Align Histidinol-phosphatase; HolPase; Histidinol-phosphate phosphatase; EC 3.1.3.15 (characterized)
to candidate AZOBR_RS10430 AZOBR_RS10430 inositol monophosphatase
Query= SwissProt::Q9K4B1 (266 letters) >FitnessBrowser__azobra:AZOBR_RS10430 Length = 284 Score = 104 bits (259), Expect = 2e-27 Identities = 93/260 (35%), Positives = 127/260 (48%), Gaps = 27/260 (10%) Query: 10 LAHVLADAADAATM----DRFKALDLKVETKPDMTPVSEADKAAEELIRGHLSRARPRDS 65 L +V+ AA+ A D + L+V K VS AD AE+L+R L +ARP Sbjct: 7 LINVMVRAAEKAARGLVRDFGEVEHLQVSRKGPADFVSAADMKAEKLLREELQKARPDFG 66 Query: 66 VHGEEFGVA-GTGPR-RWVIDPIDGTKNYVRGVPVWATLIALMEAKEGGYQPVVGLVSAP 123 EE G + G+ P RW++DP+DGT N++ G+P WA IA A++ G + V G+V P Sbjct: 67 FLMEETGASKGSDPTARWIVDPLDGTTNFLHGIPHWAISIA---AEKNG-EIVAGVVYEP 122 Query: 124 ALGRRWWAVEDHGAFTGRSLTSAHRLHVSQVSTLSDASFAYSSLSGWEEQGRLD--GFL- 180 + +WA + GAF RL VS+ L+DA A +G +GR D GFL Sbjct: 123 VHDQMFWAEKGQGAFLNH-----QRLRVSERRNLADAVIA----TGIPFKGRGDHAGFLV 173 Query: 181 ---DLTREVWRTRAYG-DFWPYMMVAEGSVDLCAEPELSLWDMAANAIIVTEAGGTFTGL 236 L +EV R +G VA G D E L+ WD AA ++VTEAGG + Sbjct: 174 EAEALMKEVAGIRRFGAASLDLAYVAAGRYDGYWERGLAPWDAAAGQLLVTEAGGFVGEI 233 Query: 237 DGRPGP-HSGNAAASNGRLH 255 G P G A+N H Sbjct: 234 GGGRNPVFGGTILAANAHFH 253 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: 223 Number of extensions: 13 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: 266 Length of database: 284 Length adjustment: 25 Effective length of query: 241 Effective length of database: 259 Effective search space: 62419 Effective search space used: 62419 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