Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 3608668 Dshi_2061 aspartate kinase (RefSeq)
Query= BRENDA::Q9WZ17 (739 letters) >FitnessBrowser__Dino:3608668 Length = 412 Score = 280 bits (715), Expect = 1e-79 Identities = 155/409 (37%), Positives = 257/409 (62%), Gaps = 9/409 (2%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 S++VMKFGG +++D++K++ AEK+ + G K +V++SAM T+ L+ Sbjct: 2 SILVMKFGGTSVADLDKIKNAAEKVQREVARGHKVIVIVSAMSGKTNELVGWVGKTSPLY 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDI-NTDI 457 D RE D ++S+GE + L+++ L++ A S+ G Q+ + T+ + +ARI +I ++ Sbjct: 62 DAREYDAVVSSGENVTAGLLALTLQEMEIPARSWQGWQVPLRTNSAHAAARIEEIPRANL 121 Query: 458 ISRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYT 517 +++ + + V+AGFQGI+ G ITTLGRGGSD TA+A A + GA C++Y DVDGVYT Sbjct: 122 DAKFDEGMQVAVIAGFQGISPEGRITTLGRGGSDTTAVAFAAAFGAVRCDIYTDVDGVYT 181 Query: 518 ADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKE---TRG 574 DPRI AR + +++EEM+EL+ GA+VLQ R+ E A ++ V + + ++ +E T G Sbjct: 182 TDPRIEDKARKLDRIAYEEMLELASLGAKVLQTRSVELAMRFKVPLRVLSSFEENTDTSG 241 Query: 575 TLIWEGTKV-ENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGM 633 TL+ + ++ E+ +V V + AK+ L V D+PG+AA I LS+ GVN+DMI+Q + Sbjct: 242 TLVCDEDEIMESNVVSGVAYSRDEAKMTLISVADRPGIAAAIFGPLSEAGVNVDMIVQNI 301 Query: 634 KSGEYNTVAFIVPESQLGKLDIDLLKTRS----EAKEIIIEKGLAKVSIVGVNLTSTPEI 689 + F P Q+ + + + + + +E++ + +AKVS+VG+ + S + Sbjct: 302 SEDGRTDMTFSCPTDQVLRAERAIKEAKELGEINFQELVADTDVAKVSVVGIGMRSHAGV 361 Query: 690 SATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDR 738 +A +F+ L +EGINI +I+ S +ISV+I+ KY+E AV+A+H FELDR Sbjct: 362 AARMFQALRDEGINIRVITTSEIKISVLIERKYMELAVQALHDAFELDR 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: 643 Number of extensions: 31 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: 412 Length adjustment: 36 Effective length of query: 703 Effective length of database: 376 Effective search space: 264328 Effective search space used: 264328 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