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_022947901.1 H035_RS0104990 lysine--tRNA ligase
Query= curated2:Q8TXG4 (431 letters) >NCBI__GCF_000421465.1:WP_022947901.1 Length = 504 Score = 141 bits (355), Expect = 5e-38 Identities = 136/459 (29%), Positives = 214/459 (46%), Gaps = 56/459 (12%) Query: 9 DVTPERDGEEVRLAGWVHEVRDLGGIKFVLLRDRTGIVQLTLPKQKVPKETFEKVPKLTK 68 D TP R VR+AG + R +G F LRD +G +QL + + +P+ + + K Sbjct: 53 DQTPLR----VRVAGRMMTRRIMGKASFCHLRDYSGQMQLYVTRDGLPEGLYREFKKWDI 108 Query: 69 ESVIRVEGTVQANEKAPGGVEVIPQRIEVLSESDTHLPLDPTGKVDADLDTRLDARVLDL 128 ++ EG + + V+V I +L++ LP G D ++ R R LDL Sbjct: 109 GDIVGAEGVLFKTKTGELSVKV--DEIRLLAKCLRPLPEKYHGLTDQEM--RYRQRYLDL 164 Query: 129 -RREEPQAIFKIRNVVTTAIREFLEERGFIEVHTPKIIASATEGGTELFPVVYF----ER 183 E + F+IR+ + +R FL ER F+EV TP + GG P V + + Sbjct: 165 IMNEVTRRTFQIRSQLVQEMRRFLIERDFLEVETPMM--QVIPGGAAARPFVTYHNTLDM 222 Query: 184 DAYLAQSPQLYKQMLMAAGFERVYEIGPIFRAEEHNTRRHLNEAISVDIEMSFIESEEDV 243 YL +P+LY + L+A GFERV+EI FR E +T+ H E ++ ++ E ++ Sbjct: 223 QLYLRIAPELYLKRLVAGGFERVFEINRNFRNEGLSTQ-HNPEFTMLEFYQAYAEYKD-- 279 Query: 244 MRVLEELLAHVFRKVREEC--EKELEALDRELPELETPFERITYEETL-----DLLSEHG 296 L +L +FR + E + + D+E+ + F+R T E+L L SE Sbjct: 280 ---LMDLTEVMFRDLAETVLGSERIVYQDQEI-DFGKSFQRFTLLESLIRFNPGLASEDV 335 Query: 297 IEVEWGEDLPTEAERKL----------GEIFE--------EPFFITEWPRETRPFYTMA- 337 +E + + E + EIFE +P FITE+P E P Sbjct: 336 DNLESARRVAEKLEIPILPGFGLGKIQTEIFEKTVEPKLLDPTFITEYPVEVSPLARRND 395 Query: 338 KDDEVTTAFDLMYQGLELASGAQR----EHRYDVLVRQIEEQGLSPEDFRH----YLEAF 389 K+ EVT F+L G E+A+G E + + Q+E + E+ H Y+ A Sbjct: 396 KNPEVTDRFELFIAGREIANGFTELNDPEEQAERFRSQLEARAAGDEEAMHFDEDYITAL 455 Query: 390 KYGMPPHGGWGLGLERTLMTITGAENIREVTLFPRDRKR 428 ++GMPP G G+G++R +M A +IR+V LFP R + Sbjct: 456 EHGMPPTAGEGIGIDRLVMLFANAPSIRDVLLFPHMRPK 494 Lambda K H 0.318 0.138 0.397 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: 525 Number of extensions: 30 Number of successful extensions: 6 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: 431 Length of database: 504 Length adjustment: 33 Effective length of query: 398 Effective length of database: 471 Effective search space: 187458 Effective search space used: 187458 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