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 N515DRAFT_1870 N515DRAFT_1870 aspartyl-tRNA synthetase
Query= SwissProt::Q51422 (591 letters) >FitnessBrowser__Dyella79:N515DRAFT_1870 Length = 589 Score = 680 bits (1755), Expect = 0.0 Identities = 341/590 (57%), Positives = 434/590 (73%), Gaps = 7/590 (1%) Query: 2 MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61 MR+HYCG ++E+L GQ VTLCGWV+ R V F+D+RD EG+AQVV + D A+ FA A Sbjct: 1 MRTHYCGLIDEALVGQTVTLCGWVNTIRLQSHVAFVDLRDHEGIAQVVVEKDNADAFAVA 60 Query: 62 DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121 + E+ +++TG VR R A N + +G++E+L ++E+LN A PF L E + E Sbjct: 61 GEIGYEYCLRVTGTVRKRL--AANDKLKTGTVELLADKVEILNAARDLPFALHE--NPNE 116 Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181 + R+ YR++DLRRPEM ++ R ++ ++RRYLD GF D+ETPIL + TPEGARDYLV Sbjct: 117 DMRMTYRYLDLRRPEMQRMMRTRIKLVQALRRYLDARGFQDIETPILTKATPEGARDYLV 176 Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241 PSR +PG F+ALPQSPQLFKQ+LM+AGFDRYYQIA+CFRDEDLRADRQPEFTQ+D+E +F Sbjct: 177 PSRVHPGQFYALPQSPQLFKQILMMAGFDRYYQIARCFRDEDLRADRQPEFTQLDLEFAF 236 Query: 242 LDESDIIGITEKMVRQLFKEVLDVEFDE-FPHMPFEEAMRRYGSDKPDLRIPLELVDVAD 300 ++E D+ E ++R +FKEV VE D FP M + EAMRR+GSDKPDLRI LELVDVAD Sbjct: 237 VEEPDVQDFVEALIRHVFKEVQGVELDAAFPRMTWAEAMRRFGSDKPDLRIALELVDVAD 296 Query: 301 QLKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNER 360 LK VEFKVF+ PANDP GRVAALR+P A++ R +ID T++V YGAKGLA++KV++ Sbjct: 297 ALKHVEFKVFAEPANDPAGRVAALRLPDGATLSRKEIDQLTEYVARYGAKGLAWLKVDDL 356 Query: 361 AKGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHDL 420 AKG EG+ SP+ KF+ +A L+ +L GA GD+VF GA K K V D +GALR+K+G D Sbjct: 357 AKGREGVNSPVAKFLDDAALDALLKATGAQSGDMVFVGAGKWKTVTDFMGALRLKLGKDR 416 Query: 421 KLLTREWAPMWVVDFPMFEENDDGS-LSALHHPFTSPKCTP-AELEANPGAALSRAYDMV 478 L+ W P+WV DFPMFE +++ ALHHPFT+PK A+L AN A+SR YDMV Sbjct: 417 GLVENSWKPLWVTDFPMFEYDEEAQRFVALHHPFTAPKVDDIADLRANAAIAVSRGYDMV 476 Query: 479 LNGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGLDR 538 LNG E+GGGSIRIH MQ AVF +LGI E E KFGFLL ALK+GAPPHGGLAFG+DR Sbjct: 477 LNGAEIGGGSIRIHRPDMQSAVFELLGIGAEEAEAKFGFLLKALKFGAPPHGGLAFGIDR 536 Query: 539 LVMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLREQP 588 + LM G SIR+VIAFPKT SA D+MT AP V L+ELH+++ +P Sbjct: 537 IAALMAGTESIRDVIAFPKTTSAQDLMTDAPSLVPDAQLKELHVKVAAEP 586 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: 1032 Number of extensions: 51 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: 589 Length adjustment: 37 Effective length of query: 554 Effective length of database: 552 Effective search space: 305808 Effective search space used: 305808 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