Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_041440117.1 TCUR_RS19370 homoserine dehydrogenase
Query= BRENDA::Q56R01 (433 letters) >NCBI__GCF_000024385.1:WP_041440117.1 Length = 443 Score = 561 bits (1447), Expect = e-164 Identities = 293/436 (67%), Positives = 344/436 (78%), Gaps = 10/436 (2%) Query: 5 RPLKVALLGCGVVGSEVARIMTTHGDDHAARIGAPVELAGVAVRRPSKVRAGIPQELITT 64 +PL+VALLGCG VGSEV R++ D ARIGAP+ELAGVAVRR + R + EL+TT Sbjct: 8 KPLRVALLGCGTVGSEVVRLLHEQAADLTARIGAPLELAGVAVRRLDRTREHVAPELLTT 67 Query: 65 DATALVKRGDIDVVIEVIGGIEPARTLITTAFEHGASVVSANKALLAEDGATLYAAAERH 124 DA LV R D+D+V+EVIGGIEPAR+L+ A + G SVV+ANKALLAEDG T++ AA + Sbjct: 68 DAMGLVTREDVDIVVEVIGGIEPARSLLLAAMKSGKSVVTANKALLAEDGETIFGAAREY 127 Query: 125 GRDLYFEAAVAGAIPLIRPLRESSPGNKVNRVLGIVNGTTNFILDRMDSSGAGYTEALDE 184 G DLY+EAAVAGAIPL+RPLRES G+ V RV+GIVNGTTN+ILDRMDS GA +++AL+E Sbjct: 128 GADLYYEAAVAGAIPLLRPLRESLVGDHVKRVIGIVNGTTNYILDRMDSCGASFSDALEE 187 Query: 185 ATALGYAEADPTADVEGFDAAAKAAILAGIAFHTRVRLDDVHREGLTEVTAADMASARRM 244 A LGYAEADPTADVEGFDAAAKAAILA +AFHT V DVHREG+TEV+AAD+A A+ M Sbjct: 188 AQELGYAEADPTADVEGFDAAAKAAILAQLAFHTPVSAADVHREGITEVSAADVAGAKAM 247 Query: 245 GCTVKLLAICERAAD-------GRSVTARVHPAMIPLSHPLASVREAYNAVFVESEAAGQ 297 VKLLAICER D GR V+ RV+PAMIP SHPLASVREAYNAVFVE+E+AG Sbjct: 248 DSVVKLLAICERVPDPEGRNNGGRGVSVRVYPAMIPRSHPLASVREAYNAVFVEAESAGS 307 Query: 298 LMFYGPGAGGAPTASAVLGDLVAVCRNKLAGATGPGESAYTQLPVSPMGEVVTRYHISLD 357 LMFYG GAGGAPTASAVLGDLVAV RN++ G GP E Y +LPV PMGE +TRY+I LD Sbjct: 308 LMFYGAGAGGAPTASAVLGDLVAVARNRVGGTRGPVEVTYAELPVLPMGETITRYYIQLD 367 Query: 358 VADKPGVLAQVATVFAEHGVSIDTVRQQGRQDSSGEASLVVVTHRAPDAALQGTVEALRS 417 VAD+ GVLAQ+A +FA H VSI VRQ+G + +A LV+VTHRAPDAAL TVE LR Sbjct: 368 VADRSGVLAQIAELFARHDVSIQAVRQEGYGE---DAQLVIVTHRAPDAALAATVEGLRR 424 Query: 418 LDTVRGVASIMRVEGE 433 LD VR V+S+MRVE + Sbjct: 425 LDIVREVSSVMRVEAD 440 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: 542 Number of extensions: 14 Number of successful extensions: 3 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: 443 Length adjustment: 32 Effective length of query: 401 Effective length of database: 411 Effective search space: 164811 Effective search space used: 164811 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