Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013842892.1 DESRU_RS14810 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000215085.1:WP_013842892.1 Length = 404 Score = 340 bits (872), Expect = 8e-98 Identities = 177/398 (44%), Positives = 260/398 (65%), Gaps = 3/398 (0%) Query: 340 VVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPD 399 +VV KFGG+++ D E++++VA ++++ + G + VV +SAMGDTTD LI L K + NP Sbjct: 2 LVVKKFGGSSVGDPERIKRVARRVVEEHQKGNQVVVAVSAMGDTTDDLISLMKQVTNNPP 61 Query: 400 PRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIIS 459 RE+D+LLSTGE S+AL+++A+R G +S TG Q+ I TD + A+I+ I T + Sbjct: 62 EREMDMLLSTGEQISIALLAMAIRDLGSDVVSLTGGQVGIYTDDVHTKAKILRIETGRVR 121 Query: 460 RYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTAD 519 L Q + VVAGFQG+ GDITTLGRGGSD TA+ALA +L AD+CE++ DVDGVYT D Sbjct: 122 EELNQGRVVVVAGFQGVNPDGDITTLGRGGSDTTAVALAAALRADVCEIFTDVDGVYTTD 181 Query: 520 PRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIWE 579 PR+V +AR + +S++EM+EL+ GAQVL R+ E A++YG+ + ++ + GT++ E Sbjct: 182 PRVVPEARKLSHISYDEMLELASLGAQVLHPRSVELAKQYGIPLHVRTSFNHMEGTIVEE 241 Query: 580 GTKVEN-PIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEY 638 +EN P+V V + +AK+ L DVPDKPGVA I + LS+ +N+DMIIQ Sbjct: 242 APDMENAPVVSGVAHDYNVAKIGLFDVPDKPGVAKTIFKALSKQSINVDMIIQSAMRNNM 301 Query: 639 NTVAFIVPESQLGKL--DIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTSTPEISATLFET 696 N + F L K I+ ++ K ++ +AKVSIVG + S P ++A +FE Sbjct: 302 NDIGFTTTIDDLRKALQIIEAIQDEVGFKGYTHDEDVAKVSIVGAGMISHPGVAADMFEA 361 Query: 697 LANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRF 734 LA+EGIN++MI+ S ++S +I E AVKA+H +F Sbjct: 362 LADEGINLEMITTSEIKVSCVIKRADTEKAVKALHKKF 399 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: 710 Number of extensions: 35 Number of successful extensions: 4 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: 404 Length adjustment: 35 Effective length of query: 704 Effective length of database: 369 Effective search space: 259776 Effective search space used: 259776 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: 52 (24.6 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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