Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate 8500213 DvMF_0971 shikimate kinase (RefSeq)
Query= curated2:Q31PU5 (190 letters) >FitnessBrowser__Miya:8500213 Length = 185 Score = 84.7 bits (208), Expect = 9e-22 Identities = 51/147 (34%), Positives = 88/147 (59%), Gaps = 5/147 (3%) Query: 14 LVGLMGSGKTTIGKLLAESLGYTYVDTDSLIENVTGRSIPEIFASDGEAGFRQIETQVLE 73 ++G+ G+GKTT+G+ LA LG+ +VDTD+LIE G + + S + F +E V+ Sbjct: 23 IIGMAGAGKTTVGRELALQLGWAHVDTDNLIEATYGTRLQAVADSMDKESFLDVEAGVIR 82 Query: 74 EVASYRRLVVATGGGIVIRPENWSYLQQ-GLVIWLDVPIPELLRRLEGDQNRPLLQTEAP 132 + + RR V++TGG +V R E ++L G +++LDV +P +L+R+ + +R L AP Sbjct: 83 RIGA-RRTVLSTGGSVVYRHEAMAHLAALGPLVYLDVSLPLILKRIAMNPDRGL--AIAP 139 Query: 133 ATTLQALWEQRRDRYAQ-ADLRIAIEA 158 T++ L+ +R Y + A +A +A Sbjct: 140 GQTIEDLYNERIALYRRYATFTVAADA 166 Lambda K H 0.316 0.134 0.376 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: 89 Number of extensions: 2 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: 190 Length of database: 185 Length adjustment: 20 Effective length of query: 170 Effective length of database: 165 Effective search space: 28050 Effective search space used: 28050 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 (21.6 bits) S2: 44 (21.6 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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