Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_058930163.1 AU252_RS07410 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_001484605.1:WP_058930163.1 Length = 452 Score = 322 bits (826), Expect = 2e-92 Identities = 180/423 (42%), Positives = 274/423 (64%), Gaps = 17/423 (4%) Query: 333 GGAEKFSVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAK 392 G A ++V KFGG+++SD E +++VA++++ +++G + VVV+SAMGDTTD L++LA Sbjct: 20 GTAVTKQLIVQKFGGSSVSDAEGVKRVAKRVVDAQRAGNEVVVVVSAMGDTTDELLDLAA 79 Query: 393 TIDENPDPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIID 452 + ++ RE+D+LLS GE S+AL+++A+ K G A SFTG+Q +ITD +G ARIID Sbjct: 80 QVTDSAPAREMDMLLSAGERISMALLAMAINKFGASAQSFTGSQAGMITDGIHGKARIID 139 Query: 453 INTDIISRYLKQDFIPVVAGFQGIT-ETGDITTLGRGGSDLTAIALAYSLGADLCELYKD 511 ++ I L + I +VAGFQG++ T +ITTLGRGGSD TA+ALA +L AD+CE+Y D Sbjct: 140 VDPHRIRTALDKGHIAIVAGFQGMSRSTNEITTLGRGGSDTTAVALAAALDADVCEIYTD 199 Query: 512 VDGVYTADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKE 571 VDG+YTADPR+V A+ I +S EEM+EL+ GA++L R E+AR++GV + ++++ + Sbjct: 200 VDGIYTADPRVVPSAQKIDTISSEEMLELAASGAKILHLRCVEYARRFGVPLHVRSSFSQ 259 Query: 572 TRGTLI----------WEGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQ 621 GT + EG +E PI+ V + AKV + VPD PG AA I + ++ Sbjct: 260 NEGTWVIPSAEDKITTQEGVALEQPIISGVAHDRSEAKVTVVGVPDIPGKAAAIFQVIAD 319 Query: 622 MGVNIDMIIQGMKS-GEYNT-VAFIVPESQLGKLDIDLLKTRSE---AKEIIIEKGLAKV 676 NIDMI+Q + + G T ++F +P + G ++ LK + I + + K+ Sbjct: 320 AHSNIDMIVQNVSTHGTGRTDISFTLPIVE-GAEALEALKAAQPDIGFENIEYNEQIGKL 378 Query: 677 SIVGVNLTSTPEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFEL 736 S++G + S P +SAT F+ L++ GINI+MIS S RISV+ ++DAV+AIH F+L Sbjct: 379 SLIGAGMRSHPGVSATFFKALSDAGININMISTSEIRISVVTHADLLDDAVRAIHKAFDL 438 Query: 737 DRE 739 D E Sbjct: 439 DSE 441 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: 33 Number of successful extensions: 5 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: 452 Length adjustment: 36 Effective length of query: 703 Effective length of database: 416 Effective search space: 292448 Effective search space used: 292448 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