Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_073039273.1 BUB04_RS10965 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_900129305.1:WP_073039273.1 Length = 417 Score = 337 bits (865), Expect = 5e-97 Identities = 184/413 (44%), Positives = 273/413 (66%), Gaps = 20/413 (4%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 ++VV K+GG +++DVE++ VA ++I+RKK+G VVVLSA TD LIELA + +P Sbjct: 2 ALVVQKYGGTSVADVERIRNVARRVIERKKAGDDLVVVLSARAGDTDRLIELAHQMSPHP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 DPRELD+LL+TGE ++AL S+A++ G++A+S TG Q IITD +G ARI I T + Sbjct: 62 DPRELDVLLATGEQITIALFSMAVKDMGFEAVSMTGYQAGIITDHHHGHARISWIETLPV 121 Query: 459 SRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 LK+ I VVAGFQG + G+ITTLGRGGSD TA+ALA +L AD CE+Y DV+GVYT Sbjct: 122 VEKLKEGKIVVVAGFQGYDDEGNITTLGRGGSDTTAVALAAALKADACEIYTDVEGVYTT 181 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIW 578 DP + AR ++++S+EEM+E++ GA+VL R+ EF KY V + ++++ + GTL+ Sbjct: 182 DPNVYSKARKLRKISYEEMLEMASMGAKVLHIRSVEFGMKYNVPIWVRSSFTDDPGTLVT 241 Query: 579 -EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKS-- 635 E ++E +V VT+ A+V + DVPD PG+A +I ++Q G+N+DMIIQG Sbjct: 242 AEDAEMEKVVVSGVTYNKNEARVTVTDVPDVPGMAFKIFEPIAQAGINVDMIIQGSSGVP 301 Query: 636 GEYNTVAFIVPESQLGKLDIDLLKTRSEAKEIIIEKG---------LAKVSIVGVNLTST 686 G N ++F VP++ D +T + A+++ E G +AK+S++GV + S Sbjct: 302 GRAN-ISFTVPKA-------DYEQTVALAEKVAREIGAGPVHGNAHIAKISVIGVGMRSH 353 Query: 687 PEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDRE 739 +++ +F++LA E INI MIS S +IS +ID KY E AV+ +H FEL ++ Sbjct: 354 TGVASLMFDSLAKENINIHMISTSEIKISCVIDEKYTELAVRVLHDAFELHKD 406 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: 759 Number of extensions: 31 Number of successful extensions: 4 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: 417 Length adjustment: 36 Effective length of query: 703 Effective length of database: 381 Effective search space: 267843 Effective search space used: 267843 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: 53 (25.0 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