Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate Ac3H11_3086 Regulatory protein of benzoate catabolism
Query= curated2:Q2W095 (195 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3086 Length = 311 Score = 96.3 bits (238), Expect = 5e-25 Identities = 63/182 (34%), Positives = 99/182 (54%), Gaps = 9/182 (4%) Query: 12 LAPLLSG------RIGRTIVLVGLMGAGKSCVGRRLAARLGLDFVDSDAEFEAASGSSIS 65 L LLSG R GR I LVGL GAGKS +G LA L + F++ E E+ +G S+ Sbjct: 123 LHELLSGGSNDTARHGR-IALVGLRGAGKSTLGPLLARALDVPFIELSREIESLAGCSVR 181 Query: 66 DYFARFGEAAFREGERKVIARLLD-GPPVVLATGGGAFVDPTTRERIKAAGTSVWIRADL 124 + +G A+R ER+ + + VV+AT GG DP T + A T+VW+RA Sbjct: 182 EIHDLYGTTAYRRYERRALEETIQIHSEVVIATPGGIVSDPATFNELLAHCTTVWLRAAP 241 Query: 125 ELLLKRTVGR-DHRPLLKQGDPREILGRLMEARYPIYAEADIIVESTDEVPEATVIRVME 183 E + R V + D RP+ + + L R+++ R Y++ADI ++++ + PE ++ + Sbjct: 242 EEHMGRVVAQGDMRPMAASKEAMDDLKRILDGRAAFYSKADITIDTSGQTPEQSLAALHA 301 Query: 184 GL 185 G+ Sbjct: 302 GV 303 Lambda K H 0.321 0.140 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: 144 Number of extensions: 7 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: 195 Length of database: 311 Length adjustment: 24 Effective length of query: 171 Effective length of database: 287 Effective search space: 49077 Effective search space used: 49077 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 (21.8 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Apr 09 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