Align shikimate kinase (EC 2.7.1.71) (characterized)
to candidate WP_013009413.1 DACET_RS00300 shikimate kinase
Query= BRENDA::A0A0M3KL09 (179 letters) >NCBI__GCF_000025725.1:WP_013009413.1 Length = 171 Score = 116 bits (291), Expect = 2e-31 Identities = 68/165 (41%), Positives = 100/165 (60%), Gaps = 2/165 (1%) Query: 8 LPNIYLVGPMGAGKTTVGRHLAELLGREFLDSDHEIERKTGATIPWIFEKEGEVGFRTRE 67 + NIYL+G MG GK++VGR LAE LG ++D+D + KTG I IFE++ E FR E Sbjct: 1 MKNIYLIGFMGTGKSSVGRLLAEDLGASYVDTDQMVIEKTGREITNIFEEDSEEDFRRLE 60 Query: 68 TVVLNELTSRKALVLATGGGAITQAPNREFLKQRGIVVYLYTPVELQLQRTYRDKN-RPL 126 T VL+E+ ++ LV++TGGG + N E ++Q G VV L L+R D+ RPL Sbjct: 61 TEVLSEVVDKENLVVSTGGGIVVTMGNLEAMRQTGFVVTLIADANTILERISSDETCRPL 120 Query: 127 LQVENPEQKLRDLLKIRDPLYREVAHYTIETNQGAARDLAQKILQ 171 L+VE P ++++ LL R Y AH+ ++T+ R+ A IL+ Sbjct: 121 LEVEEPFEEIKRLLFERASFYIN-AHHIVDTSDITPREAADCILE 164 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: 71 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: 179 Length of database: 171 Length adjustment: 19 Effective length of query: 160 Effective length of database: 152 Effective search space: 24320 Effective search space used: 24320 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: 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