Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_012470577.1 GLOV_RS12540 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000020385.1:WP_012470577.1 Length = 404 Score = 312 bits (799), Expect = 2e-89 Identities = 168/404 (41%), Positives = 262/404 (64%), Gaps = 9/404 (2%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 ++VV K+GG ++ ++++ VA++IIK ++G + VVV+SAM T+ L+ LA + + P Sbjct: 2 ALVVQKYGGTSVGTTDRIKNVAKRIIKTYEAGNEVVVVVSAMSGETNKLVALANDMVDIP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 D RE D++++TGE ++ L+S+ L+ GYKA S+ G Q+ IITD + ARI I+ + Sbjct: 62 DNREYDVVVATGEQVTIGLLSMYLKSLGYKAKSYMGWQVPIITDSTFSKARIESIDDTRM 121 Query: 459 SRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 LK I VVAGFQG+ + G++TTLGRGGSD +A+ALA +L AD+CE+Y DVDGVYT Sbjct: 122 RADLKAGNIVVVAGFQGMDKDGNLTTLGRGGSDTSAVALAAALKADVCEIYTDVDGVYTT 181 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIW 578 DP + K+AR ++++S++EM+EL+ GA+VLQ R+ EFA+K+ V + ++++ E GT++ Sbjct: 182 DPNVCKEARKVEKVSYDEMLELASLGAKVLQIRSVEFAKKFNVDIHVRSSLNENTGTMVT 241 Query: 579 -EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGE 637 E +E +V V ++ AK+ + VPDKPG+AA+I+ LS +++DMI+Q + Sbjct: 242 REDKDMEGILVSGVAYDKNEAKIAVLGVPDKPGIAAQILTPLSDAAISVDMIVQNVSHDG 301 Query: 638 YNTVAFIVPESQLGKLDIDLLKTRSEAKEIII-----EKGLAKVSIVGVNLTSTPEISAT 692 F V ++ L K LL T AKEI ++ ++K+SIVG+ + S ++ Sbjct: 302 LTDFTFTVTKADLKKA---LLITNEAAKEIQAQEVQSDENISKISIVGLGMRSHAGVATR 358 Query: 693 LFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFEL 736 +F LA INI MIS S ++SV+ID KY E AV+ +H F L Sbjct: 359 MFSVLAKNNINIGMISTSEIKVSVVIDEKYTELAVRVLHEEFGL 402 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: 678 Number of extensions: 30 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: 404 Length adjustment: 35 Effective length of query: 704 Effective length of database: 369 Effective search space: 259776 Effective search space used: 259776 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