Align Shikimate kinase 2; SK 2; EC 2.7.1.71 (uncharacterized)
to candidate BWI76_RS27615 BWI76_RS27615 putative Shikimate kinase
Query= curated2:Q7N7B0 (174 letters) >FitnessBrowser__Koxy:BWI76_RS27615 Length = 201 Score = 61.6 bits (148), Expect = 8e-15 Identities = 51/175 (29%), Positives = 83/175 (47%), Gaps = 19/175 (10%) Query: 5 LFIVGARGAGKTTVGKLLANELSYTFIDTDHHIQQTSNMTIADIVNQQGWQQF----RQL 60 LF++G G GK+TVG LLA ++Y FID D + + I + + G++++ L Sbjct: 4 LFLIGPGGVGKSTVGALLAQAMNYRFIDLDSEFCE-QLLNIRQYIQRNGYERYVRDNAAL 62 Query: 61 ESQALQQVTQINRVISTGGGII-------LSAENRQYMRQNGTVIYLQASASI-LAERLM 112 S+ L + RV+ G + + A NRQ +RQ+G I L S I +A R++ Sbjct: 63 CSRLLAENPHEKRVVVLSSGFLATDVCPEIVAGNRQLVRQSGYSILLLPSEDIDIATRIV 122 Query: 113 QQPESTQRPSLTGKSIVEEMEEV-LAARENLYCECANHIINAHLSPEKITTYVKE 166 R + G +V E EE+ R YC + + + PE++ V+E Sbjct: 123 -----VARQLMRGFGLVREKEEMKFRQRFREYCALDDCRVVSSEEPERVAELVRE 172 Lambda K H 0.317 0.130 0.355 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: 87 Number of extensions: 5 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: 174 Length of database: 201 Length adjustment: 20 Effective length of query: 154 Effective length of database: 181 Effective search space: 27874 Effective search space used: 27874 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 (21.7 bits) S2: 44 (21.6 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