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 6937701 Sama_1843 aspartyl-tRNA synthetase (RefSeq)
Query= SwissProt::Q51422 (591 letters) >FitnessBrowser__SB2B:6937701 Length = 591 Score = 777 bits (2006), Expect = 0.0 Identities = 385/592 (65%), Positives = 467/592 (78%), Gaps = 3/592 (0%) Query: 2 MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61 MRSHYCG +N+S GQEVTL GWV+R RD GGVIFLD+RDREGL QVV+DPD + F A Sbjct: 1 MRSHYCGDVNKSHVGQEVTLVGWVNRSRDLGGVIFLDLRDREGLVQVVYDPDLPDVFDVA 60 Query: 62 DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121 +R+EF V++ G VR RP+ N M +G IEVLG L ++N A+ P LD + + E Sbjct: 61 SSLRAEFCVQVKGVVRPRPDSQVNSQMKTGEIEVLGKALTIINAADPLPLSLDNHQNNSE 120 Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181 E RL+YR++DLRRPEMA +L RA++TS +RR++D NGFLD+ETPIL + TPEGARDYLV Sbjct: 121 EARLKYRYLDLRRPEMAQRLIFRAKVTSFVRRFMDGNGFLDIETPILTKATPEGARDYLV 180 Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241 PSRTY G FFALPQSPQLFKQLLM++GFDRYYQI KCFRDEDLRADRQPEFTQIDIETSF Sbjct: 181 PSRTYKGQFFALPQSPQLFKQLLMMSGFDRYYQIVKCFRDEDLRADRQPEFTQIDIETSF 240 Query: 242 LDESDIIGITEKMVRQLFKEVLDVEFDEFPHMPFEEAMRRYGSDKPDLRIPLELVDVADQ 301 + ++ TE+M+R LF E+++V+ +FP M ++EAMRR+GSDKPDLR PLELVDVAD Sbjct: 241 MTSDQVMETTERMIRNLFLELMNVDLGDFPKMTWDEAMRRFGSDKPDLRNPLELVDVADL 300 Query: 302 LKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNERA 361 LK VEF VFSGPAND +GRVAALR+PG A + R QIDDYTKFVGIYGA+GLA++KVN A Sbjct: 301 LKAVEFAVFSGPANDEEGRVAALRIPGGAELSRKQIDDYTKFVGIYGARGLAWMKVNNLA 360 Query: 362 KGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHDLK 421 GVEG+QSP+ KF+ E + I+ R A DGDI+FFGADKA +V +++GALR+K G D K Sbjct: 361 AGVEGIQSPVAKFLNEDIIKEIIARTKAADGDIIFFGADKANVVAESMGALRLKAGEDFK 420 Query: 422 LLTREWAPMWVVDFPMFEENDDGSLSALHHPFTSPK-CTPAELEANPGAALSRAYDMVLN 480 LL EW P+WVVDFPMFE+ DG A+HHPFT+P+ T AELEA+PG A+S AYDMVLN Sbjct: 421 LLEGEWRPLWVVDFPMFEK-ADGRFYAVHHPFTAPRGVTAAELEASPGKAVSDAYDMVLN 479 Query: 481 GTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGLDRLV 540 G ELGGGS+RIH+ MQ VFR+LGID+ E +EKFGFLLDAL++G PPH GLAFGLDRLV Sbjct: 480 GVELGGGSVRIHNGDMQSTVFRILGIDDEEAKEKFGFLLDALRFGTPPHAGLAFGLDRLV 539 Query: 541 MLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIR-LREQPKAE 591 MLMTGASSIR+V+AFPKT +A +T APG + L EL I L ++PK + Sbjct: 540 MLMTGASSIRDVMAFPKTTTAACPLTNAPGHANPDQLVELGIAVLPKEPKQD 591 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: 1101 Number of extensions: 40 Number of successful extensions: 2 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