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_013554590.1 NITSA_RS08365 lysine--tRNA ligase
Query= curated2:Q9X1F4 (579 letters) >NCBI__GCF_000186245.1:WP_013554590.1 Length = 520 Score = 90.5 bits (223), Expect = 1e-22 Identities = 82/269 (30%), Positives = 133/269 (49%), Gaps = 22/269 (8%) Query: 8 GELRATDEGKKVKLCGWVDRIRDLGGVRFIDLRDRYGETQIVC---DVNSEAYSVVDELT 64 GE A D + +L G + IR +G F L D G QI D+ Y+ + +L Sbjct: 52 GERIAQD--RHYRLTGRIKFIRIMGKAAFAKLEDSEGLVQIYYNRDDLPEGYYNKIKKLI 109 Query: 65 RES-VVLVEGTVRKRPEGTENPNIETGEIEVVAERIEILSLA-DPLPFYPGETPKEEMRL 122 +V EG P T TGEI + + I+S A PLP +E+R Sbjct: 110 EVGDIVEAEGF----PFVTR-----TGEITLHCTDLRIVSKAVHPLPEKFHGLTDQEIRY 160 Query: 123 KYRYIDL-RSERMKRNIILRYRISKIIRDYFDELGFLEIETPFLTRSTPEGA--RDFLVP 179 + RY+D+ + +K+ LR RI ++R +F+E GFLE+ETP + P GA R F+ Sbjct: 161 RQRYLDMIMNPEVKKTFKLRSRIVSLVRRFFEEKGFLEVETPMM-HPIPGGANARPFVTR 219 Query: 180 SRLRPGKFYALPQSPQLFKQILMISGFDRYFQIVRCFRDEDLRADRQPEFTQVDVEMSFV 239 Y L +P+L+ + L++ G + F+I R FR+E + PEFT ++ ++ Sbjct: 220 HNALGVDRY-LRIAPELYLKRLIVGGMEAVFEINRNFRNEGMDHTHNPEFTMIEYYWAWH 278 Query: 240 DVEDVLNVSEGMVSRVFKESSGIDLKVPF 268 ED++ ++E + +F E+ G+ K+P+ Sbjct: 279 TYEDLMRLTEELFDYLF-ENLGLPRKLPY 306 Score = 45.1 bits (105), Expect = 7e-09 Identities = 28/92 (30%), Positives = 48/92 (52%), Gaps = 9/92 (9%) Query: 464 AKAYDLVINGYEVGGGSIRIH-------RRDIQEKIFELLGLSEEEAQKKFGFFLEAFRY 516 A+ ++L I G E+ G ++ R +Q + E+ G ++EA ++ A Y Sbjct: 403 AERFELFIAGKEIANGFNELNDPLDQYERFKMQVEAKEVTG--DDEAMHMDLDYVRALSY 460 Query: 517 GVPPHGGIAFGLDRLVSIIAGESSIREVIAFP 548 G+ P G G+DRLV ++ + SIR+V+ FP Sbjct: 461 GMAPTAGEGIGIDRLVMLLTNQHSIRDVLLFP 492 Lambda K H 0.321 0.142 0.417 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: 840 Number of extensions: 60 Number of successful extensions: 3 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: 579 Length of database: 520 Length adjustment: 36 Effective length of query: 543 Effective length of database: 484 Effective search space: 262812 Effective search space used: 262812 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: 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