Align Shikimate kinase; Short=SK; EC 2.7.1.71 (characterized, see rationale)
to candidate NP_662291.1 CT1405 shikimate kinase
Query= uniprot:L0FT15_ECHVK (176 letters) >NCBI__GCF_000006985.1:NP_662291.1 Length = 191 Score = 99.4 bits (246), Expect = 3e-26 Identities = 69/175 (39%), Positives = 95/175 (54%), Gaps = 8/175 (4%) Query: 1 MNNSAKIVLVGMPGSGKSTLGKTLAGQLGFDFYDLDEEIVKEEGRSIPAIFMENGEGYFR 60 M + + I L G GSGKST+G LA LGF+F DLD EI G+SI IF E+GE FR Sbjct: 1 MKHHSLIFLTGFSGSGKSTIGPLLANSLGFEFIDLDREIELTAGKSINRIFAEDGEAAFR 60 Query: 61 RTETRVIEKLLQIDSAFVLSTGGGAPCFNDNMTLINRHGISVFLNVSIEQLLLRLTKNEA 120 E R +EK+ Q V+S GGG + LI HG ++L S E L LRL +++ Sbjct: 61 SLELRTLEKIGQ-QERMVVSLGGGVLENDRCFELIRSHGTLIYLKSSPEILTLRL-QHKT 118 Query: 121 DKRPMFQG-----LDTGEIRLKLQDLLADREVYYEQSKIMLSGDDISTEHLISEL 170 D RP+ +G L EI+ ++ +LL RE Y ++ ++L D + EL Sbjct: 119 D-RPLLKGPDGRKLTREEIQQRIAELLKKREPRYLKADLVLFTDSKKIGASVEEL 172 Lambda K H 0.319 0.139 0.385 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: 90 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: 176 Length of database: 191 Length adjustment: 19 Effective length of query: 157 Effective length of database: 172 Effective search space: 27004 Effective search space used: 27004 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 (21.7 bits) S2: 44 (21.6 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