Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_011989421.1 CKL_RS04210 homoserine dehydrogenase
Query= BRENDA::D8WXQ1 (432 letters) >NCBI__GCF_000016505.1:WP_011989421.1 Length = 413 Score = 286 bits (732), Expect = 8e-82 Identities = 152/368 (41%), Positives = 239/368 (64%), Gaps = 10/368 (2%) Query: 4 IQVGLLGLGTVGSGVVKIIENHQDKLMHQVGCPVKVKKILVQDLNKKRDVDVDPAQLTTN 63 I + +LG G VGSGV ++I ++DK ++ + + KILV++++K D + + LT + Sbjct: 2 INIAMLGYGVVGSGVAELIFRNRDKFKDELNEELVLSKILVRNISKHID-NKNKELLTED 60 Query: 64 ADDILQDPDIDVVIEVMGGIEETRNYLLKALSEKKHVVTANKDLMAVYGSELLTAASANG 123 DDI ++ +D+++E MGG++ + Y+ +AL+ KKHVVTANKDL+A YG ELL A NG Sbjct: 61 IDDIFKEK-VDIIVEAMGGLDPSYEYVKRALNMKKHVVTANKDLIAEYGYELLQIAKKNG 119 Query: 124 CDLFYEASVAGGIPILRSLVDGLASDRITKMMGIVNGTTNYILTKMSKHGRAYEEVLKEA 183 + +EASV GGIPIL+S+ + L + I + I+NGTTN+IL+KM+ +G +Y E L+ A Sbjct: 120 VTIHFEASVGGGIPILKSINECLVGNEIKSIKSILNGTTNFILSKMNHNGMSYTEALELA 179 Query: 184 QELGYAEADPASDVEGLDAARKMAILATLGFSMKIDLDDVKVEGITRITEEDIQYGKQLG 243 Q+LG+AEA+P SDV+G DAARK++IL+T+ ++ ++D D+ +EGIT I E D +Y K Sbjct: 180 QKLGFAEANPESDVKGYDAARKLSILSTIAYNRRVDWKDINIEGITEIDEYDFKYAKMEK 239 Query: 244 YTMKLIGIAHREGEKVEVSVQPTLLSDSHPLASVNDEYNAVYVYGEAVGETMFYGPGAGS 303 ++KL+GI+ + + +V P ++ + L + DEYNA+ V G+AVG+ MF G GAG Sbjct: 240 CSIKLMGISKLGSKHIYATVMPVMVKEDSVLGKIEDEYNAILVEGDAVGDVMFSGKGAGM 299 Query: 304 LPTATAVVSDLVGVMKNMRLGVNGANAVTPQYQKK--LKGPDEIYSKFFLRLHVKDEVGV 361 PTA+AV +D+ ++K R ++ + K LKG K+FLR+ ++ V + Sbjct: 300 FPTASAVFADIADIVKQKRKKCITFSSEKAEIDKSWGLKG------KWFLRVKTQNRVKI 353 Query: 362 FANITSIF 369 I+S F Sbjct: 354 IQGISSSF 361 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: 472 Number of extensions: 18 Number of successful extensions: 2 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: 413 Length adjustment: 32 Effective length of query: 400 Effective length of database: 381 Effective search space: 152400 Effective search space used: 152400 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 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