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 201577 SO2433 aspartyl-tRNA synthetase (NCBI ptt file)
Query= SwissProt::Q51422 (591 letters) >FitnessBrowser__MR1:201577 Length = 591 Score = 780 bits (2013), Expect = 0.0 Identities = 381/591 (64%), Positives = 470/591 (79%), Gaps = 2/591 (0%) Query: 2 MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61 MRSHYCG +N+S GQEVTL GWV+R RD GGV+FLD+RDREGL QVV+DPD E F A Sbjct: 1 MRSHYCGDVNKSHVGQEVTLVGWVNRSRDLGGVVFLDLRDREGLVQVVYDPDLPEVFNVA 60 Query: 62 DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121 +R+EF V++ G VR RP+ N M +G IEVLG L ++N +E P LD Y + E Sbjct: 61 STLRAEFCVQVKGVVRARPDSQVNAQMKTGEIEVLGKALTIINSSEPLPLSLDNYQNNSE 120 Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181 E RL+YR++DLRRPEMA +L RA++TS++RR+LD NGFLD+ETPIL + TPEGARDYLV Sbjct: 121 EQRLKYRYLDLRRPEMAQRLMFRAKVTSAVRRFLDSNGFLDIETPILTKATPEGARDYLV 180 Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241 PSRTY G FFALPQSPQLFKQLLM++GFDRYYQI KCFRDEDLRADRQPEFTQIDIETSF Sbjct: 181 PSRTYKGQFFALPQSPQLFKQLLMMSGFDRYYQIVKCFRDEDLRADRQPEFTQIDIETSF 240 Query: 242 LDESDIIGITEKMVRQLFKEVLDVEFDEFPHMPFEEAMRRYGSDKPDLRIPLELVDVADQ 301 + ++ TE+M+R LF E+L+V+ EFP M + EAMRR+GSDKPDLR PLELVDVAD Sbjct: 241 MTSEQVMNKTEEMMRGLFLEMLNVDLGEFPRMTYNEAMRRFGSDKPDLRNPLELVDVADL 300 Query: 302 LKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNERA 361 LK+VEF VFSGPAND +GRVAALR+PG AS+ R QIDDYTKFVGIYGAKGLA++K+N+ Sbjct: 301 LKDVEFAVFSGPANDEEGRVAALRIPGGASLSRKQIDDYTKFVGIYGAKGLAWMKLNDLT 360 Query: 362 KGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHDLK 421 +G+EG+QSP++KF+ E +N I++R GA GDI+ FGAD+A +V +++GALR+K G D Sbjct: 361 QGLEGIQSPVLKFLNENIVNEIINRTGAQTGDIILFGADQATVVAESMGALRLKAGEDFN 420 Query: 422 LLTREWAPMWVVDFPMFEENDDGSLSALHHPFTSPK-CTPAELEANPGAALSRAYDMVLN 480 LL +W P+WVVDFPMFE+ +GS A+HHPFT+P+ TP ELEANP +S AYDMVLN Sbjct: 421 LLEGQWRPLWVVDFPMFEK-INGSFHAVHHPFTAPRGVTPQELEANPANRVSDAYDMVLN 479 Query: 481 GTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGLDRLV 540 G ELGGGS+RIH++ MQ AVFR+LGI + E +EKFGFLL+AL+YG PPH GLAFGLDR++ Sbjct: 480 GCELGGGSVRIHNQEMQSAVFRILGITDEEAKEKFGFLLEALRYGTPPHAGLAFGLDRII 539 Query: 541 MLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLREQPKAE 591 MLMTGASSIR+V+AFPKT +A +T APG + + L EL I + + K E Sbjct: 540 MLMTGASSIRDVMAFPKTTTAACPLTNAPGFANPQQLAELGIAVVKTAKTE 590 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: 1050 Number of extensions: 40 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: 591 Length adjustment: 37 Effective length of query: 554 Effective length of database: 554 Effective search space: 306916 Effective search space used: 306916 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