Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_014148042.1 MEALZ_RS07610 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000968535.2:WP_014148042.1 Length = 436 Score = 207 bits (527), Expect = 9e-58 Identities = 139/395 (35%), Positives = 213/395 (53%), Gaps = 11/395 (2%) Query: 17 VRKVRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEI 76 ++ V+VG+ GLGTVGG +LK EI +R G + ++++ R ++ + + Sbjct: 1 MKPVKVGVLGLGTVGGGTVNVLKRNAAEIARRAGREIVVTRASTRDLERSRICDTQGIAL 60 Query: 77 AFDFDDLILNSDV--VVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIK 134 D +++ + ++ VVE IGG +A DLV +A+E G+ VVT NK LI+ +GNE Sbjct: 61 TADPYEIVNDPEIEIVVELIGGETIAKDLVLKAIENGKHVVTANKALIALHGNEIFAKAS 120 Query: 135 KRKLF--FEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEM-SKGRHFEEVL 191 + + FEA+V GGIPII +++ L ++ + GI+NGT N+ILTEM KGR F +VL Sbjct: 121 GKGVMVAFEAAVAGGIPIIKAIREGLSGNQIEWVAGIINGTGNFILTEMRDKGRDFADVL 180 Query: 192 KEAQELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIV 251 EAQ LGYAEADPT D+EG D A+K+++LA + G + V EGIT+I + + Sbjct: 181 AEAQALGYAEADPTFDVEGIDAAHKLTILASIAFGIPLQFDKVYTEGITQITRDDVDYAD 240 Query: 252 RSGKKLKLIGELDFSTNRYEVRLRE--VTPEDPFFNVDGVDNAIEVSTDLAGDFLLKGRG 309 G ++K +G ++ E+R+ + NVDGV NA+ V D G L G G Sbjct: 241 TLGYRIKHLGIARKTSEGIELRVHPTLIPARRLIANVDGVMNAVLVKGDAVGPTLYYGAG 300 Query: 310 AGGYPTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISDVEKL--EKVAEKIIKRK 367 AG PTAS+V+AD+ V + L + V + F A++D+ L E++ R Sbjct: 301 AGAEPTASSVVADVIDVV--RALTSDPENRVPHLAFQPNALADIPMLSAEQIHTAYYLRL 358 Query: 368 KSGVKPVVVLSAMGDTTDHLIELAKTIDENPDPRE 402 + +P V+ H I + I + P E Sbjct: 359 NAEDRPGVLADITRILALHDISIEAIIQKEPHENE 393 Score = 25.8 bits (55), Expect = 0.005 Identities = 12/25 (48%), Positives = 17/25 (68%) Query: 607 DKPGVAARIMRTLSQMGVNIDMIIQ 631 D+PGV A I R L+ ++I+ IIQ Sbjct: 362 DRPGVLADITRILALHDISIEAIIQ 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: 758 Number of extensions: 43 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 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