Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_012506069.1 PAES_RS07580 shikimate kinase
Query= metacyc::MONOMER-21144 (185 letters) >NCBI__GCF_000020625.1:WP_012506069.1 Length = 197 Score = 57.8 bits (138), Expect = 1e-13 Identities = 35/116 (30%), Positives = 59/116 (50%), Gaps = 1/116 (0%) Query: 21 VSIIGMAGAGKTTVGRELALQLGWAHVDTDNLIEATYGTRLQAVADSMDKESFLDVEAGV 80 + + G +G+GK+T+G LA LG+ VD D IE G + + + F D+E V Sbjct: 7 IYLTGFSGSGKSTIGPLLANSLGYDFVDLDQQIEHLAGKTINRIFTEEGEAHFRDLELMV 66 Query: 81 IRRI-GARRTVLSTGGSVVYRHEAMAHLAALGPLVYLDVSLPLILKRIAMNPDRGL 135 ++ G V+S GG ++ + + + G LVYL + ++ KR++ DR L Sbjct: 67 LQNYSGKSELVVSLGGGLLQNDRCFSLIISTGTLVYLHSNPLVLAKRLSHKSDRPL 122 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: 84 Number of extensions: 3 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: 197 Length adjustment: 20 Effective length of query: 165 Effective length of database: 177 Effective search space: 29205 Effective search space used: 29205 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: 44 (21.6 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