Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_012050677.1 SWIT_RS22745 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000016765.1:WP_012050677.1 Length = 418 Score = 273 bits (698), Expect = 1e-77 Identities = 153/413 (37%), Positives = 251/413 (60%), Gaps = 15/413 (3%) Query: 341 VVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDP 400 +VMKFGG +++ +E++ VA ++ + G + VV+SAM TD L+ + DP Sbjct: 4 IVMKFGGTSMAGIERIRNVANRVKHEVELGNEVAVVVSAMSGETDRLVNFCREASPLYDP 63 Query: 401 RELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIISR 460 RE D+++++GE + L++I L+ G KA S+ G QL I T + SARI IN++ I + Sbjct: 64 REYDVVVASGEQVTSGLLAIVLQSLGVKARSWLGWQLPIRTSDAHASARIETINSEAIGK 123 Query: 461 YLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTADP 520 + + V+ GFQG+T +TTLGRGGSD +A+A+A ++ AD C++Y DVDGVYT DP Sbjct: 124 AMAAGEVAVIPGFQGMTGDDRVTTLGRGGSDTSAVAVAAAMKADRCDIYTDVDGVYTTDP 183 Query: 521 RIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKE-----TRGT 575 RIV AR + ++++EEM+EL+ GA+VLQ R+ A K V++ + ++ + T GT Sbjct: 184 RIVPKARKLAKVTYEEMLELASVGAKVLQTRSVGLAMKEKVRLQVLSSFDQPTDNPTPGT 243 Query: 576 LI-----WEGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMII 630 +I EGT +E ++ + ++ KV L VPD+PG A I L+ +N+DMI+ Sbjct: 244 MIVGEEEIEGTTMERQLITGIAYDKNETKVTLTAVPDRPGAVASIFAPLADANINVDMIV 303 Query: 631 QGMKSGEYNT-VAFIVPESQLGKLDIDLLKTRSEA---KEIIIEKGLAKVSIVGVNLTST 686 Q + +T V F VP ++L + +D+L+ +++I + +AK+S+VGV + S Sbjct: 304 QNVAHDTGSTDVTFTVPTAELAR-SLDVLERERGTIGYEKLIHDTNVAKISVVGVGMRSH 362 Query: 687 PEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDRE 739 +++ +F+ LA GIN+ I+ S ++SV+I+ Y E AV+ +H+ + LD E Sbjct: 363 AGVASKMFDALAARGINVLAITTSEIKVSVLINEDYTELAVRVLHTAYGLDAE 415 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: 670 Number of extensions: 34 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: 418 Length adjustment: 36 Effective length of query: 703 Effective length of database: 382 Effective search space: 268546 Effective search space used: 268546 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