Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_029133415.1 A3GO_RS0110840 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000428045.1:WP_029133415.1 Length = 410 Score = 317 bits (811), Expect = 1e-90 Identities = 174/405 (42%), Positives = 261/405 (64%), Gaps = 5/405 (1%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 +++V K+GG ++ +E+++ VAEK+ + G + VVV+SAM T+ LI LAK I+E+P Sbjct: 2 ALIVQKYGGTSVGSIERIQAVAEKVAAARNRGDQVVVVVSAMSGETNRLIALAKAIEEHP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 RE+D+L+STGE ++AL+S+AL K A S+TG Q+ I+TD + ARI DI+ + Sbjct: 62 SAREMDVLVSTGEQVTIALLSMALHKIDCPAKSYTGGQVHILTDSAHSKARIQDIDDIKV 121 Query: 459 SRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 L + VVAGFQGI E G ITTLGRGGSD TA+ALA +L AD C+++ DVDGVYT Sbjct: 122 KADLDAGCVVVVAGFQGIDEQGAITTLGRGGSDTTAVALAAALKADECQIFTDVDGVYTT 181 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLI- 577 DPR+ AR + ++S+EEM+E++ G++VLQ RA EFA KY V + + ++ +E GTLI Sbjct: 182 DPRVEPKARRMSKISFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLSSFEEGEGTLIT 241 Query: 578 WEGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGE 637 +E +EN + + F AK+ + V D+PGVA RI+ +S + +DMIIQ + Sbjct: 242 FEDKGMENAKISGIAFNRDEAKLTILGVQDQPGVAYRILGPISDANIEVDMIIQNIGQDG 301 Query: 638 YNTVAFIVPESQLGKLDIDLLKTRSE---AKEIIIEKGLAKVSIVGVNLTSTPEISATLF 694 F V + K + +L ++ A+E+I + + K+S+VGV + S I++++F Sbjct: 302 TTDFTFTVHRNDYDKA-VSILNDVAKDLGAREVIGDNAIVKISLVGVGMRSHAGIASSMF 360 Query: 695 ETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDRE 739 L+ EGINI MIS S +ISV++D KY+E V+A+H F+L E Sbjct: 361 AALSKEGINIRMISTSEIKISVVVDEKYLELGVRALHEAFDLAAE 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: 731 Number of extensions: 41 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: 410 Length adjustment: 36 Effective length of query: 703 Effective length of database: 374 Effective search space: 262922 Effective search space used: 262922 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