Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate AZOBR_RS07835 AZOBR_RS07835 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >FitnessBrowser__azobra:AZOBR_RS07835 Length = 435 Score = 193 bits (491), Expect = 1e-53 Identities = 128/320 (40%), Positives = 182/320 (56%), Gaps = 14/320 (4%) Query: 20 VRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEIAFD 79 +++ +AGLGTVG + ++L+ + + IE+R G + + V RS K + + K E Sbjct: 10 LKIAVAGLGTVGAGVLKLLERQADLIEQRCGRRIEVVAVSARSRGKDRGVDLSKAEW--- 66 Query: 80 FDDLILNS-----DVVVEAIGGTD-VAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYI 133 +DD + + DVVVE IGG++ A + V ALE GR VVT NK L++ +G + Sbjct: 67 YDDPVALAAHPGVDVVVELIGGSEGAAKETVELALERGRHVVTANKALLAHHGTALAAKA 126 Query: 134 KKRKLF--FEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEM-SKGRHFEEV 190 + L FEA+V GGIPII L++ L +V+ + GI+NGT NYILTEM + GR F +V Sbjct: 127 EAAGLAIGFEAAVAGGIPIIKGLREGLAANRVSEVHGILNGTCNYILTEMRTTGRDFADV 186 Query: 191 LKEAQELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEI 250 L +AQ+LGYAEADP+ DI+G D A+K+++L V G SV EGI + Sbjct: 187 LADAQKLGYAEADPSFDIDGVDAAHKLAILTSVAFGTPVDFKSVHVEGIRHVSAVDFDYA 246 Query: 251 VRSGKKLKLIGELDFSTNRYEVRLRE--VTPEDPFFNVDGVDNAIEVSTDLAGDFLLKGR 308 G ++KL+G + + E R+ V P VDGV NA+ D L GR Sbjct: 247 DALGYRIKLLGIARRTDHGIEQRVHPCMVPKAAPIAAVDGVFNAVIAQGDFVDRVLFVGR 306 Query: 309 GAGGYPTASAVIADLFRVAK 328 GAG PTASAV+ADL +A+ Sbjct: 307 GAGEGPTASAVVADLIDIAR 326 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: 713 Number of extensions: 45 Number of successful extensions: 7 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: 435 Length adjustment: 36 Effective length of query: 703 Effective length of database: 399 Effective search space: 280497 Effective search space used: 280497 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 09 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