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 PP_1213 PP_1213 Aspartate--tRNA ligase
Query= SwissProt::Q51422 (591 letters) >FitnessBrowser__Putida:PP_1213 Length = 591 Score = 1046 bits (2705), Expect = 0.0 Identities = 517/591 (87%), Positives = 554/591 (93%) Query: 1 MMRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAK 60 MMRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLD+RDREG+AQVVFDPDRAETFA Sbjct: 1 MMRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDIRDREGMAQVVFDPDRAETFAA 60 Query: 61 ADRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVG 120 ADRVRSE+VV+ITGKVR RPEGA N NMASG+IE+LGY+L VLN+AETPPFPL+EYSDVG Sbjct: 61 ADRVRSEYVVQITGKVRKRPEGAVNANMASGAIEILGYQLNVLNEAETPPFPLNEYSDVG 120 Query: 121 EETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYL 180 EETRLRYRFIDLRRPEMA KL+LR+RITSSIRR+LD+NGFLDVETPIL R TPEGARDYL Sbjct: 121 EETRLRYRFIDLRRPEMADKLRLRSRITSSIRRFLDENGFLDVETPILTRATPEGARDYL 180 Query: 181 VPSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETS 240 VPSRT+ G FFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETS Sbjct: 181 VPSRTHAGSFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETS 240 Query: 241 FLDESDIIGITEKMVRQLFKEVLDVEFDEFPHMPFEEAMRRYGSDKPDLRIPLELVDVAD 300 FLDES+I+G+TE M+R+LFKEVLD+EF EFPHM FEEAMRRYGSDKPDLRIPLELVDVAD Sbjct: 241 FLDESEIMGLTESMIRKLFKEVLDLEFGEFPHMTFEEAMRRYGSDKPDLRIPLELVDVAD 300 Query: 301 QLKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNER 360 QLK+V+FKVF+GPANDPK RV ALR+PG ASMPRS+ID+YTKFVGIYGAKGLAYIKVNER Sbjct: 301 QLKDVDFKVFAGPANDPKCRVTALRLPGGASMPRSKIDEYTKFVGIYGAKGLAYIKVNER 360 Query: 361 AKGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHDL 420 AKGVEGLQSPIVK IPEANLN ILDRVGAVDGDIVFFGADK K+V +ALGALRI++GHD Sbjct: 361 AKGVEGLQSPIVKNIPEANLNNILDRVGAVDGDIVFFGADKFKVVSEALGALRIRLGHDF 420 Query: 421 KLLTREWAPMWVVDFPMFEENDDGSLSALHHPFTSPKCTPAELEANPGAALSRAYDMVLN 480 +LLT EWAPMWVVDFPMFEEN+DGS +ALHHPFT+PKCTP ELEANP ALSRAYDMVLN Sbjct: 421 ELLTCEWAPMWVVDFPMFEENEDGSFTALHHPFTAPKCTPEELEANPATALSRAYDMVLN 480 Query: 481 GTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGLDRLV 540 GTELGGGSIRIH K MQQAVFR+LGI+ EQEEKFGFLLDALK+GAPPHGGLAFGLDRLV Sbjct: 481 GTELGGGSIRIHRKEMQQAVFRLLGIEAEEQEEKFGFLLDALKFGAPPHGGLAFGLDRLV 540 Query: 541 MLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLREQPKAE 591 MLMTGA SIREVIAFPKTQSA VMTQAPG VD KALRELHIRLREQ K E Sbjct: 541 MLMTGAQSIREVIAFPKTQSAACVMTQAPGMVDAKALRELHIRLREQTKVE 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: 1304 Number of extensions: 39 Number of successful extensions: 1 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