Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_059152208.1 V474_RS14540 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_001046635.1:WP_059152208.1 Length = 419 Score = 270 bits (691), Expect = 8e-77 Identities = 156/414 (37%), Positives = 252/414 (60%), Gaps = 18/414 (4%) Query: 341 VVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDP 400 +VMKFGG +++ E++ +VA + +++++G + VV+SAM TD L+ + + DP Sbjct: 4 IVMKFGGTSMAGSERIRRVAGIVKRQQEAGHEVAVVVSAMSGETDRLVNFCREANALYDP 63 Query: 401 RELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIISR 460 E D+++++GE + L+++ L+ G KA S+ G Q+ I TD + ARI +I+ D + Sbjct: 64 AEYDVVVASGEQVTSGLLALTLQAIGCKARSWQGWQVPIKTDDAHAKARIEEIDADALIA 123 Query: 461 YLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTADP 520 + I V+ GFQG++ G +TTLGRGGSD +A+A+A ++ AD C++Y DVDGVYT DP Sbjct: 124 SMAAGEIAVIPGFQGVSPEGRVTTLGRGGSDTSAVAVAAAVKADRCDIYTDVDGVYTTDP 183 Query: 521 RIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKN--------AHKET 572 RIV AR + +++EEM+EL+ G++VLQ R+ A K V+V + + A Sbjct: 184 RIVAKARKLPLVTYEEMLELASVGSKVLQTRSVSLAMKEKVRVQVLSSFIDETAPAADTI 243 Query: 573 RGTLI-----WEGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNID 627 GTLI EG+ +E ++ + + AKV L VPD+PG A I L++ +N+D Sbjct: 244 PGTLIVSDEELEGSDMERQLITGIAADKNEAKVTLTRVPDRPGAVASIFAPLAESNINVD 303 Query: 628 MIIQGMKSGEYNT-VAFIVPESQLGKLDIDLLKTRSEA---KEIIIEKGLAKVSIVGVNL 683 MIIQ + + T V F VP+S L + +L+ R ++ +I + +AK+S+VGV + Sbjct: 304 MIIQNVAKDKGETDVTFTVPQSDLARAQA-MLEERKDSIGYYRLIADGNVAKISVVGVGM 362 Query: 684 TSTPEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELD 737 S +++T+F+TLA+ GINI IS S ++SV+ID E AV+ +H+ + LD Sbjct: 363 RSHAGVASTMFKTLADRGINIIAISTSEIKVSVLIDTDETELAVRVLHTAYGLD 416 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: 616 Number of extensions: 24 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: 419 Length adjustment: 36 Effective length of query: 703 Effective length of database: 383 Effective search space: 269249 Effective search space used: 269249 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 Jul 26 2024. The underlying query database was built on Jul 25 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