Align Aspartate--tRNA(Asp/Asn) ligase; Aspartyl-tRNA synthetase; AspRS; Non-discriminating aspartyl-tRNA synthetase; ND-AspRS; EC 6.1.1.23 (characterized)
to candidate WP_022948323.1 H035_RS0107245 aspartate--tRNA ligase
Query= SwissProt::Q51422 (591 letters) >NCBI__GCF_000421465.1:WP_022948323.1 Length = 598 Score = 776 bits (2003), Expect = 0.0 Identities = 378/587 (64%), Positives = 470/587 (80%), Gaps = 2/587 (0%) Query: 2 MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61 MR+H CG+LN + GQEV LCGWVHRRRDHGGVIF+D+RDREGL QVV DP E FA+A Sbjct: 1 MRTHRCGELNATHIGQEVELCGWVHRRRDHGGVIFIDLRDREGLVQVVVDPSMPEAFARA 60 Query: 62 DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121 + +RSE+V+++ G VR RPEG N + +G IEVL +L +LN+AETPPFPLD V E Sbjct: 61 EEIRSEYVIQVRGTVRPRPEGTENLALPTGQIEVLTADLVILNRAETPPFPLDSEIPVSE 120 Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181 E RLRYR++DLRRPEM AKL+ R + ++R +LD + F ++ETP L R TPEGARDYLV Sbjct: 121 EVRLRYRYLDLRRPEMQAKLRARRDVIRTLRNFLDAHEFFEIETPFLTRATPEGARDYLV 180 Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241 PSRT+P F+ALPQSPQL+KQLLM+AGFDRYYQI +CFRDEDLRADRQPEFTQ+DIETSF Sbjct: 181 PSRTHPHAFYALPQSPQLYKQLLMIAGFDRYYQIVRCFRDEDLRADRQPEFTQLDIETSF 240 Query: 242 LDESDIIGITEKMVRQLFKEVLDVEF-DEFPHMPFEEAMRRYGSDKPDLRIPLELVDVAD 300 LDE++I+ + E+M+R LFKE L V+ + FP + + EAMRR+GSDKPDLRIPLELVD+AD Sbjct: 241 LDENEIMALMEEMIRTLFKENLGVDLPNPFPRLTYAEAMRRFGSDKPDLRIPLELVDLAD 300 Query: 301 QLKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNER 360 ++ VEFKVF+GPA DP+GRVAALR+PG A + R +IDD T+FVG YGAKGLAY+KVN+R Sbjct: 301 LMQTVEFKVFAGPAADPEGRVAALRLPGGADLTRKEIDDLTRFVGNYGAKGLAYVKVNDR 360 Query: 361 AKGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHDL 420 ++G+EGLQSPI+KF+P A + IL+R A GDI+FFGADKAK+V +ALGALRIK+G D Sbjct: 361 SQGIEGLQSPILKFLPNAVIESILERTEAQTGDILFFGADKAKVVNEALGALRIKLGQDR 420 Query: 421 KLLTREWAPMWVVDFPMFEENDDGS-LSALHHPFTSPKCTPAELEANPGAALSRAYDMVL 479 L+ W P+WVV FPMFE + + +LHHPFT+P C+ +L A PG A+S+AYD+ L Sbjct: 421 GLVEAGWRPLWVVAFPMFEWDVEAKRWESLHHPFTAPACSIEDLNAEPGRAVSQAYDIAL 480 Query: 480 NGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGLDRL 539 NG E+GGGSIRIH + MQ+AVF +LGI E EEKFGFLL+ALKYG PPHGG+AFGLDRL Sbjct: 481 NGVEIGGGSIRIHTQQMQEAVFELLGIGRQEAEEKFGFLLNALKYGCPPHGGIAFGLDRL 540 Query: 540 VMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLRE 586 VMLMTG+ +IR+V+AFPKTQ+A M AP V+ + LREL I+LR+ Sbjct: 541 VMLMTGSKTIRDVMAFPKTQAAACPMVDAPARVNEEQLRELFIQLRK 587 Lambda K H 0.321 0.140 0.411 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: 1087 Number of extensions: 39 Number of successful extensions: 3 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: 591 Length of database: 598 Length adjustment: 37 Effective length of query: 554 Effective length of database: 561 Effective search space: 310794 Effective search space used: 310794 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