Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_084076347.1 BUB04_RS09250 shikimate kinase
Query= metacyc::MONOMER-21144 (185 letters) >NCBI__GCF_900129305.1:WP_084076347.1 Length = 213 Score = 72.4 bits (176), Expect = 5e-18 Identities = 48/155 (30%), Positives = 80/155 (51%), Gaps = 7/155 (4%) Query: 21 VSIIGMAGAGKTTVGRELALQLGWAHVDTDNLIEATYGTRLQAVADSMDKESFLDVEAGV 80 +++IG G GK+TVG LA +LGW VD D ++ +GT + E+F + E+ + Sbjct: 34 IALIGYRGTGKSTVGDLLAARLGWDFVDMDRVLTQRFGTSIAHFVAQNGWEAFREAESAL 93 Query: 81 IRRIGARR-TVLSTGGSVVYRHEAMAHLAALGPLVYLDVSLPLILKRIAMNPDRGL--AI 137 + +I V++TGG +V + L +V+LD LP+IL+R+A++P Sbjct: 94 LGQISREEGLVVATGGGIVEKERNGKILRDCFHVVWLDCDLPVILQRLALDPKTATQRPS 153 Query: 138 APGQTIED----LYNERIALYRRYATFTVAADALS 168 G+ ++D + R LYR A V + +LS Sbjct: 154 LTGRHVQDETSQILERRRPLYRVIAHVAVDSGSLS 188 Lambda K H 0.321 0.137 0.403 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: 103 Number of extensions: 4 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: 185 Length of database: 213 Length adjustment: 20 Effective length of query: 165 Effective length of database: 193 Effective search space: 31845 Effective search space used: 31845 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: 45 (21.9 bits)
This GapMind analysis is from Apr 10 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