Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate RR42_RS12540 RR42_RS12540 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >FitnessBrowser__Cup4G11:RR42_RS12540 Length = 436 Score = 209 bits (533), Expect = 2e-58 Identities = 125/316 (39%), Positives = 188/316 (59%), Gaps = 7/316 (2%) Query: 20 VRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEIAFD 79 ++VG+ G+GTVG + +L+ EI +R G I+ V + + ++ L + E+ D Sbjct: 4 IKVGLLGIGTVGSGTFNVLQRNQEEIRRRAGRGIEIAMVADLNTERARELTGGQVEVVAD 63 Query: 80 FDDLILNS--DVVVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIKKRK 137 ++++ D+V+E IGG +A +LV +A+E G+ VVT NK L++ +GNE E +K+ Sbjct: 64 ANEVVTRPEIDIVIELIGGYGIARELVLKAIENGKHVVTANKALLAVHGNEIFEAARKKG 123 Query: 138 LF--FEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEM-SKGRHFEEVLKEA 194 + FEA+V GGIPII L++ L ++ I GI+NGTTN+IL+EM KG F VLK+A Sbjct: 124 VIVAFEAAVAGGIPIIKALREGLTANRIEWIAGIINGTTNFILSEMRDKGLDFGTVLKQA 183 Query: 195 QELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIVRSG 254 Q LGYAEADPT DIEG D A+K+++++ + G + EGIT++ ++ G Sbjct: 184 QALGYAEADPTFDIEGIDAAHKITLMSSIAFGMPVQFDKAYVEGITKLSAVDIRYAEELG 243 Query: 255 KKLKLIGELDFSTNRYEVRLRE--VTPEDPFFNVDGVDNAIEVSTDLAGDFLLKGRGAGG 312 ++KL+G N E+R+ V + NV+G NA+ V D G L G+GAG Sbjct: 244 YRIKLLGLTRRRENGIELRVHPTLVPAKRLIANVEGAMNAVLVQGDAVGATLYYGKGAGA 303 Query: 313 YPTASAVIADLFRVAK 328 PTASAVIADL V + Sbjct: 304 EPTASAVIADLVDVTR 319 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: 763 Number of extensions: 38 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: 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 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