Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011601854.1 FRAAL_RS02615 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000058485.1:WP_011601854.1 Length = 422 Score = 322 bits (826), Expect = 2e-92 Identities = 179/406 (44%), Positives = 268/406 (66%), Gaps = 8/406 (1%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 +++V KFGG++++D +++++VAE++++ ++ G VVV+SAMGDTTD L++LA+ + P Sbjct: 2 ALLVAKFGGSSVADADRIKRVAERVVEARRDGNDVVVVVSAMGDTTDELLDLAEQVSPLP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 RELD+LL+ GE S+AL+++A+ G +A SFTG+Q +ITD +G ARIID+ I Sbjct: 62 PARELDMLLTAGERISMALLAMAITTLGAEARSFTGSQAGVITDSVHGKARIIDVTPGRI 121 Query: 459 SRYLKQDFIPVVAGFQGIT-ETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYT 517 L + I +VAGFQG++ +T DITTLGRGGSD TA+ALA +L AD CE+Y DVDGV++ Sbjct: 122 RAALDEGAIAIVAGFQGVSQDTKDITTLGRGGSDTTAVALAAALHADACEIYTDVDGVFS 181 Query: 518 ADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIK---NAHKETRG 574 ADPRIV DAR I +S+EEM+E++ GA+VL R E+AR+Y V V ++ NA T Sbjct: 182 ADPRIVPDARRIDTISYEEMLEMAACGAKVLMLRCVEYARRYSVPVHVRSSFNAKPGTWV 241 Query: 575 TLIWEGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQ-GM 633 T I E VE I+R V + AKV + PDKPGVAA + R ++ VN+DMI+Q G Sbjct: 242 TEIPEAQLVEQAIIRGVAHDVSEAKVTVVGCPDKPGVAAAVFRAVADADVNLDMIVQVGS 301 Query: 634 KSGEYNT-VAFIVPESQLGKLDIDLLKTRSEA--KEIIIEKGLAKVSIVGVNLTSTPEIS 690 +G T ++F +P++ L K + E + + + + K+S++G + S P +S Sbjct: 302 VAGSGRTDISFTLPKTDGRTALTALAKVQGEIGFERTLYDDHIGKLSLIGAGMKSHPGVS 361 Query: 691 ATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFEL 736 A F LA+ G+N+++IS S RISV++ + AV+A+H FEL Sbjct: 362 ARFFGALADAGVNVEIISTSEIRISVVVRDTDLPGAVRAVHGAFEL 407 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: 668 Number of extensions: 27 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: 422 Length adjustment: 36 Effective length of query: 703 Effective length of database: 386 Effective search space: 271358 Effective search space used: 271358 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 25 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