Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_012334463.1 M446_RS22805 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000019365.1:WP_012334463.1 Length = 411 Score = 253 bits (646), Expect = 1e-71 Identities = 149/407 (36%), Positives = 239/407 (58%), Gaps = 9/407 (2%) Query: 341 VVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDP 400 +VMKFGG +++ V+++ VA + + ++G + VV+SAM T+ L+ K Sbjct: 4 LVMKFGGTSVATVDRIRNVARHVAREVRAGYEVAVVVSAMAGKTNELVAWCKDASPLYPQ 63 Query: 401 RELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIISR 460 E D ++++GE + L++I L + G A S+ G Q+ I T ++GSARI I+ + Sbjct: 64 SEYDAVVASGEQVTSGLLAIVLAQMGIPARSWQGWQIPIETSDQHGSARIARIDGARLDA 123 Query: 461 YLKQDFIPVVAGFQGI-TETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTAD 519 + + V+AGFQGI E+G +TTLGRGGSD +A+A+A ++GA+ C++Y DVDGVYT D Sbjct: 124 GFRHGEVAVIAGFQGIHPESGRLTTLGRGGSDTSAVAVAAAIGAERCDIYTDVDGVYTTD 183 Query: 520 PRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKE----TRGT 575 PR+V AR ++ +++EEM+E++ GA+VLQ R+ E A + V ++++ + GT Sbjct: 184 PRVVPKARRLERVAFEEMLEMASLGAKVLQVRSVELAMVHRVPTTVRSSFDDPDDARPGT 243 Query: 576 LIW-EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMK 634 LI E VE I+ + F A++ L+ V DKPG+AA I L+ +N+DMIIQ + Sbjct: 244 LICDEDDIVEQQIITGIAFSKDEAQITLRRVKDKPGIAAAIFGPLADANINVDMIIQVVS 303 Query: 635 -SGEYNTVAFIVP--ESQLGKLDIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTSTPEISA 691 G + F VP + + + +D E + I + K+S +GV + S ++A Sbjct: 304 GDGATTDMTFTVPAGDYERARAILDAQAGTIEFERIEGATDVVKISAIGVGMRSHAGVAA 363 Query: 692 TLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDR 738 F LA++GINI I+ S + SV+ID Y E AV+ +H+ + LDR Sbjct: 364 KAFRALADKGINIRAITTSEIKFSVLIDAAYTELAVRTLHALYGLDR 410 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: 641 Number of extensions: 26 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: 411 Length adjustment: 36 Effective length of query: 703 Effective length of database: 375 Effective search space: 263625 Effective search space used: 263625 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