Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_074201259.1 BUQ81_RS04880 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_900141795.1:WP_074201259.1 Length = 434 Score = 191 bits (485), Expect = 7e-53 Identities = 120/319 (37%), Positives = 186/319 (58%), Gaps = 7/319 (2%) Query: 17 VRKVRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEI 76 ++ +++G+ GLGTVGG IL++ + +++R+ +S + R K + ++ Sbjct: 1 MKTIKLGLIGLGTVGGGTLAILRDSADLLQQRVNANIEVSIIAVRDLNKPRAVDTGSIQL 60 Query: 77 AFDFDDLILNSDV--VVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIK 134 D ++ + DV VVE +GGT +A +LV RA++ G+ VVT NK L++E+G+E + Sbjct: 61 TDDPTQVVNHPDVDIVVELMGGTGLARELVLRAIDNGKHVVTANKALLAEHGDEVFAAAE 120 Query: 135 KR--KLFFEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEMSK-GRHFEEVL 191 K+ ++ +EA+ GGIPII L++ L + + GI+NGT NYILTEM + G F VL Sbjct: 121 KQGVQVAYEAAAAGGIPIIKALREGLSANNIDWVAGIINGTGNYILTEMKQPGADFNAVL 180 Query: 192 KEAQELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIV 251 K AQELGYAEADPT D+EG D A+K+++LA + G V EGI+RI + ++ Sbjct: 181 KRAQELGYAEADPTFDVEGIDAAHKLTILASLAFGIPLQFEKVYTEGISRISADDMRFAD 240 Query: 252 RSGKKLKLIGELDFSTNRYEVRLR-EVTPEDPFF-NVDGVDNAIEVSTDLAGDFLLKGRG 309 G ++K +G + + +R+ + P+ NV GV NA+ D G L G G Sbjct: 241 MLGYEIKHLGIARRTDDGVSMRVHPTLIPKSVLLANVSGVMNAVMTHGDHVGPTLYYGPG 300 Query: 310 AGGYPTASAVIADLFRVAK 328 AG PTASAV+AD+ V + Sbjct: 301 AGAGPTASAVVADIVDVVR 319 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: 714 Number of extensions: 34 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: 434 Length adjustment: 36 Effective length of query: 703 Effective length of database: 398 Effective search space: 279794 Effective search space used: 279794 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 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