Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_012282998.1 HM1_RS08725 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000019165.1:WP_012282998.1 Length = 417 Score = 345 bits (886), Expect = 2e-99 Identities = 178/404 (44%), Positives = 283/404 (70%), Gaps = 6/404 (1%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 ++VV KFGG+++++ E++++VA ++++ K +G + VV++SAMGD+TD LI+LA+ I + P Sbjct: 2 AIVVQKFGGSSVANPERIQRVARRVVETKAAGNQVVVIVSAMGDSTDDLIDLARQITDKP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 RE+D+LL+TGE S+AL+++A+ K G+ +S TG Q+ I+T+ +G A+I+D+N + + Sbjct: 62 KAREMDMLLATGEQVSIALLAMAIDKLGHSVLSLTGPQVGILTEHVHGKAKILDVNPERL 121 Query: 459 SRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 L I +VAGFQG TETG+ITTLGRGGSD TA+A+A +L AD+CE++ DVDGVYT Sbjct: 122 RLELDAGNIVIVAGFQGATETGEITTLGRGGSDTTAVAVAAALKADVCEIFTDVDGVYTT 181 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIW 578 DPR+V +AR + ++++EM+EL+ GAQVL R+ E ++Y V + ++++ GT++ Sbjct: 182 DPRVVSNARKLNRITYDEMLELASLGAQVLHPRSVEVGKEYNVPIHVRSSFNYNPGTIVQ 241 Query: 579 EGT-KVE-NPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSG 636 E +VE + +VR V ++ +AK+ L DVPDKPGVA + + L++ VN+DMIIQ Sbjct: 242 EVVDEVEKDMMVRGVAYDLNVAKIGLFDVPDKPGVARTLFKALAERRVNVDMIIQSAMRD 301 Query: 637 EYNTVAFIVPESQLGKLDIDLLKTRSE---AKEIIIEKGLAKVSIVGVNLTSTPEISATL 693 + N +AF V + L +L ++++K +E A + + LAKVSIVG + S P ++A + Sbjct: 302 DKNDIAFTVGKDDL-ELAVEVVKEVNEAIGAGGLTYDADLAKVSIVGAGMVSRPGVAAMM 360 Query: 694 FETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELD 737 FE LA+EGINIDMI+ S ++S ++ + AV+AIH FEL+ Sbjct: 361 FEALADEGINIDMIATSEIKVSCVVSASEAKRAVQAIHKAFELE 404 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: 718 Number of extensions: 34 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: 417 Length adjustment: 36 Effective length of query: 703 Effective length of database: 381 Effective search space: 267843 Effective search space used: 267843 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