Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_012567832.1 RC1_RS12840 shikimate kinase
Query= metacyc::MONOMER-21144 (185 letters) >NCBI__GCF_000016185.1:WP_012567832.1 Length = 198 Score = 73.6 bits (179), Expect = 2e-18 Identities = 58/176 (32%), Positives = 85/176 (48%), Gaps = 5/176 (2%) Query: 8 LALDPARIAPDGCVSIIGMAGAGKTTVGRELALQLGWAHVDTDNLIEATYGTRLQAVADS 67 +A PA + P V ++G+ GAGKT++G+ LA +L VD D+ IE+ G +Q + D Sbjct: 1 MAQHPAFVPPRTLV-LVGLMGAGKTSIGKRLAAKLHLPFVDADHEIESAAGCTIQEIFDR 59 Query: 68 MDKESFLDVEAGVIRR-IGARRTVLSTGGSVVYRHEAMAHLAALGPLVYLDVSLPLILKR 126 + F D E VI R + + VLSTGG E A + G V+L L L++ R Sbjct: 60 FGEAQFRDGERRVIARLLEGQVRVLSTGGGAFMHPETRALIRERGLSVWLRAPLDLLVAR 119 Query: 127 IAMNPDRGLAIA--PGQTIEDLYNERIALYRRYATFTVAADALSPGGCATRIVAWL 180 +R L P + L +R +Y A TV +D P A R++A L Sbjct: 120 TGRRDNRPLLKQGNPRDILAALMAQRYPVYAE-ADITVDSDERPPEETAERVLAAL 174 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: 89 Number of extensions: 5 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: 198 Length adjustment: 20 Effective length of query: 165 Effective length of database: 178 Effective search space: 29370 Effective search space used: 29370 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