Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate YP_425834.1 Rru_A0743 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000013085.1:YP_425834.1 Length = 406 Score = 292 bits (748), Expect = 2e-83 Identities = 159/401 (39%), Positives = 251/401 (62%), Gaps = 4/401 (0%) Query: 341 VVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDP 400 +VMKFGG ++ DV+++ VA ++ +G + VV+SAM T+ L+ ++ D Sbjct: 4 IVMKFGGTSVGDVDRIRNVARRVKAEVDAGNEVAVVVSAMSGETNRLVGFCDSMTNMYDA 63 Query: 401 RELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIISR 460 RE D +++TGE ++ L++IAL+ G +A S+ G Q+ I TD+ +G ARI+ I+T ++ + Sbjct: 64 REYDAVVATGEQVTIGLLAIALQDIGVEARSWMGWQIPIHTDEAHGKARILSIDTTVLEQ 123 Query: 461 YLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTADP 520 L + VVAGFQG+ +TTLGRGGSD +A+ALA +L AD C++Y DVDGVYT DP Sbjct: 124 RLASGQVAVVAGFQGLGPNNRVTTLGRGGSDTSAVALAAALKADRCDIYTDVDGVYTTDP 183 Query: 521 RIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIW-E 579 RIV AR + +++EEM+E + GA+VLQ R+ E A K+ V+V + ++ + GTL+ E Sbjct: 184 RIVPKARKLDRITYEEMLEQASLGAKVLQTRSVEMAMKHRVRVRVLSSFSDAPGTLVCDE 243 Query: 580 GTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEYN 639 VE +V + + AK+ L V D+PGVAARI L+ +N+DMI+Q + ++ Sbjct: 244 DEIVEKELVSGIAYSRDEAKITLVKVSDRPGVAARIFGPLADANINVDMIVQNVSEDGHS 303 Query: 640 T-VAFIVPESQLGKLDIDLLKTRSEA--KEIIIEKGLAKVSIVGVNLTSTPEISATLFET 696 T + F +P S L + L R + +E+ + KVS++GV + S ++ T+F Sbjct: 304 TDLTFTLPRSDLARALKVLEGARDDINYRELTTSSAVVKVSVIGVGMRSHAGVAQTMFRA 363 Query: 697 LANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELD 737 L+ +GINI +IS S ++SV+I +Y+E AV+A+HS + LD Sbjct: 364 LSEKGINIHVISTSEIKVSVLIAEEYMELAVRALHSAYGLD 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: 597 Number of extensions: 26 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 739 Length of database: 406 Length adjustment: 35 Effective length of query: 704 Effective length of database: 371 Effective search space: 261184 Effective search space used: 261184 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: 52 (24.6 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