Align Shikimate kinase 2; SK 2; Shikimate kinase II; SKII; EC 2.7.1.71 (characterized)
to candidate BWI76_RS06185 BWI76_RS06185 shikimate kinase II
Query= SwissProt::P0A6E1 (174 letters) >FitnessBrowser__Koxy:BWI76_RS06185 Length = 175 Score = 195 bits (496), Expect = 3e-55 Identities = 98/168 (58%), Positives = 125/168 (74%) Query: 1 MTQPLFLIGPRGCGKTTVGMALADSLNRRFVDTDQWLQSQLNMTVAEIVEREEWAGFRAR 60 MTQ +FL+GPRGCGKTTVG ALA + +F DTD LQ TVA IV++E W FRA Sbjct: 1 MTQLIFLVGPRGCGKTTVGHALAKVRSFKFADTDHELQEHEQRTVAAIVQQEGWERFRAL 60 Query: 61 ETAALEAVTAPSTVIATGGGIILTEFNRHFMQNNGIVVYLCAPVSVLVNRLQAAPEEDLR 120 ET ALE V P+T+IATGGGIIL+E+NR FM+ NG+V+YL A VS L++RL+A P+ + R Sbjct: 61 ETQALERVAQPATIIATGGGIILSEYNRQFMRENGVVIYLEASVSALIDRLEAYPKAEQR 120 Query: 121 PTLTGKPLSEEVQEVLEERDALYREVAHIIIDATNEPSQVISEIRSAL 168 PTLTGKP+ EEV EVL +R+ALYR AH II+AT P +V+ +I + + Sbjct: 121 PTLTGKPIREEVGEVLAQREALYRAAAHHIINATASPDEVVEQIMTTV 168 Lambda K H 0.318 0.133 0.379 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: 101 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: 174 Length of database: 175 Length adjustment: 19 Effective length of query: 155 Effective length of database: 156 Effective search space: 24180 Effective search space used: 24180 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