Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate BPHYT_RS08955 BPHYT_RS08955 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >FitnessBrowser__BFirm:BPHYT_RS08955 Length = 443 Score = 201 bits (511), Expect = 7e-56 Identities = 145/412 (35%), Positives = 226/412 (54%), Gaps = 24/412 (5%) Query: 20 VRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYEL-LGVPKEEIAF 78 ++VG+ G GTVG + +L+ EI++R G I+++ R+P K LG +A Sbjct: 4 IKVGLLGFGTVGSGTFTVLRRNQEEIKRRAGRGIEIARIAVRNPAKATAALGSEASTVAL 63 Query: 79 --DFDDLILNS--DVVVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIK 134 DF+ ++ + D+V E IGGT VA D+V RA++ + VVT NK L++ +G E E + Sbjct: 64 TDDFNAVVDDPSIDIVAEMIGGTGVARDVVLRAIKNRKHVVTANKALLAVHGTEIFEAAR 123 Query: 135 KRKLF--FEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEM-SKGRHFEEVL 191 + FEA+V GGIPII L++ L ++ I GI+NGTTNYIL+EM +G F L Sbjct: 124 ANGVMVSFEAAVAGGIPIIKALREGLTANRIQYIAGIINGTTNYILSEMRDRGLDFATAL 183 Query: 192 KEAQELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITR---IDPEYLK 248 K AQELGYAEADPT DIEG D A+K ++++ + G + EGI++ ID +Y + Sbjct: 184 KAAQELGYAEADPTFDIEGVDAAHKATIMSAIAFGVPVQFDKAYVEGISKLAAIDIKYAE 243 Query: 249 EIVRSGKKLKLIGELDFSTNRYEVRLR-EVTPEDPFF-NVDGVDNAIEVSTDLAGDFLLK 306 E+ G ++KL+G + E+R+ + PE NV+G NA+ V D G L Sbjct: 244 EL---GYRIKLLGIARRTDKGIELRVHPTLIPEKRLLANVEGAMNAVVVHGDAVGTTLYY 300 Query: 307 GRGAGGYPTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISDVEKLEKVAEKIIKR 366 G+GAG PTASAV+ADL V + + + + + + + +++V R Sbjct: 301 GKGAGAEPTASAVVADLVDVTRLHTADPEHRVPHLAFQPDSLSSTPILPIDEVTSGYYLR 360 Query: 367 KK----SGVKPVV--VLSAMGDTTDHLIEL-AKTIDENPDPRELDLLLSTGE 411 + +GV + +L+ G + D L++ ++ +D N E D++L T E Sbjct: 361 LRVADVTGVLADITRILADTGISIDALLQKESEQVDAN-GKGETDIILITHE 411 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: 748 Number of extensions: 34 Number of successful extensions: 6 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: 739 Length of database: 443 Length adjustment: 36 Effective length of query: 703 Effective length of database: 407 Effective search space: 286121 Effective search space used: 286121 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