Align shikimate kinase (EC 2.7.1.71) (characterized)
to candidate PfGW456L13_276 Shikimate kinase I (EC 2.7.1.71)
Query= BRENDA::P0A6D7 (173 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_276 Length = 163 Score = 162 bits (410), Expect = 3e-45 Identities = 82/159 (51%), Positives = 111/159 (69%), Gaps = 1/159 (0%) Query: 13 MGAGKSTIGRQLAQQLNMEFYDSDQEIEKRTGADVGWVFDLEGEEGFRDREEKVINELTE 72 MGAGKSTIGR LA++L + F DSD+EIE RTGA++ W+FD EGE GFRDRE+ +I EL + Sbjct: 1 MGAGKSTIGRLLAKELRLPFKDSDKEIELRTGANIPWIFDKEGEPGFRDREQAMIAELCD 60 Query: 73 KQGIVLATGGGSVKSRETRNRLSARGVVVYLETTIEKQLARTQRDKKRPLLHVETPPREV 132 G+VLATGGG+V R L A G VVYL ++E+Q+ RT RD+ RPLL P + + Sbjct: 61 CDGVVLATGGGAVMREANRRALHAGGRVVYLHASVEQQVGRTSRDRNRPLLRTADPAKTL 120 Query: 133 LEALANERNPLYEEIADVTIRTDDQSAKVVANQIIHMLE 171 + LA R+PLY EIAD+ + TD++ ++V I+ L+ Sbjct: 121 RDLLA-IRDPLYREIADLVVETDERPPRMVVLDILERLQ 158 Lambda K H 0.313 0.132 0.359 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: 115 Number of extensions: 4 Number of successful extensions: 2 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: 173 Length of database: 163 Length adjustment: 18 Effective length of query: 155 Effective length of database: 145 Effective search space: 22475 Effective search space used: 22475 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 43 (21.2 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