Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_019867196.1 METMI_RS0115420 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000384075.1:WP_019867196.1 Length = 436 Score = 207 bits (526), Expect = 1e-57 Identities = 141/398 (35%), Positives = 215/398 (54%), Gaps = 17/398 (4%) Query: 17 VRKVRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEI 76 ++ ++VG+ GLGTVGG ILK EI +R G + +I++ R K + ++ Sbjct: 1 MKPIKVGVLGLGTVGGGTVNILKRNAAEIARRAGREIVITRASARDLHKPRICDTQDIQV 60 Query: 77 AFDFDDLILNSDV--VVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIK 134 D ++I + D+ +VE IGG + D++ A+ G+ +VT NK+LI+ +GNE Sbjct: 61 TNDPFEIINDPDIDIIVETIGGAGIVKDMILTAIANGKHIVTANKSLIATHGNEIFAKAS 120 Query: 135 KRKLF--FEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEM-SKGRHFEEVL 191 ++ + FEA+V GGIPII +++ L ++ + GI+NGT N+ILTEM KGR F +VL Sbjct: 121 EKGVIVAFEAAVAGGIPIIKAIREGLSGNQIQWVAGIINGTGNFILTEMRDKGRDFGDVL 180 Query: 192 KEAQELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRI---DPEYLK 248 EAQ LGYAEADP+ D+EG D A+K+++LA + G V EGIT+I D EY + Sbjct: 181 AEAQFLGYAEADPSFDVEGIDAAHKLTILASIAFGIPLQFEKVFTEGITQITRTDVEYAE 240 Query: 249 EIVRSGKKLKLIGELDFSTNRYEVRLR-EVTPEDPFF-NVDGVDNAIEVSTDLAGDFLLK 306 ++ G ++K +G + E+R+ + PE NV+GV NA+ V D G L Sbjct: 241 QL---GYRIKHLGIARKTPEGIELRVHPTLIPERRLIANVNGVMNAVLVKGDAVGATLYY 297 Query: 307 GRGAGGYPTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISDVEKL--EKVAEKII 364 G GAG PT S+V+AD+ V + L + V + F A++D+ L E + Sbjct: 298 GAGAGAEPTGSSVVADVIDVV--RALTSDPENRVPHLAFQADALADIPVLPSECIKTSYY 355 Query: 365 KRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDPRE 402 R + KP V+ DH I + I + P E Sbjct: 356 LRLNAEDKPGVLADVTKILADHNISIEAMIQKEPSKGE 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: 779 Number of extensions: 34 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 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