Align Homoserine dehydrogenase; HDH; EC 1.1.1.3 (uncharacterized)
to candidate WP_013644768.1 METBO_RS05880 homoserine dehydrogenase
Query= curated2:Q58997 (336 letters) >NCBI__GCF_000191585.1:WP_013644768.1 Length = 339 Score = 361 bits (926), Expect = e-104 Identities = 191/335 (57%), Positives = 243/335 (72%), Gaps = 2/335 (0%) Query: 1 MDIIIVGFGAIGKGIAKVLYDKKDYLKKNYE-EFKVVAITDSSGAAIDEDGLDLLKAIEV 59 M + I+GFGA+G G+ KVL K D L Y + VVA+TD SGAA++ +GLDL IE Sbjct: 1 MKLCILGFGAVGMGVVKVLSMKNDMLIDKYGLDISVVAVTDRSGAAVNPEGLDLQLLIET 60 Query: 60 KEKTGKIKNYPEKGRE-MSSIDVIKEVDADVVVEVTPSNLETGDPAKTHILESFKNKKHV 118 KE T KI +YPE G + S +V++ V+ D +VEVTP+N++ G+PA TH++E+ K + V Sbjct: 61 KENTNKISDYPEYGVPGLDSAEVVETVEFDCLVEVTPTNIDHGEPANTHMMETLKKGRDV 120 Query: 119 VTANKGPLALCYKELIEEAKKHGVIFRHEASVGGAMPIINLAKETLAGNEILSIRGILNG 178 VT+NKGPL+L + EL+E A + F++EASVGGAMPIIN A LAGN I S+ GILNG Sbjct: 121 VTSNKGPLSLYFSELVETANSNNAEFKYEASVGGAMPIINFAHNNLAGNNISSVLGILNG 180 Query: 179 TTNYILTKMEKEGLDFETALKEAKELGIAETDPTQDIEGLDTAAKIVILANSIMGMNKTI 238 TTNYIL++M EG +E LKEA+ELGIAETDPTQD+EG+D AAKIVILANS++ N TI Sbjct: 181 TTNYILSRMANEGSSYEQTLKEAQELGIAETDPTQDVEGIDAAAKIVILANSVLNRNVTI 240 Query: 239 KDVKVKGISRITPEALFLANKRGYTIKLIGQIKDGYLIVEPMLVPIDSPLNVKGTLNVAM 298 KDV ++GI+ ITPE++ LA K G+ IKLIG+ + L V P LV SP V GTLNVA Sbjct: 241 KDVHMEGITNITPESIELAKKEGFLIKLIGEASNNNLEVAPRLVKEGSPFAVDGTLNVAT 300 Query: 299 FETDLAKEVVVVGRGAGPIETASAILSDLIHIYNS 333 TDLA +V VVG+GAG IETASAILSD+I + S Sbjct: 301 VMTDLADDVTVVGKGAGSIETASAILSDIICVKKS 335 Lambda K H 0.314 0.135 0.366 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: 374 Number of extensions: 20 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: 336 Length of database: 339 Length adjustment: 28 Effective length of query: 308 Effective length of database: 311 Effective search space: 95788 Effective search space used: 95788 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 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