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_077243649.1 B1A74_RS02190 aspartate--tRNA ligase
Query= SwissProt::Q51422 (591 letters) >NCBI__GCF_001995255.1:WP_077243649.1 Length = 595 Score = 794 bits (2051), Expect = 0.0 Identities = 387/587 (65%), Positives = 478/587 (81%), Gaps = 4/587 (0%) Query: 2 MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61 MR+H CGQ+ ES EVTLCGWV+RRRDHGGVIF+D+RD GL QVVFDPDR E FA+A Sbjct: 1 MRTHLCGQVTESDLDSEVTLCGWVNRRRDHGGVIFVDLRDHAGLVQVVFDPDREEVFARA 60 Query: 62 DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121 +++RSE+V+++TG+VR RPEG NP + +G++E+LG ELEVLN A+TPPFPLD+ DVGE Sbjct: 61 EQLRSEYVIRMTGRVRRRPEGTENPELTTGAVEILGLELEVLNAAKTPPFPLDD-EDVGE 119 Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181 +TRLRYR++DLRRP M +L+LR R+T+++RR+L++ FLD+ETP+L R TPEGARDYLV Sbjct: 120 DTRLRYRYMDLRRPVMQERLRLRGRVTAAMRRFLEERDFLDLETPMLTRATPEGARDYLV 179 Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241 PSRT+ G FFALPQSPQLFKQLLM++G DRYYQI +CFRDEDLRADRQPEFTQ+D+E +F Sbjct: 180 PSRTHAGSFFALPQSPQLFKQLLMMSGMDRYYQITRCFRDEDLRADRQPEFTQLDMEMAF 239 Query: 242 LDESDIIGITEKMVRQLFKEVLDVEFDE-FPHMPFEEAMRRYGSDKPDLRIPLELVDVAD 300 +DE+D++G+TE+++R LF+EV+ +E D+ FP M EAM R+GSDKPDLRIPLE ++ + Sbjct: 240 VDEADVMGVTEELMRHLFREVMGIELDDPFPRMSHAEAMTRFGSDKPDLRIPLEFTELTE 299 Query: 301 QLKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNER 360 ++ VEFKVF+ PANDP+GRVAALRVPG A + R +ID YT+FVG YGAKGLAYIKVN+ Sbjct: 300 VMQAVEFKVFNAPANDPEGRVAALRVPGGAELTRKEIDGYTEFVGRYGAKGLAYIKVNDP 359 Query: 361 AKGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHDL 420 A GLQSPI+KF+PE + IL R GA GD++FFGAD+A +V +ALGALR++VGHD Sbjct: 360 ADPANGLQSPILKFLPEDVIREILARTGAAAGDLIFFGADRADVVNEALGALRVQVGHDR 419 Query: 421 KLLTREWAPMWVVDFPMFE-ENDDGSLSALHHPFTSPKC-TPAELEANPGAALSRAYDMV 478 L+ W P+WVVDFPMFE + DD L ALHHPFT+P +P L NP A+SRAYDMV Sbjct: 420 GLVEPGWRPLWVVDFPMFEWDPDDKRLYALHHPFTAPATDSPDALRENPREAMSRAYDMV 479 Query: 479 LNGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGLDR 538 LNGTE+GGGSIRIH+ MQQA F LGI E E EKFGFLLDAL +GAPPHGGLAFGLDR Sbjct: 480 LNGTEVGGGSIRIHNPEMQQAAFEALGIGEEEAREKFGFLLDALNFGAPPHGGLAFGLDR 539 Query: 539 LVMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLR 585 LVMLM+GA SIR+V+AFPKTQ+A ++T AP V K LREL IRLR Sbjct: 540 LVMLMSGAHSIRDVMAFPKTQTAACLLTDAPAPVGEKPLRELGIRLR 586 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: 1230 Number of extensions: 61 Number of successful extensions: 5 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: 595 Length adjustment: 37 Effective length of query: 554 Effective length of database: 558 Effective search space: 309132 Effective search space used: 309132 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