Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate CCNA_02288 CCNA_02288 tRNA synthetase class I, catalytic domain protein
Query= SwissProt::Q8DLI5 (485 letters) >FitnessBrowser__Caulo:CCNA_02288 Length = 279 Score = 140 bits (354), Expect = 4e-38 Identities = 104/282 (36%), Positives = 136/282 (48%), Gaps = 21/282 (7%) Query: 1 MTVRVRLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEG 60 MT R APSPTG LH G A +A+ + AR GG+F+LRIED D R RPEY ILE Sbjct: 1 MTFVTRFAPSPTGYLHRGHAYSALTAFEAARVTGGRFLLRIEDIDATRCRPEYEAAILED 60 Query: 61 LQWLGLTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQAPR 120 L WLGL W+ QS+ L Y AI L D+GL Y C+ T +E++ RA + P Sbjct: 61 LAWLGLNWEAPVRRQSEHLADYEAAIAGLRDRGLVYRCFKTRKEIDIGRAPHE-----PA 115 Query: 121 YDNRHRHLTPEEQAAFEAAGRTPVIRFKIEDDRQI-----------EWQDLVRGRVSWQG 169 L +E+A A G R + R+ E D R Sbjct: 116 IAYVGAPLGADEEAQRLARGEPFAWRLSLAAAREALGGFDHLSFLEEGADGSSPRTVQAL 175 Query: 170 ADLGGDMVIARAAPRGEIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALG 229 + GD+V+AR ++G Y+L VV DD G+T VIRGED T Q LL LG Sbjct: 176 PETAGDIVLARK----DVGV-AYHLAVVHDDALQGVTHVIRGEDLFEATHIQRLLQALLG 230 Query: 230 ATPPNFAHTPLILNSTGQKLSKRDGVTSISDFRAMGYLAPAL 271 P + H L+ G++ +KRD ++ + RA G A L Sbjct: 231 LPTPIYRHHGLLTGPDGKRYAKRDKAQTLRELRASGVSAQDL 272 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: 404 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: 279 Length adjustment: 30 Effective length of query: 455 Effective length of database: 249 Effective search space: 113295 Effective search space used: 113295 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: 49 (23.5 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