Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_027722491.1 H589_RS0113380 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000425265.1:WP_027722491.1 Length = 429 Score = 201 bits (511), Expect = 6e-56 Identities = 125/320 (39%), Positives = 190/320 (59%), Gaps = 8/320 (2%) Query: 17 VRKVRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRS-PQKYELLGVPKEE 75 ++ V++ IAG GTVG + RI++E + I R G+ F ++ V+ R +K + L P+ + Sbjct: 1 MQTVKLAIAGFGTVGTGLARIIEENKDVILARCGKNFKLTSVLVRDINKKRDFLPGPEVK 60 Query: 76 IAFDFDDLILNSDV--VVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYI 133 D D+ N DV VVE +GG VA ++V +AL+ G+ VVT NK+L++ +G E Sbjct: 61 FTADPDEFTSNPDVDIVVELMGGITVAKEIVIKALKAGKHVVTANKHLLAVHGIELFRVA 120 Query: 134 KKRK--LFFEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEMS-KGRHFEEV 190 + K L++EASV GGIPII +++ L ++ I GI+NGT NYIL+EMS G F+ Sbjct: 121 AENKVGLYYEASVAGGIPIIQSIKESLAANRIKSIVGILNGTANYILSEMSTNGLEFDTA 180 Query: 191 LKEAQELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEI 250 L +A+ELGYAEADPT DIEG D A+KV VLA + G+ ++ + EGIT+++ + ++ Sbjct: 181 LNQAKELGYAEADPTFDIEGIDAAHKVVVLARIAYGQDYPLDELPIEGITKVEGQDIRFA 240 Query: 251 VRSGKKLKLIGELDFSTNRYEVRLREVTPEDPFF--NVDGVDNAIEVSTDLAGDFLLKGR 308 G ++KLIG++ + E + + V G NAI V + G G+ Sbjct: 241 REFGYRIKLIGQVRDVGGKLEAGVFPALVKYTLLLARVGGNYNAIRVEGNAVGPAFFHGQ 300 Query: 309 GAGGYPTASAVIADLFRVAK 328 GAG PT SAV+AD+ ++K Sbjct: 301 GAGSLPTGSAVLADIMALSK 320 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: 768 Number of extensions: 47 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: 429 Length adjustment: 36 Effective length of query: 703 Effective length of database: 393 Effective search space: 276279 Effective search space used: 276279 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