Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_029913072.1 P166_RS0111875 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000711315.1:WP_029913072.1 Length = 408 Score = 332 bits (851), Expect = 2e-95 Identities = 179/407 (43%), Positives = 268/407 (65%), Gaps = 7/407 (1%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 +++V K+GG ++ VE+++ VA K+ K G + VV +SAM T+ L+ LAK + + P Sbjct: 2 ALIVQKYGGTSVGSVERIKNVANKVAKFVDEGHQVVVAVSAMSGETNRLMALAKEMQDEP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 RELD+LL+TGE ++AL+S+AL+++GY AIS+TG Q+ I T+ + ARI DI+ D + Sbjct: 62 SRRELDVLLTTGEQVTIALLSMALQQKGYDAISYTGWQVPIHTNNVHFKARIEDIDADKM 121 Query: 459 SRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 L Q + VVAGFQG+T GDITTLGRGGSD TA+ALA +L AD C++Y DVDGVYT Sbjct: 122 MAQLNQGKVVVVAGFQGVTPEGDITTLGRGGSDTTAVALAAALKADECQIYTDVDGVYTT 181 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLI- 577 DPR+V +A+ + ++++EM+EL+ GA+VLQ R+ EFA KY V + + ++ ++ GTL+ Sbjct: 182 DPRVVPEAKRLDVITYDEMLELASLGAKVLQIRSVEFASKYKVPLRVLSSLQDGGGTLLI 241 Query: 578 ----WEGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGM 633 +EG +E P++ + F AK+++ VPDKPGVA +I+ +S + IDMIIQ Sbjct: 242 SEEDFEGLGMEKPLISGIAFSRDEAKLMILGVPDKPGVAYKILGPISDANIEIDMIIQNQ 301 Query: 634 KSGEYNTVAFIVPESQLGKLDIDLLKTRSE--AKEIIIEKGLAKVSIVGVNLTSTPEISA 691 F V + L + K SE A+E + + + K+S+VGV + S I++ Sbjct: 302 GIDGTTDFTFTVARNDLNMAKDIIKKIASELGARETLCDDTIVKISMVGVGMKSHSGIAS 361 Query: 692 TLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDR 738 T+F+TLA+ INI MI + +ISV+ID +Y+E AVKA+H FELD+ Sbjct: 362 TMFKTLADNNINIQMIGTTEIKISVVIDEQYLETAVKALHQAFELDK 408 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: 716 Number of extensions: 27 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: 408 Length adjustment: 36 Effective length of query: 703 Effective length of database: 372 Effective search space: 261516 Effective search space used: 261516 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