Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013842894.1 DESRU_RS14820 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000215085.1:WP_013842894.1 Length = 430 Score = 211 bits (537), Expect = 6e-59 Identities = 144/423 (34%), Positives = 223/423 (52%), Gaps = 16/423 (3%) Query: 20 VRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEIAFD 79 +++G+ GLGTVG +Y+IL+E I++R G + + KV+ RS K + +P+ + Sbjct: 6 IKIGLLGLGTVGCGVYKILEENKESIQQRAGIRLEVKKVLVRSLDKKRGVELPEAMLTTS 65 Query: 80 FDDLILNSDV--VVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIKKRK 137 D+I + ++ VVE +GG + +D V AL G+ VVT NK++++EYG + ++ + Sbjct: 66 LADIIEDPEIKIVVEVLGGVNPTLDYVLAALNQGKSVVTANKDMVAEYGEQLFAAAQRNQ 125 Query: 138 --LFFEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEMSK-GRHFEEVLKEA 194 L FEASV GGIPII L+ L ++ + GI+NGTTNY+LT+M++ G F EVL EA Sbjct: 126 CDLLFEASVAGGIPIIRTLKQSLAGNQIEEVFGIINGTTNYMLTKMTQEGSPFAEVLSEA 185 Query: 195 QELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIVRSG 254 Q GYAE+DPT D+ G+D A K+++LA + ++ V EGIT+I + + G Sbjct: 186 QAKGYAESDPTADVGGFDAARKIAILASIAFNTRIPLSQVYTEGITKITVDDIAYASELG 245 Query: 255 KKLKLIGELDFSTNRYEVRLRE--VTPEDPFFNVDGVDNAIEVSTDLAGDFLLKGRGAGG 312 +KL+G + EVR+ + + P V V NA+ V + GD + G+GAG Sbjct: 246 YMIKLLGIAKARSEGVEVRVHPTFIPKDHPLAAVGDVFNAVFVRGNAVGDTMFYGKGAGE 305 Query: 313 YPTASAVIADLFRVAKYKV-----LGGAEKFSVVVMKFGGAAISDVEKLEKVAEK----I 363 PTASAV+AD+ A+ V + G F + G S KVA+K Sbjct: 306 LPTASAVVADIMDAARDIVRNVPGIIGCTCFEKKPVLDIGETFSKYYIRLKVADKPGVLA 365 Query: 364 IKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDPRELDLLLSTGEIQSVALMSIALR 423 G K V + S + TD+ EL + D L+ ++ SV ++ +R Sbjct: 366 SIALVFGNKEVSLKSVLQKATDNTAELVLITHRVQEQNVQDALMDIKQLSSVLEIANMIR 425 Query: 424 KRG 426 G Sbjct: 426 VEG 428 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: 718 Number of extensions: 40 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: 430 Length adjustment: 36 Effective length of query: 703 Effective length of database: 394 Effective search space: 276982 Effective search space used: 276982 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