Align Homoserine dehydrogenase; HDH; EC 1.1.1.3 (uncharacterized)
to candidate WP_010876056.1 MTH_RS01930 homoserine dehydrogenase
Query= curated2:Q58997 (336 letters) >NCBI__GCF_000008645.1:WP_010876056.1 Length = 340 Score = 308 bits (790), Expect = 1e-88 Identities = 168/335 (50%), Positives = 230/335 (68%), Gaps = 2/335 (0%) Query: 1 MDIIIVGFGAIGKGIAKVLYDKKDYLKKNYE-EFKVVAITDSSGAAIDEDGLDLLKAIEV 59 M I +VG GA+G+G + + K +YL++ Y + + + DSSGA D DGLD+ +E Sbjct: 4 MRICLVGLGAVGQGFLRAVQMKGEYLRERYGLDIRFTGVADSSGALHDPDGLDIRGVLEH 63 Query: 60 KEKTGKIKNYPEKGREMSSIDVIKEVDADVVVEVTPSNLETGDPAKTHILESFKNKKHVV 119 K++ G + ++P M+ +++ E + D +VE TP+N+E G+P ++ +L++ + KHVV Sbjct: 64 KKRAG-LGSHPSGYEGMTGDELLDEAEYDCLVEATPTNIEDGEPGRSLVLKAMGDGKHVV 122 Query: 120 TANKGPLALCYKELIEEAKKHGVIFRHEASVGGAMPIINLAKETLAGNEILSIRGILNGT 179 T+NKG LAL Y EL+E A + GV F EASVGGAMPIINLA+ETLA I S+ GILNGT Sbjct: 123 TSNKGHLALFYSELMEAASEAGVEFMFEASVGGAMPIINLARETLASCTIESVIGILNGT 182 Query: 180 TNYILTKMEKEGLDFETALKEAKELGIAETDPTQDIEGLDTAAKIVILANSIMGMNKTIK 239 TN+IL++M EG + AL EA+ELGIAET+P QD+EG D A K VI+ANSI+G T++ Sbjct: 183 TNFILSRMASEGSSYRQALIEAQELGIAETNPAQDVEGTDAACKAVIIANSILGRPCTLR 242 Query: 240 DVKVKGISRITPEALFLANKRGYTIKLIGQIKDGYLIVEPMLVPIDSPLNVKGTLNVAMF 299 DV+V+GI+ IT A+ LA + GY IKLI +I L V P LV + SP V GTLN+A Sbjct: 243 DVRVEGITGITQGAIELAAQEGYLIKLIAEISGDRLEVGPRLVRMGSPYAVDGTLNMATL 302 Query: 300 ETDLAKEVVVVGRGAGPIETASAILSDLIHIYNST 334 TDLA EV VGRGAG +ETASA+L+D I I+ + Sbjct: 303 RTDLAGEVTAVGRGAGSLETASAMLTDTITIWRKS 337 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: 301 Number of extensions: 11 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: 340 Length adjustment: 28 Effective length of query: 308 Effective length of database: 312 Effective search space: 96096 Effective search space used: 96096 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