Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011989176.1 CKL_RS02980 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000016505.1:WP_011989176.1 Length = 399 Score = 286 bits (733), Expect = 1e-81 Identities = 156/402 (38%), Positives = 250/402 (62%), Gaps = 8/402 (1%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 +++V K+GG+++ EK++ VA ++ + K+G VVV+SAMGDTTD LI LA+ I +NP Sbjct: 2 AIIVQKYGGSSVGTPEKIKNVANTVVNKVKAGNSLVVVVSAMGDTTDDLIALARQITDNP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 D RELD LLSTGE+ S AL+++A++ GY AIS+T Q+ I T +YG + I DIN D + Sbjct: 62 DKRELDALLSTGEMMSCALLAMAIKDLGYDAISYTAYQIGIKTSGQYGKSLIDDINADRM 121 Query: 459 SRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 + L + I + AGFQGI + GD+TTLGRGGSD TA+A+A L +CE+Y DVDG+Y+ Sbjct: 122 KKSLDEGKIIIAAGFQGINDEGDVTTLGRGGSDTTAVAIAVKLNG-VCEIYTDVDGIYSV 180 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIW 578 DPR K+A+ + E+ +EEM+ELS GAQV+ +R+ E A+KY + V + ++ RGT+I Sbjct: 181 DPRKYKNAKKLDEIDYEEMLELSSLGAQVMHSRSIELAQKYNIPVYVGLSNSNIRGTVI- 239 Query: 579 EGTKVEN----PIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMK 634 +G N P+ T ++ +A + +KD+ + + + + ++++ +N+DMI Q Sbjct: 240 KGVDTMNLESKPVTGLATSDEDIA-ITVKDIKNDINIISNLFESVAEKKINVDMISQTAP 298 Query: 635 SGEYNTVAFIVPESQLGKLDIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTSTPEISATLF 694 V+F +P+ + K + +LK+ + +I I+K + K SIVG+ + +T + A +F Sbjct: 299 IDGKVNVSFTIPKDDM-KECLTILKSYFDNNQIDIDKDITKFSIVGIGMKTTSGVVAKMF 357 Query: 695 ETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFEL 736 + I + MI+ S RI+ I + + I +F L Sbjct: 358 KLFRENNIAVKMITTSEIRITCAIKQEDKMKTISIIAEKFNL 399 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: 674 Number of extensions: 26 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: 399 Length adjustment: 35 Effective length of query: 704 Effective length of database: 364 Effective search space: 256256 Effective search space used: 256256 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