Align Homoserine dehydrogenase; HDH; EC 1.1.1.3 (uncharacterized)
to candidate WP_011306884.1 MBAR_RS10080 homoserine dehydrogenase
Query= curated2:Q58997 (336 letters) >NCBI__GCF_000195895.1:WP_011306884.1 Length = 331 Score = 328 bits (842), Expect = 9e-95 Identities = 174/329 (52%), Positives = 237/329 (72%), Gaps = 9/329 (2%) Query: 5 IVGFGAIGKGIAKVLYDKKDYLKKNYEEFKVVAITDSSGAAIDEDGLDLLKAIEVK--EK 62 I+GFGAIG+G+A+V KK+YL+ E KVVA+ DS GA ++ +G+DL + K ++ Sbjct: 8 ILGFGAIGQGVAEVFLMKKEYLESIGLEVKVVAVVDSKGATVNPEGVDLADCLVRKRRDR 67 Query: 63 TGKIKNYPEKGREMSSIDVIKEVDADVVVEVTPSNLETGDPAKTHILESFKNKKHVVTAN 122 T ++N +S ++VI+ V D+V+E TP+N+ TG ++ +FK K V+T+N Sbjct: 68 TVALEN-------ISGVEVIQSVAHDLVIETTPTNILTGGAGMQNMFAAFKTGKDVITSN 120 Query: 123 KGPLALCYKELIEEAKKHGVIFRHEASVGGAMPIINLAKETLAGNEILSIRGILNGTTNY 182 KGPL L Y+EL+E AK G FR EA+VGG+MPIINL E LAGN++ SI+GILNGT NY Sbjct: 121 KGPLTLKYRELMEAAKAAGSHFRFEATVGGSMPIINLVNEVLAGNKVKSIKGILNGTCNY 180 Query: 183 ILTKMEKEGLDFETALKEAKELGIAETDPTQDIEGLDTAAKIVILANSIMGMNKTIKDVK 242 ILT+M +E + L E+ +LGIAETDPT D+EG+DTA K+VILAN+I G++ T +V+ Sbjct: 181 ILTRMLEERASYNDILAESMQLGIAETDPTYDVEGIDTACKLVILANAIFGIDATYNNVE 240 Query: 243 VKGISRITPEALFLANKRGYTIKLIGQIKDGYLIVEPMLVPIDSPLNVKGTLNVAMFETD 302 V GI+++TPEAL +A ++G+ IKLIG++ + V P LVPI+ PL V GTLNVA ET+ Sbjct: 241 VTGITKVTPEALEMAYEKGHVIKLIGEVSRERIHVAPRLVPINHPLAVGGTLNVASVETE 300 Query: 303 LAKEVVVVGRGAGPIETASAILSDLIHIY 331 LA E+ V G+GAGPIETASAILSDLI IY Sbjct: 301 LAGEITVTGKGAGPIETASAILSDLIAIY 329 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: 339 Number of extensions: 12 Number of successful extensions: 2 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: 331 Length adjustment: 28 Effective length of query: 308 Effective length of database: 303 Effective search space: 93324 Effective search space used: 93324 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