Align Aspartate kinase Ask_Ect; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_028316098.1 G491_RS0122000 aspartate kinase
Query= SwissProt::A4VFY3 (476 letters) >NCBI__GCF_000429905.1:WP_028316098.1 Length = 472 Score = 498 bits (1283), Expect = e-145 Identities = 249/465 (53%), Positives = 330/465 (70%), Gaps = 1/465 (0%) Query: 2 HTVEKIGGTSMSRFEEVLDNIFIGRREGAALYQRIFVVSAYSGMTNLLLEHKKTGEPGVY 61 HTVEKIGGTSMSRF++VLDN+ +G R+ + LYQRI VVSAY+G+T+LLLEHKKT EPGVY Sbjct: 4 HTVEKIGGTSMSRFKDVLDNVLVGNRKESELYQRIIVVSAYAGLTDLLLEHKKTREPGVY 63 Query: 62 QRFADAQ-SEGAWREALEGVRQRMLAKNAELFSSEYELHAANQFINSRIDDASECMHSLQ 120 F D S AW +A+ V ++ML+ NAEL +L A+ F+ RI+ C+ L Sbjct: 64 GLFVDDNASSWAWGDAISKVGEKMLSINAELEPLGLDLDQADLFVKERIEGVRSCLLDLH 123 Query: 121 KLCAYGHFQLSEHLMKVREMLASLGEAHSAFNSVLALKQRGVNARLADLTGWQQEAPLPF 180 +LC+YGHFQLSEHL+ +RE+L+++GEAHSA+N+ + L+ +GVNAR DLTGW++E F Sbjct: 124 RLCSYGHFQLSEHLLTIRELLSAIGEAHSAYNTTMILQDKGVNARFVDLTGWREEENWGF 183 Query: 181 EEMISSHFAGFDFSRELVVATGYTHCAEGLMNTFDRGYSEITFAQIAAATGAREAIIHKE 240 E + F G ++ EL + TGYT C EGLM+T+DRGYSEITF+++A T AREAIIHKE Sbjct: 184 TEKVKKFFDGTNYDEELPIVTGYTQCKEGLMHTYDRGYSEITFSKVAVVTQAREAIIHKE 243 Query: 241 FHLSSADPNLVGADKVVTIGRTNYDVADQLSNLGMEAIHPRAAKTLRRAGVELRIKNAFE 300 FHLSSADP +VGA+KV TIGRTNYDVADQL++LGMEAIHP AAK LR +G++LRIKN FE Sbjct: 244 FHLSSADPKMVGAEKVQTIGRTNYDVADQLADLGMEAIHPGAAKGLRNSGIDLRIKNTFE 303 Query: 301 PEHGGTLISQDYKSEKPCVEIIAGRKDVFGIEVFDQDMLGDIGYDMEISKLLKQLKLYVV 360 P+H GTLI+ DY SE PCVEIIAGR + + DQDM+G GYD ++ K L L V Sbjct: 304 PDHPGTLITNDYVSESPCVEIIAGRTGLTEVRFMDQDMVGLTGYDQKLCKDLDDRDLRYV 363 Query: 361 NKDSDANSITYYASGSRKLINRAARLIEEQYPAAEVTVHNLAIVSAIGSDLKVKGILAKT 420 K + AN+I +Y S K R +++YP A++ + +A+VS IGS++ G++A+ Sbjct: 364 AKTTSANTIVHYFPVSMKRAGDLVRSWKKKYPEADIDMGPVAMVSPIGSNMAAPGLMARA 423 Query: 421 VAALAEAGISIQAIHQSIRQVEMQCVVNEEDYDAAIAALHRALIE 465 AL EAG+ + A+ + R VE + +V E D + LHR L+E Sbjct: 424 TTALDEAGVYVIAMQKDRRNVEAKFIVPESDLQQTVKVLHRVLVE 468 Lambda K H 0.318 0.133 0.372 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: 581 Number of extensions: 20 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: 476 Length of database: 472 Length adjustment: 33 Effective length of query: 443 Effective length of database: 439 Effective search space: 194477 Effective search space used: 194477 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: 51 (24.3 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