Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_013429770.1 CALKRO_RS03705 homoserine dehydrogenase
Query= BRENDA::D8WXQ1 (432 letters) >NCBI__GCF_000166775.1:WP_013429770.1 Length = 418 Score = 289 bits (740), Expect = 1e-82 Identities = 159/426 (37%), Positives = 266/426 (62%), Gaps = 16/426 (3%) Query: 5 QVGLLGLGTVGSGVVKIIENHQDKLMHQVGCPVKVKKILVQDLNKKRDVDVDPAQ--LTT 62 +V ++G G VGSGV +++ + + + G + VK IL D+ RD PA+ + Sbjct: 3 KVAIMGFGVVGSGVWEVLTKNASSIAKRAGEEISVKYIL--DI---RDFPDHPAKDLMIK 57 Query: 63 NADDILQDPDIDVVIEVMGGIEETRNYLLKALSEKKHVVTANKDLMAVYGSELLTAASAN 122 + D IL DP++ +V+E +GG+E Y K L KHVVT+NK+L+A +G ELL A N Sbjct: 58 DFDIILNDPEVSIVVETIGGLEPAYTYTKKLLLNGKHVVTSNKELVARHGPELLKIAKEN 117 Query: 123 GCDLFYEASVAGGIPILRSLVDGLASDRITKMMGIVNGTTNYILTKMSKHGRAYEEVLKE 182 + F+EASV GGIPI+R L + LA ++IT++ GI+NGTTNYILT+M K+ ++E+ LKE Sbjct: 118 NINYFFEASVGGGIPIIRPLQNCLAGNQITEIAGILNGTTNYILTQMKKYSLSFEDALKE 177 Query: 183 AQELGYAEADPASDVEGLDAARKMAILATLGFSMKIDLDDVKVEGITRITEEDIQYGKQL 242 AQE GYAE +P++D+EG DA RK+AIL+++ +S ++ + + EGI++IT+ED++Y ++L Sbjct: 178 AQEKGYAERNPSNDIEGHDACRKIAILSSIAYSHYVNYESIYTEGISKITKEDMEYAEEL 237 Query: 243 GYTMKLIGIAHR-EGEKVEVSVQPTLLSDSHPLASVNDEYNAVYVYGEAVGETMFYGPGA 301 G T+KLI ++ + + ++V V P ++S P A+V+D +NA+ V G+A+G+ MFYG GA Sbjct: 238 GCTIKLIAMSKKIDDKRVFARVSPLMISYKSPFANVDDVFNAILVKGDAIGDVMFYGQGA 297 Query: 302 GSLPTATAVVSDLVGVMKNMRLGVNGANAVTPQYQKKLKGPDEIYSKFFLRLHVKDEVGV 361 G LPTA+AVV D++ ++K++ A++ + + + +FF+R+ KD Sbjct: 298 GKLPTASAVVGDIIDIVKHIDKSYVYTWAISGDIE--VVDIENTSCRFFVRVKYKDYTKA 355 Query: 362 FANITSIFSEHSVSFEKILQMPLKENGLAEIVLVTHQASLQDYEDILVKLRDLNAVHEIK 421 ++ IF+ + ++ + G E VTH+ ++ + + +L ++ V ++ Sbjct: 356 KDAVSLIFN------DCMIVNTHRPIGTNEFAFVTHELKESEFREKISQLEKISVVEKVL 409 Query: 422 SSYRVE 427 S R + Sbjct: 410 SIVRYD 415 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: 459 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: 418 Length adjustment: 32 Effective length of query: 400 Effective length of database: 386 Effective search space: 154400 Effective search space used: 154400 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: 51 (24.3 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