Align aspartate-tRNAAsn ligase (EC 6.1.1.23) (characterized)
to candidate GFF789 HP15_768 lysyl-tRNA synthetase
Query= BRENDA::O07683 (436 letters) >FitnessBrowser__Marino:GFF789 Length = 511 Score = 129 bits (324), Expect = 2e-34 Identities = 131/433 (30%), Positives = 196/433 (45%), Gaps = 55/433 (12%) Query: 36 FVIVRDATGRLQVVAKEDDTPDLFETAEGLSSEDVVQVTGTLEASDQAPGGVELAPTELT 95 F +V+D TGR+Q+ A +D D G D+V V GTL S + G + + E Sbjct: 79 FKVVQDMTGRIQIYASKDVQKDTKHWDLG----DIVGVRGTLSKSGK--GDLYVTMDEYV 132 Query: 96 VVSEATDVPSIEISKDVDADLSTRLDERHLDVR-KPSTKAVFSLRSKAMGAMTDWFYDNR 154 +++++ P E K + D R R++D+ ++ VF RSK + AM +F D Sbjct: 133 LLTKSLR-PLPEKHKGL-TDTEARYRHRYVDLMVNEDSRRVFYARSKIISAMRQYFTDRD 190 Query: 155 FEEVDTPELSTAGAEGGADLFPVVYYDK----EAYLSQSPQLYKQILVASGVDRLFEVGH 210 F EV+TP L GGA P V + + YL +P+L+ + LV G +R+FE+ Sbjct: 191 FMEVETPMLQVI--PGGATARPFVTHHNALGIDMYLRIAPELFLKRLVVGGFERVFEINR 248 Query: 211 AFRAEDFGTSRHVSEIAMFDVELGYVEDHHDVMDVQEESLRHTIRHVVEHA----QRELD 266 FR E T RH E M + Y D++D+MD+ E+ LR + V+ R L Sbjct: 249 NFRNEGLST-RHNPEFTMVEFYQAYA-DYNDLMDLTEDMLRTITQKVLGTTTVVNSRTLA 306 Query: 267 ELGSDLSVPEADFPRITFEE---AREILADEYDHVPED------------DNDLDTKGER 311 + GS+ +V E DF + TFE IL D PE D + K Sbjct: 307 D-GSEETV-EYDFGK-TFERLTVVDAILRYNPDIKPEQLADDASARQVAKDLGIHLKEGW 363 Query: 312 LLG----EYFEEQGH----PAVFVVGYPDEKFYYRQDVDGDDVASRKFDLLYRGQELSSG 363 LG E FE F+ YP E + D + + +F+ G+E+++G Sbjct: 364 GLGKVQIEIFEATAEHRLMQPTFITEYPKEVSPLARCKDSNPFVTERFEFFVGGREIANG 423 Query: 364 ----GQREHDIERLTAKMREQGVEPENFEF----YLDAFRYGVPPHGGYGLGIDRLIQQL 415 E ER A++ E+ + F Y+ A YG+PP G G+GIDRL L Sbjct: 424 FSELNDAEDQAERFQAQVAEKDAGDDEAMFYDEDYVMALEYGLPPTAGEGIGIDRLAMLL 483 Query: 416 AGLDNIKEAILFP 428 +I++ ILFP Sbjct: 484 TNSPSIRDVILFP 496 Lambda K H 0.316 0.137 0.393 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: 611 Number of extensions: 29 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: 436 Length of database: 511 Length adjustment: 33 Effective length of query: 403 Effective length of database: 478 Effective search space: 192634 Effective search space used: 192634 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 (21.5 bits) S2: 51 (24.3 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