Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate RR42_RS19010 RR42_RS19010 shikimate kinase
Query= metacyc::MONOMER-21144 (185 letters) >FitnessBrowser__Cup4G11:RR42_RS19010 Length = 204 Score = 85.1 bits (209), Expect = 7e-22 Identities = 59/160 (36%), Positives = 81/160 (50%), Gaps = 3/160 (1%) Query: 24 IGMAGAGKTTVGRELALQLGWAHVDTDNLIEATYGTRLQAVADSMDKESFLDVEAGVIRR 83 +G+ GAGKTTVGR +A +L + D+D+ +EA G R+ + + + F D EA I Sbjct: 11 VGLMGAGKTTVGRTVARRLNYPFFDSDHELEARCGVRIPIIFEHEGEAGFRDREAQAIDE 70 Query: 84 IGARR-TVLSTGGSVVYRHEAMAHLAALGPLVYLDVSLPLILKRIAMNPDRGLAIA--PG 140 + RR VL+TGG V R E AHL A G +VYL S + R + +R L P Sbjct: 71 LTQRRGIVLATGGGAVLRPENRAHLKARGTVVYLRASPHDLWLRTRHDRNRPLLQTEDPK 130 Query: 141 QTIEDLYNERIALYRRYATFTVAADALSPGGCATRIVAWL 180 +E LY ER LYR A F + S A ++ L Sbjct: 131 GRLETLYGERDPLYREVADFIIETGKPSVAQLANMVLMQL 170 Lambda K H 0.321 0.137 0.403 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: 114 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: 185 Length of database: 204 Length adjustment: 20 Effective length of query: 165 Effective length of database: 184 Effective search space: 30360 Effective search space used: 30360 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 (21.8 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