Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_015819433.1 TERTU_RS12405 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000023025.1:WP_015819433.1 Length = 406 Score = 341 bits (874), Expect = 5e-98 Identities = 179/405 (44%), Positives = 269/405 (66%), Gaps = 5/405 (1%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 S++V KFGG ++ EK++ VAEK+ + G VVV+SAM T+ LI LA + E P Sbjct: 2 SLIVQKFGGTSVGTTEKIKAVAEKVAGFRDQGHDMVVVVSAMSGETNRLISLASDVQEKP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 DPRE+D+L+STGE ++AL+ +AL+ +GY A S+TG Q+KI+TD + ARI +I+ D + Sbjct: 62 DPREMDVLVSTGEQVTIALLCMALKAKGYDARSYTGGQVKILTDSAHMKARIQNIDVDNM 121 Query: 459 SRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 L + VVAGFQG+ E G+ITTLGRGGSD T +ALA +L AD C++Y DVDGVYT Sbjct: 122 RADLDAGRVVVVAGFQGVDEAGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTT 181 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIW 578 DPR+V AR + ++++EEM+E++ G++VLQ R+ EFA KY V + + ++ + GTLI Sbjct: 182 DPRVVDSARRLDKITFEEMLEMASQGSKVLQIRSVEFAGKYKVPLRVLSSFVDGPGTLIT 241 Query: 579 ---EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKS 635 E +E P+V + F AK+ + VPD PGVA++++ + + ID+I+Q + + Sbjct: 242 LDEENETMEQPVVSGIAFNRDEAKISILGVPDAPGVASKVLSPIGDANIEIDVIVQNVAA 301 Query: 636 GEYNTVAFIVPESQLGKLDIDLLKTRSE--AKEIIIEKGLAKVSIVGVNLTSTPEISATL 693 N + F V ++ L K L + A+E++ + +AK+SIVGV + S +++ + Sbjct: 302 DNTNAITFTVHKNDLEKAKSVLAGVAEDLGAREVVGDDKIAKISIVGVGMRSHAGVASKM 361 Query: 694 FETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDR 738 F+TLANE INI MI+ S +I+VII+ KY+E AV+A+HS FELD+ Sbjct: 362 FKTLANENINIQMITTSEIKITVIIEEKYLELAVRALHSAFELDK 406 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: 705 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: 406 Length adjustment: 35 Effective length of query: 704 Effective length of database: 371 Effective search space: 261184 Effective search space used: 261184 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