Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate WP_028311761.1 H566_RS0112835 hypothetical protein
Query= curated2:Q2RMW1 (188 letters) >NCBI__GCF_000482785.1:WP_028311761.1 Length = 306 Score = 94.7 bits (234), Expect = 1e-24 Identities = 64/168 (38%), Positives = 90/168 (53%), Gaps = 6/168 (3%) Query: 15 LVLVGLMGAGKTCIGRRLAQMAGVPFVDADVEIERAAKRTIAEIFATYGESEFRALERRV 74 + LVGL GAGK+ +GR LA+ G PF++ EIER A T +EI A YG + +R ERR Sbjct: 132 IALVGLRGAGKSTLGRLLAEHLGWPFIELSREIERTAGCTPSEIHALYGANAYRRYERRA 191 Query: 75 MARLL-AGRTCVLATGGGAFMAEDTRALIRLHGLSLWLRADLDLLVART-AGRTHRPLLN 132 + ++ V+AT GG T + H +LWLRA + ++R A RP+ N Sbjct: 192 LDEVIEIYPEAVIATPGGLVSEPATFNALLAHCYTLWLRASPEEHMSRVLAQGDTRPMSN 251 Query: 133 NGDAREKLAELMAKRHPVYAEADIVFD----ALDESQDASALRVRSCL 176 N A E L ++A R YA+AD+V D AL E+ D + + L Sbjct: 252 NAQAMEDLRLILAGREAFYAKADLVIDTGGRALGEAFDGMVKALAAAL 299 Lambda K H 0.323 0.136 0.386 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: 135 Number of extensions: 9 Number of successful extensions: 3 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: 188 Length of database: 306 Length adjustment: 23 Effective length of query: 165 Effective length of database: 283 Effective search space: 46695 Effective search space used: 46695 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 46 (22.3 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