Align shikimate kinase (EC 2.7.1.71) (characterized)
to candidate WP_041101536.1 SUTH_RS02930 shikimate kinase
Query= BRENDA::A0A0M3KL09 (179 letters) >NCBI__GCF_000828635.1:WP_041101536.1 Length = 164 Score = 152 bits (384), Expect = 3e-42 Identities = 77/152 (50%), Positives = 101/152 (66%) Query: 18 GAGKTTVGRHLAELLGREFLDSDHEIERKTGATIPWIFEKEGEVGFRTRETVVLNELTSR 77 GAGKTTVGR LA + R F+D+DHEIE +TG IP IF+ EGE GFR RE+ V+ EL Sbjct: 3 GAGKTTVGRQLARRMQRTFVDADHEIETRTGVRIPVIFDIEGEQGFRDRESRVIAELADE 62 Query: 78 KALVLATGGGAITQAPNREFLKQRGIVVYLYTPVELQLQRTYRDKNRPLLQVENPEQKLR 137 L++ATGGG + + NR L+Q G V+YL+ L +RT D NRPLLQV +P QK+ Sbjct: 63 SNLIVATGGGVVLRPQNRAALRQGGTVIYLHVAPRLLFERTRLDPNRPLLQVADPMQKIE 122 Query: 138 DLLKIRDPLYREVAHYTIETNQGAARDLAQKI 169 +L +RDPLYREVA I + G+ L +++ Sbjct: 123 ELFAVRDPLYREVADIVITSTGGSISHLVKQL 154 Lambda K H 0.318 0.137 0.387 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: 115 Number of extensions: 4 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: 179 Length of database: 164 Length adjustment: 18 Effective length of query: 161 Effective length of database: 146 Effective search space: 23506 Effective search space used: 23506 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 43 (21.2 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