Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate PP_4473 PP_4473 aspartokinase
Query= BRENDA::Q9WZ17 (739 letters) >FitnessBrowser__Putida:PP_4473 Length = 411 Score = 351 bits (900), Expect = e-101 Identities = 184/403 (45%), Positives = 274/403 (67%), Gaps = 4/403 (0%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 +++V KFGG ++ +E++E+VAEK+ K +++G VVVLSAM T+ LI+LAK I + P Sbjct: 2 ALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 PRELD+++STGE ++AL+++AL KRG A+S+TGNQ++I+TD + ARI+ I+ I Sbjct: 62 VPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQKI 121 Query: 459 SRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 LK+ + VVAGFQG+ E G ITTLGRGGSD T +ALA +L AD C++Y DVDGVYT Sbjct: 122 RADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTT 181 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIW 578 DPR+V AR ++++++EEM+E++ G++VLQ R+ EFA KY V + + ++ KE GTLI Sbjct: 182 DPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEGPGTLIT 241 Query: 579 --EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSG 636 E +E PI+ + F AK+ ++ VPD PGVA +I+ +S + +DMI+Q + Sbjct: 242 IDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQNVAHD 301 Query: 637 EYNTVAFIVPESQLGKLDIDLLKTRSE--AKEIIIEKGLAKVSIVGVNLTSTPEISATLF 694 F V ++ K L T E A+E+I + +AKVSIVGV + S +++ +F Sbjct: 302 NTTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHAGVASCMF 361 Query: 695 ETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELD 737 E LA E INI MIS S ++SV+++ KY+E AV+A+H+ F+LD Sbjct: 362 EALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLD 404 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: 728 Number of extensions: 35 Number of successful extensions: 3 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: 411 Length adjustment: 36 Effective length of query: 703 Effective length of database: 375 Effective search space: 263625 Effective search space used: 263625 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