Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate YP_001327133.1 Smed_1453 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000017145.1:YP_001327133.1 Length = 440 Score = 205 bits (522), Expect = 3e-57 Identities = 134/319 (42%), Positives = 185/319 (57%), Gaps = 12/319 (3%) Query: 20 VRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEIAFD 79 +++GIAGLGTVG S+ RIL++R + G I+ V R K GV I + Sbjct: 5 LKIGIAGLGTVGASLVRILQDRHETLATTCGRAIEITAVTARDRSKDR--GVDLAGITWF 62 Query: 80 FDDLILNS----DVVVEAIGGT-DVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIK 134 D + L S DV VE +GGT D A V+ AL G VVT NK L++ +G E +E + Sbjct: 63 DDAVSLASQGGIDVFVELMGGTGDPAYASVKAALTHGVHVVTANKALLAAHGIELAEIAE 122 Query: 135 KRK--LFFEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEMSK-GRHFEEVL 191 K L +EA+V GGIP+I L++ + ++R+ GIMNGT NYILT+M K G FE L Sbjct: 123 KHGALLNYEAAVAGGIPVIKALRESMTGNTISRVYGIMNGTCNYILTKMEKEGLSFEACL 182 Query: 192 KEAQELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIV 251 KEAQ LGYAEADP DIEG D A+K+S+L + G + + EGIT I E ++ Sbjct: 183 KEAQRLGYAEADPAFDIEGNDTAHKLSILTSLAFGTAIAADDIYLEGITNISIEDIQAAA 242 Query: 252 RSGKKLKLIGELDFSTNRYEVRLR-EVTPEDPFF-NVDGVDNAIEVSTDLAGDFLLKGRG 309 G ++KL+G + + E R+ + P D VDGV NA+ + +D+ G+ L+ G G Sbjct: 243 DLGYRIKLLGVAQRTESGIEQRVHPTMVPHDTVIAQVDGVTNAVAIESDILGELLMVGPG 302 Query: 310 AGGYPTASAVIADLFRVAK 328 AGG TASAV+ D+ +AK Sbjct: 303 AGGDATASAVLGDIADIAK 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: 703 Number of extensions: 34 Number of successful extensions: 4 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: 440 Length adjustment: 36 Effective length of query: 703 Effective length of database: 404 Effective search space: 284012 Effective search space used: 284012 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