Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_028990562.1 G579_RS0113315 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000423825.1:WP_028990562.1 Length = 406 Score = 311 bits (797), Expect = 4e-89 Identities = 172/403 (42%), Positives = 248/403 (61%), Gaps = 3/403 (0%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 +++V KFGG ++ E++ VA K++ G + VVV+SAM TD LI+LA+ + P Sbjct: 2 ALIVQKFGGTSVGSPERIRNVANKVLAEMAKGNQVVVVVSAMSGETDRLIKLAREMHARP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 RELD+L+STGE ++AL+++ L G A S+TG Q+ I TD + ARI+ I+ I Sbjct: 62 PERELDMLISTGEQVTIALLAMGLESLGQPARSYTGGQVAIQTDSVHTKARIVSIDEHRI 121 Query: 459 SRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 L + VVAGFQG+ G+ITTLGRGGSD TA+A+A +L AD C +Y DVDGVYT Sbjct: 122 REDLAAGRVVVVAGFQGVDAAGNITTLGRGGSDTTAVAIAAALKADECHIYTDVDGVYTT 181 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLI- 577 DPRI AR + +++EEM+E++ GA+VLQ R+ EFA KY V V + ++ E GTL+ Sbjct: 182 DPRIEPRARRLDRITFEEMLEMASLGAKVLQTRSVEFAGKYNVPVRVLSSFAEGPGTLVT 241 Query: 578 WEGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGE 637 E +E V + F AK+ + VPD+PG+A I+ +S +N+DMIIQ + Sbjct: 242 CEEAAMEEAKVSGIAFNRNEAKITIVGVPDRPGIAHSILGAVSAASINVDMIIQNVSEHG 301 Query: 638 YNTVAFIVPESQLGKL--DIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTSTPEISATLFE 695 F V + K + + +A+ + + + K+SIVGV + S I+AT+FE Sbjct: 302 KTDFTFTVERNDFDKALEIVQKIGRELDAEAVQGDNRIVKISIVGVGMRSHAGIAATMFE 361 Query: 696 TLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDR 738 TLA E INI MIS S +ISV++D KY+E AV+A+H F LD+ Sbjct: 362 TLARENINIQMISTSEIKISVVVDEKYLELAVRALHEAFGLDK 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: 673 Number of extensions: 26 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