Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_017548761.1 C792_RS14385 homoserine dehydrogenase
Query= BRENDA::D8WXQ1 (432 letters) >NCBI__GCF_000330705.1:WP_017548761.1 Length = 408 Score = 307 bits (786), Expect = 4e-88 Identities = 165/376 (43%), Positives = 241/376 (64%), Gaps = 7/376 (1%) Query: 4 IQVGLLGLGTVGSGVVKIIENHQDKLMHQVGCPVKVKKILVQDLNKKRDVDVDPAQLTTN 63 +++ LLGLGTVG+GVV ++ ++++K+ G + + +LV D+NKKR +D A +T + Sbjct: 1 MKIALLGLGTVGTGVVDVLGSNREKIAGLTGESLTISHVLVNDINKKRSSGLDGAVITDD 60 Query: 64 ADDILQDPDIDVVIEVMGGIEETRNYLLKALSEKKHVVTANKDLMAVYGSELLTAASANG 123 I++D ID+VIEVMGGIE T+N L L + HV++ANKD++A + EL+ A+ N Sbjct: 61 IGKIMEDDTIDIVIEVMGGIERTKNILKAFLEKGVHVISANKDMLAQHIDELVETANENN 120 Query: 124 CDLFYEASVAGGIPILRSLVDGLASDRITKMMGIVNGTTNYILTKMSKHGRAYEEVLKEA 183 L YEASVAGGIP++ + L S++ITK+MGI+NGTTNYIL+KM+ G +Y++ L +A Sbjct: 121 AQLLYEASVAGGIPVIHGIEHSLNSNQITKVMGILNGTTNYILSKMTIDGWSYDQALDDA 180 Query: 184 QELGYAEADPASDVEGLDAARKMAILATLGFSMKIDLDDVKVEGITRITEEDIQYGKQLG 243 +E GYAEADP +DVEG+DA RK+ +L+ L + +D+ V V GI+ + DI+Y + Sbjct: 181 KEKGYAEADPTNDVEGIDAQRKIVLLSRLAYGRTVDIGTVPVSGISGVDIADIEYAAREN 240 Query: 244 YTMKLIGIAHREGEKVEVSVQPTLLSDSHPLASVNDEYNAVYVYGEAVGETMFYGPGAGS 303 T+KL+G + + +SV+P LL H LA VN E NAV+V G AVGE MFYGPGAGS Sbjct: 241 LTLKLLGKSEFRDGALSISVEPVLLPSDHQLAGVNYEKNAVFVNGNAVGEAMFYGPGAGS 300 Query: 304 LPTATAVVSDLVGVMKNMRLGVNGANAVTPQYQKKLKGPDEIYSKFFLRLHVKDEVGVFA 363 L TA+AVVSDL+ V+++ P + G +E Y + +K G Sbjct: 301 LETASAVVSDLINVVRSRSGRHKNFAPDMPAAMENGIGMNEYY------IRMKGS-GADD 353 Query: 364 NITSIFSEHSVSFEKI 379 N+T+ E S+ F +I Sbjct: 354 NLTAALDEMSLRFSRI 369 Lambda K H 0.316 0.134 0.368 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: 458 Number of extensions: 20 Number of successful extensions: 1 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: 432 Length of database: 408 Length adjustment: 32 Effective length of query: 400 Effective length of database: 376 Effective search space: 150400 Effective search space used: 150400 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 26 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