Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate BWI76_RS07840 BWI76_RS07840 inositol monophosphatase family protein
Query= curated2:P56160 (259 letters) >FitnessBrowser__Koxy:BWI76_RS07840 Length = 269 Score = 108 bits (269), Expect = 2e-28 Identities = 79/252 (31%), Positives = 123/252 (48%), Gaps = 22/252 (8%) Query: 6 QLALELAEKAGKLTLDYFGRRS-LQVFSKRDDTP--VTEADRNAEELIRQGISAKFPDDG 62 +LA ELA+ +L +Y+ +R L V K DD V+ AD+ E ++Q I FP DG Sbjct: 14 RLACELAKAGAELAFEYYQQRDRLAVDHKGDDLQDVVSVADKRVEAFVKQRIMDAFPQDG 73 Query: 63 LFGEEFDEHPSGNGRRWIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPALGEL 122 GEE W++DPIDGT F++G+ + + +A+ +G +GV+ P EL Sbjct: 74 FLGEESGTQMPDARVLWVVDPIDGTSCFLNGLHTWCLSLAILADGEPVIGVVYDPNHREL 133 Query: 123 YQAERGSGAFMNGSPVQVSAIAENSASTVVFTEKEYLLDPPSNHPV---------DQLRI 173 + A +G GA++N +P IA + A+TV KE ++ ++H V D L Sbjct: 134 FHALKGQGAWLNDAP-----IAPHPAATV----KEGVMGVGTSHRVTPALFLPFLDALLS 184 Query: 174 DAGL-VRGWGDCYGHMLVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQSII 232 D G+ +R A+GR + M+PWD + ++ EAGG DY I Sbjct: 185 DGGMFIRNGSGALMSAWAAAGRLIGYYEPHMNPWDGLPGLVLMREAGGLSNDYLTNDGIR 244 Query: 233 DGEGLVSANNAM 244 G L+ A+ + Sbjct: 245 HGNPLLLASKTL 256 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: 174 Number of extensions: 7 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: 269 Length adjustment: 25 Effective length of query: 234 Effective length of database: 244 Effective search space: 57096 Effective search space used: 57096 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