Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate Echvi_4407 Echvi_4407 3'(2'),5'-bisphosphate nucleotidase, bacterial
Query= reanno::azobra:AZOBR_RS03845 (260 letters) >FitnessBrowser__Cola:Echvi_4407 Length = 253 Score = 68.9 bits (167), Expect = 1e-16 Identities = 45/126 (35%), Positives = 65/126 (51%), Gaps = 3/126 (2%) Query: 9 LVTLAERLADASGPVIRQYFRTP-VAVDDKADASPVTIADREAERTIRAII-EAERPDDG 66 L +A A ++G I + + P + + K D SP+T AD+ A I I+ E P Sbjct: 6 LTLVAVGAAKSAGTEIMEVYGAPDIGLAYKEDDSPLTRADKAAHHCILEILQETGLPVLS 65 Query: 67 IYGEEFG-TKNLDAEWVWVIDPIDGTKSFITGRPIFGTLIALLHRGRPVLGVIDQPIVRD 125 GEE +W W++DP+DGTK F+ F IAL+H GRPVLGV+ P++ Sbjct: 66 EEGEEVPYAVRSQWDWFWMVDPLDGTKEFVKRNGEFTVNIALIHEGRPVLGVVYAPVMGW 125 Query: 126 RWLGVE 131 + G E Sbjct: 126 MYWGSE 131 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: 178 Number of extensions: 7 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: 253 Length adjustment: 24 Effective length of query: 236 Effective length of database: 229 Effective search space: 54044 Effective search space used: 54044 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