Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 7023909 Shewana3_1129 aspartate kinase (RefSeq)
Query= BRENDA::Q9WZ17 (739 letters) >FitnessBrowser__ANA3:7023909 Length = 418 Score = 260 bits (665), Expect = 9e-74 Identities = 147/414 (35%), Positives = 255/414 (61%), Gaps = 10/414 (2%) Query: 332 LGGAEKFSVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELA 391 L G++ F V KFGG ++ +E++E VAE+I K +G V+VLSAM T+ L LA Sbjct: 7 LSGSKLF---VKKFGGTSVGSIERIEVVAEQIAKSAHNGELQVLVLSAMAGETNRLFALA 63 Query: 392 KTIDENPDPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARII 451 ID RELD+L+STGE S+ALM++AL++RG A S TG+Q++I T+ ++G A I Sbjct: 64 AQIDPRASARELDMLVSTGEQISIALMAMALQRRGINARSLTGDQVQIHTNSQFGRASIE 123 Query: 452 DINTDIISRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKD 511 ++T ++ L +P+VAGFQGI GD+TTLGRGGSD TA+ALA +L AD C+++ D Sbjct: 124 RVDTAYLTSLLNDGIVPIVAGFQGIDPNGDVTTLGRGGSDTTAVALAAALKADECQIFTD 183 Query: 512 VDGVYTADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKE 571 V GV+T DP I AR + + ++ M+E+++ GA+VL + E+A+++ V + + ++ + Sbjct: 184 VPGVFTTDPNIDSSARRLDVIGFDVMLEMAKLGAKVLHPDSVEYAQRFKVPLRVLSSFEA 243 Query: 572 TRGTLIWEGTKVENPI---VRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDM 628 GTLI G + E + V+ + +A + +K + ++ L+++ ++++ Sbjct: 244 GHGTLIQFGDESELAMAASVQGIAINKALATLTIKGLFTSSEHYQALLACLARLEIDVEF 303 Query: 629 I--IQGMKSGEYNTVAFIVPESQLGKL--DIDLLKTRSEAKEIIIEKGLAKVSIVGVNLT 684 I ++ ++ V+F++ E+++ L +++LL + ++I+E+ AKVS+VG L Sbjct: 304 ITPLKLNETSAAECVSFMLAEAKVDILLHELELLSESLDLGQLIVERQRAKVSLVGKGLQ 363 Query: 685 STPEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDR 738 + + + + L NE I+ ++S S S++S +ID + + AV+A+H FEL++ Sbjct: 364 AKVGLLTKMLDVLGNETIHAKLLSTSESKLSTVIDERDLHKAVRALHHAFELNK 417 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: 606 Number of extensions: 24 Number of successful extensions: 2 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 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