Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate 3608204 Dshi_1609 Shikimate kinase (RefSeq)
Query= metacyc::MONOMER-21144 (185 letters) >FitnessBrowser__Dino:3608204 Length = 185 Score = 83.6 bits (205), Expect = 2e-21 Identities = 54/163 (33%), Positives = 83/163 (50%), Gaps = 3/163 (1%) Query: 21 VSIIGMAGAGKTTVGRELALQLGWAHVDTDNLIEATYGTRLQAVADSMDKESFLDVEAGV 80 V ++GM GAGKT VG +A QLG +D+D+ IE ++ + + + F D E V Sbjct: 13 VVLVGMMGAGKTAVGGAVAAQLGVPFIDSDHEIEQAANAKIAEIFERDGEAFFRDRETEV 72 Query: 81 IRR-IGARRTVLSTGGSVVYRHEAMAHLAALGPLVYLDVSLPLILKRIAMNPDRGLAIA- 138 + R +G +LSTGG A +A G V+LD L L+ R+ R L + Sbjct: 73 LARLLGGVPAILSTGGGAFLAERNRALIAEKGVSVWLDAELELLWSRVRHKSTRPLLLTD 132 Query: 139 -PGQTIEDLYNERIALYRRYATFTVAADALSPGGCATRIVAWL 180 P T+ ++Y +R+ +Y + A AA LS A+R++A L Sbjct: 133 NPKATLAEIYAQRVPVYAKAALHVKAAPELSIDQMASRVIAAL 175 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: 79 Number of extensions: 5 Number of successful extensions: 3 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: 185 Length adjustment: 19 Effective length of query: 166 Effective length of database: 166 Effective search space: 27556 Effective search space used: 27556 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