Align Shikimate kinase; Short=SK; EC 2.7.1.71 (characterized, see rationale)
to candidate 8500662 DvMF_1410 Shikimate kinase (RefSeq)
Query= uniprot:AROK_DESVH (175 letters) >FitnessBrowser__Miya:8500662 Length = 177 Score = 164 bits (416), Expect = 6e-46 Identities = 84/166 (50%), Positives = 112/166 (67%) Query: 7 RVFLIGGRASGKSTVGRALAARLGWDFADTDAMVTRRAGCDIATLVAERGWDAFRDMESD 66 RV+L+G RASGK+TVG+ALAAR GW F DTDA V AG + +V GW+ FR E++ Sbjct: 10 RVYLVGPRASGKTTVGKALAARAGWHFEDTDATVAALAGMTVEQIVEREGWEGFRRRETE 69 Query: 67 ALRDAAARERVVVATGGGMVLRAENRALLREAGVTVFLSLPVEVVAARLARNPEHGQRPS 126 ALR + +VVATGGGMVL ENR +LR+ G+ +L V+++A RLAR+P QRPS Sbjct: 70 ALRATLGHDGLVVATGGGMVLAEENRRMLRDGGLVAYLCGSVDLLAGRLARDPLAAQRPS 129 Query: 127 LTGKAVADEVADVMRERAPLYAEAARHVVRGDAPVACIVEDITALL 172 LTG+ +ADEVA+V+ R PLY E A V+ + +VE + +LL Sbjct: 130 LTGRPIADEVAEVLAAREPLYRECAHVVLDAGDDLRVLVERLASLL 175 Lambda K H 0.322 0.134 0.389 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: 111 Number of extensions: 1 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: 175 Length of database: 177 Length adjustment: 19 Effective length of query: 156 Effective length of database: 158 Effective search space: 24648 Effective search space used: 24648 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 (22.0 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