Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_005459251.1 SACCYDRAFT_RS21075 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase
Query= curated2:Q2RIX1 (296 letters) >NCBI__GCF_000244975.1:WP_005459251.1 Length = 308 Score = 84.0 bits (206), Expect = 4e-21 Identities = 83/273 (30%), Positives = 122/273 (44%), Gaps = 21/273 (7%) Query: 19 TLGMALNLFDELKIEESSSPEIIITGEGEGTIPRGQENIAYRAARAVFAKVGRPPVP--L 76 T+ AL+L DE+ + S I ++GEG +P N+A RA RA+ VG+P + Sbjct: 36 TVFHALSLTDEVTVFASPEAGIEVSGEGARLVPTDDGNLAVRAVRALAEHVGKPDEANRV 95 Query: 77 KLEMHNSIPVARGLGSSAAALVGAIVGTNAILGGPLGPAELVNLATTLEGHPDNVAPAIL 136 ++ + IPVA G+ +A A++ + + L EL +A TL +V A+ Sbjct: 96 RVVIRKGIPVAGGMAGGSADAAAALLACSTLWNLDLHRDELAEVAATL---GSDVPFALY 152 Query: 137 GGLVASARDGEQVICRRLELPPGLVT-----VVAIPQFTLSTRISRGVLPAKVDLEDAVF 191 GG GEQ++ P L V+A Q LST G L D Sbjct: 153 GGTALGTGRGEQLV-------PVLSRHTFHWVLAFDQRGLSTPKVYGELDRLRQAGDPP- 204 Query: 192 NISRVAVLLAAVATGDLDLMGRMMVDKLHQPYRLPLIPGMAEVFAAAREAGALAVTLSGS 251 + LL A+A+GD + ++ + L Q + L PG+ A AGALA +SGS Sbjct: 205 RVGSPEALLEALASGDPRRLALLLGNDL-QAAAVSLRPGLRRTLRAGVSAGALAGVVSGS 263 Query: 252 GPTVIAFCRGRQPKVGPAMAAAFARKGVKCTVK 284 GPT C + +AA A GV TV+ Sbjct: 264 GPTCAFLCSDGDSAL--KVAAELAGAGVCRTVR 294 Lambda K H 0.320 0.137 0.397 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: 199 Number of extensions: 10 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: 296 Length of database: 308 Length adjustment: 27 Effective length of query: 269 Effective length of database: 281 Effective search space: 75589 Effective search space used: 75589 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: 48 (23.1 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