Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_092349926.1 BLU87_RS14070 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_900107645.1:WP_092349926.1 Length = 435 Score = 192 bits (488), Expect = 3e-53 Identities = 122/392 (31%), Positives = 209/392 (53%), Gaps = 9/392 (2%) Query: 20 VRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEIAFD 79 +++G+ G GTVG + R + IEKR+G K ++K+++R + + + D Sbjct: 4 IKIGLLGFGTVGTGVVRNFQRNAVTIEKRLGHKIELAKIVDRDATADRGVTLEPGVVTTD 63 Query: 80 FDDLILNS--DVVVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIKKR- 136 +++I N D+V+E GG + A + +A+ G+ +VT NK L++ +G E ++ Sbjct: 64 VEEVISNPEIDIVIELFGGYEPAKSFILKAIANGKHIVTANKALMAVHGQEIIAAANQQG 123 Query: 137 -KLFFEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEMSK-GRHFEEVLKEA 194 + FEA+V GGIPIIS +++ L + + I GI+NGT N+ILT+M++ G F VL EA Sbjct: 124 VSVMFEAAVAGGIPIISAIKENLCSNEFSSILGILNGTCNFILTKMTEDGSDFAPVLDEA 183 Query: 195 QELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIVRSG 254 Q+LGYAEADPT D+EG D A+K+++L+ + G + V EGI++I + + G Sbjct: 184 QKLGYAEADPTFDVEGVDTAHKIALLSALCFGTTVDFDQVYTEGISKITSMDINFAEQMG 243 Query: 255 KKLKLIGELDFSTNRYEVRLREVTPEDPF--FNVDGVDNAIEVSTDLAGDFLLKGRGAGG 312 K+KL+ ++ EVR+ + + V+GV NA+ ++ D G LL G GAG Sbjct: 244 YKIKLLAIGKNYGDQIEVRVHPTMIPNSYQLAEVNGVFNAVRLTGDFVGPTLLYGSGAGM 303 Query: 313 YPTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVK 372 TASAV+ D+ + + K+ G + ++ ++ + ++ R + + Sbjct: 304 DATASAVMGDVMAITRDKISGAQSRVPIMGYCADQIKALPIKAMSEIISHYYLRFTTVDQ 363 Query: 373 PVVVLSAMGDTTDHLIELAKTIDENPDPRELD 404 P V+ G + I + I P+ R +D Sbjct: 364 PGVLAKIAGSLGKYNISIQSMI--QPESRNVD 393 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: 723 Number of extensions: 35 Number of successful extensions: 8 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: 435 Length adjustment: 36 Effective length of query: 703 Effective length of database: 399 Effective search space: 280497 Effective search space used: 280497 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