Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate WP_011382615.1 AMB_RS00855 helix-turn-helix domain-containing protein
Query= curated2:A5GQN5 (195 letters) >NCBI__GCF_000009985.1:WP_011382615.1 Length = 290 Score = 80.1 bits (196), Expect = 4e-20 Identities = 52/160 (32%), Positives = 84/160 (52%), Gaps = 5/160 (3%) Query: 21 LVGMMGSGKSTVGPLLAKALGYRFLDADAVISQAAGCSIPEIFERDGEEGFRQLERQVLQ 80 L+G+ G+GK+T+G +A F ++I Q AG + EI G++G+R+LE L+ Sbjct: 122 LIGLRGAGKTTLGEAVAGRFAAPFRRITSMIEQMAGMDMTEILLSTGQKGYRKLEYSALE 181 Query: 81 Q-LSQWHSLVVATGGGIVTVPANWGELRQG-VVIWLDVAEEELMRRLQADPGGRPLLAGD 138 L ++V+ GG +V+ P + L Q IW+ + E+ MRR+ RP +AG Sbjct: 182 NTLEAQPTMVLEAGGSLVSEPRTFELLLQSCFTIWVQASPEDHMRRVMGQGDLRP-IAGQ 240 Query: 139 DPAGR--LHGLLEKRQPLYGQADLRVSAQGEGASDISERI 176 A L +LE R+ LYG+AD ++ G +D E + Sbjct: 241 QMAAMEDLKAILEARRHLYGRADAVINTSGRSIADSVEEM 280 Lambda K H 0.316 0.137 0.408 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: 144 Number of extensions: 7 Number of successful extensions: 3 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: 195 Length of database: 290 Length adjustment: 23 Effective length of query: 172 Effective length of database: 267 Effective search space: 45924 Effective search space used: 45924 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: 46 (22.3 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