Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_005459952.1 SACCYDRAFT_RS23295 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000244975.1:WP_005459952.1 Length = 420 Score = 325 bits (834), Expect = 2e-93 Identities = 167/405 (41%), Positives = 274/405 (67%), Gaps = 7/405 (1%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 ++VV K+GG+++ +++++VAE+I+ KK+G + VVV SAMGDTTD L++LA+ ++ P Sbjct: 2 ALVVQKYGGSSLESADRIKRVAERIVATKKAGNQVVVVCSAMGDTTDELLDLAQQVNPVP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 RE+D+LL+ GE S AL+++A+ +G +A SFTG+Q ++T +G+ARIID+ + Sbjct: 62 PEREMDMLLTAGERISNALVAMAISAQGAEAWSFTGSQAGVVTTSVHGNARIIDVTPSRV 121 Query: 459 SRYLKQDFIPVVAGFQGIT-ETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYT 517 + L+Q +I +VAGFQG++ +T DITTLGRGGSD TA+A+A +L AD+CE+Y DVDGVYT Sbjct: 122 TEALEQGYIALVAGFQGVSQDTKDITTLGRGGSDTTAVAVAAALDADVCEIYSDVDGVYT 181 Query: 518 ADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLI 577 ADPRIV +AR + + +EEM+EL+ G+++L R+ E+AR+YGV + +++++ + GT + Sbjct: 182 ADPRIVSNARKLDTIPYEEMLELAASGSKILHLRSVEYARRYGVPIRVRSSYSDKPGTTV 241 Query: 578 W---EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMK 634 E VE ++ V + AK+ + VPD G A RI R ++ ++IDM++Q + Sbjct: 242 TGSIEEIPVEQALITGVAHDRSEAKITVTGVPDHAGAAGRIFRAVADAEIDIDMVLQNIS 301 Query: 635 SGEYNT-VAFIVPESQLGKL--DIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTSTPEISA 691 + T + F + ++ K +++ +K + ++ + + KVS+VG + S P ++A Sbjct: 302 NTTGRTDITFTLSKANGPKAVSELEKIKAELDFSAVLYDDHVGKVSLVGAGMRSHPGVTA 361 Query: 692 TLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFEL 736 T E LA G+NI++I+ S RISV+I + ++DAV+AIH FEL Sbjct: 362 TFCEALAKAGVNIEIINTSEIRISVLIRDEQLDDAVRAIHEAFEL 406 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: 659 Number of extensions: 23 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: 420 Length adjustment: 36 Effective length of query: 703 Effective length of database: 384 Effective search space: 269952 Effective search space used: 269952 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