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_004302467.1 C665_RS05700 aspartate--tRNA ligase
Query= SwissProt::Q51422 (591 letters) >NCBI__GCF_000310185.1:WP_004302467.1 Length = 599 Score = 750 bits (1936), Expect = 0.0 Identities = 379/595 (63%), Positives = 460/595 (77%), Gaps = 7/595 (1%) Query: 2 MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61 MR+HYCG++ + Q VT+CGWVHRRRDHGGVIF+D+RDREGL QVV DPDRAE F A Sbjct: 1 MRTHYCGKVTAADLDQIVTICGWVHRRRDHGGVIFIDLRDREGLVQVVCDPDRAEMFKTA 60 Query: 62 DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121 + VR+EFV+K++GKVR RP G N N+ SG IE+L +++EVLN A TPPF LD+ ++ E Sbjct: 61 ESVRNEFVLKLSGKVRRRPAGTENANLVSGEIEILCHDIEVLNAAATPPFQLDD-ENLSE 119 Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181 RL R IDLRRP+M L LR + T + RR+LD GF+DVETP+L + TPEGARDYLV Sbjct: 120 TVRLTNRVIDLRRPQMQKNLMLRYKTTMAFRRFLDGAGFIDVETPMLTKSTPEGARDYLV 179 Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241 PSR +PG FFALPQSPQLFKQLLMVAG+DRYYQI KCFRDEDLRADRQPEFTQ+D+ETSF Sbjct: 180 PSRVHPGQFFALPQSPQLFKQLLMVAGYDRYYQIVKCFRDEDLRADRQPEFTQVDLETSF 239 Query: 242 LDESDIIGITEKMVRQLFKEVLDVEFD-EFPHMPFEEAMRRYGSDKPDLRIPLELVDVAD 300 ++E +I + E+M+R +FKE + VE FP M + EAMRRYGSDKPDLR+ LEL DV D Sbjct: 240 MNEHEITALVEEMIRYVFKEAMAVELPAPFPRMTYAEAMRRYGSDKPDLRVTLELTDVTD 299 Query: 301 QLKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNER 360 +++V FKVFSGPA GRVAA+RVPG S+ R +ID+YTKFV IYGA+GLAYIKVN+ Sbjct: 300 AVQDVAFKVFSGPATS-GGRVAAMRVPGGNSLTRGEIDEYTKFVAIYGARGLAYIKVNDV 358 Query: 361 AKGVE-GLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHD 419 + E GLQSPIVK + E L IL+R GA GD++FFGADK K+V DA+GALRIK+GH+ Sbjct: 359 TQPNEHGLQSPIVKNLHETALRTILERTGAQSGDLIFFGADKTKVVNDAMGALRIKLGHE 418 Query: 420 LKLLTRE-WAPMWVVDFPMFE-ENDDGSLSALHHPFTSPKCTPAE-LEANPGAALSRAYD 476 +T E W P+WVVDFPMFE + DD +A HHPFTSPK + LE+NPG L++AYD Sbjct: 419 KGYVTGEAWRPLWVVDFPMFEYDEDDKRWTACHHPFTSPKDEHIDLLESNPGECLAKAYD 478 Query: 477 MVLNGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGL 536 + LNG E+GGGS+RIH +Q VF L I EQ+ KFGFLLDALKYGAPPHGGLAFGL Sbjct: 479 LALNGWEIGGGSVRIHRADVQARVFEALNIGPEEQQAKFGFLLDALKYGAPPHGGLAFGL 538 Query: 537 DRLVMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLREQPKAE 591 DR+V +MTGA SIR+VIAFPKTQ A ++T AP VD K LRELHIRLR++ + + Sbjct: 539 DRIVTMMTGAESIRDVIAFPKTQRAQCLLTDAPSGVDEKQLRELHIRLRQKVETQ 593 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: 1096 Number of extensions: 48 Number of successful extensions: 8 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 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