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 WP_013835377.1 THICY_RS04270 lysine--tRNA ligase
Query= curated2:B1GZY6 (584 letters) >NCBI__GCF_000214825.1:WP_013835377.1 Length = 506 Score = 89.4 bits (220), Expect = 3e-22 Identities = 91/300 (30%), Positives = 141/300 (47%), Gaps = 33/300 (11%) Query: 19 IAVCGWVHSRRDHGGVIFIDLRDREGILQI-VFQPENKEIFEAAEKLRSEY--VIAVKGW 75 + V G + RR G F L+D G +Q V + E E F + R + ++ V G+ Sbjct: 70 VKVAGRMMLRRIMGKASFATLQDMSGRIQAYVTRDELPEGFYNEQFKRWDLGDIVGVSGY 129 Query: 76 VRNRPFGTLNTNMSTGNVELVAVELKILNTSPGLPFEISDYIDTSEELRLKYRYLDL-RR 134 + F T NT+ + +VE + + K L P + D +E+R + RYLDL Sbjct: 130 L----FKT-NTDELSIHVESIELITKALRPLPDKFHGLQD-----QEVRYRQRYLDLIMS 179 Query: 135 PNLQKNFVMRHKISKEIRNFLNEEGFLEIETPFLTKSTPEGARDFLVPSRLHHGNFFALP 194 ++ F R K+ +R F +GF+E+ETP + + P GA P HH N +P Sbjct: 180 EQSRRTFETRSKVIHAMREFFVRKGFMEVETPMM-QVIPGGAS--AKPFVTHH-NALDMP 235 Query: 195 Q----SPQLFKQILMSAGFDKYYQIVRCFRDEDLRADRQPEFTQVDVEMSFVDEEDVMVV 250 +P+L+ + L+ GF+K ++I R FR+E L PEFT V+ ++ D D+M Sbjct: 236 LYLRIAPELYLKRLLVGGFEKVFEINRNFRNEGLSTRHNPEFTMVEFYEAYADYIDMMDY 295 Query: 251 IERMLARVFKMTLNLDIKMPFERMPYSEAMLRFGSDKPDTRFEVEIKDFSRELKNSGFSV 310 E M + +M L ++PY + F DKP R + +KD S L N G V Sbjct: 296 TEEMFKELAQMVLGSG------QVPYQGQVFHF--DKPFAR--ITMKD-SIALYNEGVKV 344 Score = 44.7 bits (104), Expect = 9e-09 Identities = 30/111 (27%), Positives = 49/111 (44%), Gaps = 5/111 (4%) Query: 453 PKDADSLTKEN-AGRAKAKAYDVVLNGIELGGGSIRIHKSGIQKKIF----NILDISDES 507 P + L + N A +++ + G EL G ++ + Q + F D D+ Sbjct: 396 PAEVSPLARRNDANPFVTDRFELFIGGRELANGFSELNDAEDQAERFMDQVRAKDAGDDE 455 Query: 508 AEKKFGFLLKALTYGAPPHGGAALGFDRLCALISGEDSIREVIAFPKTQKA 558 A + AL +G PP G +G DRL L + SI++V+ FP + A Sbjct: 456 AMHYDADFITALEHGMPPAAGQGIGIDRLVMLFTDAASIKDVLLFPHMRPA 506 Lambda K H 0.320 0.139 0.404 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: 616 Number of extensions: 30 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: 584 Length of database: 506 Length adjustment: 35 Effective length of query: 549 Effective length of database: 471 Effective search space: 258579 Effective search space used: 258579 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 (21.8 bits) S2: 52 (24.6 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