Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_004511964.1 GMET_RS09500 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000012925.1:WP_004511964.1 Length = 405 Score = 328 bits (842), Expect = 2e-94 Identities = 172/401 (42%), Positives = 268/401 (66%), Gaps = 3/401 (0%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 ++VV K+GG ++ +E++ VA+++ K +G VVV+SAM T+ L+ LA + E P Sbjct: 2 ALVVQKYGGTSMGSIERIRNVAKRVAKTYDAGNDMVVVVSAMSGETNKLVALANEVCEFP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 D RE D+L+++GE S+AL+++ L+ GYKA S+ G Q+ IITD + ARI +I + Sbjct: 62 DNREYDVLVASGEQVSIALLAMCLKSMGYKAKSYHGWQVPIITDSVFSKARIEEIPDAKV 121 Query: 459 SRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 LK I VVAGFQGI + G++TTLGRGGSD +A+A+A ++ AD+CE+Y DVDGVYT Sbjct: 122 RADLKDGTIVVVAGFQGIDKDGNVTTLGRGGSDTSAVAMAAAMKADVCEIYTDVDGVYTT 181 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIW 578 DP I +DAR I ++S++EM+EL+ GA+VLQ R+ EFA+KY V + ++++ + +GT++ Sbjct: 182 DPNICEDARKIDKISYDEMLELASLGAKVLQIRSVEFAKKYNVDIHVRSSFNDNQGTMVT 241 Query: 579 EGTK-VENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGE 637 + K +E +V + ++ AK+ + VPDKPG+AA+I+ +LS +++DMI+Q + G+ Sbjct: 242 KEDKDMEAVLVSGIAYDKNEAKIAVLGVPDKPGIAAKILSSLSDANISVDMIVQNVSGGD 301 Query: 638 YNTVAFIVPESQLGK-LDIDL-LKTRSEAKEIIIEKGLAKVSIVGVNLTSTPEISATLFE 695 F V ++ K L I + T +A + ++ ++KVSIVGV + S ++ +F+ Sbjct: 302 LTDFTFTVTKADFKKALAITKEIATEIKATGVSADESISKVSIVGVGMRSHAGVATKMFQ 361 Query: 696 TLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFEL 736 TLANEGINI MIS S ++SV+ID KY E AV+ +H F L Sbjct: 362 TLANEGINIQMISTSEIKVSVVIDAKYTELAVRVLHEAFGL 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: 686 Number of extensions: 26 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: 405 Length adjustment: 35 Effective length of query: 704 Effective length of database: 370 Effective search space: 260480 Effective search space used: 260480 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: 52 (24.6 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