Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_020177124.1 A3OQ_RS0119490 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000385335.1:WP_020177124.1 Length = 412 Score = 265 bits (678), Expect = 3e-75 Identities = 153/408 (37%), Positives = 245/408 (60%), Gaps = 10/408 (2%) Query: 341 VVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDP 400 +VMKFGG +++DV+++ VA + + ++G VV+SAM T+ L++ + DP Sbjct: 4 LVMKFGGTSVADVDRIRNVARHVQREVEAGYDIAVVVSAMSGKTNELVDWCRVASRFYDP 63 Query: 401 RELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDIN-TDIIS 459 RE D +++ GE + L++I L+ G A S+ G Q+ I+T +GSARI DI+ + I Sbjct: 64 REYDAVVAAGEQVTAGLLAIVLQDMGIPARSWQGWQVPILTSDAHGSARIADIDGSAIFK 123 Query: 460 RYLKQDFIPVVAGFQGI-TETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 + ++ + V+AGFQG+ ETG I+TLGRGGSD +A+A+A ++ A+ C++Y DVDGVYT Sbjct: 124 AFEERKEVAVIAGFQGLHQETGRISTLGRGGSDTSAVAIAAAIKAERCDIYTDVDGVYTT 183 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKE----TRG 574 DPRIV AR + +++EEM+E++ GA+VLQ R+ E A Y VK ++++ + G Sbjct: 184 DPRIVAKARRLDRVAFEEMLEMASLGAKVLQVRSVELAMVYKVKTFVRSSFDDPLDPKPG 243 Query: 575 TLIWEGTKV-ENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGM 633 TLI + + E +V + F A++ L+ V D PGVAA I L++ +N+DMIIQ + Sbjct: 244 TLICDEEDILEQQVVTGIAFSREEAQITLRRVADNPGVAAAIFMPLAEANINVDMIIQVV 303 Query: 634 KSGEYNT-VAFIVPESQLGKLDIDLLKTRSEAKEIIIE--KGLAKVSIVGVNLTSTPEIS 690 T + F VP + L K + + ++ + K+S +GV + S P ++ Sbjct: 304 SDNTVATDITFTVPVVDFERARAILEKAQPQIGYGTLQGASDVVKISAIGVGMRSHPGVA 363 Query: 691 ATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDR 738 A F+ LA +GINI I+ S + SV+I+ Y E AV+ +HS + LD+ Sbjct: 364 ARAFKALAEKGINIRAITTSEIKFSVLIEAAYTELAVRTLHSLYGLDK 411 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: 676 Number of extensions: 28 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: 412 Length adjustment: 36 Effective length of query: 703 Effective length of database: 376 Effective search space: 264328 Effective search space used: 264328 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