Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate SM_b20362 SM_b20362 inositol monophosphatase
Query= reanno::Phaeo:GFF2154 (250 letters) >FitnessBrowser__Smeli:SM_b20362 Length = 266 Score = 99.4 bits (246), Expect = 7e-26 Identities = 76/212 (35%), Positives = 102/212 (48%), Gaps = 11/212 (5%) Query: 29 DPVTIADRAAEQAMRSVLSELRPEDSILGEEFGETHGQSGRTWVLDPIDGTRGFISGTPT 88 D V+IADR E +R ++E PED +LGEE+G G+SG TW +DPIDGT F++G P Sbjct: 47 DLVSIADREVENLIRDRIAEAYPEDGVLGEEYGLVPGRSGFTWAVDPIDGTSPFVNGMPN 106 Query: 89 WGVLIALGDADGPFLGIVDQPYIGERFIGT-PEGASLTG---PLGHSALVTRATDSLSEA 144 W V IAL A P +G++ P GE + GA L G L S + L A Sbjct: 107 WCVSIALVHAGIPVVGVIAAPCHGELYAAALGLGARLNGKALTLDGSRTIRNHVTGLG-A 165 Query: 145 TLFTTFPEVGTEAERAAFQRVSAQVRLTRYGMDCYAYALLAAGQCDLVIEAGLNAYDIQA 204 + VG E + A R G A +AAG+ E ++A+D A Sbjct: 166 NNYVKPAFVGQMVE----SLLEAGGTFMRNGSGALMLAYVAAGRLVGYYEPYMHAWDCLA 221 Query: 205 PIAVIQAAGGVVTNW--QGEPAHEGGQVLAAA 234 ++Q AGG + +GE G VLAAA Sbjct: 222 GYCLVQEAGGWYLPFPTEGESLTRGSIVLAAA 253 Lambda K H 0.317 0.134 0.392 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: 169 Number of extensions: 8 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: 250 Length of database: 266 Length adjustment: 24 Effective length of query: 226 Effective length of database: 242 Effective search space: 54692 Effective search space used: 54692 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