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 15984 b1866 aspartyl-tRNA synthetase (NCBI)
Query= SwissProt::Q51422 (591 letters) >FitnessBrowser__Keio:15984 Length = 590 Score = 754 bits (1946), Expect = 0.0 Identities = 375/585 (64%), Positives = 457/585 (78%), Gaps = 4/585 (0%) Query: 2 MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61 MR+ YCGQL S GQ+VTLCGWV+RRRD G +IF+D+RDREG+ QV FDPDRA+ A Sbjct: 1 MRTEYCGQLRLSHVGQQVTLCGWVNRRRDLGSLIFIDMRDREGIVQVFFDPDRADALKLA 60 Query: 62 DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121 +R+EF +++TG VR R E N +MA+G IEVL L ++N+A+ PLD E Sbjct: 61 SELRNEFCIQVTGTVRARDEKNINRDMATGEIEVLASSLTIINRADV--LPLDSNHVNTE 118 Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181 E RL+YR++DLRRPEMA +LK RA+ITS +RR++DD+GFLD+ETP+L + TPEGARDYLV Sbjct: 119 EARLKYRYLDLRRPEMAQRLKTRAKITSLVRRFMDDHGFLDIETPMLTKATPEGARDYLV 178 Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241 PSR + G F+ALPQSPQLFKQLLM++GFDRYYQI KCFRDEDLRADRQPEFTQID+ETSF Sbjct: 179 PSRVHKGKFYALPQSPQLFKQLLMMSGFDRYYQIVKCFRDEDLRADRQPEFTQIDVETSF 238 Query: 242 LDESDIIGITEKMVRQLFKEVLDVEFDEFPHMPFEEAMRRYGSDKPDLRIPLELVDVADQ 301 + + + E +VR L+ EV V+ +FP M F EA RRYGSDKPDLR P+EL DVAD Sbjct: 239 MTAPQVREVMEALVRHLWLEVKGVDLGDFPVMTFAEAERRYGSDKPDLRNPMELTDVADL 298 Query: 302 LKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNERA 361 LK VEF VF+GPANDPKGRVAALRVPG AS+ R QID+Y FV IYGAKGLAYIKVNERA Sbjct: 299 LKSVEFAVFAGPANDPKGRVAALRVPGGASLTRKQIDEYGNFVKIYGAKGLAYIKVNERA 358 Query: 362 KGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHDLK 421 KG+EG+ SP+ KF+ + ILDR A DGD++FFGAD KIV DA+GALR+KVG DL Sbjct: 359 KGLEGINSPVAKFLNAEIIEDILDRTAAQDGDMIFFGADNKKIVADAMGALRLKVGKDLG 418 Query: 422 LLTR-EWAPMWVVDFPMFEENDDGSLSALHHPFTSPK-CTPAELEANPGAALSRAYDMVL 479 L +WAP+WV+DFPMFE++ +G L+A+HHPFTSPK T AEL+A P A++ AYDMV+ Sbjct: 419 LTDESKWAPLWVIDFPMFEDDGEGGLTAMHHPFTSPKDMTAAELKAAPENAVANAYDMVI 478 Query: 480 NGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGLDRL 539 NG E+GGGS+RIH+ MQQ VF +LGI+E EQ EKFGFLLDALKYG PPH GLAFGLDRL Sbjct: 479 NGYEVGGGSVRIHNGDMQQTVFGILGINEEEQREKFGFLLDALKYGTPPHAGLAFGLDRL 538 Query: 540 VMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRL 584 ML+TG +IR+VIAFPKT +A +MT+AP + AL EL I++ Sbjct: 539 TMLLTGTDNIRDVIAFPKTTAAACLMTEAPSFANPTALAELSIQV 583 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: 1078 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: 590 Length adjustment: 37 Effective length of query: 554 Effective length of database: 553 Effective search space: 306362 Effective search space used: 306362 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