Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011446941.1 SARO_RS16780 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000013325.1:WP_011446941.1 Length = 418 Score = 263 bits (672), Expect = 1e-74 Identities = 154/416 (37%), Positives = 245/416 (58%), Gaps = 18/416 (4%) Query: 341 VVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDP 400 +VMKFGG +++ E++ +VA + +++ +G + VV+SAM TD L+ + + DP Sbjct: 4 IVMKFGGTSMAGTERIRRVARIVQRQQAAGHEVAVVVSAMAGETDRLVNFCREANPLYDP 63 Query: 401 RELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIISR 460 E D+++++GE + L+++ L+ G KA S+ G QL I TD + ARI I+++ + Sbjct: 64 AEYDVVVASGEQVTSGLLAMHLQALGCKARSWLGWQLPIHTDDAHSKARIEGIDSEALLA 123 Query: 461 YLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTADP 520 + I V+ GFQG+T +TTLGRGGSD +A+A+A ++ AD C++Y DVDGVYT DP Sbjct: 124 SMGAGEIAVIPGFQGLTADNRVTTLGRGGSDTSAVAVAAAVKADRCDIYTDVDGVYTTDP 183 Query: 521 RIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKN--------AHKET 572 RIV AR +K +++EEM+EL+ G++VLQ R+ A K GV+V + + A Sbjct: 184 RIVAKARKLKNVTYEEMLELASVGSKVLQTRSVSLAMKEGVRVQVLSSFIDDDAPAADTI 243 Query: 573 RGTLI-----WEGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNID 627 GT+I EG +E ++ + + AKV L + D+PG A I L+ +N+D Sbjct: 244 PGTMIVSDEELEGLDMERQLITGIAADKNEAKVTLTRIADRPGAVAAIFGPLAAANINVD 303 Query: 628 MIIQGMKSGEYNT-VAFIVPESQLGKLDIDLLKTRSEA---KEIIIEKGLAKVSIVGVNL 683 MIIQ + + T V F VP S L + LL+ R + ++ +AK+S+VGV + Sbjct: 304 MIIQNIAKDKGETDVTFTVPISDLARTQA-LLEERKDTIGYYRMLANSKVAKISVVGVGM 362 Query: 684 TSTPEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDRE 739 S +++T+F LA+ GINI I+ S ++SV+ID E AV+ +H+ + LD E Sbjct: 363 RSHAGVASTMFRALADRGINIQAITTSEIKVSVLIDEDETELAVRVLHTAYGLDGE 418 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: 637 Number of extensions: 27 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 739 Length of database: 418 Length adjustment: 36 Effective length of query: 703 Effective length of database: 382 Effective search space: 268546 Effective search space used: 268546 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