Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate Dsui_2907 Dsui_2907 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >FitnessBrowser__PS:Dsui_2907 Length = 436 Score = 217 bits (553), Expect = 9e-61 Identities = 145/402 (36%), Positives = 216/402 (53%), Gaps = 9/402 (2%) Query: 17 VRKVRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEI 76 ++ + VG+ G+GTVGG + +LK EI +R G IS V +R+ + ++ Sbjct: 1 MKAINVGLLGIGTVGGGTFTVLKRNAEEITRRAGRPIEISIVADRNLDLARQVTGGACKV 60 Query: 77 AFDFDDLIL--NSDVVVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIK 134 D ++ N D+VVE IGG VA DLV +A+E G+ VVT NK L++ +GNE + Sbjct: 61 TDDAFAVVSDPNVDIVVELIGGYGVAKDLVMKAIENGKHVVTANKALLATHGNEIFAAAQ 120 Query: 135 KRKLF--FEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEM-SKGRHFEEVL 191 K+ + FEA+V GGIPII L++ L ++ + GI+NGTTN+IL+EM KG F +VL Sbjct: 121 KKGVIVAFEAAVAGGIPIIKALREGLSANRIEWVAGIINGTTNFILSEMRDKGLSFADVL 180 Query: 192 KEAQELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIV 251 KEAQ LGYAEADPT D+EG D A+K+++++ + G + EGIT++D +K Sbjct: 181 KEAQRLGYAEADPTFDVEGVDAAHKLTIMSAIAFGIPMSFDKAHVEGITKLDAIDIKYAE 240 Query: 252 RSGKKLKLIGELDFSTNRYEVRLR-EVTPEDPFF-NVDGVDNAIEVSTDLAGDFLLKGRG 309 + G ++KL+G + E+R+ + PE NV+G NA+ V D G L G+G Sbjct: 241 QLGYRIKLLGVTKRTPEGVELRVHPTLIPEKRLIANVEGAMNAVLVKGDAVGATLYYGKG 300 Query: 310 AGGYPTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISDVEKLEKVAEKIIKRKKS 369 AG PTASAVIADL V + + + + + L +V R + Sbjct: 301 AGAEPTASAVIADLVDVTRLHTSDPEHRVPHLAFQPDAVVDLPILPLAEVQTAYYLRLRV 360 Query: 370 GVKPVVVLSAMGDTTDHLIELAKTIDENPDPREL--DLLLST 409 KP V+ D I + I + P E+ D++L T Sbjct: 361 EDKPGVLADITRILADQSISIDAMIQKEPGEGEVQTDIILLT 402 Score = 33.1 bits (74), Expect = 3e-05 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 14/72 (19%) Query: 605 VPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEYNTVAFIVPESQLGKLDIDLLKTRSEA 664 V DKPGV A I R L+ ++ID +IQ + GE G++ D++ + Sbjct: 360 VEDKPGVLADITRILADQSISIDAMIQ-KEPGE-------------GEVQTDIILLTHQT 405 Query: 665 KEIIIEKGLAKV 676 +E ++ +AK+ Sbjct: 406 REKNVDAAIAKI 417 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: 805 Number of extensions: 41 Number of successful extensions: 7 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: 436 Length adjustment: 36 Effective length of query: 703 Effective length of database: 400 Effective search space: 281200 Effective search space used: 281200 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