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_092991957.1 BLP65_RS01725 aspartate--tRNA ligase
Query= SwissProt::Q51422 (591 letters) >NCBI__GCF_900102855.1:WP_092991957.1 Length = 596 Score = 782 bits (2020), Expect = 0.0 Identities = 388/585 (66%), Positives = 466/585 (79%), Gaps = 3/585 (0%) Query: 2 MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61 MRSHYCG L+E+ Q+V L GWVHRRRDHGGVIF+D+RDREGL QVV DPD E FA A Sbjct: 1 MRSHYCGHLHETHLDQDVHLYGWVHRRRDHGGVIFIDLRDREGLVQVVIDPDDPEIFATA 60 Query: 62 DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLD-EYSDVG 120 +RVR+EFV+++ G+VR RPEG NP++ +G IEVLG EL +LN++ETPPF LD E +V Sbjct: 61 ERVRNEFVLEVKGRVRRRPEGTVNPDLPTGQIEVLGKELNILNRSETPPFMLDIEDDEVS 120 Query: 121 EETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYL 180 EE RLRYR++DLRRP+M +LKLR+++T +R YLD + FLDVETP+L R TPEGARDYL Sbjct: 121 EEHRLRYRYVDLRRPDMFKRLKLRSQVTQVLRNYLDHHAFLDVETPMLTRATPEGARDYL 180 Query: 181 VPSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETS 240 VPSRT+ GHFFALPQSPQLFKQLLMV+G DRYYQI +CFRDEDLRADRQPEFTQ+DIETS Sbjct: 181 VPSRTHQGHFFALPQSPQLFKQLLMVSGVDRYYQIVRCFRDEDLRADRQPEFTQLDIETS 240 Query: 241 FLDESDIIGITEKMVRQLFKEVLDVEFDEFPHMPFEEAMRRYGSDKPDLRIPLELVDVAD 300 F+DE +I+ + E MV LF V VE EFP + + EAMRR+ SDKPDLRIPLELVDV D Sbjct: 241 FMDEEEIMELMEGMVADLFTRVQGVELPEFPRLTYAEAMRRFASDKPDLRIPLELVDVDD 300 Query: 301 QLKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNER 360 +KEVEFKVFSGPANDP R+AAL VPG + R ID+YTKFVGIYGAKGLAYIKVN+ Sbjct: 301 LMKEVEFKVFSGPANDPNSRLAALHVPGGGELSRKAIDEYTKFVGIYGAKGLAYIKVNDL 360 Query: 361 AKGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHDL 420 A G EGLQSPI+KF+P+ + I+ R GA DGD+VFFGADKAK+V +ALGALR+K+GHDL Sbjct: 361 AAGREGLQSPILKFLPDEVVEQIMARTGAKDGDVVFFGADKAKVVNEALGALRVKIGHDL 420 Query: 421 KLLTREWAPMWVVDFPMFE-ENDDGSLSALHHPFTSPKCTPAE-LEANPGAALSRAYDMV 478 ++ + W P WVVDFPMFE + D ++HHPFTSPK + L++ P SRAYDMV Sbjct: 421 DMVEQGWRPCWVVDFPMFEWDEKDNRWYSMHHPFTSPKEEHIDLLDSEPEKCYSRAYDMV 480 Query: 479 LNGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGLDR 538 LNGTE+GGGS+RI+ +Q+ V + LGI + E + KFGFLL ALKYG PPHGG+AFGLDR Sbjct: 481 LNGTEIGGGSMRIYRSEVQKRVLKALGIGDEEAQAKFGFLLTALKYGCPPHGGIAFGLDR 540 Query: 539 LVMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIR 583 LVMLM+GA SIR+V+AFPKTQSA D+MT+AP V + L EL IR Sbjct: 541 LVMLMSGARSIRDVMAFPKTQSAADLMTEAPSEVPPEQLVELGIR 585 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: 1150 Number of extensions: 47 Number of successful extensions: 4 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