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_026608385.1 METAC_RS0120015 aspartate--tRNA ligase
Query= curated2:A5G126 (595 letters) >NCBI__GCF_000427445.1:WP_026608385.1 Length = 633 Score = 723 bits (1867), Expect = 0.0 Identities = 378/634 (59%), Positives = 444/634 (70%), Gaps = 48/634 (7%) Query: 1 MHEYRTHDCGALRAADAGITARLSGWVNVKRDHGGLLFIDLRDHYGITQCVFPAGSPVFA 60 MH YR+H CG LR A AG T RLSGW + RDHGG+LFIDLRDHYG+TQCV S FA Sbjct: 1 MHRYRSHSCGDLREALAGETTRLSGWCHRIRDHGGVLFIDLRDHYGVTQCVVDPDSKAFA 60 Query: 61 AAEALRAESVITVTGRVVKRDADTVNPRLPTGEIELVAETVEVQSTADVLPIQVAGEAQF 120 AE LR+E V+ + G V KR T NP +PTG +E+ +EV A LP+ V GE + Sbjct: 61 LAEKLRSEWVVRIDGLVRKRPDGTENPEMPTGFVEVYVTEIEVLGPAAELPLPVFGEHNY 120 Query: 121 PEELRLRYRFLDLRREKLHRNIMLRANVIAWLRREMTARGFTEFTTPILTASSPEGARDF 180 PE++RLRYRFLDLRR+KLH+NIMLR +I LR M RGF EF TPILTASSPEGARDF Sbjct: 121 PEDMRLRYRFLDLRRDKLHKNIMLRGQIIDSLRARMKERGFFEFQTPILTASSPEGARDF 180 Query: 181 LVPSRVHPGQFYALPQAPQQFKQLLMVAGFDRYFQIAPCFRDEASRADRAPGEFYQLDFE 240 LVPSR+HPG+FYALPQAPQQFKQL+MVAGFDRYFQIAPCFRDE +RADR+PGEFYQLD E Sbjct: 181 LVPSRLHPGKFYALPQAPQQFKQLIMVAGFDRYFQIAPCFRDEDARADRSPGEFYQLDVE 240 Query: 241 MSFVTQEDVFATIEPVLGGLFREFGGGRGVTQWPFPRIAYDEALLKYGSDKPDLRNPLLI 300 MSFVTQEDVFA +EPVL G+F EFGGGR VT FP I+Y A+ +G+DKPDLRNPLLI Sbjct: 241 MSFVTQEDVFAEVEPVLRGIFEEFGGGRPVTP-KFPLISYSAAIRAFGTDKPDLRNPLLI 299 Query: 301 TDVTEAFRDSGFGLFAKIVAGG--GVVRAIPAPGTGGNPRSFFDKLNDWARSEGAGGLGY 358 DVT AFRDSGFG+FAK +A V AIPAP GG R+F D+++ WA+SEG GL Y Sbjct: 300 HDVTNAFRDSGFGVFAKRLAADPEAAVWAIPAP--GGGQRTFCDRMDSWAKSEGQPGLAY 357 Query: 359 IIF--APDGAKGPIAKNLEPARAEAIREA------------------------------- 385 I + + GP+AKN+ R E IR Sbjct: 358 IFWREGEEAGAGPVAKNIGLERGEHIRRGLSGRSGEWVQLPAPETLDDERFPLEVAEPYR 417 Query: 386 ----TGASVGDAVFFAAGKPLEAAKFAGTVRTKLGTDLGLIDGAKFEFCWIVDFPMYERD 441 G GDAVFF GKP + KFAG R K+G +L L G FEFCWIVDFPMYE + Sbjct: 418 RLRPDGLMAGDAVFFVLGKPKDIYKFAGAARLKIGKELNLSSGDVFEFCWIVDFPMYEWN 477 Query: 442 EETGQIVFSHNPFSMPQ------GGLEALNGQDPLTIKAFQYDIVCNGVELSSGAIRNHR 495 E+ +I FSHNPFSMP GL+A + + L IKAFQYDIVCNG+ELSSGAIRNHR Sbjct: 478 EDEKKIDFSHNPFSMPNFEHETFVGLDAADEKTVLGIKAFQYDIVCNGIELSSGAIRNHR 537 Query: 496 PDIMLRAFEIAGYGAEEVEARFGGMLNAFRYGAPPHGGSAPGVDRMVMLLADEPNLREVI 555 PDIM +AF +AGY +E +FGGM AF+YGAPPHGG APGVDR+VMLLA E NLRE++ Sbjct: 538 PDIMRKAFALAGYDESVLEEKFGGMYRAFQYGAPPHGGIAPGVDRIVMLLAGEENLREIV 597 Query: 556 AFPLNQQGQDLLMGAPAPVPAARLKELSLAIALP 589 FP+NQ+ +DLLMGAP+ V A +L+EL + + LP Sbjct: 598 LFPMNQRAEDLLMGAPSTVTAKQLRELHIRLNLP 631 Lambda K H 0.322 0.140 0.423 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: 1193 Number of extensions: 47 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 595 Length of database: 633 Length adjustment: 37 Effective length of query: 558 Effective length of database: 596 Effective search space: 332568 Effective search space used: 332568 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 (21.9 bits) S2: 53 (25.0 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