Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_013009413.1 DACET_RS00300 shikimate kinase
Query= metacyc::MONOMER-21144 (185 letters) >NCBI__GCF_000025725.1:WP_013009413.1 Length = 171 Score = 55.5 bits (132), Expect = 5e-13 Identities = 41/145 (28%), Positives = 69/145 (47%), Gaps = 5/145 (3%) Query: 21 VSIIGMAGAGKTTVGRELALQLGWAHVDTDNLIEATYGTRLQAVADSMDKESFLDVEAGV 80 + +IG G GK++VGR LA LG ++VDTD ++ G + + + +E F +E V Sbjct: 4 IYLIGFMGTGKSSVGRLLAEDLGASYVDTDQMVIEKTGREITNIFEEDSEEDFRRLETEV 63 Query: 81 IRR-IGARRTVLSTGGSVVYRHEAMAHLAALGPLVYLDVSLPLILKRIAMNPDRGLAIAP 139 + + V+STGG +V + + G +V L IL+RI+ + P Sbjct: 64 LSEVVDKENLVVSTGGGIVVTMGNLEAMRQTGFVVTLIADANTILERISSDE----TCRP 119 Query: 140 GQTIEDLYNERIALYRRYATFTVAA 164 +E+ + E L A+F + A Sbjct: 120 LLEVEEPFEEIKRLLFERASFYINA 144 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: 69 Number of extensions: 2 Number of successful extensions: 1 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: 171 Length adjustment: 19 Effective length of query: 166 Effective length of database: 152 Effective search space: 25232 Effective search space used: 25232 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