Align shikimate kinase (EC 2.7.1.71) (characterized)
to candidate Synpcc7942_0894 Synpcc7942_0894 shikimate kinase
Query= BRENDA::A0A0M3KL09 (179 letters) >FitnessBrowser__SynE:Synpcc7942_0894 Length = 190 Score = 120 bits (302), Expect = 1e-32 Identities = 72/167 (43%), Positives = 105/167 (62%), Gaps = 3/167 (1%) Query: 10 NIYLVGPMGAGKTTVGRHLAELLGREFLDSDHEIERKTGATIPWIFEKEGEVGFRTRETV 69 +++LVG MG+GKTT+G+ LAE LG ++D+D IE TG +IP IF +GE GFR ET Sbjct: 11 DLFLVGLMGSGKTTIGKLLAESLGYTYVDTDSLIENVTGRSIPEIFASDGEAGFRQIETQ 70 Query: 70 VLNELTSRKALVLATGGGAITQAPNREFLKQRGIVVYLYTPVELQLQRTYRDKNRPLLQV 129 VL E+ S + LV+ATGGG + + N +L Q+G+V++L P+ L+R D+NRPLLQ Sbjct: 71 VLEEVASYRRLVVATGGGIVIRPENWSYL-QQGLVIWLDVPIPELLRRLEGDQNRPLLQT 129 Query: 130 ENPEQKLRDLLKIRDPLYREV-AHYTIETNQGAARDLAQKILQLILS 175 E P L+ L + R Y + IE ++ + Q+IL++I S Sbjct: 130 EAPATTLQALWEQRRDRYAQADLRIAIEASEDPEVTM-QRILEVIPS 175 Lambda K H 0.318 0.137 0.387 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: 80 Number of extensions: 3 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: 179 Length of database: 190 Length adjustment: 19 Effective length of query: 160 Effective length of database: 171 Effective search space: 27360 Effective search space used: 27360 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