Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 6936867 Sama_1049 aspartate kinase (RefSeq)
Query= BRENDA::Q9WZ17 (739 letters) >FitnessBrowser__SB2B:6936867 Length = 403 Score = 256 bits (654), Expect = 2e-72 Identities = 144/402 (35%), Positives = 236/402 (58%), Gaps = 6/402 (1%) Query: 340 VVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPD 399 + V KFGG ++ E++E VA+ I K G + V+VLSAM T+ L +A ID Sbjct: 4 IYVKKFGGTSVGTFERIEAVADAIAKAHFEGERQVLVLSAMAGETNRLYAMAANIDPLAP 63 Query: 400 PRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIIS 459 RELD+L+S GE S+ALMSIAL +RG A S G+Q+K+ T+ ++G A I ++T ++ Sbjct: 64 ARELDMLVSAGEQVSIALMSIALARRGVNARSLLGSQVKVRTNSQFGRASIESVDTGLLM 123 Query: 460 RYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTAD 519 + L + +PV+AGFQG+ E GD+TTLGRGGSD TA+A+A +L A C+++ DV GV+T D Sbjct: 124 QLLDEGAVPVIAGFQGVNEQGDVTTLGRGGSDTTAVAIAAALEAAECQIFTDVTGVFTTD 183 Query: 520 PRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLI-W 578 P I DA+ + +S+E M E++R GA+VL + AR++GV + + ++ + GTLI + Sbjct: 184 PNIDPDAQKLDSISFEAMYEMARQGAKVLHPDSVACARRHGVVLRVLSSFESGSGTLIRF 243 Query: 579 EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEY 638 + + + + G V + + D+P + + L+ V+ D+++Q E Sbjct: 244 DEPEHSGSGIVGIAVTRGQGLVSVAGLVDQPQAEVALFQALANASVDTDLVVQ---LAEE 300 Query: 639 NTVAFIVPESQLGKL--DIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTSTPEISATLFET 696 +AF + + L K+ ID L ++ E LAKVS+V E+ A + E Sbjct: 301 KALAFTLAQGALDKVLTLIDRLALEQPLADVRHESPLAKVSLVSTGKAVMAEVGARVTEL 360 Query: 697 LANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDR 738 L + I + ++S S ++SV+ID +++ AV+++H F+L++ Sbjct: 361 LEAQNIRVKLLSTSEIKLSVVIDEVHLQHAVRSLHRAFDLNK 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: 598 Number of extensions: 30 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: 403 Length adjustment: 35 Effective length of query: 704 Effective length of database: 368 Effective search space: 259072 Effective search space used: 259072 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 09 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