Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_078716958.1 B5D49_RS06950 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_900167125.1:WP_078716958.1 Length = 413 Score = 289 bits (739), Expect = 2e-82 Identities = 156/403 (38%), Positives = 253/403 (62%), Gaps = 2/403 (0%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 S+VV KFGG +++++E + +V K+ + G K VVVLSAM T+ L+ +A P Sbjct: 2 SLVVQKFGGTSVANLECMRQVLAKVKRPLSRGDKVVVVLSAMSGETNRLLAMADEWAAQP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 DP E+D L+STGE SVAL +I L+ +G +A S G Q+ I T+ +G ARI+DI+ + Sbjct: 62 DPAEVDSLVSTGEQASVALFAILLKAQGIRARSVLGFQVPIRTNCAHGKARILDIDGSKL 121 Query: 459 SRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 L + + VVAGFQG + ITTLGRGGSD +A+ALA +L AD+CE+Y DV GV+T Sbjct: 122 HTMLDEHDVLVVAGFQGCDDCQRITTLGRGGSDTSAVALAAALEADVCEIYTDVSGVFTT 181 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLIW 578 DP I AR I +++++EM+E++ GA+VLQ R+ EFA+KY V V +++ + GT++ Sbjct: 182 DPNICSTARKIDKVAYDEMLEMASMGAKVLQIRSVEFAKKYNVIVHVRSTFCDEPGTIVC 241 Query: 579 EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEY 638 + ++E +V + ++ A++ L V D+PGV+A++ ++ + +DMI+Q Sbjct: 242 QEDQMEAVLVSGIAYDKDQARITLVHVEDRPGVSAQVFSAIAAKKILVDMIVQNPSKDGK 301 Query: 639 NTVAFIVPESQLGKL--DIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTSTPEISATLFET 696 + F VP + L + ++ LK ++ +K +AK+S++GV + + +++ F+ Sbjct: 302 TDLTFTVPRADLKQTIRILEGLKYEIGFGDLRYDKHVAKISVIGVGMRNHSGVASKAFQA 361 Query: 697 LANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDRE 739 L++EGINI MIS S +++ +I+ KY E AV+ +H F+LD E Sbjct: 362 LSDEGINILMISTSEIKVTCLIEEKYTELAVRTVHKAFDLDSE 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: 611 Number of extensions: 28 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 739 Length of database: 413 Length adjustment: 36 Effective length of query: 703 Effective length of database: 377 Effective search space: 265031 Effective search space used: 265031 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