Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_092482509.1 BM299_RS05755 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_900115975.1:WP_092482509.1 Length = 408 Score = 247 bits (631), Expect = 7e-70 Identities = 147/413 (35%), Positives = 235/413 (56%), Gaps = 23/413 (5%) Query: 341 VVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGD-----TTDHLIELAKTID 395 +V+KFGG ++ E E+VA KII K G PVVV+SA+G TD LI L K Sbjct: 4 IVLKFGGTSLVSPELRERVAGKIIAAKDEGYVPVVVVSAIGREGDPYATDTLISLVKQTY 63 Query: 396 ENPDPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINT 455 + RE+D+L+S GEI S +M+ L+ GY A+ TG Q IITD+ Y ARI+ + Sbjct: 64 HDLPAREMDMLMSCGEIISGVVMAATLQAMGYPAVFLTGAQAGIITDRNYSGARILQVQA 123 Query: 456 DIISRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGV 515 ++RY ++ +I VVAGFQG TE G+ITTLGRGGSD TA AL +L A ++Y DVDG+ Sbjct: 124 KNVTRYTQEGYIVVVAGFQGTTEDGEITTLGRGGSDTTAAALGVALNAVYVDIYTDVDGI 183 Query: 516 YTADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGT 575 TADPRIV +A+ ++ ++++E+ L+ GA+V+ RA E A + + + +++ ++ GT Sbjct: 184 MTADPRIVAEAKALEVITYDEICHLAHEGAKVVHPRAVEIAMQKSIPLRVRSTFSDSPGT 243 Query: 576 LIWEGTKV--------ENPIVRAVTFEDGMAKVVLKDVPDKPGV--AARIMRTLSQMGVN 625 L+ +V ++ IV +T+ G+A+ +++ G+ R+ R L+ G++ Sbjct: 244 LVTNSGEVYKGTIDITKDRIVTGITYISGIAQFIVRIGATGEGLKQQRRMFRALALAGIS 303 Query: 626 IDMIIQGMKSGEYNTVAFIVPESQLGKLDIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTS 685 ID I V + + + + +L+ E+I G AKVS VG ++ Sbjct: 304 IDFI------NILPEVVLFTVKDDVAEKAVKVLENTGYMSEVI--TGCAKVSAVGAGMSG 355 Query: 686 TPEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDR 738 P + A + E L + I I + S + + V++ + +E AV+A+H +F+LD+ Sbjct: 356 VPGVIADIVEALTKDDIQILQCNDSHTTVWVLVRREEMEKAVRALHRQFKLDQ 408 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: 711 Number of extensions: 40 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: 408 Length adjustment: 36 Effective length of query: 703 Effective length of database: 372 Effective search space: 261516 Effective search space used: 261516 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