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_019894107.1 A377_RS0100535 aspartate--tRNA ligase
Query= SwissProt::Q51422 (591 letters) >NCBI__GCF_000384235.1:WP_019894107.1 Length = 598 Score = 763 bits (1970), Expect = 0.0 Identities = 371/590 (62%), Positives = 469/590 (79%), Gaps = 6/590 (1%) Query: 1 MMRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAK 60 MMR+HYCG++ E+L+ Q VT+ GWVHRRRDHGGVIF+D+RDREGL QVV +P A F Sbjct: 1 MMRTHYCGEVTEALEAQTVTVSGWVHRRRDHGGVIFIDLRDREGLVQVVVNPTDAAMFEI 60 Query: 61 ADRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVG 120 A+RVRSEFV+KI+G+V LR NP M +G IEV+ +LEVL+++E PF +D+ V Sbjct: 61 AERVRSEFVLKISGQVTLRTPETVNPKMTTGKIEVVASQLEVLSRSEPIPFQMDD-PHVS 119 Query: 121 EETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYL 180 EE RL YR++DLRR M ++ R ++T S+RR+LDDNGF+D+ETPIL + TPEGARDYL Sbjct: 120 EEVRLTYRYLDLRREPMQLAMRTRYKVTRSMRRFLDDNGFMDIETPILTKSTPEGARDYL 179 Query: 181 VPSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETS 240 VPSRT+ FFALPQSPQLFKQLLM++GFDRYYQI +CFRDEDLRADRQPEFTQ+DIETS Sbjct: 180 VPSRTHLNRFFALPQSPQLFKQLLMMSGFDRYYQITRCFRDEDLRADRQPEFTQLDIETS 239 Query: 241 FLDESDIIGITEKMVRQLFKEVLDVEFD-EFPHMPFEEAMRRYGSDKPDLRIPLELVDVA 299 F++E +++ + E + + +F+E +DV+FD +FP M + +A+ +YG D+PDLRIPLELVDVA Sbjct: 240 FMEEEEVMQVMEGLAKTIFREAVDVQFDGDFPRMTYAQAIEKYGIDRPDLRIPLELVDVA 299 Query: 300 DQLKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNE 359 D L+++EFKVF+ PA DP GRVAALRVP + R +ID+YTKFVGIYGAKGLAYIKVN+ Sbjct: 300 DLLQDIEFKVFAAPAKDPMGRVAALRVPNGGKLSRKEIDEYTKFVGIYGAKGLAYIKVND 359 Query: 360 RAKGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHD 419 + G+EGLQSPIVKF P+ + I+ RVGA DGDIVFFGADKAK+V +ALGALR K+G D Sbjct: 360 LSAGLEGLQSPIVKFFPDQAME-IMQRVGAQDGDIVFFGADKAKVVNEALGALRCKLGED 418 Query: 420 LKLLTREWAPMWVVDFPMFE-ENDDGSLSALHHPFTSPKCTPAEL--EANPGAALSRAYD 476 L ++ ++WAP+WVVDFPMFE + + ++A+HHPFT PK T E+ P LSRAYD Sbjct: 419 LGMIEKDWAPVWVVDFPMFEMDEETARMTAIHHPFTQPKATTEEILNHDAPHQMLSRAYD 478 Query: 477 MVLNGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGL 536 +V+NG E+GGGS+RIHD MQ AV ++LGID+ E +EKFGFLL+ALKYG PPH G+AFGL Sbjct: 479 LVINGIEVGGGSVRIHDTEMQSAVLKLLGIDQEEADEKFGFLLNALKYGCPPHAGMAFGL 538 Query: 537 DRLVMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLRE 586 DRLVMLM G SIR+VIAFPKTQSA ++T APG VD L+EL +R R+ Sbjct: 539 DRLVMLMAGRDSIRDVIAFPKTQSAACMLTDAPGGVDNAQLKELDLRFRK 588 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: 1138 Number of extensions: 32 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: 598 Length adjustment: 37 Effective length of query: 554 Effective length of database: 561 Effective search space: 310794 Effective search space used: 310794 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