Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013075566.1 BTUS_RS07805 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000092905.1:WP_013075566.1 Length = 407 Score = 211 bits (537), Expect = 6e-59 Identities = 139/411 (33%), Positives = 215/411 (52%), Gaps = 23/411 (5%) Query: 340 VVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGD-----TTDHLIELAKTI 394 ++V KFGG +++ E + + K + VVV+SAMG TD L+ L Sbjct: 3 ILVQKFGGTSLAGDEPRQWAVHHVEKALAQEFRVVVVVSAMGRQGAPYATDTLLGLIPPG 62 Query: 395 DENPDPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDIN 454 P RE DLLLS GEI S + LR +A + TG Q I+T+ +G+A I+++ Sbjct: 63 ASTP--RETDLLLSCGEIISAVSFAALLRTHKIRATALTGGQAGIVTESEFGAAPILEVK 120 Query: 455 TDIISRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDG 514 I R L+Q + VVAGFQG T G+ITTLGRGGSD TA AL +L A+ +++ DV+G Sbjct: 121 PGRIIRELEQGHVVVVAGFQGRTADGEITTLGRGGSDTTAAALGVALDAERVDIFTDVEG 180 Query: 515 VYTADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRG 574 + TADPRIV+DAR + + ++ E+ L+ GA+V+ RA E A + + V ++ + G Sbjct: 181 IMTADPRIVRDARRLPQATYTEICNLAYQGAKVIHPRAVEIAMRKNIPVRVRATMSDDEG 240 Query: 575 TLI--------WEGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNI 626 TL+ EG + +V +T + ++ + P V + + ++ G+++ Sbjct: 241 TLVTNVEDDGRLEGRDPGDRLVTGITQTSRIVQIKIAQPSGAPPVHRAVFQAMADAGISV 300 Query: 627 DMIIQGMKSGEYNTVAFIVPESQLGKLDIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTST 686 D I G VAF V E++ G+ + L R+ E+ I AKVS+VG + Sbjct: 301 DFINVGP-----GGVAFTVSEAEAGRAEKIL---RNLGVEVEIVPDCAKVSVVGAGIAGV 352 Query: 687 PEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELD 737 P + A + LA EG+ I + S + I ++ + AV A+H RF LD Sbjct: 353 PGVMARIVGALAEEGVEILQSADSHTTIWCLVREGDMNRAVCALHRRFGLD 403 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: 695 Number of extensions: 33 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: 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 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