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_086511348.1 BZY95_RS18410 aspartate--tRNA ligase
Query= SwissProt::Q51422 (591 letters) >NCBI__GCF_002151265.1:WP_086511348.1 Length = 592 Score = 899 bits (2324), Expect = 0.0 Identities = 443/590 (75%), Positives = 505/590 (85%), Gaps = 1/590 (0%) Query: 2 MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61 MRSHYCGQLNE++ Q VTLCGWVHRRRDHGGVIFLD+RDR+G+AQVV DPD AE FA A Sbjct: 1 MRSHYCGQLNETMVDQTVTLCGWVHRRRDHGGVIFLDMRDRDGIAQVVVDPDTAEAFATA 60 Query: 62 DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121 DR RSE+V++I+G+VRLRPEG +NP M +G IEVL E+EVLN A TPPF LDE+ VGE Sbjct: 61 DRARSEYVLRISGRVRLRPEGTQNPKMPTGMIEVLAKEVEVLNTAATPPFQLDEHGKVGE 120 Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181 E RL++R+IDLRRPEM KL+LR+RI+ +R +L+ GFLD+ETPIL R TPEGARDYLV Sbjct: 121 EVRLKHRYIDLRRPEMIEKLRLRSRISHHVRAFLEGQGFLDIETPILTRATPEGARDYLV 180 Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241 PSRT+PG FFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIE SF Sbjct: 181 PSRTHPGSFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIEASF 240 Query: 242 LDESDIIGITEKMVRQLFKEVLDVEFDEFPHMPFEEAMRRYGSDKPDLRIPLELVDVADQ 301 ++E+DI+G+TE M+R+LF++VLDVE EFP M + EAM RYGSDKPDLRIPL LVDV D Sbjct: 241 VEENDIMGVTEAMIRELFQDVLDVELPEFPRMSWAEAMDRYGSDKPDLRIPLTLVDVDDL 300 Query: 302 LKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNERA 361 +K+V+F+VFSGPAN GRVAAL+VPG ASM R IDDYTKFVGIYGAKGLA+IKVNERA Sbjct: 301 MKQVDFQVFSGPANAADGRVAALKVPGGASMSRKVIDDYTKFVGIYGAKGLAWIKVNERA 360 Query: 362 KGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHDLK 421 KG+EGLQSPIVKF+ E + +LDRVGA DGDIVFFGADKA+IV +ALGALR+K+G DL Sbjct: 361 KGLEGLQSPIVKFM-ENVIEELLDRVGAADGDIVFFGADKARIVNEALGALRVKLGEDLN 419 Query: 422 LLTREWAPMWVVDFPMFEENDDGSLSALHHPFTSPKCTPAELEANPGAALSRAYDMVLNG 481 L TR WAP+WVVDFPMFE +D+G LS LHHPFTSP C+P EL+ANP ALSRAYDMVLNG Sbjct: 420 LYTRPWAPLWVVDFPMFEADDNGRLSPLHHPFTSPSCSPEELKANPAGALSRAYDMVLNG 479 Query: 482 TELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGLDRLVM 541 TELGGGSIRIHD+ MQ VF +LGI E E EKFGFLLDAL YGAPPHGGLAFGLDRLVM Sbjct: 480 TELGGGSIRIHDQQMQSTVFEILGIGEEEAREKFGFLLDALHYGAPPHGGLAFGLDRLVM 539 Query: 542 LMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLREQPKAE 591 LM G+ +IREVIAFPKTQSA +MT APG V G LREL+IRLR++ KAE Sbjct: 540 LMAGSRTIREVIAFPKTQSAACLMTDAPGEVSGDQLRELNIRLRQKAKAE 589 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: 1226 Number of extensions: 43 Number of successful extensions: 2 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: 592 Length adjustment: 37 Effective length of query: 554 Effective length of database: 555 Effective search space: 307470 Effective search space used: 307470 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