Align Homoserine dehydrogenase; HDH; EC 1.1.1.3 (uncharacterized)
to candidate WP_013684244.1 ARCVE_RS07875 homoserine dehydrogenase
Query= curated2:Q58997 (336 letters) >NCBI__GCF_000194625.1:WP_013684244.1 Length = 330 Score = 326 bits (835), Expect = 6e-94 Identities = 168/330 (50%), Positives = 237/330 (71%), Gaps = 8/330 (2%) Query: 3 IIIVGFGAIGKGIAKVLYDKKDYLKKNYEEFKVVAITDSSGAAIDEDGLDLLKAIEVKEK 62 I I GFGA+G+G+A++L ++ + +++ E++VVA+ DS G+ DE+G+ L +A+E K+K Sbjct: 4 IAIFGFGAVGQGVAEILMNR-ERIERWIGEYRVVAVADSKGSICDENGISLKEALEAKKK 62 Query: 63 TGKIKNYPEKGREMSSIDVIKEVDADVVVEVTPSNLETGDPAKTHILESFKNKKHVVTAN 122 MS +D+I +D DV +E TP+N+ETG+P ++I HVVT+N Sbjct: 63 GSLPPG-------MSVMDIIDSIDFDVAIEATPTNIETGEPGLSYIKACLNKGCHVVTSN 115 Query: 123 KGPLALCYKELIEEAKKHGVIFRHEASVGGAMPIINLAKETLAGNEILSIRGILNGTTNY 182 KGPL + YKEL E A++ GV EA+VGGAMP+I LAK +AGNEILSI+GILNGT NY Sbjct: 116 KGPLVVAYKELAELAERKGVRLMFEATVGGAMPLIKLAKRDIAGNEILSIKGILNGTCNY 175 Query: 183 ILTKMEKEGLDFETALKEAKELGIAETDPTQDIEGLDTAAKIVILANSIMGMNKTIKDVK 242 IL++ME+E L + L EA+EL IAE + + D+EG+D+AAK+VILAN++MGM+ + DV+ Sbjct: 176 ILSRMEQERLSYHQILSEAQELKIAEANASYDVEGIDSAAKLVILANAVMGMDVSFNDVE 235 Query: 243 VKGISRITPEALFLANKRGYTIKLIGQIKDGYLIVEPMLVPIDSPLNVKGTLNVAMFETD 302 V GI+ ITPEA +A ++GYTI+LI + L V P L+P+ PL V+GTLN + +TD Sbjct: 236 VVGITSITPEAFEIAMEKGYTIRLIAEASRDGLRVSPRLLPLHHPLAVRGTLNAVLIQTD 295 Query: 303 LAKEVVVVGRGAGPIETASAILSDLIHIYN 332 LA+E+ V+GRGAG IETASAI+SDLI IY+ Sbjct: 296 LAREIFVIGRGAGKIETASAIISDLIDIYS 325 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: 324 Number of extensions: 9 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: 330 Length adjustment: 28 Effective length of query: 308 Effective length of database: 302 Effective search space: 93016 Effective search space used: 93016 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