Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_014149274.1 MEALZ_RS13830 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000968535.2:WP_014149274.1 Length = 409 Score = 323 bits (829), Expect = 8e-93 Identities = 176/401 (43%), Positives = 264/401 (65%), Gaps = 3/401 (0%) Query: 342 VMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDPR 401 V KFGG ++ VE+++ VAEK+ + G + V+V+SAM T+ LI LA I + P+ R Sbjct: 5 VYKFGGTSVGSVERIKAVAEKVKQAHDQGDQLVIVVSAMSGETNRLIALANEIQKYPNSR 64 Query: 402 ELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIISRY 461 E+D+LLSTGE + +L+S+AL + G A S+TG Q+KI+TD + ARII+I+ + Sbjct: 65 EMDVLLSTGEQVTTSLLSMALHELGCPACSYTGGQVKILTDSSHTKARIINIDDKRMRED 124 Query: 462 LKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTADPR 521 L + VVAGFQG+ + G+ITTLGRGGSD TA+ALA +L AD C ++ DVDGVYT DPR Sbjct: 125 LTAGRVVVVAGFQGVDDKGNITTLGRGGSDTTAVALAAALKADECCIFTDVDGVYTTDPR 184 Query: 522 IVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLI-WEG 580 + +AR ++++++EEM+E++ G++VLQ R+ EFA KY V + + ++ E +GTLI +E Sbjct: 185 VEPNARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLSSFTEGKGTLITYED 244 Query: 581 TKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEYNT 640 ++E ++ + F AK+ + VPD PGVA +I+ ++ + +DMIIQ + E Sbjct: 245 DQMEQALISGIAFNRDEAKLTITGVPDLPGVAYKILGPIADANIEVDMIIQNIAGDETTD 304 Query: 641 VAFIVPESQLGKLD--IDLLKTRSEAKEIIIEKGLAKVSIVGVNLTSTPEISATLFETLA 698 F V + K +D + AK + + + K+SIVGV + S I++T+F+ LA Sbjct: 305 FTFTVHRNDYEKAKELLDSICAELGAKAVTGDVKIVKISIVGVGMRSHAGIASTMFKALA 364 Query: 699 NEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDRE 739 +EGINI MIS S +ISV++D KY+E AV+A+HS FELDRE Sbjct: 365 DEGINIRMISTSEIKISVVVDEKYLELAVRALHSAFELDRE 405 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: 706 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: 409 Length adjustment: 36 Effective length of query: 703 Effective length of database: 373 Effective search space: 262219 Effective search space used: 262219 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