Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_025273850.1 HALAL_RS0109855 homoserine dehydrogenase
Query= BRENDA::Q56R01 (433 letters) >NCBI__GCF_000527155.1:WP_025273850.1 Length = 425 Score = 480 bits (1235), Expect = e-140 Identities = 258/430 (60%), Positives = 319/430 (74%), Gaps = 8/430 (1%) Query: 7 LKVALLGCGVVGSEVARIMTTHGDDHAARIGAPVELAGVAVRRPSKVRA--GIPQELITT 64 +K+ALLGCG VGSEV R+M + A RIG P+E+AGVAVRR K R+ G+ +L TT Sbjct: 1 MKLALLGCGTVGSEVVRLMRMRATELANRIGEPLEIAGVAVRRAGKDRSHLGLDPDLFTT 60 Query: 65 DATALVKRGDIDVVIEVIGGIEPARTLITTAFEHGASVVSANKALLAEDGATLYAAAERH 124 DAT L+KR DID+V+E GGIEPA+T ITTA G SVV+ANKALLA DG L AAAE Sbjct: 61 DATELIKRPDIDLVVEAAGGIEPAKTWITTALSEGKSVVTANKALLASDGPALAAAAESG 120 Query: 125 GRDLYFEAAVAGAIPLIRPLRESSPGNKVNRVLGIVNGTTNFILDRMDSSGAGYTEALDE 184 DLY+EAA A AIPL+RPLR+S G+ +N VLGIVNGTTN+I RM +G + EAL E Sbjct: 121 RADLYYEAAAAAAIPLMRPLRDSFQGDTINAVLGIVNGTTNYICTRMTEAGMSFGEALAE 180 Query: 185 ATALGYAEADPTADVEGFDAAAKAAILAGIAFHTRVRLDDVHREGLTEVTAADMASARRM 244 A LGYAEADP+AD++G+DAAAKAA++A +AFHT + L DVHREG++ +T+AD+A+A Sbjct: 181 AGDLGYAEADPSADLDGYDAAAKAALIASLAFHTHIDLGDVHREGISSLTSADIAAATAD 240 Query: 245 GCTVKLLAICERAADGRSVTARVHPAMIPLSHPLASVREAYNAVFVESEAAGQLMFYGPG 304 G +K L I R DG SV RVHPAMIP HPLA+V AYNAVF+E+E+AGQLMFYG G Sbjct: 241 GRVIKPLCIATRDDDGISV--RVHPAMIPRHHPLANVNGAYNAVFIEAESAGQLMFYGAG 298 Query: 305 AGGAPTASAVLGDLVAVCRNKLAGATG-PGESAYTQLPVSPMGEVVTRYHISLDVADKPG 363 AGG TASAVLGD+V V RN+ +GA P E+A+ + PV +G+ +TRY++SLDV D+PG Sbjct: 299 AGGTETASAVLGDIVTVARNRRSGARAFPPEAAWQERPVKEIGQALTRYYVSLDVVDEPG 358 Query: 364 VLAQVATVFAEHGVSIDTVRQQGRQDSSGEASLVVVTHRAPDAALQGTVEALRSLDTVRG 423 VLA+VA+ FA HGVS+ TV Q G + +A LVVVTH APDA L T+E L+ L VR Sbjct: 359 VLARVASTFAHHGVSLATVSQTGHGE---DAQLVVVTHLAPDAELAATLEELKQLALVRH 415 Query: 424 VASIMRVEGE 433 V+S MRVEGE Sbjct: 416 VSSTMRVEGE 425 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: 490 Number of extensions: 26 Number of successful extensions: 5 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: 425 Length adjustment: 32 Effective length of query: 401 Effective length of database: 393 Effective search space: 157593 Effective search space used: 157593 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