Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011802264.1 PNAP_RS14430 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000015505.1:WP_011802264.1 Length = 422 Score = 282 bits (722), Expect = 2e-80 Identities = 166/419 (39%), Positives = 259/419 (61%), Gaps = 20/419 (4%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTI---- 394 +++V K+GG ++ E++ VA+++ K ++G + VVV SAM T+ L+ LAK + Sbjct: 2 ALIVHKYGGTSMGSTERIRNVAKRVAKWARAGHQMVVVPSAMSGETNRLLGLAKELAPAQ 61 Query: 395 DENPDPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDIN 454 ++ RELD L +TGE S AL++IAL+ G A+S+ G Q+ I T+ Y ARI I+ Sbjct: 62 SDDTYSRELDALAATGEQASSALLAIALQAEGMPAVSYAGWQVTIKTNSAYTKARIESID 121 Query: 455 TDIISRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDG 514 + + L + ++ GFQG+ E G++TTLGRGGSD +A+A+A +L A C +Y DVDG Sbjct: 122 DEKVRADLDAGKVVIITGFQGMDEGGNVTTLGRGGSDTSAVAIAAALKAHECLIYTDVDG 181 Query: 515 VYTADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNA------ 568 VYT DPR+V +AR ++ +S+EEM+E++ G++VLQ R+ EFA KY V + + ++ Sbjct: 182 VYTTDPRVVPEARRLQTVSFEEMLEMASMGSKVLQIRSVEFAGKYKVPLRVLSSFTDWNI 241 Query: 569 --HKETR-GTLI--WEGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMG 623 ++E R GTLI E K+E IV + F AK+ + VPD PG+A +I+ ++ Sbjct: 242 DINEEARSGTLISFEEDEKMEKAIVSGIAFNRDEAKISVLGVPDTPGIAYQILGAVADAN 301 Query: 624 VNIDMIIQGMKSGEYNTVAFIVPESQLGKLDIDLLKTR----SEAKEIIIEKGLAKVSIV 679 + +D+IIQ + +F V + K +DLLK++ A+E+ + + KVSIV Sbjct: 302 IEVDVIIQNISKDGKTDFSFTVHRNDFAK-TLDLLKSKVVPALGAQEVTGDARICKVSIV 360 Query: 680 GVNLTSTPEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDR 738 G+ + S I++ +F LA EGINI MIS S + SV+ID KY+E AV+A+H F+LD+ Sbjct: 361 GIGMRSHVGIASKMFRVLAEEGINIQMISTSEIKTSVVIDEKYMELAVRALHKAFDLDQ 419 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: 693 Number of extensions: 38 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: 422 Length adjustment: 36 Effective length of query: 703 Effective length of database: 386 Effective search space: 271358 Effective search space used: 271358 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