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_074201023.1 BUQ81_RS03535 aspartate--tRNA ligase
Query= SwissProt::Q51422 (591 letters) >NCBI__GCF_900141795.1:WP_074201023.1 Length = 599 Score = 778 bits (2010), Expect = 0.0 Identities = 378/593 (63%), Positives = 477/593 (80%), Gaps = 9/593 (1%) Query: 3 RSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKAD 62 RSHYCG + E+L + VT+ GWVHRRRDHGGVIF+D+RD GL QVV DPD + FA A+ Sbjct: 10 RSHYCGTVTENLMDETVTVSGWVHRRRDHGGVIFIDLRDSSGLVQVVVDPDTPQAFAAAE 69 Query: 63 RVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGEE 122 R+R+E V+++TG+VR RPEG NPN+ +G IE+L +L+VL+ AE PF LDE VGE+ Sbjct: 70 RLRAECVIQVTGRVRARPEGTTNPNLPTGQIEILAKDLQVLSMAEPIPFQLDE--KVGED 127 Query: 123 TRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLVP 182 RL+YR+IDLRR +M LKLR ++T ++R YLDDNGF+++ETP+L + TPEGARDYLVP Sbjct: 128 VRLKYRYIDLRRDDMQRNLKLRYQVTRAMRNYLDDNGFMEIETPMLTKSTPEGARDYLVP 187 Query: 183 SRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSFL 242 SRT+P FFALPQSPQLFKQLLM++GFDRY+QI +CFRDEDLRADRQPEFTQ+D+ETSFL Sbjct: 188 SRTHPHKFFALPQSPQLFKQLLMMSGFDRYFQITRCFRDEDLRADRQPEFTQLDLETSFL 247 Query: 243 DESDIIGITEKMVRQLFKEVLDVEFDE-FPHMPFEEAMRRYGSDKPDLRIPLELVDVADQ 301 E ++ + E +V+ +FKE + VEF E FP M + EA+R+YG D+PDLRIPLEL+DVAD Sbjct: 248 TEEGVMALMEGLVKHIFKEGIGVEFSEDFPRMTYAEAIRKYGVDRPDLRIPLELMDVADL 307 Query: 302 LKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNERA 361 L++++FKVF+GPA DPKGRVAAL+VPG A + R +ID+YTKFVGIYGAKGLA+IKVN+ + Sbjct: 308 LQDIDFKVFAGPAKDPKGRVAALKVPGGARLTRKEIDEYTKFVGIYGAKGLAWIKVNDLS 367 Query: 362 KGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHDLK 421 +G+EGLQSPIVKF P+ + I++RVGA DGDIVFFGADKAK+V ++LGALR+K+G DL Sbjct: 368 RGIEGLQSPIVKFFPDQVME-IMERVGAQDGDIVFFGADKAKVVNESLGALRVKLGEDLG 426 Query: 422 LLTREWAPMWVVDFPMFEEND-DGSLSALHHPFTSPKCTPAELEA----NPGAALSRAYD 476 +L EWAP+W+VDFPMFEE++ L+A+HHPFT PK T EL A LSRAYD Sbjct: 427 MLEGEWAPVWIVDFPMFEEDEKTARLTAIHHPFTQPKATTEELRALEQEEKHQLLSRAYD 486 Query: 477 MVLNGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGL 536 +V+NG E+GGGS+RIHD +MQ VF++LGI + E +EKFGF L ALKYGAPPH G+AFGL Sbjct: 487 LVINGIEVGGGSVRIHDSAMQAEVFKLLGISDEEAQEKFGFFLQALKYGAPPHAGMAFGL 546 Query: 537 DRLVMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLREQPK 589 DRLVMLM G +IR+VIAFPKTQSA ++T+APG V + LREL +R RE K Sbjct: 547 DRLVMLMAGCDTIRDVIAFPKTQSAACLLTEAPGEVAPEQLRELGLRFREAVK 599 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: 1136 Number of extensions: 54 Number of successful extensions: 6 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: 599 Length adjustment: 37 Effective length of query: 554 Effective length of database: 562 Effective search space: 311348 Effective search space used: 311348 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 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