Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate YP_004140819.1 Mesci_1612 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000185905.1:YP_004140819.1 Length = 417 Score = 271 bits (693), Expect = 5e-77 Identities = 150/414 (36%), Positives = 250/414 (60%), Gaps = 15/414 (3%) Query: 341 VVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDP 400 +VMKFGG +++D+ ++ VA + + +G + VV+SAM T+ L+ + D Sbjct: 4 IVMKFGGTSVADIARIRNVARHVKREVDAGHEVAVVVSAMAGKTNELVGWTREASPMHDA 63 Query: 401 RELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIISR 460 RE D ++++GE + L++I L+ G A S+ G Q+ I TD +G+ARI+DI+ + + Sbjct: 64 REYDAVVASGEQVTAGLLAITLQNMGVHARSWQGWQIPIKTDNAHGAARILDIDGAFLIK 123 Query: 461 YLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTADP 520 + + V+AGFQGI I TLGRGGSD +A+A+A ++ AD C++Y DVDGVYT DP Sbjct: 124 RFGEGQVAVIAGFQGIGPDNRIATLGRGGSDTSAVAIAAAVKADRCDIYTDVDGVYTTDP 183 Query: 521 RIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKE--------- 571 RI AR + ++S+EEM+E++ GA+VLQ R+ E A + V+ ++++ + Sbjct: 184 RIEPKARRLAKISFEEMLEMASLGAKVLQVRSVELAMVHRVRTFVRSSFDDPDAPGMGDL 243 Query: 572 --TRGTLIWEGTK-VENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDM 628 GTLI + + VE +V + + A++ L+ V D+PGVAA I L++ +N+DM Sbjct: 244 LNPPGTLICDEEEIVEQQVVTGIAYAKDEAQISLRRVGDRPGVAAGIFGPLAEANINVDM 303 Query: 629 IIQGM-KSGEYNTVAFIVPESQLGK--LDIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTS 685 I+Q + + G++ + F VP + K ++ LK + E G++KVS++G+ + S Sbjct: 304 IVQNISEDGKFTDMTFTVPSGDVDKALAVLERLKASIGYDVVQSEAGMSKVSVIGIGMRS 363 Query: 686 TPEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDRE 739 ++AT F+ LA++ INI I+ S +IS++IDG Y E AV+ +HS + LD++ Sbjct: 364 HAGVAATAFKALADKSINIRAITTSEIKISILIDGPYTELAVRTLHSVYGLDKQ 417 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: 677 Number of extensions: 32 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: 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