Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_012970316.1 ALVIN_RS05455 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000025485.1:WP_012970316.1 Length = 409 Score = 320 bits (820), Expect = 9e-92 Identities = 173/402 (43%), Positives = 265/402 (65%), Gaps = 4/402 (0%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 +++V K+GG ++ +E+++ VAE++ + + G + VVV+SAM TD LI+LAK + E P Sbjct: 2 ALIVQKYGGTSVGSIERIQAVAERVKRWRDQGDQVVVVVSAMSGETDRLIKLAKQLQERP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 +PRELD+LLSTGE ++AL+S+AL +G A S+TG Q+ I+TD + ARI DI+ + Sbjct: 62 EPRELDVLLSTGEQVTIALLSMALTAQGCPARSYTGAQVHILTDSAHNKARIRDIDAARV 121 Query: 459 SRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 L+ + VVAGFQGI E GDITTLGRGGSD +A+A+A +L AD C++Y DVDGVYT Sbjct: 122 RADLEAGRVVVVAGFQGIDEQGDITTLGRGGSDTSAVAIAAALKADECQIYTDVDGVYTT 181 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLI- 577 DPR+ AR + +++EEM+E++ G++VLQ R+ EFA KY V + + ++ +E GTLI Sbjct: 182 DPRVEPKARKLDRITFEEMLEMASLGSKVLQIRSVEFAGKYRVPLRVLSSFEEGEGTLIS 241 Query: 578 WEGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGE 637 +E VE+ + + F AK+ + VPD+PGVA RI+ +++ + +DMI+Q + + E Sbjct: 242 FEDNDVEDAKISGIAFSRDEAKLTVLGVPDQPGVAHRILGPIAEANIEVDMIVQNVGADE 301 Query: 638 YNT-VAFIVPESQLGKLDIDLLKTRSE--AKEIIIEKGLAKVSIVGVNLTSTPEISATLF 694 T F V + L +T +E A+++ + + K+S+VGV + S I++ +F Sbjct: 302 STTDFTFTVHRNDYAPALEILQRTANELGARQVTGDASIVKISLVGVGMRSHAGIASRMF 361 Query: 695 ETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFEL 736 +LA EGINI MIS S +ISV++D KY+E V+ +H F L Sbjct: 362 ASLAKEGINIRMISTSEIKISVVVDEKYLELGVRTLHDAFGL 403 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: 696 Number of extensions: 28 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 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