Align Aspartate kinase Ask_Ect; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_029911010.1 P166_RS0108215 aspartate kinase
Query= SwissProt::A4VFY3 (476 letters) >NCBI__GCF_000711315.1:WP_029911010.1 Length = 478 Score = 486 bits (1250), Expect = e-142 Identities = 250/477 (52%), Positives = 332/477 (69%), Gaps = 9/477 (1%) Query: 3 TVEKIGGTSMSRFEEVLDNIFIGRREGAALYQRIFVVSAYSGMTNLLLEHKKTGEPGVYQ 62 +VEKIGGTSMS ++ V DNI + Y+RI VVSAY GMTN LLEHKKTG+PGVY Sbjct: 2 SVEKIGGTSMSDYQAVRDNIVFYPQNP---YRRILVVSAYGGMTNDLLEHKKTGQPGVYG 58 Query: 63 RFA-----DAQSEGAWREALEGVRQRMLAKNAELFSSEYELHAANQFINSRIDDASECMH 117 FA D +E +WREAL + +M N ELF + AAN+FI+ RI+ + Sbjct: 59 LFAYNDESDDGTEHSWREALRDLSAKMQQFNEELFDEDDMKAAANRFISERIEHTENLLM 118 Query: 118 SLQKLCAYGHFQLSEHLMKVREMLASLGEAHSAFNSVLALKQRGVNARLADLTGWQQEAP 177 LQ LC +GHF L +HL+ VRE+LAS+GEAHSA+N LK G+NA DLTGWQ + Sbjct: 119 HLQNLCHHGHFSLEDHLLTVRELLASIGEAHSAWNLTQLLKSEGINAIWIDLTGWQDDEK 178 Query: 178 LPFEEMISSHFAGFDFSRELVVATGYTHCAEGLMNTFDRGYSEITFAQIAAATGAREAII 237 LP +E+I + ++ L + TGY HC E LMNTFDRGYSE+TF++IA A +A+I Sbjct: 179 LPLDEVIHNKLCHLNYDEVLPIVTGYAHCEENLMNTFDRGYSEMTFSRIAVLCQATQAVI 238 Query: 238 HKEFHLSSADPNLVGADKVVTIGRTNYDVADQLSNLGMEAIHPRAAKTLRRAGVELRIKN 297 HKE+HLSSADP LVG ++ V IG+TNYD+ADQL+NLGMEAIHP+AAK LR+A + L IKN Sbjct: 239 HKEYHLSSADPRLVGEEQAVPIGKTNYDIADQLANLGMEAIHPKAAKGLRQAQIPLLIKN 298 Query: 298 AFEPEHGGTLISQDYKSEKPCVEIIAGRKDVFGIEVFDQDMLG-DIGYDMEISKLLKQLK 356 FEPEH GT+I +DY SE P VEIIAGR+++ +EVFD +M+G Y+ I ++ K+L+ Sbjct: 299 TFEPEHHGTIIREDYVSEFPQVEIIAGRQNLIAVEVFDAEMMGQQTDYEQAIWEITKRLR 358 Query: 357 LYVVNKDSDANSITYYASGSRKLINRAARLIEEQYPAAEVTVHNLAIVSAIGSDLKVKGI 416 V+ KD +AN+IT Y S + R A +E + P A+++ +++VSA+GSD+++KG+ Sbjct: 359 CQVLTKDFNANTITLYLQASLRKAKRLAGQLEVRLPTAKISTSKVSLVSAMGSDMRIKGL 418 Query: 417 LAKTVAALAEAGISIQAIHQSIRQVEMQCVVNEEDYDAAIAALHRALIEPENHGDVI 473 LA+ V L EAGI+IQA+HQ++RQVEMQ V E+DY+ A+ LH +LIE NHG I Sbjct: 419 LAQAVQTLFEAGINIQALHQNLRQVEMQFFVKEQDYERAVKRLHASLIEVHNHGKAI 475 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: 603 Number of extensions: 25 Number of successful extensions: 5 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: 478 Length adjustment: 33 Effective length of query: 443 Effective length of database: 445 Effective search space: 197135 Effective search space used: 197135 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