Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate BPHYT_RS06160 BPHYT_RS06160 glutamyl-Q tRNA(Asp) ligase
Query= SwissProt::Q8DLI5 (485 letters) >FitnessBrowser__BFirm:BPHYT_RS06160 Length = 296 Score = 145 bits (367), Expect = 1e-39 Identities = 91/270 (33%), Positives = 136/270 (50%), Gaps = 11/270 (4%) Query: 1 MTVRVRLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEG 60 MT R R APSPTG LH G+ +A+ +WL AR G +++R+ED D R+ P E+IL Sbjct: 1 MTYRGRFAPSPTGPLHFGSLVSALASWLDARAHRGAWLVRVEDIDGPRTVPGAAEDILAT 60 Query: 61 LQWLGLTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQAPR 120 L+ G+ DE P +QS R+ Y++A++ L G+ Y C CT +E+ + Sbjct: 61 LERFGMHADEPPVWQSARMPRYQEALEQLKANGVIYPCGCTRKEIADSLLNAHTRNTTLA 120 Query: 121 YDNRHRHLTPEEQAAFEAAGRTPVIRFKIEDDRQIEWQDLVRGRVSWQGADLGGDMVIAR 180 Y R R +R D I ++D +G+ + A GD V+ R Sbjct: 121 YPGTCR------DGLHGKPARAWRLRVPDGDSAVITFEDRWQGKQTQNLATEVGDFVLKR 174 Query: 181 AAPRGEIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGATPPNFAHTPL 240 A + Y L VVVDD GIT ++RG D + +T +QI L LG P + H P+ Sbjct: 175 ADDQW-----AYQLAVVVDDADAGITHIVRGADLMDSTARQIYLQRCLGVPTPEYLHVPV 229 Query: 241 ILNSTGQKLSKRDGVTSISDFRAMGYLAPA 270 + N G+KLSK++G T++ + L+ A Sbjct: 230 VTNEAGEKLSKQNGATALDSEKPFEALSAA 259 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: 357 Number of extensions: 18 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: 296 Length adjustment: 30 Effective length of query: 455 Effective length of database: 266 Effective search space: 121030 Effective search space used: 121030 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 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