Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_036262203.1 DL86_RS12820 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000746085.1:WP_036262203.1 Length = 412 Score = 258 bits (658), Expect = 5e-73 Identities = 151/410 (36%), Positives = 242/410 (59%), Gaps = 10/410 (2%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 S +VMKFGG +++D+E++ VA + + +K+G VV+SAM T+ L+ + Sbjct: 2 SRLVMKFGGTSVADIERIRNVARHVERERKAGNDIAVVVSAMSGKTNELVRWCEEASGLC 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDIN-TDI 457 D RE D ++++GE + L++I L++ G A S+ G Q+ I+T +GSARI + I Sbjct: 62 DQREYDAVVASGEQVTAGLLAIVLQEIGIPARSWQGWQVPILTSNSHGSARIAHVEGRAI 121 Query: 458 ISRYLKQDFIPVVAGFQGIT-ETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVY 516 + + + + VVAGFQG+ ETG I TLGRGGSD +A+A+A ++GA C++Y DVDGVY Sbjct: 122 LEGFSARGEVAVVAGFQGLNKETGRIATLGRGGSDTSAVAIAAAIGASRCDIYTDVDGVY 181 Query: 517 TADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETR--- 573 T DPRIV A+ + +++EEM+E++ GA+VLQ R+ E A + VK ++++ + R Sbjct: 182 TTDPRIVPKAKRLDRVAFEEMLEMASLGAKVLQVRSVELAMAHKVKTFVRSSFDDPRDPK 241 Query: 574 -GTLIW-EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQ 631 GTLI E VE +V + F A++ L+ V D PGVAA I L++ +N+DMI+Q Sbjct: 242 PGTLICDEEDIVEQQVVTGIAFSRDEAQITLRQVADHPGVAAAIFMPLAEANINVDMIVQ 301 Query: 632 -GMKSGEYNTVAFIVPESQLGKLDIDLLKTRSEA--KEIIIEKGLAKVSIVGVNLTSTPE 688 + + F V + + L K + + + + + K+S +GV + S Sbjct: 302 VASEDSGATDMTFTVSTADFERTKAILQKAQPQIGFQSLNGASDVVKISAIGVGMRSHAG 361 Query: 689 ISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDR 738 ++A F+ LA +GINI I+ S + SV+I+ Y E AV+ +HS + LD+ Sbjct: 362 VAARAFKALAEKGINIRAITTSEIKFSVLIEAAYTELAVRTLHSLYGLDK 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: 647 Number of extensions: 28 Number of successful extensions: 6 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