Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_078430173.1 BK574_RS22615 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_002019605.1:WP_078430173.1 Length = 409 Score = 322 bits (825), Expect = 2e-92 Identities = 170/403 (42%), Positives = 267/403 (66%), Gaps = 5/403 (1%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 S++V K+GG ++ VE++E VA ++ K + G + VVV+SAMG TTD L+ LA I + P Sbjct: 2 SIIVQKYGGTSVGSVERIEHVAGRVAKTVEQGNQVVVVVSAMGKTTDQLVTLASEISDKP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 RE+D+LL+TGE +++L+++AL++RG AIS TG Q I+T++ +GSARIIDI T+ + Sbjct: 62 SKREMDMLLTTGEQVTISLLAMALQQRGLGAISMTGWQAGIVTEENHGSARIIDIQTEKM 121 Query: 459 SRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 L + +VAGFQG +E G+ITTLGRGGSD TA+ALA +L A+ C++Y DV GVYT Sbjct: 122 ETQLSLGNVVIVAGFQGSSEHGEITTLGRGGSDTTAVALAAALKAERCDIYTDVTGVYTT 181 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIW 578 DPR + +AR + +S++EM+E++ GA VL RA EFA+ Y VK+++ ++ E GTLI Sbjct: 182 DPRYIDEARKLHSISYDEMLEMANLGAGVLHPRAVEFAKNYQVKLMVASSIVEEVGTLIE 241 Query: 579 EGTKVE-NPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGE 637 E +E N +VR + FE+ + K+ + +P++ G + + LS G+N+D+IIQ + + Sbjct: 242 EEVSMEQNLVVRGIAFENDVTKITVSGLPNEIGTLSDVFTLLSNHGINVDIIIQNQIAEQ 301 Query: 638 YNTVAFIVPESQLGKLDIDLLKTRSEA---KEIIIEKGLAKVSIVGVNLTSTPEISATLF 694 ++V+F S L + + +LK E +E++ E LAKVSI+G + S P ++A +F Sbjct: 302 KSSVSFSTSRSSLEE-TLSVLKKHQEELQFEEVVHEGDLAKVSIIGSGMISNPGVAAQMF 360 Query: 695 ETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELD 737 + LA I I M+S S ++S +++ + AV+A+H F+LD Sbjct: 361 KILAEHEILIKMVSTSEIKVSALVEEGVMVPAVEALHRAFQLD 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: 633 Number of extensions: 32 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: 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