Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23; Aspartyl-tRNA synthetase; AspRS; Non-discriminating aspartyl-tRNA synthetase; ND-AspRS (uncharacterized)
to candidate Dsui_2863 Dsui_2863 lysyl-tRNA synthetase (class II)
Query= curated2:A5GPL9 (611 letters) >FitnessBrowser__PS:Dsui_2863 Length = 500 Score = 96.3 bits (238), Expect = 3e-24 Identities = 85/284 (29%), Positives = 137/284 (48%), Gaps = 35/284 (12%) Query: 17 SVQLCGWVDRRRDHGGVIFIDLRDRTGTVQITVDPDL-GAEAFAVAEHLRSETVLQISGK 75 SV++ G + RR G F ++D +G +Q+ V DL GAEA+ +H ++ G Sbjct: 63 SVKVAGRIMLRRLMGKASFATIQDVSGRIQLYVKVDLVGAEAYDDFKHWDIGDIVGAEGT 122 Query: 76 VRARPAESLNEKLATGAVEVLASGITVLNSVKGNLPFPVSVHDEENTREELRLRHRYLDL 135 + K TG + + S I +L+ K P P H T E R R RYLDL Sbjct: 123 LF---------KTRTGELTIQVSEIRLLS--KALRPLPEKFHGL--TDMEQRHRQRYLDL 169 Query: 136 RRKRMNDNLRL----RAQTIQAARRFLEDEGFIEVETPVLTRSTPEGA--RDYVLPSRVC 189 MN++ R R++ IQ+ R ++ F+EVETP++ P GA + ++ Sbjct: 170 I---MNESSRFTFVARSRMIQSIRNYMISHHFLEVETPMM-HPIPGGASAKPFITHHNAL 225 Query: 190 GGEWFALPQSPQLFKQLLMVGGIERYYQVARCFRDEDLRADRQPEFTQLDIEMSFMDQEE 249 E F L +P+L+ + L+VGG E+ ++V R FR+E L PEFT ++ ++ D + Sbjct: 226 DMELF-LRIAPELYLKRLVVGGFEKVFEVNRNFRNEGLSTRHNPEFTMMEFYEAYADYKL 284 Query: 250 ILQLNESLICSIWKAVKG----------IDLPRPFPRMTWHDAM 283 ++ E L+ + G +DL +PF R+T A+ Sbjct: 285 LMDFTEGLLRHAARDALGTEVFQYQGRELDLSKPFARLTMVQAV 328 Score = 48.5 bits (114), Expect = 7e-10 Identities = 28/92 (30%), Positives = 45/92 (48%), Gaps = 4/92 (4%) Query: 489 QAYDLVLNGLELGGGSLRIHDSALQRQVLQTVGLPLEEAQEQFGFL----MDALDVGAPP 544 + ++L + G E+ G ++D Q + E+ F + AL+ G PP Sbjct: 407 ERFELFIVGREIANGFSELNDPEDQAARFLEQAKAKDAGDEEAMFYDADYIKALEFGLPP 466 Query: 545 HGGLAFGVDRMVMLLAGEESIRDTIAFPKTQQ 576 GG G+DR+VMLL +IRD I FP+ ++ Sbjct: 467 TGGCGIGIDRLVMLLTDTANIRDVILFPQMRK 498 Lambda K H 0.319 0.137 0.406 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: 698 Number of extensions: 44 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 611 Length of database: 500 Length adjustment: 36 Effective length of query: 575 Effective length of database: 464 Effective search space: 266800 Effective search space used: 266800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 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