Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate Dsui_2134 Dsui_2134 aspartate kinase, monofunctional class
Query= BRENDA::Q9WZ17 (739 letters) >FitnessBrowser__PS:Dsui_2134 Length = 407 Score = 321 bits (823), Expect = 4e-92 Identities = 171/405 (42%), Positives = 266/405 (65%), Gaps = 5/405 (1%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 +++V K+GG ++ E+++ VA+++ + K G VVV SAM T+ LI LAK I P Sbjct: 2 ALIVQKYGGTSVGSTERIKNVAKRVARWKAMGHDVVVVPSAMSGETNRLIGLAKEISATP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 PRELD++ STGE ++ L+++A+++ G KA S+TG+Q++++TD + ARI+ I+ + + Sbjct: 62 SPRELDVIASTGEQVTIGLLAMAIQEEGLKAKSYTGSQVRVLTDSTFTKARILQIDDERM 121 Query: 459 SRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 + L + + VVAGFQG E G+ITTLGRGGSD +A+ALA +L AD C++Y DVDGVYT Sbjct: 122 RKDLAEGNVVVVAGFQGADENGNITTLGRGGSDTSAVALAAALKADECQIYTDVDGVYTT 181 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKV-LIKNAHKETRGTLI 577 DPR+V +AR + +++EEM+E++ G++VLQ R+ EFA KY VK+ ++ + E GTLI Sbjct: 182 DPRVVPEARKLDTITFEEMLEMASLGSKVLQIRSVEFAGKYKVKLRVLSSFQDEGEGTLI 241 Query: 578 W--EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKS 635 + +E PI+ + F AK+ + VPD+PG+A +I+ ++ +++DMIIQ + Sbjct: 242 TVEDDKNMEQPIISGIAFNRDEAKLTVLGVPDRPGIAYQILGPIADANIDVDMIIQNVGV 301 Query: 636 GEYNTVAFIVPESQLGK--LDIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTSTPEISATL 693 +F V S+ K ++ +K A+EI+ + KVS VGV + S P +++ + Sbjct: 302 DGTTDFSFTVNRSEYTKAMAVLEQVKQHVGAREIVGDNKTCKVSAVGVGMRSHPGVASQM 361 Query: 694 FETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDR 738 F TLA EGINI MIS S +ISV+ID KY+E AV+ +H F LD+ Sbjct: 362 FRTLAEEGINIQMISTSEIKISVVIDEKYLELAVRILHKTFGLDQ 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: 710 Number of extensions: 27 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 739 Length of database: 407 Length adjustment: 36 Effective length of query: 703 Effective length of database: 371 Effective search space: 260813 Effective search space used: 260813 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 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