Align Aspartate kinase Ask_Ect; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate Ac3H11_4087 Aspartokinase (EC 2.7.2.4)
Query= SwissProt::A4VFY3 (476 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4087 Length = 473 Score = 384 bits (985), Expect = e-111 Identities = 210/461 (45%), Positives = 296/461 (64%), Gaps = 8/461 (1%) Query: 3 TVEKIGGTSMSRFEEVLDNIFIGRREGAALYQRIFVVSAYSGMTNLLLEHKKTGEPGVYQ 62 +VEKIGGTSM+ F +VL +I + + +Y RI+VVSAYSG+TN LLEHKKTGE G+Y Sbjct: 10 SVEKIGGTSMTAFGDVLRHIML--HDPKRIYGRIYVVSAYSGVTNQLLEHKKTGERGIYA 67 Query: 63 RFADAQSEGAWREALEGVRQRMLAKNAELFSSEYELHAANQFINSRIDDASECMHSLQKL 122 FA+ + +++AL + + NA L A+ FI+ RI A E + ++Q + Sbjct: 68 LFAEGKG---YQDALVNLATSLKKLNAGYADLGLPLDVADAFIDQRIGQAREYLSAMQHV 124 Query: 123 CAYGHFQLSEHLMKVREMLASLGEAHSAFNSVLALKQRGVNARLADLTGWQQEAPLPFEE 182 A G+ + L+ RE+LAS+GE+HSAFNSV LK GV A L DL G+ +E Sbjct: 125 LASGYLSRHDVLLAAREVLASIGESHSAFNSVEILKANGVKAVLMDLAGFDDNEAWTIDE 184 Query: 183 MISSHFAGFDFSRELVVATGYTHCAEGLMNTFDRGYSEITFAQIAAATGAREAIIHKEFH 242 I+ F G D S ++VVATGYT EG+M FDRGYSE+TF++IA EA+IHKEFH Sbjct: 185 RIAHSFKGLDLSDKVVVATGYTKGTEGIMREFDRGYSEVTFSKIAVEVRPAEAVIHKEFH 244 Query: 243 LSSADPNLVGADKVVTIGRTNYDVADQLSNLGMEAIHPRAAKTLRRAGVELRIKNAFEPE 302 LSSADPNLVG + + +G TNYDVADQL+++GMEAIHP+AAK + AG+ +R+KN FEP+ Sbjct: 245 LSSADPNLVGLENAIVVGATNYDVADQLADVGMEAIHPKAAKPMELAGIPIRLKNTFEPD 304 Query: 303 HGGTLISQDYKSEKPCVEIIAGRKDVFGIEVFDQDMLGDIGYDMEISKLLKQLKLYVVNK 362 H GTLI++D+ E+ VEI+ G V IE+ D M+G +G+D + + + ++ + K Sbjct: 305 HPGTLITKDFVGERARVEIVTGTDKVTLIEIHDPSMVGTVGFDAGLMNVFCKHEVSYILK 364 Query: 363 DSDANSITYYASGSRKLINRAARLIEEQYPAAEVTVHNLAIVSAIGSDLKVKGILAKTVA 422 ++ANSI + S+ A L ++ Y VT+ AIV IGS++ + G+LAK Sbjct: 365 ATNANSIAHLMWDSQVTPELVAEL-QKDYQV--VTIKPSAIVCTIGSNIGIPGVLAKAAQ 421 Query: 423 ALAEAGISIQAIHQSIRQVEMQCVVNEEDYDAAIAALHRAL 463 ALA+A +++ + Q++RQV MQ V+ EDY AI AL+ AL Sbjct: 422 ALADAQVNVNCVSQTLRQVNMQFVIEREDYKTAIKALNMAL 462 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: 566 Number of extensions: 29 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: 476 Length of database: 473 Length adjustment: 33 Effective length of query: 443 Effective length of database: 440 Effective search space: 194920 Effective search space used: 194920 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 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