Align Homoserine dehydrogenase; HDH; EC 1.1.1.3 (uncharacterized)
to candidate PP_0664 PP_0664 homoserine dehydrogenase
Query= curated2:Q58997 (336 letters) >FitnessBrowser__Putida:PP_0664 Length = 347 Score = 214 bits (546), Expect = 2e-60 Identities = 131/339 (38%), Positives = 192/339 (56%), Gaps = 9/339 (2%) Query: 3 IIIVGFGAIGKGIAKVLYDKKDYLKKNYE-EFKVVAITDSS-GAAIDEDGLDLLKAIEVK 60 I +VGFG + + +A+++ ++ + K+V +TD G+ ID DGLD + Sbjct: 6 IALVGFGGVNRALAQLIAERNARWQHELGFGLKIVGVTDLFLGSVIDRDGLDAAVLAALP 65 Query: 61 EKTGKIKNYPEKGREMSSIDVIKEVDADVVVEVTPSNLETGDPAKTHILESFKNKKHVVT 120 + G + + P+ E + VIK+ AD++ E T +N + G+PA T + + KHVVT Sbjct: 66 AQKGALAHIPQGSAEAFNEAVIKQSGADIIAEATFTNPKDGEPAATFCRWALEAGKHVVT 125 Query: 121 ANKGPLALCYKELIEEAKKHGVIFRHEASVGGAMPIINLAKETLAGNEILSIRGILNGTT 180 NKGP+AL + L AK + V F +E +V P++ +A++TLAG ++ GILNGT+ Sbjct: 126 TNKGPIALHAQALKALAKANNVSFEYEGAVMSGTPVLRMARQTLAGAGLVGFEGILNGTS 185 Query: 181 NYILTKMEKEGLDFETALKEAKELGIAETDPTQDIEGLDTAAKIVILANSIMGMNKTIKD 240 NY+LT+ME EGL F A+ +A+ LG AE DPT D+EG D K+VILAN ++G + D Sbjct: 186 NYVLTRME-EGLGFNEAVAQAQALGFAEADPTADVEGHDVRLKVVILANELLGACLQVGD 244 Query: 241 VKVKGISRITPEALFLANKRGYTIKLIGQIK-----DGYLIVEPMLVPIDSPL-NVKGTL 294 V GIS I A+ A G KLIG + VE L+P PL + G Sbjct: 245 VACSGISAIDSAAIERARAAGERWKLIGSARREAGGSVRASVEAKLLPGHHPLAGILGAT 304 Query: 295 NVAMFETDLAKEVVVVGRGAGPIETASAILSDLIHIYNS 333 N F+T+L V V G GAG IETA A+LSD++ I+ + Sbjct: 305 NALAFDTELLGAVTVSGPGAGRIETAFALLSDIVAIHTA 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: 280 Number of extensions: 15 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: 347 Length adjustment: 29 Effective length of query: 307 Effective length of database: 318 Effective search space: 97626 Effective search space used: 97626 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 09 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