Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013450993.1 CALNI_RS04345 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000183405.1:WP_013450993.1 Length = 409 Score = 332 bits (851), Expect = 2e-95 Identities = 181/400 (45%), Positives = 267/400 (66%), Gaps = 4/400 (1%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 S+VVMKFGG ++ +E+++ VA +K+K+ G VVV SAM TD LI L K I Sbjct: 2 SLVVMKFGGTSVGSIERIKNVARIAVKKKEEGHDVVVVSSAMAGETDRLINLLKEISPKY 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 D RE D L+STGE ++ L++ A+++ G+ AISFTG Q+ +ITD + ARI+ I + I Sbjct: 62 DLREYDQLVSTGETAAIPLVTQAIKELGHDAISFTGFQIGMITDGAHSKARIVKITAERI 121 Query: 459 SRYLKQDFIPVVAGFQGI-TETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYT 517 + LK+ I VVAGFQGI ETGDITTLGRGGSD TA+A+A ++ AD+CE+Y DVDGVYT Sbjct: 122 FKALKEGKICVVAGFQGIFPETGDITTLGRGGSDTTAVAIAAAINADVCEIYTDVDGVYT 181 Query: 518 ADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLI 577 ADPRIVK+A+ + +S+EEM+EL+ GA+VLQ+R+ E KY V +L+ ++ ++ GTL+ Sbjct: 182 ADPRIVKNAKKLDRISYEEMLELASLGAKVLQSRSVELGMKYNVPILVLSSIEDKPGTLV 241 Query: 578 WEGTK-VENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSG 636 + K +E IV VT + AK+ + VPD+PG+AA I L++ +N+DMIIQ + Sbjct: 242 VKEDKDMEKVIVSGVTADKNQAKITIVGVPDRPGIAAEIFGKLAEANINVDMIIQNVGLD 301 Query: 637 EYNTVAFIVPESQLGKL--DIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTSTPEISATLF 694 ++F V ++ L + + +KT A +++ ++ +AKVSIVGV + S ++A +F Sbjct: 302 GKTDLSFTVAKTDLLRAIDACEAVKTSIGASKVVSDENIAKVSIVGVGMKSHAGVAAKMF 361 Query: 695 ETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRF 734 + L+ INI MIS S +IS +ID K+ E AV+ +H +F Sbjct: 362 KLLSENNINIQMISTSEIKISCVIDEKFAELAVRVLHEKF 401 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: 706 Number of extensions: 32 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: 409 Length adjustment: 36 Effective length of query: 703 Effective length of database: 373 Effective search space: 262219 Effective search space used: 262219 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