Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate 14290 b0144 glutamyl-Q tRNA(Asp) synthetase (RefSeq)
Query= SwissProt::Q8DLI5 (485 letters) >FitnessBrowser__Keio:14290 Length = 308 Score = 140 bits (353), Expect = 6e-38 Identities = 93/250 (37%), Positives = 129/250 (51%), Gaps = 27/250 (10%) Query: 6 RLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEGLQWLG 65 R APSP+G LH G+ A+ ++L AR R G++++RIED D R P E IL L+ G Sbjct: 19 RFAPSPSGELHFGSLIAALGSYLQARARQGRWLVRIEDIDPPREVPGAAETILRQLEHYG 78 Query: 66 LTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQAPRYDNRH 125 L WD +QS R D YR+A+ L ++GL+YYC CT ++++ YD Sbjct: 79 LHWDGDVLWQSQRHDAYREALAWLHEQGLSYYCTCTRARIQSI---------GGIYDGHC 129 Query: 126 R--HLTPEEQAAFEAAGRTPVIRFKIEDDRQIEWQDLVRGRVSWQGADLGGDMVIARAAP 183 R H P + AA + PV +F D +RG + D +I R Sbjct: 130 RVLHHGP-DNAAVRIRQQHPVTQF----------TDQLRGIIHADEKLAREDFIIHR--- 175 Query: 184 RGEIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGATPPNFAHTPLILN 243 G YNL VVVDD G+T+++RG D I T +QI LY+ G P++ H PL LN Sbjct: 176 --RDGLFAYNLAVVVDDHFQGVTEIVRGADLIEPTVRQISLYQLFGWKVPDYIHLPLALN 233 Query: 244 STGQKLSKRD 253 G KLSK++ Sbjct: 234 PQGAKLSKQN 243 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: 445 Number of extensions: 27 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: 308 Length adjustment: 30 Effective length of query: 455 Effective length of database: 278 Effective search space: 126490 Effective search space used: 126490 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