Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_005808827.1 DHAF_RS18265 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000021925.1:WP_005808827.1 Length = 409 Score = 226 bits (575), Expect = 2e-63 Identities = 147/417 (35%), Positives = 230/417 (55%), Gaps = 33/417 (7%) Query: 340 VVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDT-----TDHLIELAKTI 394 V+V KFGG ++S E+ +VA K+ + + G PVVV+SA+G + TD I L I Sbjct: 3 VLVQKFGGTSVSSAERRAQVAAKVSEAVREGYSPVVVVSAIGRSGDPYATDTFINLVNGI 62 Query: 395 DENPDPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDIN 454 RE+DLL+S GEI S +++ L+ G +AI TG Q IIT+ YG ARII + Sbjct: 63 TLESPKREMDLLMSCGEIISGVVLTSTLKSMGLEAILLTGGQAGIITNDCYGDARIIRVE 122 Query: 455 TDIISRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDG 514 I +L + + VV GFQG+TE G +TTLGRGGSD TA AL +L A+ ++Y DV+G Sbjct: 123 PKGILDHLSEGRVVVVTGFQGVTEDGQVTTLGRGGSDTTASALGVALNAEAIDIYTDVEG 182 Query: 515 VYTADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRG 574 + TADPRIV+DAR++ +++ E+ L+ GA+V+ RA E A + + + IK + RG Sbjct: 183 IMTADPRIVEDARILDVVTYNEICHLAHQGAKVIHPRAVEIAMQRNIPIWIKCTFSDARG 242 Query: 575 TLIWE-------GTKVENPIVRAVTFEDGMA--------KVVLKDVPDKPGVAARIMRTL 619 TL+ GT + R +T G+A +V DV D V +I + + Sbjct: 243 TLVTSIQPDMGAGTDITGD--RTIT---GIAHTPNVTQIQVPTHDVADVLQVDKQIFKGM 297 Query: 620 SQMGVNIDMIIQGMKSGEYNTVAFIVPESQLGKLDIDLLKTRSEAKEIIIEKGLAKVSIV 679 + +++D I S + +V + VP+ ++ + + +L + G AKVSIV Sbjct: 298 ALADISVDFI-----SVQPESVLYTVPD-EIAEKAMKILDNLGFKPTAV--PGCAKVSIV 349 Query: 680 GVNLTSTPEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFEL 736 G + P + A + E L++ G+ I + S + I V+++ + + AV+A+H +F L Sbjct: 350 GAGIAGVPGVMANMVEALSDAGVRILQSADSHTTIWVLVNKEDMVPAVQALHKKFLL 406 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: 40 Number of successful extensions: 3 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