Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_077280321.1 B1C78_RS16900 homoserine kinase
Query= curated2:Q0AHY7 (316 letters) >NCBI__GCF_002000365.1:WP_077280321.1 Length = 310 Score = 147 bits (370), Expect = 4e-40 Identities = 91/270 (33%), Positives = 139/270 (51%), Gaps = 7/270 (2%) Query: 8 TKKQLAVWLQNYSLGSLTDLQGISSGIENTNYFVTTTQGKFILTLFEKLTSTELPFYLNL 67 T+++L +L++Y+LG L D Q G + T G+F L + +T PF L Sbjct: 19 TREELVAFLRHYALGELRDFQ---PGRRGRRGRLITDAGRFWL-VGPGMTD---PFLEAL 71 Query: 68 MAYLSEQGIPCPKPIESQDHALLGTLNGKPASIVSFLPGQSMTQIREEQCAQVGEILAKM 127 + +L+ G+P P + D + +L P ++V + GQ ++ + CA+VG++L ++ Sbjct: 72 LEHLAGHGLPVPTVVRGHDGRWIRSLGEYPGALVRWPEGQHPQRLEPDACARVGDLLGRI 131 Query: 128 HLAGLNYNGKNRNPRGLDWWQTAAGTVMPFLSRSEQSLLDEELQFQIKQRTTNLPQGIIH 187 HLAGL + R W + + + P L+ ++LL EE++FQ R T+LPQG IH Sbjct: 132 HLAGLEFTQSRPPHRDHRWRRQSTDALAPDLTPEARTLLHEEIRFQGLYRHTDLPQGTIH 191 Query: 188 ADLFRDNVLFTSTGIGGIIDFYFACNDALLYDLAITANDWCTLGDGVMDKARMHALVKAY 247 R ++ TG G+ F A ALL D+A+ ND C DG +D+ AL+ AY Sbjct: 192 GAPNRRRLVIDETGRVGLTGFGHASRCALLVDVAVAVNDCCIGSDGRLDRTLSAALLNAY 251 Query: 248 QAARPLTAEEYPAWPAMLRAGALRFWLSRL 277 RPL E AWP +LR AL WL L Sbjct: 252 HRLRPLRPIERGAWPVLLRLAALDGWLETL 281 Lambda K H 0.320 0.136 0.415 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: 233 Number of extensions: 16 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: 316 Length of database: 310 Length adjustment: 27 Effective length of query: 289 Effective length of database: 283 Effective search space: 81787 Effective search space used: 81787 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 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