Align Shikimate kinase 2; SK 2; Shikimate kinase II; SKII; EC 2.7.1.71 (characterized)
to candidate WP_035240990.1 Q366_RS16545 shikimate kinase AroL
Query= SwissProt::P0A6E1 (174 letters) >NCBI__GCF_000745975.1:WP_035240990.1 Length = 177 Score = 122 bits (306), Expect = 3e-33 Identities = 70/152 (46%), Positives = 97/152 (63%), Gaps = 2/152 (1%) Query: 3 QPLFLIGPRGCGKTTVGMALADSLNRRFVDTDQWLQSQLNMTVAEIVEREEWAGFRARET 62 +P+FLIG R GKT+ G LA+ LN+ F+DTD L+S ++A++V R W FR +ET Sbjct: 2 RPIFLIGYRCTGKTSTGKYLAELLNKNFIDTDLVLESTFGTSIAQMVARHGWPYFRTKET 61 Query: 63 AALEAVTAPST-VIATGGGIILTEFNRHFMQNNGIVVYLCAPVSVLVNRLQAAPEE-DLR 120 L + S VIATGGGIIL E NR F++ NG+VVYL AP SVL +R++ R Sbjct: 62 ETLTNLDLESAPVIATGGGIILAEENRAFLKENGVVVYLYAPASVLTDRIRKDENNTGRR 121 Query: 121 PTLTGKPLSEEVQEVLEERDALYREVAHIIID 152 P LT L+ E +++LE R+ LY+ +A I I+ Sbjct: 122 PDLTRDSLALETKKMLEIRNPLYQALAEISIN 153 Lambda K H 0.318 0.133 0.379 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: 6 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: 177 Length adjustment: 19 Effective length of query: 155 Effective length of database: 158 Effective search space: 24490 Effective search space used: 24490 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 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