Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate 16632 b2533 inositol monophosphatase (NCBI)
Query= reanno::Korea:Ga0059261_2035 (260 letters) >FitnessBrowser__Keio:16632 Length = 267 Score = 87.0 bits (214), Expect = 4e-22 Identities = 74/255 (29%), Positives = 114/255 (44%), Gaps = 15/255 (5%) Query: 8 IDLAGRLADAAGAAIRPYFRAEHGLESKDDSSP--VTLADKAAEAAMRRLIIAERPMDAI 65 +++A R A AG I + +E+ S VT DKAAEA + I P I Sbjct: 5 LNIAVRAARKAGNLIAKNYETPDAVEASQKGSNDFVTNVDKAAEAVIIDTIRKSYPQHTI 64 Query: 66 IGEEEDDRPGTSGRI-WVLDPIDGTRSFIVGRPIFGTLIALLEDGWPVLGIIDQPIIKER 124 I EE + GT + WV+DP+DGT +FI P F IA+ G + ++ P+ E Sbjct: 65 ITEESGELEGTDQDVQWVIDPLDGTTNFIKRLPHFAVSIAVRIKGRTEVAVVYDPMRNEL 124 Query: 125 WLGVTGRETLFNGKPARARTCRELSKALLATTSPALFTDGQLHAFEHV-------DAAVM 177 + G+ NG R T R+L +LAT P + +A ++ + Sbjct: 125 FTATRGQGAQLNGYRLRGSTARDLDGTILATGFP---FKAKQYATTYINIVGKLFNECAD 181 Query: 178 STVLGGDCYNYGLVASGHLDIVIEAGLKLHDFAALVPVVEGAGGRMCDWQGDPLHAGSNG 237 G + VA+G +D E GL+ DFAA +V AGG + D+ G + + Sbjct: 182 FRRTGSAALDLAYVAAGRVDGFFEIGLRPWDFAAGELLVREAGGIVSDFTGGHNYMLTGN 241 Query: 238 EVIAAGDPARIEELV 252 I AG+P ++ ++ Sbjct: 242 --IVAGNPRVVKAML 254 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: 150 Number of extensions: 8 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: 267 Length adjustment: 25 Effective length of query: 235 Effective length of database: 242 Effective search space: 56870 Effective search space used: 56870 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