Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate CA265_RS06215 CA265_RS06215 inositol monophosphatase
Query= reanno::Korea:Ga0059261_2035 (260 letters) >FitnessBrowser__Pedo557:CA265_RS06215 Length = 263 Score = 82.0 bits (201), Expect = 1e-20 Identities = 59/201 (29%), Positives = 91/201 (45%), Gaps = 4/201 (1%) Query: 32 LESKDDSSPVTLADKAAEAAMRRLIIAERPMDAIIGEEEDDRPGTSGRIWVLDPIDGTRS 91 +E K + V+ DK AE + + + P I EE+ W++DP+DGT + Sbjct: 33 IEYKGLNDMVSYVDKTAEQKLVQNLEKLIPDAGFITEEKTINRTGKTYTWIIDPLDGTTN 92 Query: 92 FIVGRPIFGTLIALLEDGWPVLGIIDQPIIKERWLGVTGRETLFNGKPARARTCRELSKA 151 FI G P +G +AL EDG PV+G++ + E + G L N K + +L + Sbjct: 93 FIHGIPAYGISVALYEDGLPVIGVVYELNRGEMFYSYKGGPALMNKKEIKVSANPDLKSS 152 Query: 152 LLATTSPALFTDGQLHAFEHVDAAVMST----VLGGDCYNYGLVASGHLDIVIEAGLKLH 207 LLAT P D Q + + + + +G + A G D E L+ Sbjct: 153 LLATGFPYYQFDKQPQYLKLLTEMMQKSHGVRRIGAAAIDLVYTACGRFDAFFEYNLQQW 212 Query: 208 DFAALVPVVEGAGGRMCDWQG 228 DFAA +V+ AGG + D+ G Sbjct: 213 DFAAGCFIVQQAGGEVYDFAG 233 Lambda K H 0.320 0.138 0.419 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: 140 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: 260 Length of database: 263 Length adjustment: 25 Effective length of query: 235 Effective length of database: 238 Effective search space: 55930 Effective search space used: 55930 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