Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate SMc02438 SMc02438 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >FitnessBrowser__Smeli:SMc02438 Length = 424 Score = 264 bits (675), Expect = 6e-75 Identities = 155/424 (36%), Positives = 252/424 (59%), Gaps = 30/424 (7%) Query: 341 VVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLI----ELAKTIDE 396 +VMKFGG +++D+ ++ VA + + +G + VV+SAM T+ L+ + K Sbjct: 4 IVMKFGGTSVADLNRIHNVARHVKREVDAGHEVAVVVSAMSGKTNELVGWVENMPKVAGS 63 Query: 397 NP---DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDI 453 N D RE D ++++GE + L++IAL+ G A S+ G QL I TD +G+ARI++I Sbjct: 64 NAPFYDAREYDAVVASGEQVTSGLLAIALQSMGINARSWQGWQLPIKTDNAHGAARILEI 123 Query: 454 NTDIISRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVD 513 + + R + + + VVAGFQG+ + TLGRGGSD +A+A+A ++ AD C++Y DVD Sbjct: 124 DGADVIRRMGEGQVAVVAGFQGLGPDNRLATLGRGGSDTSAVAIAAAVKADRCDIYTDVD 183 Query: 514 GVYTADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKE-- 571 GVYT DPRI AR +K++++EEM+E++ GA+VLQ R+ E A + V+ ++++ ++ Sbjct: 184 GVYTTDPRIEPKARRLKKIAFEEMLEMASLGAKVLQVRSVELAMVHKVRTFVRSSFEDPD 243 Query: 572 ---------TRGTLIW-EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQ 621 GTLI E VE +V + + A++ L+ + D+PGV+A I L++ Sbjct: 244 APGMGDLMNPPGTLICDEDEIVEQEVVTGIAYAKDEAQISLRRLADRPGVSAAIFGPLAE 303 Query: 622 MGVNIDMIIQGM-KSGEYNTVAFIVPESQLGKLDIDLLKTRSEAKE------IIIEKGLA 674 +N+DMI+Q + + G + F VP + K L+ + KE I E GL Sbjct: 304 AHINVDMIVQNISEDGSKTDMTFTVPSGDVDK----ALRVLGDNKEKIGYDVIQSESGLV 359 Query: 675 KVSIVGVNLTSTPEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRF 734 KVS++G+ + S ++A+ F LA++GINI I+ S +IS++IDG Y E AV+ +HS + Sbjct: 360 KVSVIGIGMRSHAGVAASAFRALADKGINIKAITTSEIKISILIDGPYAELAVRTLHSVY 419 Query: 735 ELDR 738 LD+ Sbjct: 420 GLDK 423 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: 35 Number of successful extensions: 5 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: 424 Length adjustment: 36 Effective length of query: 703 Effective length of database: 388 Effective search space: 272764 Effective search space used: 272764 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