Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_077244462.1 B1A74_RS09290 hypothetical protein
Query= curated2:Q9RAM6 (319 letters) >NCBI__GCF_001995255.1:WP_077244462.1 Length = 262 Score = 46.6 bits (109), Expect = 7e-10 Identities = 31/75 (41%), Positives = 39/75 (52%), Gaps = 9/75 (12%) Query: 220 IAIAVNDWCVNADCTLDAVRVRAFLDAYHAIRPLTGEEHAAWPGMLRVAAMRFWLSRLND 279 IA+AV+ VN LD R RA L YH RPL+ E A P +LR+AA+ WL R+ Sbjct: 176 IALAVS---VNEAGELDRERYRALLGGYHQERPLSAIERGAAPTLLRMAALDDWLERI-- 230 Query: 280 LYFPQAGELTHAKDP 294 +AG DP Sbjct: 231 ----EAGRAPAGPDP 241 Lambda K H 0.324 0.137 0.430 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: 226 Number of extensions: 16 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: 319 Length of database: 262 Length adjustment: 26 Effective length of query: 293 Effective length of database: 236 Effective search space: 69148 Effective search space used: 69148 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 48 (23.1 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