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 GFF2090 HP15_2044 aspartyl-tRNA synthetase
Query= SwissProt::Q51422 (591 letters) >FitnessBrowser__Marino:GFF2090 Length = 602 Score = 894 bits (2311), Expect = 0.0 Identities = 433/588 (73%), Positives = 499/588 (84%) Query: 2 MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61 MRSHYCG +NES QEVTLCGWVHRRRDHGGVIFLD+RDR+G++QVV DPD E+FA A Sbjct: 1 MRSHYCGGINESHIDQEVTLCGWVHRRRDHGGVIFLDLRDRDGMSQVVVDPDTPESFALA 60 Query: 62 DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121 ++VRSEFV+K+TG+VR RP G N NM +G +E+LG EL +LN A TPPFPLDE+ DVGE Sbjct: 61 EKVRSEFVIKVTGRVRRRPAGTENNNMPTGQVELLGKELTILNAAATPPFPLDEHVDVGE 120 Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181 + RLRYRF+DLRRPEM +L+ R+R+TS IR YLD NGF+DVETPIL R TPEGARDYLV Sbjct: 121 DVRLRYRFVDLRRPEMINRLRFRSRVTSYIRNYLDSNGFMDVETPILTRATPEGARDYLV 180 Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241 PSRT+ G FFALPQSPQLFKQLLMV+G DRYYQIAKCFRDEDLRADRQPEFTQ+DIE SF Sbjct: 181 PSRTHEGSFFALPQSPQLFKQLLMVSGVDRYYQIAKCFRDEDLRADRQPEFTQVDIEASF 240 Query: 242 LDESDIIGITEKMVRQLFKEVLDVEFDEFPHMPFEEAMRRYGSDKPDLRIPLELVDVADQ 301 +DE ++ + E M+R LFK+VL+VE FP MP+ EAM+RYGSDKPDLRIPLEL+DV D Sbjct: 241 IDEETLMKLNEDMIRALFKDVLEVELPSFPQMPYAEAMQRYGSDKPDLRIPLELLDVNDL 300 Query: 302 LKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNERA 361 ++ V+FKVF+GPA DPKGRVAALRVP + R QIDDYTKFVGIYGAKGLAYIKVN+ + Sbjct: 301 VEGVDFKVFAGPAKDPKGRVAALRVPKGGELTRKQIDDYTKFVGIYGAKGLAYIKVNDLS 360 Query: 362 KGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHDLK 421 KGVEGLQSPI+KF+ + I++RVGA DGDIVFFGADK +V +ALGALRIK+GHDL Sbjct: 361 KGVEGLQSPIIKFLGDDVALAIMERVGAEDGDIVFFGADKTNVVNEALGALRIKIGHDLD 420 Query: 422 LLTREWAPMWVVDFPMFEENDDGSLSALHHPFTSPKCTPAELEANPGAALSRAYDMVLNG 481 +LT EWAP+WVVDFPMFEE DG L+A+HHPFT+P C+P +L A+P ALSRAYDMVLNG Sbjct: 421 MLTSEWAPLWVVDFPMFEETPDGGLTAIHHPFTAPSCSPEDLAADPANALSRAYDMVLNG 480 Query: 482 TELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGLDRLVM 541 TELGGGSIRIHD+ MQ+AVFR+LGI E E KFGFLLDALK+G PPHGGLAFGLDRLVM Sbjct: 481 TELGGGSIRIHDEKMQEAVFRILGIGEEEARAKFGFLLDALKFGCPPHGGLAFGLDRLVM 540 Query: 542 LMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLREQPK 589 LMTGASSIR+VIAFPKTQSA +MTQAPG VD K LRELHIRLR+ K Sbjct: 541 LMTGASSIRDVIAFPKTQSATCLMTQAPGEVDEKQLRELHIRLRKPSK 588 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: 1258 Number of extensions: 51 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: 602 Length adjustment: 37 Effective length of query: 554 Effective length of database: 565 Effective search space: 313010 Effective search space used: 313010 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