Align Aspartate kinase Ask_Ect; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_046011231.1 OLEAN_RS15785 aspartate kinase
Query= SwissProt::A4VFY3 (476 letters) >NCBI__GCF_000967895.1:WP_046011231.1 Length = 477 Score = 521 bits (1341), Expect = e-152 Identities = 256/477 (53%), Positives = 342/477 (71%), Gaps = 2/477 (0%) Query: 1 MHTVEKIGGTSMSRFEEVLDNIFIGRREGAALYQRIFVVSAYSGMTNLLLEHKKTGEPGV 60 MHT+EKIGGTSMS +E V DN+ +G + L+QR+FVVSAY G+TN LLEHKK+G+PG+ Sbjct: 1 MHTIEKIGGTSMSNYESVRDNVVLGGKR-TTLFQRVFVVSAYGGITNELLEHKKSGQPGI 59 Query: 61 YQRFADAQSEGAWREALEGVRQRMLAKNAELFSSEYELHAANQFINSRIDDASECMHSLQ 120 ++ FA+ + AW + + +RQ++ N +LF L AN+F++ R+ +A +C+ LQ Sbjct: 60 FELFANGMEDNAWMQKFDDLRQQLYVINQDLFGETPLLLKANKFLDERLMNAKQCLLDLQ 119 Query: 121 KLCAYGHFQLSEHLMKVREMLASLGEAHSAFNSVLALKQRGVNARLADLTGWQQEAPLPF 180 LC +GHF+L HL VREMLAS+GEAHSA+N+ L++ GVNA DLTGW+ + Sbjct: 120 SLCQHGHFELESHLETVREMLASIGEAHSAWNTAELLRRDGVNACFVDLTGWRTNKHISL 179 Query: 181 EEMISSHFAGFDFSRELVVATGYTHCAEGLMNTFDRGYSEITFAQIAAATGAREAIIHKE 240 +E I F D +L + TGY H GLM++FDRGYSE+TF+++A T AREA+IHKE Sbjct: 180 DERIRLAFDNIDLDSQLPIVTGYAHSDSGLMSSFDRGYSEMTFSRLAVLTDAREAVIHKE 239 Query: 241 FHLSSADPNLVGADKVVTIGRTNYDVADQLSNLGMEAIHPRAAKTLRRAGVELRIKNAFE 300 FHLSSADP LVG D V IGRTNYDVADQL++LGMEAIHP+AAK LR+ + LR+KN FE Sbjct: 240 FHLSSADPRLVGEDNAVPIGRTNYDVADQLASLGMEAIHPKAAKGLRQNNIPLRVKNTFE 299 Query: 301 PEHGGTLISQDYKSEKPCVEIIAGRKDVFGIEVFDQDMLGDI-GYDMEISKLLKQLKLYV 359 PEH GTLI+ DY S+ PCVEIIAG K +F ++VFDQDM G + YD E+ +L++ K ++ Sbjct: 300 PEHTGTLITGDYISDSPCVEIIAGCKGIFALQVFDQDMSGSLHDYDREVLAILRRFKAHI 359 Query: 360 VNKDSDANSITYYASGSRKLINRAARLIEEQYPAAEVTVHNLAIVSAIGSDLKVKGILAK 419 V+KD +AN+IT+Y S S K + R IEE+YP AEV +AIVSAIGSD+K+ GILAK Sbjct: 360 VSKDINANTITHYLSASLKTVKRIRAAIEEKYPTAEVDQQKVAIVSAIGSDMKIPGILAK 419 Query: 420 TVAALAEAGISIQAIHQSIRQVEMQCVVNEEDYDAAIAALHRALIEPENHGDVIAAA 476 V A+A IS+ A HQ++RQV+MQ +VNE DY+ + +LH +L+E +HG I A Sbjct: 420 AVKAVASKTISVLAFHQTMRQVDMQFIVNECDYEETVKSLHTSLVEVHDHGRAICLA 476 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: 636 Number of extensions: 18 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: 477 Length adjustment: 33 Effective length of query: 443 Effective length of database: 444 Effective search space: 196692 Effective search space used: 196692 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