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_013820279.1 METME_RS18575 aspartate--tRNA ligase
Query= SwissProt::Q51422 (591 letters) >NCBI__GCF_000214665.1:WP_013820279.1 Length = 596 Score = 792 bits (2045), Expect = 0.0 Identities = 389/587 (66%), Positives = 474/587 (80%), Gaps = 2/587 (0%) Query: 2 MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61 MRSH CG+LN GQ V LCGWVHRRRDHGGVIF+D+RDR GL QVVFDPD +++FA A Sbjct: 1 MRSHKCGELNTQHLGQTVALCGWVHRRRDHGGVIFIDLRDRAGLVQVVFDPDLSDSFAIA 60 Query: 62 DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121 + VRSE+V++I G VR RPEG N NM +G IEVLG +EVLN++ETPPFPL+ +V E Sbjct: 61 ESVRSEYVLRIEGVVRDRPEGTHNANMFTGQIEVLGKHIEVLNESETPPFPLESEIEVNE 120 Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181 ETRLR+R+IDLRR M ++K+R +T +R+YLDDN F ++ETP L + TPEGARDY+V Sbjct: 121 ETRLRFRYIDLRRTVMQQRMKVRRDVTRHLRQYLDDNEFFEIETPYLTKATPEGARDYIV 180 Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241 PSRT+P FFALPQSPQL+KQLLMVAG +RYYQ+ +CFRDEDLRADRQPEFTQ+DIETSF Sbjct: 181 PSRTHPNAFFALPQSPQLYKQLLMVAGMERYYQVVRCFRDEDLRADRQPEFTQLDIETSF 240 Query: 242 LDESDIIGITEKMVRQLFKEVLDVEF-DEFPHMPFEEAMRRYGSDKPDLRIPLELVDVAD 300 ++E I+ I E+M+R+LFK++++V+ D FP M EAMRRYGSD+PDLRIPLELVD+AD Sbjct: 241 MNEQQIMAIMEEMIRRLFKDIINVDLGDPFPVMSHAEAMRRYGSDRPDLRIPLELVDIAD 300 Query: 301 QLKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNER 360 +++EV+FKVFSGPANDP GRV A+RVP M RS ID+ +KFVGIYGAKGLAYIKVN+ Sbjct: 301 EMREVDFKVFSGPANDPHGRVVAMRVPEGGEMSRSVIDELSKFVGIYGAKGLAYIKVNDL 360 Query: 361 AKGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHDL 420 A G EGLQSPIVKF P+ ++ +VGA +GD+VFFGADKA IV +A+GALR+K+G D Sbjct: 361 AAGAEGLQSPIVKFAPDEVWAKVMAKVGAQNGDLVFFGADKADIVNEAMGALRVKLGLDR 420 Query: 421 KLLTREWAPMWVVDFPMFEENDDGS-LSALHHPFTSPKCTPAELEANPGAALSRAYDMVL 479 LLT +W P+WVVDFPMF +D +A+HHPFT+P C+ EL+A+PG ALSRAYD+VL Sbjct: 421 NLLTGDWKPLWVVDFPMFAWDDKAQRYTAIHHPFTAPSCSVEELKADPGHALSRAYDLVL 480 Query: 480 NGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGLDRL 539 NGTE+GGGSIRI+ MQQ VF +LGI E EKFGFLLDALKYGAPPHGG+AFGLDRL Sbjct: 481 NGTEVGGGSIRINRTEMQQIVFAILGIGHEEAREKFGFLLDALKYGAPPHGGIAFGLDRL 540 Query: 540 VMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLRE 586 VMLMTGASSIR+VIAFPKTQ+A + AP V + L+EL IRLR+ Sbjct: 541 VMLMTGASSIRDVIAFPKTQTAACPLFNAPALVSDEQLKELGIRLRK 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: 1143 Number of extensions: 44 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: 596 Length adjustment: 37 Effective length of query: 554 Effective length of database: 559 Effective search space: 309686 Effective search space used: 309686 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