Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_092994380.1 BLP65_RS06305 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_900102855.1:WP_092994380.1 Length = 436 Score = 206 bits (523), Expect = 3e-57 Identities = 143/405 (35%), Positives = 220/405 (54%), Gaps = 13/405 (3%) Query: 20 VRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEIAFD 79 V+VG+ GLGTVGG +L+E EI +R G + R K + ++ D Sbjct: 4 VKVGLLGLGTVGGGTINLLQENAEEIMRRAGRGIEVIHACARDLNKPRICDTEGISLSTD 63 Query: 80 FDDLILNSDV--VVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIKKRK 137 ++++ N DV ++E IGG +A D++ RA+E G+ +VT NK LI+++GNE + R Sbjct: 64 PNEVVDNPDVDVILELIGGEGMARDVMLRAIENGKHIVTANKALIAKHGNEIFAAAEARG 123 Query: 138 LF--FEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEM-SKGRHFEEVLKEA 194 + FEA+V GGIPII L++ L ++ + GI+NGT N+ILTEM + R F +VL EA Sbjct: 124 VIVAFEAAVAGGIPIIKGLREGLAANRIEWLAGIINGTGNFILTEMRDEDRDFADVLAEA 183 Query: 195 QELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIVRSG 254 Q LGYAEADPT D+EG D A+K++++A + G + V EGIT + + + G Sbjct: 184 QRLGYAEADPTFDVEGIDAAHKLAIMASIAFGMPLKFDRVYTEGITHVTRDDVTFAEELG 243 Query: 255 KKLKLIGELDFSTNRYEVRLR-EVTPEDPFF-NVDGVDNAIEVSTDLAGDFLLKGRGAGG 312 ++K +G + N E+R+ + PE NVDGV NA+ V ++ G L G GAG Sbjct: 244 YRIKHLGIARRTWNGIELRVHPTLIPERQLIANVDGVMNAVVVKGNMVGPTLYYGAGAGA 303 Query: 313 YPTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISD--VEKLEKVAEKIIKRKKSG 370 PTASAV+ADL V + L A + V + A++D + +++V R + Sbjct: 304 EPTASAVVADLIDVV--RALSCAPESRVPHLGVHPHALADESILAMDEVETAYYLRMQVV 361 Query: 371 VKPVVVLSAMGDTTDHLIELAKTIDENPDPRE--LDLLLSTGEIQ 413 +P V+ D I + + + P P E + ++L T +Q Sbjct: 362 DRPGVLADLTRTFADLEISIEAVVQKEPPPGESLVTIILLTRTVQ 406 Score = 27.7 bits (60), Expect = 0.001 Identities = 10/27 (37%), Positives = 19/27 (70%) Query: 605 VPDKPGVAARIMRTLSQMGVNIDMIIQ 631 V D+PGV A + RT + + ++I+ ++Q Sbjct: 360 VVDRPGVLADLTRTFADLEISIEAVVQ 386 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: 737 Number of extensions: 35 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 739 Length of database: 436 Length adjustment: 36 Effective length of query: 703 Effective length of database: 400 Effective search space: 281200 Effective search space used: 281200 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