Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_011613860.1 TERY_RS22050 homoserine dehydrogenase
Query= BRENDA::D8WXQ1 (432 letters) >NCBI__GCF_000014265.1:WP_011613860.1 Length = 434 Score = 336 bits (861), Expect = 1e-96 Identities = 179/433 (41%), Positives = 281/433 (64%), Gaps = 14/433 (3%) Query: 5 QVGLLGLGTVGSGVVKIIENHQDKLMHQVGCPVKVKKILVQDLNKKRDVDVDPAQLTTNA 64 ++GLLGLGTVG G KI+ + Q + H + +++ ++ V+D++K RD+++ P LTT+ Sbjct: 4 KIGLLGLGTVGIGTAKILLSPQGR--HPLINELEIYRVGVRDISKTRDINISPNILTTDL 61 Query: 65 DDILQDPDIDVVIEVMGGIEETRNYLLKALSEKKHVVTANKDLMAVYGSELLTAASANGC 124 + I DPD+D++IE++GG+E R+ +LKA+ KH+VTANK +++ YG E+ AA+ Sbjct: 62 EAIATDPDVDIIIELIGGLEPARSLILKAIEHGKHIVTANKAVISRYGPEIFDAANKKSV 121 Query: 125 DLFYEASVAGGIPILRSLVDGLASDRITKMMGIVNGTTNYILTKMSKHGRAYEEVLKEAQ 184 + EASV GGIP+++ L + L +RI + GI+NGTTNYILTKM K G + +VL +AQ Sbjct: 122 YVMLEASVGGGIPVIQPLKESLTVNRIHSITGIINGTTNYILTKMQKEGADFADVLADAQ 181 Query: 185 ELGYAEADPASDVEGLDAARKMAILATLGFSMKIDLDDVKVEGITRITEEDIQYGKQLGY 244 +LGYAEA+P +DVEGLDA K+AIL +L FS I L+D+ EGI +IT DI Y QL + Sbjct: 182 KLGYAEANPTADVEGLDAKDKIAILGSLAFSGFIKLEDIYCEGIRQITAADITYAAQLNF 241 Query: 245 TMKLIGIAHR-------EGEKVEVSVQPTLLSDSHPLASVNDEYNAVYVYGEAVGETMFY 297 +KL+ IA + +K+++ V PTL+ +HPLAS+ND NA+++ GE +G+ MF+ Sbjct: 242 VIKLLAIAKQAPKNTNFTSDKLQLRVHPTLIPKTHPLASINDVDNAIFIEGEPIGQVMFF 301 Query: 298 GPGAGSLPTATAVVSDLVGVMKNMRLGV----NGANAVTPQYQKKLKGPDEIYSKFFLRL 353 GPGAG+ PTA+AVVSD++ + ++ + + T Q ++ E+ ++F+ R Sbjct: 302 GPGAGAGPTASAVVSDIMNIAAILQTETEPIPHPLLSCTHQKYCEIVPIKELITRFYARF 361 Query: 354 HVKDEVGVFANITSIFSEHSVSFEKILQMPLKENGLAEIVLVTHQASLQDYEDILVKLRD 413 +D+ GV + S F ++SVS E ++Q + N LAEIV+VT ++ L +++ Sbjct: 362 LTQDKPGVIGKLGSCFGKYSVSLESVVQTGI-HNQLAEIVVVTRDVREGNFRQALEEIQS 420 Query: 414 LNAVHEIKSSYRV 426 L+ ++ I S RV Sbjct: 421 LDVINSIPSILRV 433 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: 464 Number of extensions: 25 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: 434 Length adjustment: 32 Effective length of query: 400 Effective length of database: 402 Effective search space: 160800 Effective search space used: 160800 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 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