Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate 199481 SO0286 shikimate kinase (NCBI ptt file)
Query= metacyc::MONOMER-21144 (185 letters) >FitnessBrowser__MR1:199481 Length = 171 Score = 68.2 bits (165), Expect = 8e-17 Identities = 52/160 (32%), Positives = 76/160 (47%), Gaps = 3/160 (1%) Query: 21 VSIIGMAGAGKTTVGRELALQLGWAHVDTDNLIEATYGTRLQAVADSMDKESFLDVEAGV 80 + ++G GAGK+T+GR LA L D+D IE G + V D +E F EA V Sbjct: 7 IFLVGPMGAGKSTIGRHLAQMLHLEFHDSDQEIEQRTGADIAWVFDVEGEEGFRRREAQV 66 Query: 81 IRRIGARR-TVLSTGGSVVYRHEAMAHLAALGPLVYLDVSLPLILKRIAMNPDRGLAIA- 138 I + ++ VL+TGG V + HL+A G +VYL+ ++ + R + R L Sbjct: 67 IADLSEKQGIVLATGGGSVQSKDIRNHLSARGIVVYLETTIDKQVARTQRDKRRPLLQVD 126 Query: 139 -PGQTIEDLYNERIALYRRYATFTVAADALSPGGCATRIV 177 P + +E L R LY A V D S A +I+ Sbjct: 127 DPREVLESLAEIRNPLYEEIADVVVKTDDQSAKVVANQII 166 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: 78 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: 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 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