Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013074687.1 BTUS_RS03195 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000092905.1:WP_013074687.1 Length = 415 Score = 325 bits (834), Expect = 2e-93 Identities = 170/399 (42%), Positives = 262/399 (65%), Gaps = 3/399 (0%) Query: 341 VVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDP 400 +VMKFGG++++ E++ KVA+++ K K G + VV+SAMGDTTD LI LAK ++E P Sbjct: 4 IVMKFGGSSVATAERMVKVAQRVAKTKAEGHQVAVVVSAMGDTTDDLIALAKQVNERPPA 63 Query: 401 RELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIISR 460 RELD+LLSTGE S+A++++AL+ G A S TG Q ++ +G ARI+++ D + Sbjct: 64 RELDMLLSTGEQVSIAVLTMALQGLGVPATSLTGGQAGFRVEQVFGKARILEVRPDRVDA 123 Query: 461 YLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTADP 520 L+ + VVAGFQG+T+ G+I TLGRGGSD TA+ALA +L AD+CE+Y DVDGVYT DP Sbjct: 124 LLRDGHVAVVAGFQGVTDDGEIATLGRGGSDTTAVALAAALKADVCEIYTDVDGVYTTDP 183 Query: 521 RIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIWEG 580 RIVK+A I E+S++EM+EL+ GA VL RA E+A+ Y V ++++++ + GT + E Sbjct: 184 RIVKEAAKIPEISYDEMLELANLGAVVLHPRAVEYAKLYRVPLVVRSSFHDGPGTWVKEE 243 Query: 581 TKVE-NPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEYN 639 VE +VR + + +AKV L VP++ ++ L++ VN+D+I+Q + + + Sbjct: 244 ANVEQGQVVRGIAHDLNVAKVSLVGVPNRQDSLGKVFHALAEENVNVDIIVQSIVHNDVH 303 Query: 640 TVAFIVPESQLGKL--DIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTSTPEISATLFETL 697 ++F V L ++ L+ A EI+ E+ LAKVSIVG + S P ++A +F+ L Sbjct: 304 DISFTVCRDDLPVTLRVLEDLRVALGAGEIVTEEDLAKVSIVGAGMISNPGVAARMFDAL 363 Query: 698 ANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFEL 736 G++I M+S S ++S ++D + V+ AV+ +H FEL Sbjct: 364 IEAGMSIRMVSTSEIKVSCVVDARDVKRAVQVLHQAFEL 402 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: 625 Number of extensions: 30 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: 415 Length adjustment: 36 Effective length of query: 703 Effective length of database: 379 Effective search space: 266437 Effective search space used: 266437 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