Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_089302655.1 CHB84_RS17170 homoserine dehydrogenase
Query= BRENDA::Q56R01 (433 letters) >NCBI__GCF_900188115.1:WP_089302655.1 Length = 447 Score = 513 bits (1322), Expect = e-150 Identities = 272/431 (63%), Positives = 332/431 (77%), Gaps = 8/431 (1%) Query: 6 PLKVALLGCGVVGSEVARIMTTHGDDHAARIGAPVELAGVAVRRPSKVRAGIPQELITTD 65 P++VALLGCG VGSEVAR++T + AAR GAPVELAG+AVRRP K +P +L+T+D Sbjct: 20 PVRVALLGCGTVGSEVARLLTEEAAEFAARAGAPVELAGIAVRRPDK-HPELPADLLTSD 78 Query: 66 ATALVKRGDIDVVIEVIGGIEPARTLITTAFEHGASVVSANKALLAEDGATLYAAAERHG 125 L+ D+DVV+E++GGIEPAR+ + TA G SVV+ANKALLA+ L AA+ G Sbjct: 79 VEGLIA-SDVDVVVELVGGIEPARSWLLTALRSGKSVVTANKALLADCSRELSEAADASG 137 Query: 126 RDLYFEAAVAGAIPLIRPLRESSPGNKVNRVLGIVNGTTNFILDRMDSSGAGYTEALDEA 185 DLY+EAAVAGAIPL+RPLRES G+++ RV+GIVNGTTN+IL MDS+GAGY + L+EA Sbjct: 138 ADLYYEAAVAGAIPLVRPLRESLAGDRITRVMGIVNGTTNYILSAMDSTGAGYVDTLEEA 197 Query: 186 TALGYAEADPTADVEGFDAAAKAAILAGIAFHTRVRLDDVHREGLTEVTAADMASARRMG 245 + LGYAEADPTADV+G+DAA+KAAILA +AFHTR+ DV+REG+ V+AAD+A+A+ +G Sbjct: 198 SNLGYAEADPTADVDGYDAASKAAILASLAFHTRIAASDVYREGIGSVSAADVAAAKMIG 257 Query: 246 CTVKLLAICERAA--DG-RSVTARVHPAMIPLSHPLASVREAYNAVFVESEAAGQLMFYG 302 TVKLLAICER DG SV+ RVHP MIP SH LA V A+NAV+VE++ AG+LMF+G Sbjct: 258 RTVKLLAICERVVGPDGSESVSVRVHPVMIPRSHQLAGVGGAFNAVYVEADGAGELMFFG 317 Query: 303 PGAGGAPTASAVLGDLVAVCRNKLAGATGPGESAYTQLPVSPMGEVVTRYHISLDVADKP 362 GAGGAPTASAVLGDLV V RN+ G GP ESA+ L V PMGE TRYHISL VAD+P Sbjct: 318 QGAGGAPTASAVLGDLVDVARNRAGGGRGPRESAHAGLAVRPMGETPTRYHISLQVADRP 377 Query: 363 GVLAQVATVFAEHGVSIDTVRQQGRQDSSGEASLVVVTHRAPDAALQGTVEALRSLDTVR 422 GVLAQV+ VFA+H VSI VRQ +D ASLVVVTH APDAAL+ TV+ + LD V Sbjct: 378 GVLAQVSQVFAKHDVSIAAVRQ---RDKHSTASLVVVTHAAPDAALRATVDDIGELDVVH 434 Query: 423 GVASIMRVEGE 433 V S+MRVEGE Sbjct: 435 EVVSVMRVEGE 445 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: 555 Number of extensions: 26 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: 447 Length adjustment: 32 Effective length of query: 401 Effective length of database: 415 Effective search space: 166415 Effective search space used: 166415 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