Align shikimate kinase (EC 2.7.1.71) (characterized)
to candidate WP_029994987.1 SWIT_RS00040 shikimate kinase
Query= reanno::Caulo:CCNA_03103 (200 letters) >NCBI__GCF_000016765.1:WP_029994987.1 Length = 180 Score = 185 bits (470), Expect = 4e-52 Identities = 96/167 (57%), Positives = 123/167 (73%), Gaps = 1/167 (0%) Query: 32 KTIVLVGLMGVGKSSVGRRLANVLGLPFRDADNEVEAAAGRSISEIFAELGEPAFRDGER 91 + +VL+GLMG GKS++G+RLA + LPF DAD E+E AAG +ISEIFA GE FRDGER Sbjct: 14 RPLVLIGLMGAGKSTIGKRLAARVHLPFVDADQEIERAAGLTISEIFARFGEKEFRDGER 73 Query: 92 RVIARLLDEPPHVLATGGGAFVNAETRALINEKAVSVWLKADVELLARRVSRKD-NRPLV 150 RVIARL+D P V+ATGGGAF+ ETRALI ++A +VWL AD+E+LA RV R++ RPL+ Sbjct: 74 RVIARLIDGRPKVIATGGGAFMQEETRALILDRATAVWLDADIEVLADRVGRREGTRPLL 133 Query: 151 RGKDPVKVLTELAEARYPAYAEAQVHVETGDTPHMVAVEAILTALRQ 197 + +D +VL ELA R P YA A +H+ + PH V+AIL AL Q Sbjct: 134 KDRDAREVLAELAAVRNPVYALAPIHIRSQPLPHDATVDAILKALTQ 180 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: 137 Number of extensions: 8 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: 180 Length adjustment: 20 Effective length of query: 180 Effective length of database: 160 Effective search space: 28800 Effective search space used: 28800 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: 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