Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_041099485.1 SUTH_RS11835 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000828635.1:WP_041099485.1 Length = 413 Score = 332 bits (851), Expect = 2e-95 Identities = 177/410 (43%), Positives = 271/410 (66%), Gaps = 9/410 (2%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 +++V K+GG ++ E++ VA+++ + K G + VVV+SAM T+ LI LAK + P Sbjct: 2 ALIVQKYGGTSMGSPERIRNVAKRVARWKAQGHQLVVVVSAMSGETNRLIALAKDVSPQP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 D RELD+++STGE ++AL+++A+R G KA S+TG Q+K++TD + ARI++I+ + Sbjct: 62 DARELDVMISTGEQVTIALLAMAIRDLGLKARSYTGGQVKVLTDSTFTKARILEIDDANM 121 Query: 459 SRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 R L D + +VAGFQG+ G+ITTLGRGGSD +A+A+A +L AD C++Y DVDGVYT Sbjct: 122 RRDLDDDTVIIVAGFQGVDADGNITTLGRGGSDTSAVAMAAALAADECQIYTDVDGVYTT 181 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAH----KETRG 574 DPRIV +AR + +++EEM+E++ G++VLQ R+ EFA KY VK+ + ++ +ET G Sbjct: 182 DPRIVPEARKLDRITFEEMLEMASLGSKVLQIRSVEFAGKYKVKLRVLSSFEEEGQETSG 241 Query: 575 TLIW--EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQG 632 TLI E T +E PI+ + F AK+ + VPD+PG+A +I+ ++ +++DMIIQ Sbjct: 242 TLITLEEDTTMEQPIISGIAFNRDEAKLTVLGVPDRPGIAYQILGPIADANIDVDMIIQN 301 Query: 633 MKSGEYNTVAFIVPESQLG---KLDIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTSTPEI 689 + +F V S+ KL D +K A+ I + + KVS VGV + S P + Sbjct: 302 VGHDGTTDFSFTVNRSEFARTKKLLEDQIKPHIGARAIEGDNKICKVSAVGVGMRSHPGV 361 Query: 690 SATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDRE 739 ++ +F TLA EGINI MIS S +ISV++D KY+E AV+ +H FELD++ Sbjct: 362 ASKMFRTLAEEGINIQMISTSEIKISVVVDEKYLELAVRVLHKVFELDQQ 411 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: 709 Number of extensions: 27 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 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