Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_052664755.1 NITAL_RS03510 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000969705.1:WP_052664755.1 Length = 415 Score = 328 bits (842), Expect = 3e-94 Identities = 170/407 (41%), Positives = 274/407 (67%), Gaps = 7/407 (1%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 ++VV K+GG ++ D +++++VA+++ + + G + VVV+SAMG TTD L+ +A+ I + P Sbjct: 2 AIVVQKYGGTSVGDTDRMKRVADRVARTHRDGNQTVVVVSAMGKTTDDLVAMAQRISDAP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 RELD+LL++GE S++L+++AL + G A SFTG+Q IITD +G ARI++I + Sbjct: 62 PQRELDILLTSGERISMSLLAMALAEHGVPAKSFTGSQAGIITDAVHGKARILEITPGRV 121 Query: 459 SRYLKQDFIPVVAGFQGIT-ETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYT 517 L + + +VAGFQG++ +T DIT+LGRGGSD TA+ALA +LGAD+CE+Y DVDGV+T Sbjct: 122 QEALDEGNVVIVAGFQGVSQDTKDITSLGRGGSDTTAVALAAALGADVCEIYTDVDGVFT 181 Query: 518 ADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLI 577 ADPRIV AR + +S+EE +E++ HGA VLQ R+ EF R +GV++ ++++ T GT + Sbjct: 182 ADPRIVATARKLSYVSYEEALEMTAHGAGVLQTRSVEFGRNHGVRIHVRSSFSYTPGTWV 241 Query: 578 W--EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKS 635 E + VE+ I+ V + AKV + V D+PG+AA++ TL+ +NIDMI+Q + + Sbjct: 242 GPREESTVEDAIISGVAHDTSEAKVTVMKVSDQPGIAAKLFSTLADAKINIDMIVQNVSA 301 Query: 636 GEYNTVAFIVPESQLGKLDIDLLKTRSE---AKEIIIEKGLAKVSIVGVNLTSTPEISAT 692 ++F +P + +L+ +E A+ +++++ +AKVS+VG + + P ++A Sbjct: 302 DGRTDISFTLPRGDTNQARA-ILEPYAEAIGAEGVLVDENVAKVSLVGAGMKTHPGVAAR 360 Query: 693 LFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDRE 739 +F L+ G+NI+MIS S+ R+SV+I VE AV A+H F L + Sbjct: 361 MFSALSAAGVNIEMISTSTIRVSVVIAKDQVEPAVLAVHEAFGLSED 407 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: 629 Number of extensions: 20 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: 415 Length adjustment: 36 Effective length of query: 703 Effective length of database: 379 Effective search space: 266437 Effective search space used: 266437 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