Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate WP_028989244.1 G579_RS0104615 gluconate kinase
Query= curated2:Q67N09 (174 letters) >NCBI__GCF_000423825.1:WP_028989244.1 Length = 161 Score = 48.1 bits (113), Expect = 7e-11 Identities = 49/145 (33%), Positives = 72/145 (49%), Gaps = 15/145 (10%) Query: 1 MNIVLVGLMGSGKTAVGRLLAERLGRPFVDTDRL-VEADAGRTVADI-FAAEGEEGFRRR 58 M I+L+G+ GSGK+ VGRLLA+ LG + D D A+ + I E + + Sbjct: 1 MVIILMGVAGSGKSTVGRLLADTLGWRYCDADDFHPRANVEKMARGIPLNDEDRQPWLAA 60 Query: 59 EAEVVARA-AAGDNQVIATGGGAVLRTENREAL---RRTGFVIWLDAEPETLYDRARGQG 114 +VAR+ AAG++ V+A + L+ RE L R +++L A+PE + R + Sbjct: 61 LQRLVARSVAAGEDMVLAC---SALKHSYRERLRVDRAAVRLVYLKADPELI----RRRL 113 Query: 115 LHRRPLLSGPDPLGRLRALAAARRP 139 RR GPD L LAA P Sbjct: 114 AQRRGHFLGPDLLA--SQLAALEEP 136 Lambda K H 0.321 0.138 0.395 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: 3 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: 174 Length of database: 161 Length adjustment: 18 Effective length of query: 156 Effective length of database: 143 Effective search space: 22308 Effective search space used: 22308 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 (21.9 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