Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate Ga0059261_2519 Ga0059261_2519 aspartate kinase (EC 2.7.2.4)
Query= BRENDA::Q9WZ17 (739 letters) >FitnessBrowser__Korea:Ga0059261_2519 Length = 419 Score = 267 bits (682), Expect = 9e-76 Identities = 159/411 (38%), Positives = 249/411 (60%), Gaps = 16/411 (3%) Query: 341 VVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDP 400 +VMKFGG +++ +E++ VA ++ ++G + VV+SAM TD L+ + D Sbjct: 4 IVMKFGGTSMAGIERIRNVANRVKAEWEAGNQVAVVVSAMAGETDRLVGFCREASPLYDL 63 Query: 401 RELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIISR 460 RE D ++S GE + L++IAL+ G A S+ G QL I T + SARI I+T ++ Sbjct: 64 REYDTVVSAGEQVTSGLLAIALQAIGVPARSWLGWQLPIHTSSAHASARIGTIDTTELNA 123 Query: 461 YLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTADP 520 L + V+ GFQG+ E +TTLGRGGSD +A+A+A ++ AD C++Y DVDGVYT DP Sbjct: 124 SLADGNVAVIPGFQGLAEDNRVTTLGRGGSDTSAVAVAAAMKADRCDIYTDVDGVYTTDP 183 Query: 521 RIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKET------RG 574 RIV AR + ++++EEM+EL+ GA+VLQ R+ A K GV+V + ++ ++ RG Sbjct: 184 RIVPRARKLSKVTYEEMLELASVGAKVLQTRSVGLAMKEGVRVRVLSSLEDNRDEEGHRG 243 Query: 575 TLI---WEGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQ 631 TLI E VE ++ + + AKV L +VPD+PG I L++ G+N+DMI+Q Sbjct: 244 TLIVGEEEINDVERQLITGIAADKNEAKVTLTNVPDRPGAVGHIFTPLAEAGINVDMIVQ 303 Query: 632 GMKSGEYNT-VAFIVPESQLGKLDIDLLKTRSEA----KEIIIEKGLAKVSIVGVNLTST 686 + +T V F VP ++L + +D+L+ +S+A +I + +AK+S+VGV + S Sbjct: 304 NVAHATGSTDVTFTVPRAELARA-LDVLE-KSKAPIGYDALIHDTKVAKISVVGVGMRSH 361 Query: 687 PEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELD 737 ++AT+FETL INI I+ S ++SV+I E AV+ +H+ + LD Sbjct: 362 AGVAATMFETLGERRINILAITTSEIKVSVLIHEDETELAVRVLHTAYGLD 412 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: 646 Number of extensions: 27 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: 419 Length adjustment: 36 Effective length of query: 703 Effective length of database: 383 Effective search space: 269249 Effective search space used: 269249 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 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