Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate SMc03994 SMc03994 inositol monophosphatase
Query= reanno::azobra:AZOBR_RS03845 (260 letters) >FitnessBrowser__Smeli:SMc03994 Length = 266 Score = 86.7 bits (213), Expect = 5e-22 Identities = 70/209 (33%), Positives = 97/209 (46%), Gaps = 8/209 (3%) Query: 37 KADASPVTIADREAERTIRAIIEAERPDDGIYGEEFGT-KNLDAEWVWVIDPIDGTKSFI 95 K A V+ ADR+AER IR + RP G GEE K D W++DP+DGT +F+ Sbjct: 36 KGPADYVSQADRKAERIIREELMKARPTYGFLGEEGEEIKGTDGAHRWIVDPLDGTTNFL 95 Query: 96 TGRPIFGTLIALLHRGRPVLGVIDQPIVRDRWLGVEGRPTLFNGQPARVRECAGGLAAAT 155 G P F +AL +G V V+ P + + G N + RV L+ A Sbjct: 96 HGIPHFAISVALERQGEIVGAVVFNPATDELYTAERGGGAFLNDRRLRV-GARKALSDAV 154 Query: 156 LGTTSPDLFPGADQD---AFRRVAG-AAKVSVYGGDCYSYGLLAAGYYDLVVESGLKLYD 211 +GT +P L G R V G A + G +AAG +D E L +D Sbjct: 155 IGTGTPHLGRGNHGKYLVELRHVMGEVAGIRRMGSASLDLAYVAAGRFDGFWERDLAAWD 214 Query: 212 FAALVPVVTGAGGLMTDWD--GRPLDATS 238 AA + ++ AGG TD + G+PL+A S Sbjct: 215 MAAGLLLIREAGGWSTDAEGGGKPLEAGS 243 Lambda K H 0.320 0.139 0.424 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: 185 Number of extensions: 15 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: 260 Length of database: 266 Length adjustment: 25 Effective length of query: 235 Effective length of database: 241 Effective search space: 56635 Effective search space used: 56635 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 (21.8 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