Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate WP_051957978.1 Q366_RS10275 shikimate kinase
Query= curated2:P72796 (189 letters) >NCBI__GCF_000745975.1:WP_051957978.1 Length = 170 Score = 84.7 bits (208), Expect = 8e-22 Identities = 59/143 (41%), Positives = 75/143 (52%), Gaps = 8/143 (5%) Query: 11 QGVNLFLIGMMGSGKSTVGPLLAEQLGYRFFDADVLIERVAGKAIADIFAEDGEDTFRDL 70 Q +++ LIGM GKSTVG LLA+QLGY F D D+LI+ +A I + G F D+ Sbjct: 4 QNLSVALIGMPAVGKSTVGVLLAKQLGYDFLDTDILIQTKENMTLAQIIGKKGVQGFLDI 63 Query: 71 ETEVLGHL--AAQTRSVIATGGGVVLRRQNWSYLHH-GLVIWLDGSLELLLARLQGDEAR 127 E GHL R VI+TGG V+ R Q +L VI+L L LL RL EAR Sbjct: 64 EA---GHLLGLGGKRRVISTGGSVIYREQAMRHLKKIATVIYLHADLSTLLTRLSDLEAR 120 Query: 128 PLLQVENLEERLGNLLAQRQPLY 150 + N + L +R PLY Sbjct: 121 GVAIDPN--SNIDALYKERTPLY 141 Lambda K H 0.320 0.139 0.399 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: 83 Number of extensions: 3 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: 189 Length of database: 170 Length adjustment: 19 Effective length of query: 170 Effective length of database: 151 Effective search space: 25670 Effective search space used: 25670 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 (21.8 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