Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_037574568.1 BS73_RS20470 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000744815.1:WP_037574568.1 Length = 425 Score = 324 bits (831), Expect = 5e-93 Identities = 172/412 (41%), Positives = 272/412 (66%), Gaps = 13/412 (3%) Query: 340 VVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPD 399 +VV K+GG++++D E +++VA +I+ KK+G + VVV+SAMGDTTD LI+LA+ + P Sbjct: 3 LVVQKYGGSSVADAEGIKRVARRIVDTKKAGHEVVVVVSAMGDTTDELIDLAEEVSPIPG 62 Query: 400 PRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIIS 459 RELD+LL+ GE S+AL+++A++ G++A SFTG+Q +ITD + ARIID+ I Sbjct: 63 GRELDMLLTAGERISMALLAMAIKSLGHEAQSFTGSQAGVITDSVHNKARIIDVTPGRIR 122 Query: 460 RYLKQDFIPVVAGFQGIT-ETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 L + I +VAGFQG++ ++ +ITTLGRGGSD TA+ALA +L A++CE+Y DVDGV+TA Sbjct: 123 TSLDEGNIAIVAGFQGVSQDSKNITTLGRGGSDTTAVALAAALDAEVCEIYTDVDGVFTA 182 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIW 578 DPR+VK AR I E+++E+M+EL+ G++VL R E+AR+Y + + ++++ +GT + Sbjct: 183 DPRVVKKARKIDEIAFEDMLELASSGSKVLLHRCVEYARRYNIPIHVRSSFSGLQGTWVR 242 Query: 579 E------GTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQG 632 ++E I+ V + AK+ + VPDKPG AARI R ++ +NIDM++Q Sbjct: 243 NKEESEGAAEMEQAIISGVAHDTSEAKITVVGVPDKPGEAARIFRAIADAEINIDMVVQN 302 Query: 633 MKSG--EYNTVAFIVPESQLGKLDIDLLKTRSEA---KEIIIEKGLAKVSIVGVNLTSTP 687 + ++F +P+++ G+ I+ L+ + + + K+S+VG + S P Sbjct: 303 VSQATTSLTDISFTLPKTE-GRKAIEALEKVQAGIGYDSLRYDDQIGKISLVGAGMRSNP 361 Query: 688 EISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDRE 739 ++AT FE L+N G+NI++IS S RISV+ V AV+A+HS F LD + Sbjct: 362 GVTATFFEALSNAGVNIELISTSEIRISVVTRADDVNQAVQAVHSAFGLDSD 413 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: 672 Number of extensions: 34 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: 425 Length adjustment: 36 Effective length of query: 703 Effective length of database: 389 Effective search space: 273467 Effective search space used: 273467 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