Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_085123520.1 B9O00_RS15090 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_900177295.1:WP_085123520.1 Length = 407 Score = 288 bits (737), Expect = 4e-82 Identities = 162/402 (40%), Positives = 255/402 (63%), Gaps = 5/402 (1%) Query: 341 VVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDP 400 +VMKFGG +++D++++ VA+K+ +G + VV+SAM T+ L+ A D Sbjct: 4 IVMKFGGTSVADLDRIRNVADKVAAEVAAGNEVAVVVSAMAGVTNQLVGYAGQAARLYDL 63 Query: 401 RELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIISR 460 RE D ++S+GE + L+SI L+ RG +A S+ G Q+ I+TD +GSARI I + + R Sbjct: 64 REYDAVVSSGENVTAGLLSIVLQDRGVQARSWQGWQIPILTDGAHGSARIEKIEVEDLLR 123 Query: 461 YLKQDFIPVVAGFQGITETGD-ITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTAD 519 + + VVAGFQG ITTLGRGGSD +A+ALA +L AD C++Y DVDGVYT D Sbjct: 124 RMAAGEVAVVAGFQGFEPVRRRITTLGRGGSDTSAVALAAALKADRCDIYTDVDGVYTCD 183 Query: 520 PRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIWE 579 PRIV+ AR I +++EEM+E++ GA+VLQ R+ E A K+ V V + ++ +E GTL+ + Sbjct: 184 PRIVQRARKIDRITYEEMLEMASQGAKVLQTRSVEMAMKHRVPVRVLSSFQEGTGTLVVD 243 Query: 580 GTK-VENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEY 638 + VE +V VT+ AK+ L++V D+PGVAA I L++ VN+DMI+Q + + + Sbjct: 244 EEEIVEQAVVSGVTYSRDEAKITLRNVTDRPGVAAAIFGPLAEASVNVDMIVQNISADQQ 303 Query: 639 NT-VAFIVPESQLGKL--DIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTSTPEISATLFE 695 T + F V + L + I+ + + + K + I+K + KVS++GV + S ++ +F Sbjct: 304 TTDMTFTVTRADLERAVEVIEANRDKFDFKAMSIDKNVVKVSVIGVGMRSHAGVAQMMFS 363 Query: 696 TLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELD 737 LA +GINI +I+ S ++SV+I +Y E A++++HS + LD Sbjct: 364 ALAEKGINIQVITTSEIKVSVLIAEEYTELALRSLHSAYGLD 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: 617 Number of extensions: 22 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: 407 Length adjustment: 36 Effective length of query: 703 Effective length of database: 371 Effective search space: 260813 Effective search space used: 260813 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