Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate WP_011841801.1 RSPH17029_RS13355 nucleoside/nucleotide kinase family protein
Query= curated2:A0LUH0 (172 letters) >NCBI__GCF_000015985.1:WP_011841801.1 Length = 198 Score = 39.3 bits (90), Expect = 4e-08 Identities = 44/145 (30%), Positives = 62/145 (42%), Gaps = 16/145 (11%) Query: 4 VVVLIGPPGAGKSTVGRALASRLAV--------SFEDTDDVIEQRA---GKRIAEIFLTD 52 +V L GPPGAGKST+G AL + L F D V+ +R K E F Sbjct: 21 IVALAGPPGAGKSTLGEALVAGLGPGARLVPMDGFHFDDRVLARRGLSNRKGAPETFDIW 80 Query: 53 GEAAFRQLEKA--VVADRLAAHTGVLALGGGAILDDDTRALLADHTVIYLEVEFSEAVRR 110 G A + +A VA + + LA ++ D R L+ + + L+ E RR Sbjct: 81 GFLALMERLRAGGEVAIPVFDRSMELARAAADVVTDQDRILVVEGNYLLLD---EEPWRR 137 Query: 111 VGLNRDRPLLLGNPRAQLRALMDAR 135 + D L L P A+L + AR Sbjct: 138 LRGFFDLTLFLDVPEAELERRLLAR 162 Lambda K H 0.319 0.136 0.377 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: 88 Number of extensions: 4 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: 172 Length of database: 198 Length adjustment: 19 Effective length of query: 153 Effective length of database: 179 Effective search space: 27387 Effective search space used: 27387 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 (21.7 bits) S2: 44 (21.6 bits)
This GapMind analysis is from Apr 16 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