Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_074201598.1 BUQ81_RS06570 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_900141795.1:WP_074201598.1 Length = 404 Score = 339 bits (869), Expect = 2e-97 Identities = 183/404 (45%), Positives = 271/404 (67%), Gaps = 5/404 (1%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 +++V K+GG ++ VE+++ VA+K+I+ G + VVV+SAM T+ L +A+ I P Sbjct: 2 ALIVQKYGGTSVGSVERIQNVADKVIRTVDEGHQVVVVVSAMSGETNRLTAMAQEIQPRP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 +PRE+D+LLSTGE ++AL+S+AL +RGY A+S+TG Q+ I+T+ + ARI IN D + Sbjct: 62 NPREMDVLLSTGEQVTIALLSMALMQRGYPAVSYTGWQVPILTNNVHTKARIEKINDDKL 121 Query: 459 SRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 L I VVAGFQG+T +ITTLGRGGSD TA+ALA +L AD C++Y DVDGVYT Sbjct: 122 RSELNAGKIVVVAGFQGVTLNNEITTLGRGGSDTTAVALAAALKADECQIYTDVDGVYTT 181 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIW 578 DPR+V +AR + ++++EM+EL+ GA+VLQ R+ EFA KY V + + ++ KE GTLI Sbjct: 182 DPRVVPNARRLDVITYDEMLELASLGAKVLQIRSVEFASKYRVPLRVLSSMKEGGGTLIT 241 Query: 579 EGTKV-ENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGE 637 KV E P++ + F AK+++ VPDKPGVA +I+ +S ++IDMIIQ Sbjct: 242 SEDKVMEKPLISGIAFNRDEAKLMILGVPDKPGVAYQIVGPISDANIDIDMIIQNQGVDG 301 Query: 638 YNTVAFIVPESQLGKLDIDLLKTRSE---AKEIIIEKGLAKVSIVGVNLTSTPEISATLF 694 F V + +++LK ++E A+E++ + G+ KVS+VG+ + S I+A +F Sbjct: 302 TTDFTFTVHRNDC-PAALEILKRQAEKLGAREVLADDGIVKVSLVGIGMKSHAGIAARMF 360 Query: 695 ETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDR 738 E LA GINI MI + +ISVII+ KY+E+AV+A+H FEL+R Sbjct: 361 EVLAERGINIQMIGTTEIKISVIIEEKYLEEAVQALHDAFELER 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: 730 Number of extensions: 33 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