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_012399800.1 BPHY_RS01895 aspartate--tRNA ligase
Query= SwissProt::Q51422 (591 letters) >NCBI__GCF_000020045.1:WP_012399800.1 Length = 599 Score = 729 bits (1882), Expect = 0.0 Identities = 370/593 (62%), Positives = 446/593 (75%), Gaps = 9/593 (1%) Query: 2 MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61 MRS YCG + E L GQ V+LCGWV RRRDHGGVIF+D+RDREGL QVV DPDRAE F A Sbjct: 3 MRSEYCGLVTEHLLGQTVSLCGWVSRRRDHGGVIFIDLRDREGLVQVVCDPDRAEMFKTA 62 Query: 62 DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121 + VR+EF V++ G VR RPEG N + SG IEVL +EL VLN + TPPF LD+ ++ E Sbjct: 63 EGVRNEFCVQVKGVVRNRPEGTTNAGLKSGKIEVLCHELNVLNASVTPPFQLDD-DNLSE 121 Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181 TRL +R +DLRRP+M L+LR R+ +R+YLD GF+D+ETP+L + TPEGARDYLV Sbjct: 122 TTRLTHRVLDLRRPQMQHNLRLRYRVAMEVRKYLDSRGFIDIETPMLTKSTPEGARDYLV 181 Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241 PSR G FFALPQSPQLFKQLLMVA FDRYYQI KCFRDEDLRADRQPEFTQID ETSF Sbjct: 182 PSRVNAGQFFALPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRADRQPEFTQIDCETSF 241 Query: 242 LDESDIIGITEKMVRQLFKEVLDVEFD-EFPHMPFEEAMRRYGSDKPDLRIPLELVDVAD 300 L E +I + E M R +FKE + VE D +F MP+ EAM R+GSDKPDLR+ LE ++ D Sbjct: 242 LSEQEIRDLFEDMTRHVFKETIGVELDAKFAVMPYSEAMSRFGSDKPDLRVKLEFTELTD 301 Query: 301 QLKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNER 360 +K+V+FKVFS PAN GRVAALRVP + R ID YT+FV IYGAKGLA+IK+NE Sbjct: 302 AMKDVDFKVFSTPANTKDGRVAALRVPKGGELSRGDIDSYTEFVRIYGAKGLAWIKINEV 361 Query: 361 AKGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHD- 419 AKG +GLQSPIVK + +A + I++R GA DGDI+FF AD+AK+V D+LGALR+K+GH Sbjct: 362 AKGRDGLQSPIVKNLHDAAIAAIIERTGAQDGDIIFFAADRAKVVNDSLGALRLKIGHSE 421 Query: 420 ----LKLLTREWAPMWVVDFPMFE-ENDDGSLSALHHPFTSPKCTPAE-LEANPGAALSR 473 L+ W P+WVVDFPMFE + ++ A HHPFTSPK E LE +PG L++ Sbjct: 422 FGKANGLVEAGWKPLWVVDFPMFEYDEEENRYVAAHHPFTSPKDEHLEYLETDPGRCLAK 481 Query: 474 AYDMVLNGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLA 533 AYD+VLNG E+GGGS+RI + +Q VFR L I E KFGFLLDAL+YGAPPHGG+A Sbjct: 482 AYDIVLNGWEIGGGSVRIFQEDVQSKVFRALKIGAEEARLKFGFLLDALQYGAPPHGGIA 541 Query: 534 FGLDRLVMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLRE 586 FGLDR+V +M GA SIR+VIAFPKTQ A D++TQAP VD + LRELHIRLR+ Sbjct: 542 FGLDRIVTMMAGADSIRDVIAFPKTQRAQDLLTQAPSEVDERQLRELHIRLRQ 594 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: 1089 Number of extensions: 53 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: 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