Align Homoserine dehydrogenase; HDH; EC 1.1.1.3 (uncharacterized)
to candidate WP_012964601.1 FERP_RS00305 homoserine dehydrogenase
Query= curated2:Q58997 (336 letters) >NCBI__GCF_000025505.1:WP_012964601.1 Length = 330 Score = 302 bits (773), Expect = 9e-87 Identities = 156/330 (47%), Positives = 231/330 (70%), Gaps = 9/330 (2%) Query: 3 IIIVGFGAIGKGIAKVLYDKKDYLKKNYEEFKVVAITDSSGAAIDEDGLDLLKAIEVKEK 62 I I+GFG +G+G+A++L K+ ++ +FKVVA+ DS + + E +DL KA+ K K Sbjct: 4 IAIIGFGTVGQGVAELLLRKRSEIEGRIGKFKVVAVADSKSSVVGE--VDLEKALNEKRK 61 Query: 63 TGKIKNYPEKGREMSSIDVIKEVDADVVVEVTPSNLETGDPAKTHILESFKNKKHVVTAN 122 ++ +++++++I+ V+ DV+ E TP+N+E+G+P THI + K K+V+T+N Sbjct: 62 KRRLSG------DITAMEIIENVEYDVLFECTPTNVESGEPGLTHIKAALKRGKNVITSN 115 Query: 123 KGPLALCYKELIEEAKKHGVIFRHEASVGGAMPIINLAKETLAGNEILSIRGILNGTTNY 182 KGPL + Y EL + A+K+ EA+VGGAMP+I L K LAG+ IL IRGILNGT NY Sbjct: 116 KGPLVVAYNELCKLAEKNSCKLGFEATVGGAMPLIKLVKNDLAGSGILRIRGILNGTCNY 175 Query: 183 ILTKMEKEGLDFETALKEAKELGIAETDPTQDIEGLDTAAKIVILANSIMGMNKTIKDVK 242 IL++ME E + +E L EA ELGIAE+DP+ D++G+D AAK+VI+AN+++ N +DV Sbjct: 176 ILSRMEVEKMPYEQILSEAIELGIAESDPSYDVKGIDAAAKLVIIANALLERNVRFEDVH 235 Query: 243 VKGISRITPEALFLANKRGYTIKLIGQIKDGYLIVEPMLVPIDSPLNVKGTLNVAMFETD 302 ++GI +TPEA +A K+GYTI+LI ++ D L V P LVP++ PLN+ GTLN A T+ Sbjct: 236 IEGIEDLTPEAFEVALKKGYTIRLIAEVGDS-LRVSPRLVPLNHPLNIYGTLNAAEIVTE 294 Query: 303 LAKEVVVVGRGAGPIETASAILSDLIHIYN 332 A V V+GRGAG +ETASA++SDLI +Y+ Sbjct: 295 TAGRVFVIGRGAGKLETASAMISDLIDMYD 324 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: 321 Number of extensions: 18 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