Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_012674034.1 SULAZ_RS07315 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000021545.1:WP_012674034.1 Length = 411 Score = 314 bits (804), Expect = 6e-90 Identities = 171/403 (42%), Positives = 262/403 (65%), Gaps = 13/403 (3%) Query: 340 VVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPD 399 ++V K+GG ++ ++E+++ VA KI K G + VVV SAM TD LI L + + P+ Sbjct: 3 LIVQKYGGTSVGNIERIKNVARKIKKAVDEGNQVVVVSSAMTGETDRLIGLTRELSNRPN 62 Query: 400 PRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIIS 459 PRE D++++TGE ++ L++IAL++ G AIS TG Q+ IITD + ARI I+T I Sbjct: 63 PREQDMVVATGEQVAIGLVAIALQELGVPAISLTGWQVPIITDNVHTKARIKKIDTHRIR 122 Query: 460 RYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTAD 519 ++L + + +VAGFQG++E GDITTLGRGGSD +A+ALA +L AD+CE+Y DV GV+TAD Sbjct: 123 KHLDEGKVVIVAGFQGVSEDGDITTLGRGGSDTSAVALAAALKADVCEIYTDVPGVFTAD 182 Query: 520 PRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIW- 578 PRIV++AR I +S+EEM+E++ G++V+Q R+ EF KYGVK+ ++++ + GT I Sbjct: 183 PRIVENARKIPVISYEEMMEMASLGSKVMQIRSVEFGAKYGVKIHVRSSFNDEEGTWIME 242 Query: 579 EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEY 638 E ++E +VR ++ E +++ + VPDKPGVAA++ + L + +DMI+Q + + Sbjct: 243 ENEEMEKVVVRGISHELKESRITVVRVPDKPGVAAKLFKALGDKNIVVDMIVQNVSHKGF 302 Query: 639 NTVAFIVPESQLGKLDIDLLK--TRSEAKEIIIE-----KGLAKVSIVGVNLTSTPEISA 691 ++F V K D D + R AKE+ E +AK+S+VG+ + + ++ Sbjct: 303 TDISFTV-----NKTDADYAEEIAREVAKEVGAEDVERNDKIAKISVVGLGMKTHSGVAG 357 Query: 692 TLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRF 734 +FE L EGINI IS S +IS +ID KY E AV+A+H F Sbjct: 358 KMFEVLYKEGINIYAISTSEIKISCLIDEKYAELAVRALHEAF 400 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: 726 Number of extensions: 39 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 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