Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_012283362.1 HM1_RS10585 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000019165.1:WP_012283362.1 Length = 404 Score = 220 bits (560), Expect = 1e-61 Identities = 143/407 (35%), Positives = 227/407 (55%), Gaps = 20/407 (4%) Query: 340 VVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGD-----TTDHLIELAKTI 394 + V+KFGG ++++ K ++I + + G + V V+SAMG TD L+ L + + Sbjct: 3 IAVLKFGGTSVANETKRNHAVQRIREALEEGCRVVAVVSAMGRKPEPYATDTLLSLVQEL 62 Query: 395 DENPDPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDIN 454 D N RE DLL++ GEI S +M+ +L + G +A S TG Q IIT +++G ARI + Sbjct: 63 DFNLPLREKDLLMACGEIISSVVMTASLLRAGIEATSLTGWQAGIITTEQFGDARIQRVE 122 Query: 455 TDIISRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDG 514 + I R L+QD + V+AGFQG +E G+I TLGRGGSD TA+A+ +LGA++ +++ DV G Sbjct: 123 VERIRRELEQDRVAVIAGFQGASENGEIATLGRGGSDTTAVAVGAALGAEVVDIFTDVRG 182 Query: 515 VYTADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRG 574 VYTADPR+V DAR++ +S++E+ +L++ GA+V+ RA E A K V +++ +G Sbjct: 183 VYTADPRLVSDARILSCVSYQEVCQLAQEGAKVIHPRAVEIAMKNHQAVRVRSTEFHDKG 242 Query: 575 TLIWEGTKV--ENPIVRAVTFEDGMA-----KVVLKDVPDKPGVAARIMRTLSQMGVNID 627 TLI E R +T MA KV PD + + L++ G+++D Sbjct: 243 TLICAPHHAGDEYCCDRLITGIAHMAPITQIKVNTSQWPDPALTGQTVFQALAEAGISVD 302 Query: 628 MIIQGMKSGEYNTVAFIVPESQLGKLDIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTSTP 687 I + V F VP+ K +L+ E + +G AKV++VG+N+T P Sbjct: 303 FI-----NVHPAAVIFTVPDEITAKA-TRVLEELGLCPE--VRQGCAKVAVVGINMTGVP 354 Query: 688 EISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRF 734 + A + L E + I + S + I +I K + A+ A+H +F Sbjct: 355 GVMAQIVVALNREKVPILQSADSYTTIWCLIPIKDLTVALNALHRQF 401 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: 559 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: 404 Length adjustment: 35 Effective length of query: 704 Effective length of database: 369 Effective search space: 259776 Effective search space used: 259776 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: 52 (24.6 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