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_011766962.1 AZO_RS16275 aspartate--tRNA ligase
Query= SwissProt::Q51422 (591 letters) >NCBI__GCF_000061505.1:WP_011766962.1 Length = 599 Score = 759 bits (1959), Expect = 0.0 Identities = 385/595 (64%), Positives = 465/595 (78%), Gaps = 7/595 (1%) Query: 2 MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61 MR+ YCGQ+ + Q VTLCGWVHRRRDHGGVIF+D+RDREGL QVV DPDRAE F A Sbjct: 1 MRTQYCGQVTAAHLDQIVTLCGWVHRRRDHGGVIFIDLRDREGLVQVVCDPDRAEMFKTA 60 Query: 62 DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121 + VR+EFV+K+TGKVR RP G N N+ SG IEVL +E+EVLN + TPPF LD+ ++ E Sbjct: 61 ESVRNEFVLKMTGKVRRRPAGTENANLTSGEIEVLCHEIEVLNTSATPPFQLDD-ENLSE 119 Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181 RL R IDLRRP+M L LR ++ + RR+LD GF+DVETP+L + TPEGARDYLV Sbjct: 120 TVRLTNRVIDLRRPQMQKNLMLRYKVAMAFRRFLDGAGFIDVETPMLTKSTPEGARDYLV 179 Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241 PSR +PG FFALPQSPQLFKQLLMVAGFDRYYQI KCFRDEDLRADRQPEFTQ+DIETSF Sbjct: 180 PSRVHPGQFFALPQSPQLFKQLLMVAGFDRYYQITKCFRDEDLRADRQPEFTQVDIETSF 239 Query: 242 LDESDIIGITEKMVRQLFKEVLDVEF-DEFPHMPFEEAMRRYGSDKPDLRIPLELVDVAD 300 L+E++I + E+M+R +FKE L V+ FP M + EAMRRYGSDKPDLR+ LEL +V D Sbjct: 240 LNETEITALMEEMIRFVFKESLGVDLPSPFPRMTYAEAMRRYGSDKPDLRVTLELTEVTD 299 Query: 301 QLKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNER 360 +K+V FKVFSGPAN GRVAA+RVPG A++ R +ID+YTKFVGIYGAKGLAYIKVN+ Sbjct: 300 LMKDVAFKVFSGPANS-GGRVAAMRVPGGATLTRGEIDEYTKFVGIYGAKGLAYIKVNDA 358 Query: 361 AKGVE-GLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHD 419 ++ E GLQSPIVK + EA L +++R GA GD++FFGADKAK+V DA+GALRIK+GH+ Sbjct: 359 SQPNETGLQSPIVKNLSEAALRGVIERTGAQSGDLIFFGADKAKVVNDAIGALRIKLGHE 418 Query: 420 LKLLTRE-WAPMWVVDFPMFE-ENDDGSLSALHHPFTSPKCTPAE-LEANPGAALSRAYD 476 +T + W P+WVVDFPMFE + DD +A HHPFTSPK E L+ NPG L++AYD Sbjct: 419 KGYVTGDAWRPLWVVDFPMFEYDEDDKRWTACHHPFTSPKDEHVELLKTNPGECLAKAYD 478 Query: 477 MVLNGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGL 536 + LNG E+GGGS+RIH +Q VF L I EQ+ KFGFLLDALK+GAPPHGGLAFGL Sbjct: 479 LALNGWEIGGGSVRIHRADVQATVFEALNIGAEEQQVKFGFLLDALKFGAPPHGGLAFGL 538 Query: 537 DRLVMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLREQPKAE 591 DR+V +M GA SIR+VIAFPKTQ A ++T APG VD K LRELHIRLR++ + + Sbjct: 539 DRVVTMMAGAESIRDVIAFPKTQRAQCLLTNAPGEVDEKQLRELHIRLRQKVETQ 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: 1119 Number of extensions: 51 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