Align Aspartate kinase Ask_Ect; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_059153662.1 V474_RS23850 aspartate kinase
Query= SwissProt::A4VFY3 (476 letters) >NCBI__GCF_001046635.1:WP_059153662.1 Length = 484 Score = 435 bits (1118), Expect = e-126 Identities = 235/475 (49%), Positives = 308/475 (64%), Gaps = 3/475 (0%) Query: 2 HTVEKIGGTSMSRFEEVLDNIFIGRREGAALYQRIFVVSAYSGMTNLLLEHKKTGEPGVY 61 H+VEKIGGTSM+ V DN+ + REGA LY RIFVVSAY+GMT+LLLEHKK+G GV+ Sbjct: 5 HSVEKIGGTSMAATSTVFDNVLVAGREGADLYNRIFVVSAYAGMTDLLLEHKKSGRAGVH 64 Query: 62 QRFADAQSEGAWREALEGVRQRMLAKNAELFSSEYELHAANQFINSRIDDASECMHSLQK 121 F ++ GAWR AL V M +NAE+F+ A+ F+ RI C+ L + Sbjct: 65 AHFIRNETPGAWRAALGEVMDAMTVRNAEMFARIESRAEADAFVTKRIAALETCLDDLDR 124 Query: 122 LCAYGHFQLSEHLMKVREMLASLGEAHSAFNSVLALKQRGVNARLADLTGWQQEAPLPFE 181 L A+G F L E + VREMLA LGEAHSA ++ L L+ RGV+A DLT W E + Sbjct: 125 LRAHGRFCLKEQMTTVREMLAGLGEAHSAHSTALMLRDRGVDAVFVDLTLWDNEDMRSLD 184 Query: 182 EMISSHFAGFDFSRELVVATGYTHCAEGLMNTFDRGYSEITFAQIAAATGAREAIIHKEF 241 + I A D +R++ + TGY C G++ + RGYSE+TF++IA T AREAIIHKEF Sbjct: 185 DRIVEALAPIDLARQMPIVTGYAGCEGGMVRRYARGYSEMTFSRIAVLTQAREAIIHKEF 244 Query: 242 HLSSADPNLVGADKVVTIGRTNYDVADQLSNLGMEAIHPRAAKTLRRAGVELRIKNAFEP 301 HLSSADP LVG IGRTNYDVADQL+NLGMEAIHPRA + LR++G+ LR++N F+ Sbjct: 245 HLSSADPRLVGEAVARKIGRTNYDVADQLANLGMEAIHPRAGRGLRQSGIPLRVRNTFDR 304 Query: 302 EHGGTLISQDYKSEKPCVEIIAGRKDVFGIEVFDQDMLGDIGYDMEISKLLKQLKLYVVN 361 GGTLI DY SE P VEI+ G V ++VF+QDM+G+ GYD I L + ++V+ Sbjct: 305 HDGGTLICGDYVSEHPRVEIVTGLSSVQALQVFEQDMVGEKGYDAAILDTLTRHGAWIVS 364 Query: 362 KDSDANSITYYASG--SRKLINRAARLIEEQYPAAEVTVHNLAIVSAIGSDLKVKGILAK 419 K S+AN+IT+Y SG S ++ A IE +P A VTV +A+VS IGSDL G++ + Sbjct: 365 KSSNANTITHYLSGTDSAQMAGIVAD-IEAHWPGAAVTVQPVAMVSVIGSDLAEPGLVPR 423 Query: 420 TVAALAEAGISIQAIHQSIRQVEMQCVVNEEDYDAAIAALHRALIEPENHGDVIA 474 + AL AGI + A+ IR V++Q VV ED+D A+ LH+ L+E DV A Sbjct: 424 ALMALGGAGIGMAAMQHQIRNVDVQFVVAVEDFDPAVRVLHKVLVEGAALTDVKA 478 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: 598 Number of extensions: 24 Number of successful extensions: 3 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: 484 Length adjustment: 34 Effective length of query: 442 Effective length of database: 450 Effective search space: 198900 Effective search space used: 198900 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 Jul 26 2024. The underlying query database was built on Jul 25 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