Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 8499506 DvMF_0276 aspartate kinase (RefSeq)
Query= BRENDA::Q9WZ17 (739 letters) >FitnessBrowser__Miya:8499506 Length = 409 Score = 315 bits (808), Expect = 2e-90 Identities = 169/403 (41%), Positives = 259/403 (64%), Gaps = 3/403 (0%) Query: 340 VVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPD 399 ++V KFGG +++++E +++V EK+ + + G KPVVVLSA T+ L+ LA+ +PD Sbjct: 3 ILVQKFGGTSVANLECMKQVREKVRRALRDGYKPVVVLSARSGETNRLLALAEEWSTDPD 62 Query: 400 PRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIIS 459 P E+D L++TGE SVAL S+ L+ G KA S TG Q+ I T +G ARI+DI+ + Sbjct: 63 PAEVDALIATGEQVSVALFSMLLKDSGIKARSMTGFQVPITTSDAFGRARIMDIDASRLR 122 Query: 460 RYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTAD 519 + L+ + VVAGFQG+T G +TTLGRGGSD +A+ALA +LG+ CE+Y DVDGVYT D Sbjct: 123 KELETHDVIVVAGFQGVTSEGRVTTLGRGGSDTSAVALAAALGSVECEIYTDVDGVYTTD 182 Query: 520 PRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLI-W 578 P + AR + +S++EM+E++ GA+VLQ R+ EFA+KY V V +++ +T GT++ Sbjct: 183 PNLCSTARKLDRVSYDEMLEMASMGAKVLQIRSVEFAKKYKVPVHVRSTFTDTPGTMVTQ 242 Query: 579 EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEY 638 E ++E +V + ++ A+V L+ VPDKPGV+A I LSQ G+ +DMI+Q Sbjct: 243 EDCEMEAVLVSGIAYDKDQARVTLRSVPDKPGVSAAIFGPLSQQGILVDMIVQNPSRDGV 302 Query: 639 NTVAFIVPESQLGK--LDIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTSTPEISATLFET 696 + F VP L K ++ ++ R+ A+E++ + +AKVS +GV + + ++A F Sbjct: 303 TDMTFTVPRKDLKKTLALMEEIRARTGAQEVLHDTQVAKVSAIGVGMRNHSGVAAKAFAA 362 Query: 697 LANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDRE 739 L E INI MIS S +I+ +I+ KY E AV+ +H F L+ + Sbjct: 363 LHAENINILMISTSEIKITCLIEEKYTELAVRTLHDAFGLNHD 405 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: 626 Number of extensions: 29 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: 409 Length adjustment: 36 Effective length of query: 703 Effective length of database: 373 Effective search space: 262219 Effective search space used: 262219 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 09 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