Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_085772645.1 B1812_RS16990 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_002117405.1:WP_085772645.1 Length = 411 Score = 268 bits (684), Expect = 5e-76 Identities = 157/407 (38%), Positives = 243/407 (59%), Gaps = 8/407 (1%) Query: 341 VVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDP 400 +VMKFGG +++ VE++ VA + + +G VV+SAM T+ L+ K D Sbjct: 4 LVMKFGGTSVATVERIHNVARHVKREIAAGYDVAVVVSAMSGKTNELVAWCKEAARLHDM 63 Query: 401 RELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIISR 460 RE D ++++GE + L++IAL+ +G A S+ G Q ++TD +G+ARI+ I + I Sbjct: 64 REYDAVVASGEQVTSGLLAIALQAQGVAARSWQGWQTPVLTDASHGAARIMSIEPEGIIE 123 Query: 461 YLKQDFIPVVAGFQGITE-TGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTAD 519 + VVAGFQGI + +G ITTLGRGGSD +A+ALA ++GA+ C++Y DVDGVYT D Sbjct: 124 GFGRKETAVVAGFQGIHKPSGRITTLGRGGSDTSAVALAAAIGAERCDIYTDVDGVYTTD 183 Query: 520 PRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKE----TRGT 575 PR+V AR + +++EEM+E++ GA+V+Q R+ E A K+ + ++++ + GT Sbjct: 184 PRVVSKARRMDRIAFEEMLEMASLGAKVMQVRSVELALKHDMPTYVRSSFDDPDDPRPGT 243 Query: 576 LIW-EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMK 634 LI E +E+ +V V F A++ L+ V DKPGVAA + L++ G+N+DMI+Q + Sbjct: 244 LICREEDIMESQVVTGVAFSRDEAQITLRRVIDKPGVAASVFMPLAEAGINVDMIVQTIS 303 Query: 635 SGEYNTVAFIVPESQLGKLDIDLLKTRSEA--KEIIIEKGLAKVSIVGVNLTSTPEISAT 692 + F V S + L K + E + K +AKVS+VGV + S ++A Sbjct: 304 DDSMTDMTFTVAASDFDRARALLEKAKGEIGFAALAGAKDVAKVSVVGVGMRSHAGVAAK 363 Query: 693 LFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDRE 739 F LA +G+NI IS S + SV+ID Y E AV+ +H+ + LD E Sbjct: 364 GFRALAEKGVNIRAISTSEIKFSVLIDAAYTELAVRTLHTLYGLDGE 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: 646 Number of extensions: 28 Number of successful extensions: 6 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: 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