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_012969945.1 ALVIN_RS03570 aspartate--tRNA ligase
Query= SwissProt::Q51422 (591 letters) >NCBI__GCF_000025485.1:WP_012969945.1 Length = 592 Score = 805 bits (2080), Expect = 0.0 Identities = 391/589 (66%), Positives = 486/589 (82%), Gaps = 5/589 (0%) Query: 2 MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61 MR+ YCG LN GQEV LCGWV RRRDHGGVIF+D+RDREGL QVVFDPDRAE FA+A Sbjct: 1 MRTQYCGDLNSQHTGQEVVLCGWVQRRRDHGGVIFIDLRDREGLVQVVFDPDRAEVFARA 60 Query: 62 DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYS-DVG 120 ++VRSE+V+KITG+VR RPEG NP++++G IE+LG +LE+LN AETPP LD ++ D Sbjct: 61 EQVRSEYVLKITGRVRPRPEGTINPDLSTGEIEILGLDLEILNAAETPPIQLDSHAADAS 120 Query: 121 EETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYL 180 EE RLRYR++DLRRPEM A+L+ R+R+T ++RR+LD+ GFLD+ETPIL + TPEGARDYL Sbjct: 121 EELRLRYRYLDLRRPEMQARLRTRSRVTQAMRRFLDERGFLDIETPILTKSTPEGARDYL 180 Query: 181 VPSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETS 240 VPSRT+PG FFALPQSPQLFKQLLM++G DRYYQIA+CFRDEDLRADRQPEFTQ+DIE S Sbjct: 181 VPSRTHPGEFFALPQSPQLFKQLLMMSGLDRYYQIARCFRDEDLRADRQPEFTQLDIEVS 240 Query: 241 FLDESDIIGITEKMVRQLFKEVLDVEF-DEFPHMPFEEAMRRYGSDKPDLRIPLELVDVA 299 F+ E +++G+ E M+R LF EV+ VE D FP + + EAMRR+GSD+PDLR+PLEL+DVA Sbjct: 241 FMSEDELMGLMEGMIRSLFSEVIGVELPDPFPRLTYAEAMRRFGSDRPDLRVPLELIDVA 300 Query: 300 DQLKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNE 359 D + V+F+VF+GPA DP+GRV ALR+P + R +ID YT+FVGIYGAKGLAYIKVNE Sbjct: 301 DLMDGVDFQVFAGPAKDPEGRVVALRLPKGGELSRKEIDGYTQFVGIYGAKGLAYIKVNE 360 Query: 360 -RAKGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGH 418 AKG EGLQSPI+KF+P+A + I+ R GAVDGD++FFGADKA++V +++GALR+K+G Sbjct: 361 WAAKGREGLQSPILKFLPDATVEGIMARTGAVDGDLIFFGADKARVVNESIGALRVKLGQ 420 Query: 419 DLKLLTREWAPMWVVDFPMFEEND-DGSLSALHHPFTSPKCTP-AELEANPGAALSRAYD 476 D LL EW P+WVVDFPMFE + +G ALHHPFT+PK LE++PGA LSRAYD Sbjct: 421 DRGLLEGEWRPLWVVDFPMFEHDPANGRWVALHHPFTAPKDEHLGLLESDPGACLSRAYD 480 Query: 477 MVLNGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGL 536 MVLNGTELGGGSIRIH ++Q+ VF++L I + + EE+FGFLL AL++G PPHGGLAFGL Sbjct: 481 MVLNGTELGGGSIRIHRDAVQRQVFKLLNISDEQAEERFGFLLKALRFGCPPHGGLAFGL 540 Query: 537 DRLVMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLR 585 DRLVMLMTGA SIR+V+AFPKTQ+A ++T AP +VD L+EL +RLR Sbjct: 541 DRLVMLMTGAGSIRDVMAFPKTQTAACLLTDAPSTVDEAQLKELSLRLR 589 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: 1157 Number of extensions: 59 Number of successful extensions: 6 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: 592 Length adjustment: 37 Effective length of query: 554 Effective length of database: 555 Effective search space: 307470 Effective search space used: 307470 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