Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_012468657.1 GLOV_RS02785 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000020385.1:WP_012468657.1 Length = 407 Score = 291 bits (746), Expect = 3e-83 Identities = 159/401 (39%), Positives = 251/401 (62%), Gaps = 3/401 (0%) Query: 341 VVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDP 400 VV K+GG+A++ E++ K+AE+II+ VVV+SA T+ LIE+A+ + Sbjct: 4 VVQKYGGSAVTSPEQIRKIAERIIQSYNDRNDVVVVISARAGETNRLIEMAQEMCPRQTG 63 Query: 401 RELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIISR 460 E DLL+S GE S+ L+++ + GYK ++ G Q+ IITD + A I I+ I Sbjct: 64 SEYDLLISAGEQVSIGLLALCISSLGYKVRTYLGWQVPIITDSLHTRASIEYIDPAKIRA 123 Query: 461 YLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTADP 520 L I +VAGFQGI +G ITTLGRGG D +A+ALA++LGA++CELY DVDG++TADP Sbjct: 124 DLNHGAIVLVAGFQGIDRSGTITTLGRGGGDTSAVALAHALGAEVCELYSDVDGIFTADP 183 Query: 521 RIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTL-IWE 579 I DAR I+++S++EM+EL+ GA+ +Q RA E+A+K+ V + +++A RGTL + E Sbjct: 184 AICDDARKIEKISYDEMLELASQGARGVQIRAIEYAKKHNVTIHVRSAFTAERGTLVVKE 243 Query: 580 GTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEYN 639 +E +V + + AK+ + VPDKPG AA+I+ L+ +++DMI+Q + Sbjct: 244 HMPMEGVVVTGIVADKNEAKIAVLGVPDKPGSAAKILTGLADKDISVDMIVQNVGQDGLA 303 Query: 640 TVAFIVPESQLGKLDIDLLKTRSE--AKEIIIEKGLAKVSIVGVNLTSTPEISATLFETL 697 + F + ++ L K + E A+E++ ++ ++KVSIVG+ + + ++A +F L Sbjct: 304 DITFSISKTDLEKAHQITTQIAKEVNAREVLADRNISKVSIVGLGMKNHAGVAARMFTAL 363 Query: 698 ANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDR 738 A INI MIS S ++SV I+ KY E AV+ +H F++D+ Sbjct: 364 AYNNINIQMISTSEIKVSVAIEEKYTELAVRVLHEAFKVDQ 404 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: 696 Number of extensions: 27 Number of successful extensions: 4 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: 407 Length adjustment: 36 Effective length of query: 703 Effective length of database: 371 Effective search space: 260813 Effective search space used: 260813 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: 52 (24.6 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