Align Homoserine dehydrogenase; HDH; EC 1.1.1.3 (uncharacterized)
to candidate WP_078428931.1 BK574_RS13245 homoserine dehydrogenase
Query= curated2:Q58997 (336 letters) >NCBI__GCF_002019605.1:WP_078428931.1 Length = 345 Score = 256 bits (655), Expect = 4e-73 Identities = 145/341 (42%), Positives = 214/341 (62%), Gaps = 11/341 (3%) Query: 3 IIIVGFGAIGKGIAKVLYDKKDYLKKNYE-EFKVVAITDS-SGAAIDEDGLDLLKAIEVK 60 + ++GFG +G+G+A++L KKD LK E KVVAI+D G+ D +G+D+ KA+ + Sbjct: 4 LALLGFGTVGQGLAEILLQKKDALKAETGWEGKVVAISDMIKGSIYDPEGIDIEKALAIV 63 Query: 61 EKTGKIKNYPEKG---REMSSIDVIKEVDADVVVEVTPSNLETGDPAKTHILESFKNKKH 117 +KTG + +YPE R++ S + I++ +AD +VEVT ++++TG PA H +F KH Sbjct: 64 KKTGTLDDYPESEGLIRDLDSFETIEQTNADTIVEVTFTDVKTGQPAIDHCKTAFAAGKH 123 Query: 118 VVTANKGPLALCYKELIEEAKKHGVIFRHEASVGGAMPIINLAKETLAGNEILSIRGILN 177 VV +NKGP+AL YKEL + A +HGV + E +V P + + LAGN+I I GILN Sbjct: 124 VVMSNKGPVALAYKELSQLANQHGVRWGFEGTVMSGTPALRMPLTALAGNDINEISGILN 183 Query: 178 GTTNYILTKMEKEGLDFETALKEAKELGIAETDPTQDIEGLDTAAKIVILANSIMGMNKT 237 GTTNY+L +ME EGL +E AL EA+ G AE DPT D+EG D KIVILAN++M Sbjct: 184 GTTNYMLLRME-EGLSYEEALTEAQNKGFAEADPTSDVEGYDARYKIVILANTVMNTTLK 242 Query: 238 IKDVKVKGISRITPEALFLANKRGYTIKLIGQIKDGYLI----VEPMLVPIDSPL-NVKG 292 + DV GI+++TP + A +G KLI +++ + + V+P ++ PL V+G Sbjct: 243 VDDVACDGITQLTPYDIKKAKAQGKRWKLIARVRKEHGVVKASVQPEMMDETHPLAQVQG 302 Query: 293 TLNVAMFETDLAKEVVVVGRGAGPIETASAILSDLIHIYNS 333 +N FE DLA + + G GAG ET ++L DL++IY + Sbjct: 303 VINAVSFECDLAGTITLSGPGAGRTETGYSLLIDLLNIYRN 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: 321 Number of extensions: 28 Number of successful extensions: 6 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: 345 Length adjustment: 28 Effective length of query: 308 Effective length of database: 317 Effective search space: 97636 Effective search space used: 97636 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