Align Aspartate kinase Ask_Ect; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_033394393.1 F612_RS0100940 aspartate kinase
Query= SwissProt::A4VFY3 (476 letters) >NCBI__GCF_000381085.1:WP_033394393.1 Length = 481 Score = 469 bits (1206), Expect = e-136 Identities = 241/472 (51%), Positives = 323/472 (68%), Gaps = 4/472 (0%) Query: 3 TVEKIGGTSMSRFEEVLDNIFIGRREGAALYQRIFVVSAYSGMTNLLLEHKKTGEPGVYQ 62 ++EKIGGTSMS + V DNI + Y R+ VVSAY G+T+ LLEHKKTG+PGV+ Sbjct: 10 SIEKIGGTSMSDYPVVRDNIVLYSNNP---YNRVLVVSAYGGITDDLLEHKKTGQPGVFG 66 Query: 63 RFADAQSEGAWREALEGVRQRMLAKNAELFSSEYELHAANQFINSRIDDASECMHSLQKL 122 FA S+ W A + + Q++ N LF+ +L AN FIN RI E ++ LQ L Sbjct: 67 LFAHNDSKSDWFIAFQKLGQKLNQINQTLFTDAQQLDKANGFINERIVKTKELLNHLQDL 126 Query: 123 CAYGHFQLSEHLMKVREMLASLGEAHSAFNSVLALKQRGVNARLADLTGWQQEAPLPFEE 182 C++GHF L EHL+ VRE+LAS+GEAHSA+N L+ GV R DLTGWQ + +E Sbjct: 127 CSHGHFSLEEHLLTVRELLASIGEAHSAWNLSQLLQNEGVKTRFVDLTGWQADTKHSLDE 186 Query: 183 MISSHFAGFDFSRELVVATGYTHCAEGLMNTFDRGYSEITFAQIAAATGAREAIIHKEFH 242 +I+ + DF++EL + TGY HC+E LM+TFDRGYSE+ F++IA A EA+IHKE+H Sbjct: 187 VITENMKDIDFTKELAIVTGYAHCSENLMDTFDRGYSEMVFSRIAVLCNATEAVIHKEYH 246 Query: 243 LSSADPNLVGADKVVTIGRTNYDVADQLSNLGMEAIHPRAAKTLRRAGVELRIKNAFEPE 302 LSSADP LVG + + IG+TNYD+ADQL+NLGMEAIHP AAK LR+A + LRIKNAFEPE Sbjct: 247 LSSADPRLVGETQAIPIGKTNYDIADQLANLGMEAIHPHAAKGLRQAKIALRIKNAFEPE 306 Query: 303 HGGTLISQDYKSEKPCVEIIAGRKDVFGIEVFDQDMLGDIG-YDMEISKLLKQLKLYVVN 361 H GTLI+ DY SE P VEIIAG + + +E+FDQ+M+G G Y+ + + +L+ V+ Sbjct: 307 HHGTLITDDYVSESPQVEIIAGMQRLIALEIFDQEMMGQQGRYEKILIDMSARLQCQVIT 366 Query: 362 KDSDANSITYYASGSRKLINRAARLIEEQYPAAEVTVHNLAIVSAIGSDLKVKGILAKTV 421 KD +AN+IT + + S K R A + EQ P A + +++VS +GSD+++KG+LAK+V Sbjct: 367 KDFNANTITVFLNTSLKKAKRLATQLLEQLPTATLNTSRVSLVSVMGSDMRIKGLLAKSV 426 Query: 422 AALAEAGISIQAIHQSIRQVEMQCVVNEEDYDAAIAALHRALIEPENHGDVI 473 L I+I+A+HQ+IRQVEMQ VNE+DY+ I ALH LIE +HG I Sbjct: 427 QTLFTHDINIEAMHQNIRQVEMQFFVNEKDYEKTIKALHLNLIEIHDHGKAI 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: 559 Number of extensions: 17 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: 481 Length adjustment: 34 Effective length of query: 442 Effective length of database: 447 Effective search space: 197574 Effective search space used: 197574 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