Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_043766820.1 U743_RS07145 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000733765.1:WP_043766820.1 Length = 434 Score = 182 bits (463), Expect = 2e-50 Identities = 130/388 (33%), Positives = 201/388 (51%), Gaps = 14/388 (3%) Query: 20 VRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEIAFD 79 +R+G+ GLGTVG + R+ + I +R G + +I+ R + + +I + Sbjct: 5 LRLGLLGLGTVGQGVVRLAQRNAALITERTGRRVVITAASARDTSRQRDCDL--SDIRIE 62 Query: 80 FDDLIL----NSDVVVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIKK 135 D + + + DVVVE IGG D A L++ A++ G+ VVT NK LI+E GN E Sbjct: 63 TDPMAVVRADDVDVVVELIGGLDPAEALLQAAIDAGKPVVTANKALIAERGNALFERAAA 122 Query: 136 R--KLFFEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEMS-KGRHFEEVLK 192 + FEA+V GGIP+I L++ L ++ + GI+NGT NYILT M+ +G F+EVL Sbjct: 123 AGVPVAFEAAVAGGIPVIKALREGLAGNRIDGLSGIINGTGNYILTRMADEGVAFDEVLA 182 Query: 193 EAQELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIVR 252 +AQ LGYAEADP+ D++G D A+K+++LA + G ++V EGI I + + + Sbjct: 183 DAQRLGYAEADPSFDVDGIDAAHKLAILAAIAFGMPLSFDAVTCEGIRGIVTKDIDLARQ 242 Query: 253 SGKKLKLIGELDFSTNRYEVRLR-EVTPEDPFF-NVDGVDNAIEVSTDLAGDFLLKGRGA 310 G ++K +G + + E+R++ + PE VDGV N + +S D GD G GA Sbjct: 243 LGYRIKHLGIAKWRGDAVELRVQPTLLPETELLAKVDGVLNTVVISGDAVGDTGYFGPGA 302 Query: 311 GGYPTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISDVEKLEKVAEKIIKRKKSG 370 GG TASAV AD+ +A+ GG + + G V L + R + Sbjct: 303 GGDATASAVWADIIDIARD---GGRSRVPALSSGDGAIRPMPVRSLAETRSSHYLRLQVA 359 Query: 371 VKPVVVLSAMGDTTDHLIELAKTIDENP 398 + V+ + DH I + P Sbjct: 360 DETGVLRAITSILADHAISVEAIYQREP 387 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: 749 Number of extensions: 33 Number of successful extensions: 6 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: 434 Length adjustment: 36 Effective length of query: 703 Effective length of database: 398 Effective search space: 279794 Effective search space used: 279794 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 Jul 25 2024. The underlying query database was built on Jul 25 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