Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate Pf1N1B4_2861 glutamyl-Q-tRNA synthetase
Query= SwissProt::Q8DLI5 (485 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2861 Length = 298 Score = 133 bits (335), Expect = 7e-36 Identities = 94/277 (33%), Positives = 134/277 (48%), Gaps = 27/277 (9%) Query: 6 RLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEGLQWLG 65 R AP+P+G+LH G+ A+ ++L AR GG++++R+ED D R P IL+ L+ G Sbjct: 12 RFAPTPSGHLHFGSLVAALASYLDARSVGGRWLVRMEDLDPPREEPGAQAAILKALESYG 71 Query: 66 LTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQAPRYDNRH 125 WD QS+R Y + I L ++GLAY C C+ ++LE G P + Sbjct: 72 FEWDGDMVRQSERHAAYDEVINRLFNQGLAYACTCSRKQLEPYH------GIYPGFCRNA 125 Query: 126 RHLTPEEQAAFEAAGRTPVIRFKIEDDRQIEWQDLVRGRVSWQGADLGGDMVIARAAPRG 185 H T E AA R P + + D Q E++ + V GD VI R Sbjct: 126 GHGT--ENAAIRL--RVPELEYHFIDRVQGEFRQHLGREV--------GDFVIRR----- 168 Query: 186 EIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGATPPNFAHTPLILNST 245 G Y L VV+DD GITD++RG D + +TP+Q+ L E LG P + H PLI Sbjct: 169 RDGLYAYQLAVVLDDAWQGITDIVRGADLLDSTPRQLYLQELLGLPQPRYLHIPLITQPD 228 Query: 246 GQKLSKRDGVTSISDFRAMGYLAPALANYMTLLGWSP 282 G KL K +++ +A P L + LG P Sbjct: 229 GHKLGKSYRSPPLTEDQA----TPLLLRALRALGHKP 261 Lambda K H 0.320 0.136 0.418 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: 424 Number of extensions: 25 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: 485 Length of database: 298 Length adjustment: 30 Effective length of query: 455 Effective length of database: 268 Effective search space: 121940 Effective search space used: 121940 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: 50 (23.9 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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