Align shikimate kinase (EC 2.7.1.71) (characterized)
to candidate PP_5079 PP_5079 Shikimate kinase
Query= BRENDA::A0A0M3KL09 (179 letters) >FitnessBrowser__Putida:PP_5079 Length = 172 Score = 172 bits (437), Expect = 2e-48 Identities = 90/167 (53%), Positives = 117/167 (70%), Gaps = 4/167 (2%) Query: 10 NIYLVGPMGAGKTTVGRHLAELLGREFLDSDHEIERKTGATIPWIFEKEGEVGFRTRETV 69 N+ LVGPMGAGK+T+GR LA+ L F DSD EIE + GA IPWIF+KEGE GFR RE Sbjct: 3 NLILVGPMGAGKSTIGRLLAKELRLLFKDSDKEIELRCGANIPWIFDKEGEPGFRDREQA 62 Query: 70 VLNELTSRKALVLATGGGAITQAPNREFLKQRGIVVYLYTPVELQLQRTYRDKNRPLLQV 129 ++ EL + +VLATGGGA+ + NR+ L Q G V+YL+ VE Q+ RT RD+NRPLL+ Sbjct: 63 MIAELCALDGVVLATGGGAVMREANRQALHQGGRVIYLHASVEQQVGRTARDRNRPLLRT 122 Query: 130 ENPEQKLRDLLKIRDPLYREVAHYTIETNQGAAR----DLAQKILQL 172 NPE LR LL+ RDPLYRE+A +ET++ R D+ +++ QL Sbjct: 123 ANPEATLRTLLETRDPLYREIADLVVETDERPPRMVVIDILERLQQL 169 Lambda K H 0.318 0.137 0.387 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: 103 Number of extensions: 1 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: 179 Length of database: 172 Length adjustment: 19 Effective length of query: 160 Effective length of database: 153 Effective search space: 24480 Effective search space used: 24480 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 (21.7 bits) S2: 44 (21.6 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