Align Homoserine dehydrogenase; HDH; EC 1.1.1.3 (uncharacterized)
to candidate WP_011654697.1 RL_RS25505 homoserine dehydrogenase
Query= curated2:Q58997 (336 letters) >NCBI__GCF_000009265.1:WP_011654697.1 Length = 353 Score = 217 bits (553), Expect = 3e-61 Identities = 128/340 (37%), Positives = 197/340 (57%), Gaps = 9/340 (2%) Query: 2 DIIIVGFGAIGKGIAKVLYDKKDYLKKNYE-EFKVVAITDSS-GAAIDEDGLDLLKAIEV 59 +I ++GFG + + + +++ K +++ +VA++D G+ I +GLD ++ Sbjct: 5 NIALIGFGGVNRALTELIAAKNQLWERDLGFRLNIVAVSDLYLGSVISPNGLDAKTLVDA 64 Query: 60 KEKTGKIKNYPEKGREMSSIDVIKEVDADVVVEVTPSNLETGDPAKTHILESFKNKKHVV 119 K + G E + +IK AD+VVE T +N + G+PA +H + + KHVV Sbjct: 65 KFEKGGFGQLSGGSAEADNETIIKTAPADIVVEATYTNPKDGEPAVSHCRWALETGKHVV 124 Query: 120 TANKGPLALCYKELIEEAKKHGVIFRHEASVGGAMPIINLAKETLAGNEILSIRGILNGT 179 T NKGP+A+ L AK +GV F +E +V P+I +A+ TLAG E+ GILNGT Sbjct: 125 TTNKGPVAIAAPALKAFAKTNGVRFEYEGAVMSGTPVIRMAERTLAGAELKGFEGILNGT 184 Query: 180 TNYILTKMEKEGLDFETALKEAKELGIAETDPTQDIEGLDTAAKIVILANSIMGMNKTIK 239 +N++L +ME GLDF +A+KEA++LG AE DPT D+EG D K+VILAN ++G N + Sbjct: 185 SNFVLGRME-SGLDFASAVKEAQKLGYAEADPTADVEGFDVRLKVVILANELLGANLKPE 243 Query: 240 DVKVKGISRITPEALFLANKRGYTIKLIG---QIKDGYLI--VEPMLVPIDSPL-NVKGT 293 D+ KG+S ++ + A K KLIG + DG + V P + +D PL V G Sbjct: 244 DISCKGVSGLSLSDIEEAAKANSRWKLIGAAVRNDDGSVTGSVSPKRLGLDHPLAGVNGA 303 Query: 294 LNVAMFETDLAKEVVVVGRGAGPIETASAILSDLIHIYNS 333 N +T+L V + G GAG IETA A+LSD++ I+++ Sbjct: 304 TNAVSLDTELLGAVTITGPGAGRIETAYALLSDIVAIHSA 343 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: 311 Number of extensions: 22 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: 353 Length adjustment: 29 Effective length of query: 307 Effective length of database: 324 Effective search space: 99468 Effective search space used: 99468 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