Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_013842894.1 DESRU_RS14820 homoserine dehydrogenase
Query= BRENDA::D8WXQ1 (432 letters) >NCBI__GCF_000215085.1:WP_013842894.1 Length = 430 Score = 414 bits (1063), Expect = e-120 Identities = 210/427 (49%), Positives = 300/427 (70%), Gaps = 2/427 (0%) Query: 2 EAIQVGLLGLGTVGSGVVKIIENHQDKLMHQVGCPVKVKKILVQDLNKKRDVDVDPAQLT 61 + I++GLLGLGTVG GV KI+E +++ + + G ++VKK+LV+ L+KKR V++ A LT Sbjct: 4 KVIKIGLLGLGTVGCGVYKILEENKESIQQRAGIRLEVKKVLVRSLDKKRGVELPEAMLT 63 Query: 62 TNADDILQDPDIDVVIEVMGGIEETRNYLLKALSEKKHVVTANKDLMAVYGSELLTAASA 121 T+ DI++DP+I +V+EV+GG+ T +Y+L AL++ K VVTANKD++A YG +L AA Sbjct: 64 TSLADIIEDPEIKIVVEVLGGVNPTLDYVLAALNQGKSVVTANKDMVAEYGEQLFAAAQR 123 Query: 122 NGCDLFYEASVAGGIPILRSLVDGLASDRITKMMGIVNGTTNYILTKMSKHGRAYEEVLK 181 N CDL +EASVAGGIPI+R+L LA ++I ++ GI+NGTTNY+LTKM++ G + EVL Sbjct: 124 NQCDLLFEASVAGGIPIIRTLKQSLAGNQIEEVFGIINGTTNYMLTKMTQEGSPFAEVLS 183 Query: 182 EAQELGYAEADPASDVEGLDAARKMAILATLGFSMKIDLDDVKVEGITRITEEDIQYGKQ 241 EAQ GYAE+DP +DV G DAARK+AILA++ F+ +I L V EGIT+IT +DI Y + Sbjct: 184 EAQAKGYAESDPTADVGGFDAARKIAILASIAFNTRIPLSQVYTEGITKITVDDIAYASE 243 Query: 242 LGYTMKLIGIAHREGEKVEVSVQPTLLSDSHPLASVNDEYNAVYVYGEAVGETMFYGPGA 301 LGY +KL+GIA E VEV V PT + HPLA+V D +NAV+V G AVG+TMFYG GA Sbjct: 244 LGYMIKLLGIAKARSEGVEVRVHPTFIPKDHPLAAVGDVFNAVFVRGNAVGDTMFYGKGA 303 Query: 302 GSLPTATAVVSDLVGVMKNMRLGVNGANAVTPQYQKKLKGPDEIYSKFFLRLHVKDEVGV 361 G LPTA+AVV+D++ +++ V G T +K + E +SK+++RL V D+ GV Sbjct: 304 GELPTASAVVADIMDAARDIVRNVPGIIGCTCFEKKPVLDIGETFSKYYIRLKVADKPGV 363 Query: 362 FANITSIFSEHSVSFEKILQMPLKENGLAEIVLVTHQASLQDYEDILVKLRDLNAVHEIK 421 A+I +F VS + +LQ + AE+VL+TH+ Q+ +D L+ ++ L++V EI Sbjct: 364 LASIALVFGNKEVSLKSVLQK--ATDNTAELVLITHRVQEQNVQDALMDIKQLSSVLEIA 421 Query: 422 SSYRVEG 428 + RVEG Sbjct: 422 NMIRVEG 428 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: 471 Number of extensions: 14 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: 430 Length adjustment: 32 Effective length of query: 400 Effective length of database: 398 Effective search space: 159200 Effective search space used: 159200 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 25 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