Align shikimate kinase (EC 2.7.1.71) (characterized)
to candidate WP_012972712.1 AZL_RS00465 shikimate kinase
Query= reanno::Caulo:CCNA_03103 (200 letters) >NCBI__GCF_000010725.1:WP_012972712.1 Length = 228 Score = 188 bits (477), Expect = 7e-53 Identities = 97/174 (55%), Positives = 126/174 (72%), Gaps = 1/174 (0%) Query: 23 SDDLAPLRAKTIVLVGLMGVGKSSVGRRLANVLGLPFRDADNEVEAAAGRSISEIFAELG 82 ++D PL +T+VLVGLMG GKS++GRRLA L +PFRDAD E+EAAAG SI+EIFA G Sbjct: 11 AEDAKPLLPRTVVLVGLMGAGKSAIGRRLATRLHMPFRDADAEIEAAAGCSIAEIFARDG 70 Query: 83 EPAFRDGERRVIARLL-DEPPHVLATGGGAFVNAETRALINEKAVSVWLKADVELLARRV 141 EP FR ERR+I RLL DEP H+LATGGGAF++ ETRA I + VSVWL A++++L R Sbjct: 71 EPVFRSVERRMITRLLKDEPVHILATGGGAFMDPETRAAIRQHGVSVWLHAELDVLVSRT 130 Query: 142 SRKDNRPLVRGKDPVKVLTELAEARYPAYAEAQVHVETGDTPHMVAVEAILTAL 195 +R+ +RP++ DP +L L E RYP YAEA + V + + P V VE ++ AL Sbjct: 131 ARRTHRPILNQGDPRAILERLMEQRYPTYAEADLTVVSDERPPDVTVELVIDAL 184 Lambda K H 0.316 0.132 0.369 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: 165 Number of extensions: 6 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: 200 Length of database: 228 Length adjustment: 22 Effective length of query: 178 Effective length of database: 206 Effective search space: 36668 Effective search space used: 36668 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: 45 (21.9 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