Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_017600365.1 D471_RS0120565 homoserine dehydrogenase
Query= BRENDA::Q56R01 (433 letters) >NCBI__GCF_000341125.1:WP_017600365.1 Length = 428 Score = 548 bits (1412), Expect = e-160 Identities = 293/427 (68%), Positives = 347/427 (81%), Gaps = 7/427 (1%) Query: 7 LKVALLGCGVVGSEVARIMTTHGDDHAARIGAPVELAGVAVRRPSKVRAGIPQELITTDA 66 +KVALLGCGVVG+EV R++ D+ AAR+G +E+ G+AVRR + R G+ L+TTDA Sbjct: 3 MKVALLGCGVVGAEVVRLIEEQSDELAARVGTRIEVGGIAVRRMDRDR-GVDPALLTTDA 61 Query: 67 TALVKRGDIDVVIEVIGGIEPARTLITTAFEHGASVVSANKALLAEDGATLYAAAERHGR 126 TALV R DID+V+EVIGGIEPAR+LI A + G SVV+ANKALLAEDG TL+ AA G Sbjct: 62 TALVTRPDIDLVVEVIGGIEPARSLILAAVKAGKSVVTANKALLAEDGQTLHTAARDAGV 121 Query: 127 DLYFEAAVAGAIPLIRPLRESSPGNKVNRVLGIVNGTTNFILDRMDSSGAGYTEALDEAT 186 DLY+EAAVAGAIPL+RPLR+S G++VNRVLGIVNGTTN+ILDRMDS GAG+TE+L+EA Sbjct: 122 DLYYEAAVAGAIPLLRPLRDSLAGDRVNRVLGIVNGTTNYILDRMDSLGAGFTESLEEAQ 181 Query: 187 ALGYAEADPTADVEGFDAAAKAAILAGIAFHT-RVRLDDVHREGLTEVTAADMASARRMG 245 ALGYAEADPTADVEGFDAAAKAAILA +AFHT RV DVHREG+T V+AAD+ASAR MG Sbjct: 182 ALGYAEADPTADVEGFDAAAKAAILARLAFHTQRVTAADVHREGITAVSAADIASARAMG 241 Query: 246 CTVKLLAICERAADGRSVTARVHPAMIPLSHPLASVREAYNAVFVESEAAGQLMFYGPGA 305 C VKLLAIC+R+ DG SV RVHP M+P+ HPLASV+EAYNAVFVE+E+AG+LMFYG GA Sbjct: 242 CVVKLLAICQRSEDGGSVGVRVHPVMLPVEHPLASVKEAYNAVFVEAESAGRLMFYGAGA 301 Query: 306 GGAPTASAVLGDLVAVCRNKLAGATGPGESAY-TQLPVSPMGEVVTRYHISLDVADKPGV 364 GG PTASAVLGDLVAV RN+LA T E A+ T LPV MG +T YH+SLDVAD+PGV Sbjct: 302 GGTPTASAVLGDLVAVARNRLA-HTSVAEGAHDTGLPVHDMGHTITSYHVSLDVADRPGV 360 Query: 365 LAQVATVFAEHGVSIDTVRQQGRQDSSGEASLVVVTHRAPDAALQGTVEALRSLDTVRGV 424 L++VA VFA+HGVSI VRQ+G S +A LV+V+H APD+AL TVE LR + VR V Sbjct: 361 LSKVAEVFADHGVSIKNVRQEG---SGEDAQLVLVSHPAPDSALSSTVERLRGHELVREV 417 Query: 425 ASIMRVE 431 AS+MRVE Sbjct: 418 ASVMRVE 424 Lambda K H 0.317 0.132 0.371 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: 515 Number of extensions: 17 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: 433 Length of database: 428 Length adjustment: 32 Effective length of query: 401 Effective length of database: 396 Effective search space: 158796 Effective search space used: 158796 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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