Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_028485478.1 A377_RS0110715 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000384235.1:WP_028485478.1 Length = 439 Score = 199 bits (506), Expect = 2e-55 Identities = 134/414 (32%), Positives = 222/414 (53%), Gaps = 15/414 (3%) Query: 17 VRKVRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEI 76 + K++VG+ GLGTVGG IL++ EIE+R+G + I G+ + + Sbjct: 1 MEKIKVGLLGLGTVGGGTLTILRDTLTEIERRLGGQTTIEVTHAAVRDLERARGLNTDSL 60 Query: 77 AFDFDDLIL----NSDVVVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEY 132 D + + D+V+E +GGT +A + + A++ G+ +VT NK LI+E+GNE Sbjct: 61 VLTDDPKAVAGHPDVDIVIELMGGTTLAKECLEAAIKAGKHIVTANKALIAEHGNELFAL 120 Query: 133 IKKRKLF--FEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEMSKGR-HFEE 189 ++ ++ +EA+V GGIPII L++ L ++ + GI+NGT NYILTEM+ F + Sbjct: 121 AEQHQVMIAYEAAVAGGIPIIKALREGLSANRIEWVAGIINGTGNYILTEMNDPEADFYQ 180 Query: 190 VLKEAQELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKE 249 VL+ AQELGYAEADPT D+EG D A+K++++A + G + V EGI+ I E ++ Sbjct: 181 VLRTAQELGYAEADPTFDVEGTDAAHKLTIMASIAFGIELQFDKVYTEGISEITAEDIQF 240 Query: 250 IVRSGKKLKLIGELDFSTNRYEVRLR-EVTPEDPFFN-VDGVDNAIEVSTDLAGDFLLKG 307 + G ++K +G + + + +R+ + PE + ++GV NA+ V + G L G Sbjct: 241 AQKLGYQVKHLGIASRTDDGFSLRVHPTLVPESVLLSQINGVMNAVMVKGNHVGPTLYYG 300 Query: 308 RGAGGYPTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISDVEKLEKVAE----KI 363 GAGG PTASAV+ADL V +++ A++ + + V +E++ + Sbjct: 301 PGAGGGPTASAVVADLIDVIRWRHQPAADRVPALGFAANSLSTQSVAPVEEIETAYYLRF 360 Query: 364 IKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDPRELDLLLSTGEIQSVAL 417 SGV + +S + D IEL +P + L++ T + A+ Sbjct: 361 FAHDNSGV--LAKVSTILAEFDINIELLHQEPSAVNPNDATLVMLTNVVPEKAM 412 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: 745 Number of extensions: 37 Number of successful extensions: 5 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: 439 Length adjustment: 36 Effective length of query: 703 Effective length of database: 403 Effective search space: 283309 Effective search space used: 283309 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 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