 GQVLAANDALHSKL 262 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: 177 Number of extensions: 11 Number of successful extensions: 4 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: 271 Length adjustment: 25 Effective length of query: 234 Effective length of database: 246 Effective search space: 57564 Effective search space used: 57564 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