Align histidinol-phosphatase (EC 3.1.3.15); inositol-phosphate phosphatase (EC 3.1.3.25) (characterized)
to candidate 7025121 Shewana3_2284 inositol monophosphatase (RefSeq)
Query= BRENDA::Q6NPM8 (346 letters) >FitnessBrowser__ANA3:7025121 Length = 267 Score = 110 bits (275), Expect = 4e-29 Identities = 73/223 (32%), Positives = 117/223 (52%), Gaps = 9/223 (4%) Query: 94 ADASGEVIRKYFRK--KFDIVDKDDMSPVTIADQMAEEAMVSIIFQNLPSHAIYGEEKGW 151 A A+G+ I + + + + ++ K VT D+ AE A+ I ++ P H I GEEKG Sbjct: 12 ARAAGQTIMRAYTELDRVEVSAKGVNDFVTSVDKEAEAAITYQIRKSYPDHTIVGEEKGE 71 Query: 152 RCKEESADYVWVLDPIDGTKSFITGKPVFGTLIALLYKGKPILGLIDQPILKERWIGMNG 211 + E+ DYVW++DP+DGT +F+ G P F IAL +KGK + ++ P+ +E + + G Sbjct: 72 N-RGENKDYVWIVDPLDGTNNFVRGIPHFAVSIALQHKGKTEVAVVYDPVREELFTAIRG 130 Query: 212 RRTKLNGEDISTRSCPKLSQAYLYTTSPHLFSEEAEKAYSRVRDKV-----KVPLYGCDC 266 + KLN I + +L+ + T P + E +Y + +V + G Sbjct: 131 KGAKLNDFRIRVTNVTELAPTIIGTGFPFKARQHTE-SYMAIFGEVFGQCSDLRRAGSAA 189 Query: 267 YAYALLASGFVDLVIESGLKPYDFLALVPVIEGAGGTITDWTG 309 A +A+G +D E GLKP+D A + AGGT+TD+TG Sbjct: 190 LDLAYVAAGRLDGFFEIGLKPWDIAAGDLICREAGGTVTDFTG 232 Lambda K H 0.318 0.133 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: 185 Number of extensions: 9 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: 346 Length of database: 267 Length adjustment: 27 Effective length of query: 319 Effective length of database: 240 Effective search space: 76560 Effective search space used: 76560 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: 48 (23.1 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