Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate WP_078430849.1 BK574_RS11810 shikimate kinase
Query= curated2:B7HPD4 (165 letters) >NCBI__GCF_002019605.1:WP_078430849.1 Length = 169 Score = 165 bits (418), Expect = 3e-46 Identities = 76/165 (46%), Positives = 121/165 (73%) Query: 1 MKSIYITGYMGAGKTTIGKALSKELHMDVIDTDQKIEEKQEKEIRDIFAEEGEMAFREYE 60 M+ I++TG+MGAGK+TIGK L+++L+ ++DTD+ IE Q K I IF+E+GE FR YE Sbjct: 1 MRIIFLTGFMGAGKSTIGKVLAEKLNYRLLDTDEWIESIQGKSIPRIFSEDGETGFRSYE 60 Query: 61 SEMLRSLPVENVIITTGGGIIEREENRKWMKENGTVVYLYCDPHVIAERLREDTTRPLFQ 120 + L+ LP E++++TTGGGI+ +EENRK M++ G ++YL+C+ I R + DTTRPL Q Sbjct: 61 TNALKDLPDEDMVVTTGGGIVVKEENRKIMRKKGIIIYLHCEIDEILVRTKGDTTRPLLQ 120 Query: 121 KKDIDAFVMKFELRRAYYEEAHIHIDTTNKSVKQIMDELKEKINE 165 K ID F+ R+A+YE+A +DTT+ S+ +I++++++ +N+ Sbjct: 121 NKSIDQVSDLFKQRKAFYEDADYQVDTTSLSIPEIVEKIEKILND 165 Lambda K H 0.316 0.134 0.373 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: 100 Number of extensions: 1 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: 165 Length of database: 169 Length adjustment: 18 Effective length of query: 147 Effective length of database: 151 Effective search space: 22197 Effective search space used: 22197 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 (21.6 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