Align Histidinol-phosphatase; HolPase; Histidinol-phosphate phosphatase; EC 3.1.3.15 (characterized)
to candidate N515DRAFT_3936 N515DRAFT_3936 myo-inositol-1(or 4)-monophosphatase
Query= SwissProt::Q9K4B1 (266 letters) >FitnessBrowser__Dyella79:N515DRAFT_3936 Length = 267 Score = 109 bits (273), Expect = 5e-29 Identities = 82/227 (36%), Positives = 110/227 (48%), Gaps = 17/227 (7%) Query: 31 LKVETKPDMTPVSEADKAAEELIRGHLSRARPRDSVHGEEFGVAGTGPRRWVIDPIDGTK 90 L + K M SE D+ AE I L RA P ++ EE G G GP WVIDP+DGT Sbjct: 30 LNIVEKQRMDFASEVDRLAEAEIVKELRRAYPSHAILAEESGAMGKGPLTWVIDPLDGTH 89 Query: 91 NYVRGVPVWATLIALMEAKEGGYQPVVGLVSAPALGRRWWAVEDHGAFTGRSLTSAHRLH 150 NY+RG+P ++ IAL+E E PV G+V P G + A + GA+ + R+ Sbjct: 90 NYLRGIPHFSVSIALLEKGE----PVYGVVFDPLRGELFTASKGDGAY-----LNDRRIR 140 Query: 151 VSQVSTLSDASFAYSSLSGWEEQGRLDGFLDLTREVWR-----TRAYGDFWPYMMVAEGS 205 VS+ L A A + ++ L+ L++TR + R+ VA G Sbjct: 141 VSKREDLGGAMIATG--YPYRQRQHLEAQLNMTRVLLGQAEDIRRSGSAALDLSYVAAGR 198 Query: 206 VDLCAEPELSLWDMAANAIIVTEAGGTFTGLDGRPG-PHSGNAAASN 251 D E L WDMAA ++V EAGG + GR G P SGN A N Sbjct: 199 YDGYFEIGLKPWDMAAGVLLVREAGGRYGDFAGRDGIPASGNIIAGN 245 Lambda K H 0.318 0.135 0.418 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: 12 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: 266 Length of database: 267 Length adjustment: 25 Effective length of query: 241 Effective length of database: 242 Effective search space: 58322 Effective search space used: 58322 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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