Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_012566497.1 RC1_RS06230 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000016185.1:WP_012566497.1 Length = 430 Score = 189 bits (480), Expect = 2e-52 Identities = 131/325 (40%), Positives = 184/325 (56%), Gaps = 20/325 (6%) Query: 18 RKVRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQK---YELLGVP-- 72 + +++GIAGLGTVGG + +IL+ + +E R G +++ V RS K +L G+ Sbjct: 3 KPLKIGIAGLGTVGGGVLQILRRNADLLETRCGRPVVVTAVSARSRGKDRGADLSGLRWY 62 Query: 73 KEEIAFDFDDLILNSDVVVEAIGGTD-VAVDLVRRALELGRIVVTPNKNLISEYGNEFSE 131 + A D + DVV E IGG+D VA LV AL GR VVT NK L++ +G + Sbjct: 63 DDAAALAHDPEV---DVVCELIGGSDGVAKALVETALANGRHVVTANKALLARHGTALAL 119 Query: 132 YIKKR--KLFFEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEM-SKGRHFE 188 + R L +EA+V GGIP+I L++ L +V + GI+NGT NYILTEM + GR F Sbjct: 120 AAESRGLTLAYEAAVAGGIPVIKGLREGLAANRVREVHGILNGTCNYILTEMRTTGRDFA 179 Query: 189 EVLKEAQELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRI---DPE 245 +VL +AQ LGYAEADP DI+G D A+K+++L V G ++V EGI I D + Sbjct: 180 DVLADAQRLGYAEADPGFDIDGVDAAHKLAILTAVAFGCQVDFDAVHVEGIRHISSLDIQ 239 Query: 246 YLKEIVRSGKKLKLIGELDFSTNRYEVRLRE--VTPEDPFFNVDGVDNAIEVSTDLAGDF 303 Y E+ G +++L+ + E R+ V P DGV NA+ D Sbjct: 240 YADEL---GYRIRLLAIGRRTERGIEQRVHPCMVPVGSPIGATDGVFNAVVADGDFVDKV 296 Query: 304 LLKGRGAGGYPTASAVIADLFRVAK 328 +L GRGAG PTASAV+ADL +A+ Sbjct: 297 VLVGRGAGAGPTASAVVADLLDIAQ 321 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: 728 Number of extensions: 32 Number of successful extensions: 5 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: 430 Length adjustment: 36 Effective length of query: 703 Effective length of database: 394 Effective search space: 276982 Effective search space used: 276982 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