Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_085218826.1 B9N75_RS10910 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_900177405.1:WP_085218826.1 Length = 413 Score = 274 bits (700), Expect = 7e-78 Identities = 149/407 (36%), Positives = 248/407 (60%), Gaps = 8/407 (1%) Query: 341 VVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDP 400 +VMKFGG +++ +E++ VA + + ++G + VV+SAM TD L++L + DP Sbjct: 4 IVMKFGGTSMAGIERIRHVAGLVRREAEAGNQVAVVVSAMAGETDRLVQLCREAASLYDP 63 Query: 401 RELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIISR 460 RE D+++++GE + L++I L+ G A S+ G QL I T + +A I I+ D++ R Sbjct: 64 REYDVVVASGEQVTSGLLAITLQGMGLNARSYMGWQLPIRTSPAHSAALIDGIDVDVLER 123 Query: 461 YLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTADP 520 I V+ GFQG+ G + TLGRGGSD +A+ALA ++ AD C++Y DVDGVYT DP Sbjct: 124 VFDGGGIAVIPGFQGVAADGSVATLGRGGSDTSAVALAAAMRADRCDIYTDVDGVYTTDP 183 Query: 521 RIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIWEG 580 RIV AR + +++EEM+EL+ GA+VLQ R+ A + + V + ++ ++ GT+I + Sbjct: 184 RIVPRARKLAAVTYEEMLELASVGAKVLQTRSVGLAMREKMPVTVLSSFEDKPGTMIVDD 243 Query: 581 TKV-----ENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGM-K 634 ++ E ++ + ++ A+V L +PD+PG A I L++ +N+DMI+Q + + Sbjct: 244 DRIEELDMERQLITGIAYDKNEARVTLTGLPDQPGAVAAIFGALAEANINVDMIVQSVPR 303 Query: 635 SGEYNTVAFIVPESQLGKLDIDLLKTRSEA--KEIIIEKGLAKVSIVGVNLTSTPEISAT 692 +GE + + F VP + L + L + +SE E++ + + KVS VGV + S I+A Sbjct: 304 AGEPSVLTFTVPTASLPQTTEVLGRIKSEVGFGEVLTDTNVVKVSAVGVGMRSNAGIAAQ 363 Query: 693 LFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDRE 739 +F LA+ GINI I+ S ++SV+I +Y E AV+ +H+ + LD + Sbjct: 364 MFRALADRGINILAITTSEIKVSVLIAEEYTELAVRVLHTAYGLDAD 410 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: 681 Number of extensions: 44 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: 413 Length adjustment: 36 Effective length of query: 703 Effective length of database: 377 Effective search space: 265031 Effective search space used: 265031 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 Jul 26 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