Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_028312931.1 H566_RS0120680 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000482785.1:WP_028312931.1 Length = 418 Score = 311 bits (796), Expect = 5e-89 Identities = 174/414 (42%), Positives = 261/414 (63%), Gaps = 16/414 (3%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 +++V K+GG ++ E++ VA ++ K ++G + VVV SAM T+ L+ LAK + NP Sbjct: 2 ALIVHKYGGTSMGSTERIRNVARRVAKWVRAGHQIVVVPSAMSGETNRLLGLAKELTSNP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 DPRELD++ STGE SV L+++AL+ G A+S+ G Q+ + TD Y ARI I+ + Sbjct: 62 DPRELDMIASTGEQVSVGLLALALQAEGVPAVSYAGWQVPVRTDSAYTKARISSIDDTRV 121 Query: 459 SRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 L + V+ GFQGI E G ITTLGRGGSD +A+A+A +L A+ C +Y DVDGVYT Sbjct: 122 RADLDAGKVVVITGFQGIDELGSITTLGRGGSDTSAVAVAAALKAEECLIYTDVDGVYTT 181 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNA---------H 569 DPR+V +AR +K +S+EEM+E++ G++VLQ R+ EFA KY V+ + ++ Sbjct: 182 DPRVVPEARRLKVISFEEMLEMASLGSKVLQIRSVEFAGKYRVRTRVLSSLTDPLMPLED 241 Query: 570 KETRGTLIW--EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNID 627 + GTLI E K+E ++ + F AKV + VPDKPGVA +I+ +++ +++D Sbjct: 242 EMISGTLITFEEDEKMETAVISGIAFSRDEAKVTVLGVPDKPGVAFKILGPIAEANIDVD 301 Query: 628 MIIQGMKSGEYNTVAFIVPESQLGKLDIDLLKTRSE----AKEIIIEKGLAKVSIVGVNL 683 +IIQ + +F V +L K +D+L T+ + AKEI+ + + KVS VG+ + Sbjct: 302 VIIQNQSVEGFTDFSFTVARGELAKA-LDVLNTKVKPEIGAKEIVGDPAVCKVSAVGIGM 360 Query: 684 TSTPEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELD 737 S I++ +FETL NEGINI MIS S +ISV+I KY+E AV+A+H F L+ Sbjct: 361 RSHVGIASKMFETLFNEGINIQMISTSEIKISVVIADKYMELAVRALHKAFGLE 414 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: 748 Number of extensions: 37 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: 418 Length adjustment: 36 Effective length of query: 703 Effective length of database: 382 Effective search space: 268546 Effective search space used: 268546 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 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