Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_090216211.1 CV091_RS06185 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_002796795.1:WP_090216211.1 Length = 412 Score = 295 bits (755), Expect = 3e-84 Identities = 161/408 (39%), Positives = 259/408 (63%), Gaps = 9/408 (2%) Query: 340 VVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPD 399 V+VMKFGG ++++++++ + A+++ G +V++SAM T+ L+ D Sbjct: 3 VLVMKFGGTSVANLDRIRRAAKRVGVEVAKGYDVIVIVSAMSGKTNELVGWVNETSPLYD 62 Query: 400 PRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIIS 459 RE D ++S+GE + LM++ L++ G A S+ G Q+ + TD + ARI +I TD ++ Sbjct: 63 AREYDAIVSSGENVTAGLMALTLQEMGVPARSWQGWQVPLKTDSAHSQARIEEIPTDNLN 122 Query: 460 -RYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 R+ + + VVAGFQGI+ G ITTLGRGGSD TA+A A + GA+ C++Y DVDGVYT Sbjct: 123 GRFNEGMKVAVVAGFQGISPEGRITTLGRGGSDTTAVAFAAAFGAERCDIYTDVDGVYTT 182 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKE---TRGT 575 DPRI AR + ++++EEM+EL+ GA+VLQ R+ E A +Y VK+ + ++ +E GT Sbjct: 183 DPRICTKARKLDKIAFEEMLELASLGAKVLQTRSVELAMRYKVKLRVLSSFEEQSDEAGT 242 Query: 576 LIWEGTKV-ENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMK 634 L+ + ++ E+ +V V + AK+ L V D+PG+AA I TLS GVN+DMIIQ + Sbjct: 243 LVCDEEEIMESNVVNGVAYSRDEAKMTLVSVADRPGIAATIFNTLSDAGVNVDMIIQNIS 302 Query: 635 SGEYNTVAFIVPESQLGKLDIDLLKTRSEAK----EIIIEKGLAKVSIVGVNLTSTPEIS 690 + F P Q+ + + L+ + + + E++ + +AKVS+VG+ + S ++ Sbjct: 303 EEGRTDMTFSCPTDQVARAEQSLVAIKDQGELNYAELVADTDVAKVSVVGIGMRSQSGVA 362 Query: 691 ATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDR 738 A +F+ L++EGINI +I+ S +ISV+ID KY+E AV+A+H FELD+ Sbjct: 363 AKMFKVLSDEGINIKVITTSEIKISVLIDRKYMELAVQALHDAFELDK 410 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: 657 Number of extensions: 27 Number of successful extensions: 6 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: 412 Length adjustment: 36 Effective length of query: 703 Effective length of database: 376 Effective search space: 264328 Effective search space used: 264328 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 Jul 26 2024. The underlying query database was built on Jul 25 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