Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_017600365.1 D471_RS0120565 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000341125.1:WP_017600365.1 Length = 428 Score = 179 bits (455), Expect = 2e-49 Identities = 141/438 (32%), Positives = 216/438 (49%), Gaps = 31/438 (7%) Query: 20 VRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEIAFD 79 ++V + G G VG + R+++E+ +E+ R+G + + + R + GV + D Sbjct: 3 MKVALLGCGVVGAEVVRLIEEQSDELAARVGTRIEVGGIAVRRMDRDR--GVDPALLTTD 60 Query: 80 FDDLILNSDV--VVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIKKR- 136 L+ D+ VVE IGG + A L+ A++ G+ VVT NK L++E G + Sbjct: 61 ATALVTRPDIDLVVEVIGGIEPARSLILAAVKAGKSVVTANKALLAEDGQTLHTAARDAG 120 Query: 137 -KLFFEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEM-SKGRHFEEVLKEA 194 L++EA+V G IP++ L+D L +V R+ GI+NGTTNYIL M S G F E L+EA Sbjct: 121 VDLYYEAAVAGAIPLLRPLRDSLAGDRVNRVLGIVNGTTNYILDRMDSLGAGFTESLEEA 180 Query: 195 QELGYAEADPTNDIEGYDVAYKVSVLAGVV--TGRFPGINSVQFEGITRIDPEYLKEIVR 252 Q LGYAEADPT D+EG+D A K ++LA + T R + V EGIT + + Sbjct: 181 QALGYAEADPTADVEGFDAAAKAAILARLAFHTQRVTAAD-VHREGITAVSAADIASARA 239 Query: 253 SGKKLKLIGELDFSTNRYEVRLR----EVTPEDPFFNVDGVDNAIEVSTDLAGDFLLKGR 308 G +KL+ S + V +R + E P +V NA+ V + AG + G Sbjct: 240 MGCVVKLLAICQRSEDGGSVGVRVHPVMLPVEHPLASVKEAYNAVFVEAESAGRLMFYGA 299 Query: 309 GAGGYPTASAVIADLFRVAKYK-----VLGGAEKFSVVVMKFGGAAISDVEKLEKVAEKI 363 GAGG PTASAV+ DL VA+ + V GA + V G S L+ VA+ Sbjct: 300 GAGGTPTASAVLGDLVAVARNRLAHTSVAEGAHDTGLPVHDMGHTITSYHVSLD-VAD-- 356 Query: 364 IKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDPRELDLLLSTGEIQSVALMSIALR 423 +P V+ DH + + K + + + L+L + AL S R Sbjct: 357 --------RPGVLSKVAEVFADHGVSI-KNVRQEGSGEDAQLVLVSHPAPDSALSSTVER 407 Query: 424 KRGYKAISFTGNQLKIIT 441 RG++ + + +++ T Sbjct: 408 LRGHELVREVASVMRVET 425 Score = 25.4 bits (54), Expect = 0.006 Identities = 10/28 (35%), Positives = 17/28 (60%) Query: 604 DVPDKPGVAARIMRTLSQMGVNIDMIIQ 631 DV D+PGV +++ + GV+I + Q Sbjct: 353 DVADRPGVLSKVAEVFADHGVSIKNVRQ 380 Lambda K H 0.318 0.137 0.377 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: 597 Number of extensions: 30 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 739 Length of database: 428 Length adjustment: 36 Effective length of query: 703 Effective length of database: 392 Effective search space: 275576 Effective search space used: 275576 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: 53 (25.0 bits)
This GapMind analysis is from Apr 09 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