Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011384021.1 AMB_RS08140 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000009985.1:WP_011384021.1 Length = 406 Score = 288 bits (738), Expect = 3e-82 Identities = 161/401 (40%), Positives = 255/401 (63%), Gaps = 4/401 (0%) Query: 341 VVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDP 400 +VMKFGG +++D+E+++ VA ++ + +G + VV+SAM T+ L+ + D Sbjct: 4 IVMKFGGTSVADIERIKNVANRVKREFDAGNQVAVVVSAMSGATNQLVAWCNQVAPLHDA 63 Query: 401 RELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIISR 460 RE D +++TGE + L++IAL++ G A S+ G QL I TD +G ARI+ I TD + Sbjct: 64 REYDAVVATGEQVTTGLLAIALQELGVNARSWCGWQLPIRTDGVHGKARIMSIETDEMIA 123 Query: 461 YLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTADP 520 + + + VVAGFQG+ I TLGRGGSD +A+ALA +L AD C++Y DVDGVYT DP Sbjct: 124 RMGKGEVAVVAGFQGLGPDNRIATLGRGGSDTSAVALAAALHADRCDIYTDVDGVYTTDP 183 Query: 521 RIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIW-E 579 RIV A+ + ++++EEM+EL+ GA+VLQ R+ E A K+ V+V + ++ ++ GTL+ E Sbjct: 184 RIVSVAKKLDKITYEEMLELASVGAKVLQTRSVEMAMKHRVRVQVLSSFEDKPGTLVCDE 243 Query: 580 GTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGM-KSGEY 638 VE +V + + AK+ L V D+PGVAA I L++ VN+DMI+Q + + G+ Sbjct: 244 DEIVEKELVSGIAYSRDEAKITLVRVADRPGVAASIFGPLAEAAVNVDMIVQNVSEDGKS 303 Query: 639 NTVAFIVPESQL--GKLDIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTSTPEISATLFET 696 + F V + L K ++ K ++++ + + KVS++GV + S I+ +F+T Sbjct: 304 TDLTFTVGNADLERAKKVLEDAKGNLGFEKLLADPNVVKVSVIGVGMRSHAGIAQKMFQT 363 Query: 697 LANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELD 737 LA+EGINI +IS S +ISV+I+ KY E A++A+H+ + LD Sbjct: 364 LASEGINIQVISTSEIKISVLIEEKYTELALRALHTAYGLD 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: 662 Number of extensions: 24 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: 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 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