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_011800201.1 PNAP_RS03905 aspartate--tRNA ligase
Query= SwissProt::Q51422 (591 letters) >NCBI__GCF_000015505.1:WP_011800201.1 Length = 605 Score = 733 bits (1893), Expect = 0.0 Identities = 372/591 (62%), Positives = 453/591 (76%), Gaps = 8/591 (1%) Query: 2 MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61 MRS+YCG + ESL GQ V+LCGWV+RRRDHGGVIF+D+RDREG QVV DPDRAE F A Sbjct: 11 MRSNYCGLVTESLMGQTVSLCGWVNRRRDHGGVIFIDLRDREGYVQVVCDPDRAEMFGIA 70 Query: 62 DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121 + VR+EF V++ G VR RPEG N ++ SG +EVL +EL VLN + TPPF LD+ ++ E Sbjct: 71 EDVRNEFCVQVKGIVRARPEGTANASLKSGQVEVLCHELIVLNASVTPPFQLDD-DNLSE 129 Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181 TRL +R +DLRRP M L LR R+ R++LD NGF+D+ETP+L + TPEGARDYLV Sbjct: 130 TTRLTHRVLDLRRPYMQNNLMLRYRVAMETRKFLDANGFIDIETPMLTKSTPEGARDYLV 189 Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241 PSR G FFALPQSPQLFKQLLMVAGFDRYYQI KCFRDEDLRADRQPEFTQIDIETSF Sbjct: 190 PSRVNEGQFFALPQSPQLFKQLLMVAGFDRYYQITKCFRDEDLRADRQPEFTQIDIETSF 249 Query: 242 LDESDIIGITEKMVRQLFKEVLDVEFDEFPHMPFEEAMRRYGSDKPDLRIPLELVDVADQ 301 + E +I + + M+ +FK VL+ + EFP M + +AM RYGSDKPDLR+ LE ++ D Sbjct: 250 MGEQEIRDMFQGMISNMFKTVLNTDLGEFPVMAYADAMHRYGSDKPDLRVNLEFTELTDV 309 Query: 302 LKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNERA 361 + +V+FKVFS PA P GRV ALRVPG A + RS+ID YT+FV IYGAKGLA+IKVN+ + Sbjct: 310 MADVDFKVFSAPATTPGGRVVALRVPGGAEISRSEIDAYTEFVKIYGAKGLAWIKVNDVS 369 Query: 362 KGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHDL- 420 KG EGLQSPIVK I +A + IL R GA +GDI+FFGADK+K+V D++GALR+KVGH + Sbjct: 370 KGREGLQSPIVKNIHDAAVAEILKRTGAQNGDILFFGADKSKVVNDSIGALRLKVGHSVF 429 Query: 421 ----KLLTREWAPMWVVDFPMFEENDDGS-LSALHHPFTSPKCTPAE-LEANPGAALSRA 474 L T+ W P+WVVDFPMFE ++DG SA+HHPFT+PK + ++ +PG +++A Sbjct: 430 GKKSGLFTKGWKPLWVVDFPMFEYDEDGKRWSAVHHPFTAPKDGHEDWMDTDPGRCIAKA 489 Query: 475 YDMVLNGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAF 534 YDMVLNG ELGGGS+RIH +Q VF L I E + KFGFLLDAL+YGAPPHGGLAF Sbjct: 490 YDMVLNGWELGGGSVRIHRADVQSKVFSALNIGPEEAQLKFGFLLDALQYGAPPHGGLAF 549 Query: 535 GLDRLVMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLR 585 GLDR+V +MTGA SIR+VIAFPKTQ A ++T AP VD K LRELHIRLR Sbjct: 550 GLDRIVTMMTGAESIRDVIAFPKTQRAQCLLTHAPSPVDEKQLRELHIRLR 600 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: 1084 Number of extensions: 46 Number of successful extensions: 5 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: 605 Length adjustment: 37 Effective length of query: 554 Effective length of database: 568 Effective search space: 314672 Effective search space used: 314672 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