Align Aspartate kinase Ask_Ect; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_014149670.1 MEALZ_RS15850 aspartate kinase
Query= SwissProt::A4VFY3 (476 letters) >NCBI__GCF_000968535.2:WP_014149670.1 Length = 480 Score = 524 bits (1350), Expect = e-153 Identities = 266/476 (55%), Positives = 345/476 (72%), Gaps = 1/476 (0%) Query: 2 HTVEKIGGTSMSRFEEVLDNIFIGRREGAALYQRIFVVSAYSGMTNLLLEHKKTGEPGVY 61 HTVEKIGGTSMS + V DNI + LYQRIFVVSAY G+T++LLEHKK G+ G+Y Sbjct: 4 HTVEKIGGTSMSDYVAVRDNIILKPVHREDLYQRIFVVSAYGGITDMLLEHKKNGQAGIY 63 Query: 62 QRFADAQSEGAWREALEGVRQRMLAKNAELFSSEYELHAANQFINSRIDDASECMHSLQK 121 +FA++ ++ W+ +L ++Q M A NA +F + + A+ FI R+DDA C+ LQ Sbjct: 64 GQFANSVNDDGWQASLVALKQAMFAINANIFDTADAIKKADTFIGERLDDAERCLADLQH 123 Query: 122 LCAYGHFQLSEHLMKVREMLASLGEAHSAFNSVLALKQRGVNARLADLTGWQQEAPLPFE 181 LC +GHF L HL VREMLASLGEAHSA+N+V L+Q G+NA DLTGWQ + + + Sbjct: 124 LCRHGHFSLDAHLSTVREMLASLGEAHSAWNTVQLLQQDGINAVFVDLTGWQTDKHMTLD 183 Query: 182 EMISSHFAGFDFSRELVVATGYTHCAEGLMNTFDRGYSEITFAQIAAATGAREAIIHKEF 241 E I + FA D ++L +ATGY H +GLM+TFDRGYSE+TF++IA T A EAIIHKEF Sbjct: 184 ERIKNAFAEIDLRQQLPIATGYAHSIDGLMSTFDRGYSEMTFSRIAVLTKADEAIIHKEF 243 Query: 242 HLSSADPNLVGADKVVTIGRTNYDVADQLSNLGMEAIHPRAAKTLRRAGVELRIKNAFEP 301 HLSSADP LVG DK V IGRTNYDVADQL+NLGMEAIHP+AAK LR+ + LR++N FEP Sbjct: 244 HLSSADPRLVGEDKAVPIGRTNYDVADQLANLGMEAIHPKAAKGLRQNDIALRVRNTFEP 303 Query: 302 EHGGTLISQDYKSEKPCVEIIAGRKDVFGIEVFDQDMLGDI-GYDMEISKLLKQLKLYVV 360 +H GTLI+ DY S KPCVEIIAG K V+ EVFDQ+M G+I YD EI +++ + ++V Sbjct: 304 DHAGTLITGDYVSSKPCVEIIAGCKGVYAFEVFDQNMAGEIHNYDREILGQIRRFRAHIV 363 Query: 361 NKDSDANSITYYASGSRKLINRAARLIEEQYPAAEVTVHNLAIVSAIGSDLKVKGILAKT 420 +KD +AN+IT+Y S S K I R ++E YP AE+ ++IVSAIGSD+K+ GILAKT Sbjct: 364 SKDINANTITHYLSASLKTIRRIRDALQEIYPDAEINQQKVSIVSAIGSDMKIPGILAKT 423 Query: 421 VAALAEAGISIQAIHQSIRQVEMQCVVNEEDYDAAIAALHRALIEPENHGDVIAAA 476 V+ALAE IS+ A+HQS+RQV+MQ V++E+ Y A+ +LH L+E +HG I A Sbjct: 424 VSALAEKQISVLAMHQSMRQVDMQFVIDEDAYTDAMKSLHCHLVEVHDHGIAICLA 479 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: 620 Number of extensions: 23 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: 480 Length adjustment: 34 Effective length of query: 442 Effective length of database: 446 Effective search space: 197132 Effective search space used: 197132 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