Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate Synpcc7942_0922 Synpcc7942_0922 Glutamate--tRNA ligase
Query= metacyc::MONOMER-13959 (483 letters) >FitnessBrowser__SynE:Synpcc7942_0922 Length = 300 Score = 134 bits (338), Expect = 3e-36 Identities = 96/317 (30%), Positives = 153/317 (48%), Gaps = 35/317 (11%) Query: 6 RVRYAPSPTGHLHIGNARTALFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQLNYLKW 65 R R+AP+P+G LH+G+ A+ +YL R+Q G +++R++D D R + G L+ Sbjct: 6 RGRFAPTPSGDLHLGSLVAAVGSYLHVRSQCGTWLLRIDDLDAPRVVPGASDRIQTCLEA 65 Query: 66 LGIDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEELEKEREEQIAR 125 G+ WDE V Y Q + + Y+ E+L G Y+C C+ ++L + + Sbjct: 66 FGLHWDEVV--------YFQQPQQEHYQAALEQLTATGRVYRCQCSRKQLSQSGDSVSVD 117 Query: 126 GEMPRYSGKHRDLTQEEQEKFIAEGRKPSIRFRVPEGKVIAFNDIVKGEISFE-SDGIGD 184 G + RY G RD + EG S R V IA D +G + + +GD Sbjct: 118 GSL-RYPGFCRDRQLSSE----IEG---SDRLNVQNLPAIALEDAWQGRYQQDLAQAVGD 169 Query: 185 FVIVKKDGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAFGWDIPQFGHMTL 244 F++ ++D +Y+ A +DD +T V+RG D +++TP+QI + Q P +GH+ L Sbjct: 170 FILRRRDRLFSYHLATVVDDARQGITEVIRGLDLLASTPRQIALQQLLNLPTPHYGHLPL 229 Query: 245 IVNESRKKLSKRDESIIQFIEQYKELGYLPEALFNFIGLLG--------WSPVGEEELFT 296 +V + KLSK+ ++ +L P L IG LG +PVGE+ + Sbjct: 230 VVWPNGDKLSKQTKA------PPLDLRQAPALLSQAIGHLGLALPSDLQGAPVGEQLAWA 283 Query: 297 KEQFIEIFDVNRLSKSP 313 I F RLSK P Sbjct: 284 ----IAHFPAPRLSKQP 296 Lambda K H 0.316 0.137 0.394 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: 322 Number of extensions: 12 Number of successful extensions: 3 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: 483 Length of database: 300 Length adjustment: 30 Effective length of query: 453 Effective length of database: 270 Effective search space: 122310 Effective search space used: 122310 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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