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_010961029.1 MCA_RS08730 aspartate--tRNA ligase
Query= SwissProt::Q51422 (591 letters) >NCBI__GCF_000008325.1:WP_010961029.1 Length = 599 Score = 797 bits (2059), Expect = 0.0 Identities = 384/592 (64%), Positives = 471/592 (79%), Gaps = 2/592 (0%) Query: 2 MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61 MRSH CG++NESL GQEV LCGWVHRRRDHGGVIF+D+RDREGL QVVFDPD E F+ A Sbjct: 1 MRSHRCGEVNESLLGQEVGLCGWVHRRRDHGGVIFVDLRDREGLVQVVFDPDHPEPFSLA 60 Query: 62 DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121 + VRSE+V+++ G+VR RPEG NPN+ SG +EVL LE+LN++ETPPFP++ +V E Sbjct: 61 ETVRSEYVIRVVGQVRARPEGTENPNLKSGRVEVLATSLEILNRSETPPFPIESDIEVNE 120 Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181 E RLRYR+IDLRRP M +++LR IT +R +LD +GF ++ETP L + TPEGARDYLV Sbjct: 121 EMRLRYRYIDLRRPVMQQRMRLRRDITRFLRNFLDHHGFYEIETPFLTKATPEGARDYLV 180 Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241 PSRT+P FFALPQSPQL+KQLLM++G DRYYQ+ +CFRDEDLRADRQPEFTQ+DIETSF Sbjct: 181 PSRTHPHSFFALPQSPQLYKQLLMISGMDRYYQVVRCFRDEDLRADRQPEFTQLDIETSF 240 Query: 242 LDESDIIGITEKMVRQLFKEVLDVEF-DEFPHMPFEEAMRRYGSDKPDLRIPLELVDVAD 300 ++E I+ + E M+R LF+E L+ E D FP M + EAMRRY SDKPDLRIPLELVD+AD Sbjct: 241 MNEDQIMTLMEAMIRDLFRETLNEELPDPFPRMTYAEAMRRYASDKPDLRIPLELVDIAD 300 Query: 301 QLKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNER 360 + VEFKVF+GPA DP+GRV AL++PG + R IDD T+FVGIYGAKGLAY+KVN+ Sbjct: 301 LMAGVEFKVFAGPAADPEGRVVALKLPGGGDLSRKDIDDLTRFVGIYGAKGLAYVKVNDL 360 Query: 361 AKGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHDL 420 G+EGLQSPI+KF+PE+ + IL+R A GD++FFGADKA+IV +++GALR+K+G D Sbjct: 361 GAGLEGLQSPILKFMPESTIRGILERTEAQTGDLIFFGADKARIVNESMGALRVKLGQDR 420 Query: 421 KLLTREWAPMWVVDFPMFE-ENDDGSLSALHHPFTSPKCTPAELEANPGAALSRAYDMVL 479 L+ + W P+WV DFPMFE + G ALHHPFT+PKC+ +L NPG ALSRAYDMVL Sbjct: 421 GLVEKGWRPLWVTDFPMFEWDEKSGRWVALHHPFTAPKCSEEQLRQNPGRALSRAYDMVL 480 Query: 480 NGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGLDRL 539 NGTE+GGGS+RIH MQQ VF +LGI E E ++KFGFLL+AL+YG PPHGGLAFGLDRL Sbjct: 481 NGTEIGGGSVRIHRTEMQQTVFDLLGIGEEEAQQKFGFLLNALRYGCPPHGGLAFGLDRL 540 Query: 540 VMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLREQPKAE 591 VMLM+GASSIREV+AFPKTQSA + AP V+ L EL IRLR+ P E Sbjct: 541 VMLMSGASSIREVMAFPKTQSAWCPLIDAPAQVNDAQLHELGIRLRKNPAVE 592 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: 1166 Number of extensions: 45 Number of successful extensions: 3 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