Align Homoserine dehydrogenase; HDH; EC 1.1.1.3 (uncharacterized)
to candidate YP_002822914.1 NGR_b07030 homoserine dehydrogenase
Query= curated2:Q58997 (336 letters) >NCBI__GCF_000018545.1:YP_002822914.1 Length = 359 Score = 222 bits (565), Expect = 1e-62 Identities = 131/340 (38%), Positives = 197/340 (57%), Gaps = 9/340 (2%) Query: 2 DIIIVGFGAIGKGIAKVLYDKKDYLKKNYE-EFKVVAITDSS-GAAIDEDGLDLLKAIEV 59 +I ++GFG + + +A+++ K +++ +VA++D G+ I +GLD +E Sbjct: 12 NIALIGFGGVNRALAELIATKNPLWERDLGFRLNIVAVSDLYLGSVISPNGLDAKTLVEA 71 Query: 60 KEKTGKIKNYPEKGREMSSIDVIKEVDADVVVEVTPSNLETGDPAKTHILESFKNKKHVV 119 G E + +IK AD++VE T +N + G+PA +H + ++ KHVV Sbjct: 72 NFAKGGFGQLSGGSAEADNETIIKTAPADLIVEATFTNPKDGEPAVSHCRWALQSGKHVV 131 Query: 120 TANKGPLALCYKELIEEAKKHGVIFRHEASVGGAMPIINLAKETLAGNEILSIRGILNGT 179 T NKGP+A+ +EL A +GV F +E SV P+I +A+ TLAG E+ GILNGT Sbjct: 132 TTNKGPVAIAAQELKAVAHANGVHFEYEGSVMSGTPVIRMAERTLAGAEVKGFEGILNGT 191 Query: 180 TNYILTKMEKEGLDFETALKEAKELGIAETDPTQDIEGLDTAAKIVILANSIMGMNKTIK 239 +N++L +ME GLDF TA+KEA+ LG AE DPT D+EG D K+VILAN ++G + + Sbjct: 192 SNFVLGRME-GGLDFATAVKEAQILGYAEADPTADVEGFDVRLKVVILANELLGASLKPE 250 Query: 240 DVKVKGISRITPEALFLANKRGYTIKLIGQI---KDGYLI--VEPMLVPIDSPL-NVKGT 293 +V KGIS+++P + A KL+G +DG + V P +P + PL V G Sbjct: 251 EVTCKGISKLSPSDIENAAAANSRWKLVGSAVRNEDGTVTGSVSPKQLPFEHPLAGVNGA 310 Query: 294 LNVAMFETDLAKEVVVVGRGAGPIETASAILSDLIHIYNS 333 N T+L V + G GAG IETA A+LSD+I I+N+ Sbjct: 311 TNAVSLNTELLGSVTITGPGAGRIETAYALLSDIIAIHNA 350 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: 298 Number of extensions: 14 Number of successful extensions: 4 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: 359 Length adjustment: 29 Effective length of query: 307 Effective length of database: 330 Effective search space: 101310 Effective search space used: 101310 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