Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_015943399.1 DHAF_RS06940 homoserine dehydrogenase
Query= BRENDA::D8WXQ1 (432 letters) >NCBI__GCF_000021925.1:WP_015943399.1 Length = 342 Score = 266 bits (680), Expect = 7e-76 Identities = 149/330 (45%), Positives = 213/330 (64%), Gaps = 16/330 (4%) Query: 4 IQVGLLGLGTVGSGVVKIIENHQDKLMHQVGCPVKVKKILVQDLNKKRDVDVDPAQLTTN 63 +++GLLG G VG GV+K I H +K++ ++G + V K LVQD++K+R ++ LT Sbjct: 6 VKIGLLGCGNVGQGVIKGILLHSNKILRKLGATLVVSKALVQDISKERAIE--GVVLTQK 63 Query: 64 ADDILQDPDIDVVIEVMGGIEETRNYLLKALSEKKHVVTANKDLMAVYGSELLTAASANG 123 DIL DP+I+VV+EVMGG T +++ +AL++ KHVVTANK L+A++G+EL A G Sbjct: 64 PQDILDDPEIEVVVEVMGGEHPTYSFIKEALAKGKHVVTANKLLLALHGAELQEIAQRKG 123 Query: 124 CDLFYEASVAGGIPILRSLVDGLASDRITKMMGIVNGTTNYILTKMSKHGRAYEEVLKEA 183 L YE SV GGIPILR++ GLA D++ K+ GI+NGTTNYILT+M++ G+ YEE L+EA Sbjct: 124 ICLLYEGSVLGGIPILRTIQYGLAGDQVKKICGILNGTTNYILTQMAESGKGYEEALREA 183 Query: 184 QELGYAEADPASDVEGLDAARKMAILATLGFSMKIDLDDVKVEGITRITEEDIQYGKQLG 243 QE GYAE+DP DV GLDAA K+ IL F + I L++V++ GI +T E++ K+ G Sbjct: 184 QEAGYAESDPTMDVTGLDAACKLVILCRECFELNIPLEEVEINGIQGLTPEEVAEQKEQG 243 Query: 244 YTMKLIGIA------------HREGEKVEVSVQPTLLSDSHPLASVNDEYNAVYVYGEAV 291 KL+ A REG + +VSVQ LS L+ V+ N + + + V Sbjct: 244 RVPKLVAEAAIIEHSSSEPEKRREGIRAKVSVQ--WLSGEAILSHVSGVDNGLSLETQLV 301 Query: 292 GETMFYGPGAGSLPTATAVVSDLVGVMKNM 321 G+ + GPGAG L T AV+SD+V + K + Sbjct: 302 GDLFWKGPGAGGLATGGAVLSDIVEIAKKV 331 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: 363 Number of extensions: 14 Number of successful extensions: 3 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: 342 Length adjustment: 30 Effective length of query: 402 Effective length of database: 312 Effective search space: 125424 Effective search space used: 125424 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