Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_084276585.1 B8779_RS05980 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_900176045.1:WP_084276585.1 Length = 401 Score = 338 bits (866), Expect = 4e-97 Identities = 177/400 (44%), Positives = 269/400 (67%), Gaps = 1/400 (0%) Query: 340 VVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPD 399 ++V K+GG ++ +E++E VA+++ K K++G VVV+SAM T+ LI+ AK P Sbjct: 2 LIVQKYGGTSVGSLERIENVAKRVAKTKEAGNDVVVVVSAMSGETNKLIDYAKHFSPTPS 61 Query: 400 PRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIIS 459 R++DLLLS+GE + AL+SIAL + G+ ++ TG Q I+TDK + ARI IN + + Sbjct: 62 RRDMDLLLSSGERVTAALLSIALNEMGFPTVAMTGRQAGIVTDKSHTVARIEKINPEPMQ 121 Query: 460 RYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTAD 519 LK+ I VVAGFQGITE G +TTLGRGGSDLTA+A+A +LGAD CE+Y DVDGVYT D Sbjct: 122 NALKEGKIIVVAGFQGITEDGQVTTLGRGGSDLTAVAIAGALGADKCEIYSDVDGVYTTD 181 Query: 520 PRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIW- 578 PRI A+ + ++S++EM+EL+ GA+VLQ R+ E A+K GV + +++ + GT+I Sbjct: 182 PRIEPKAKKLDKISYDEMLELASLGAKVLQNRSVELAKKLGVVIEARSSFNDNPGTIITK 241 Query: 579 EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEY 638 E +E P+V + + A+V L+ V D+PG+AA I + L+ +N+DMI+Q + Sbjct: 242 EEDIMEKPLVSGIALDKNQARVSLRGVKDRPGIAAEIFKALANENINVDMIVQTIGEDGK 301 Query: 639 NTVAFIVPESQLGKLDIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTSTPEISATLFETLA 698 + F VP+++L + + + + E +++ + +AKVSIVGV + S +++ FET+A Sbjct: 302 TNLDFTVPQNELELVKKVMEQFKDEYEKVEYDPDVAKVSIVGVGMKSHSGVASKAFETMA 361 Query: 699 NEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDR 738 E INI+MIS S +IS+IID KY E AV+A+H+ +ELD+ Sbjct: 362 KENINIEMISTSEIKISMIIDEKYGELAVRALHAAYELDK 401 Lambda K H 0.318 0.137 0.377 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: 737 Number of extensions: 34 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: 739 Length of database: 401 Length adjustment: 35 Effective length of query: 704 Effective length of database: 366 Effective search space: 257664 Effective search space used: 257664 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: 52 (24.6 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