Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate GFF4537 PS417_23220 inositol monophosphatase
Query= curated2:P56160 (259 letters) >FitnessBrowser__WCS417:GFF4537 Length = 271 Score = 107 bits (266), Expect = 3e-28 Identities = 80/262 (30%), Positives = 126/262 (48%), Gaps = 11/262 (4%) Query: 1 MTPDLQLALELAEKAGKLTLDYFGRR-SLQVFSKRDDTPVTEADRNAEELIRQGISAKFP 59 M P L +AL A A +L R +++V K V+E DR AE+ I + +P Sbjct: 1 MQPMLNIALRAARSASELIFRSIERLDTIKVDEKDAKDYVSEVDRAAEQKIIDALRKAYP 60 Query: 60 DDGLFGEEFDEHP-SGNGRR--WIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINF 116 G+ GEE H SG G WIIDP+DGT +F+ G+P + V IA + G ++ V+ Sbjct: 61 THGILGEETGLHKGSGEGEDYLWIIDPLDGTTNFLRGIPHFAVSIACKYRGRLEHAVVLD 120 Query: 117 PALGELYQAERGSGAFMNGSPVQVS--AIAENSASTVVFTEKEYLLDPPSNHPVDQLRI- 173 P E + A RG GA +NG ++VS + + F ++ +D N+ + R Sbjct: 121 PVRQEEFTASRGRGAQLNGRRLRVSGRTSLDGALLGTGFPFRDDQMDNLENY-LGMFRAL 179 Query: 174 ---DAGLVRGWGDCYGHMLVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQS 230 AG+ R VA+GR + + +S WD AA +++EAGG D+ G Sbjct: 180 VGQTAGIRRAGAASLDLAYVAAGRFDAFWESGLSEWDMAAGALLIQEAGGLVSDFTGGHD 239 Query: 231 IIDGEGLVSANNAMGRNLIAAI 252 ++ +V+ N + ++ AI Sbjct: 240 FLEKGHVVAGNTKCFKAVLTAI 261 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: 184 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: 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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