Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate Ga0059261_2339 Ga0059261_2339 glutamyl-tRNA synthetase, bacterial family
Query= SwissProt::Q8DLI5 (485 letters) >FitnessBrowser__Korea:Ga0059261_2339 Length = 441 Score = 242 bits (617), Expect = 2e-68 Identities = 182/464 (39%), Positives = 232/464 (50%), Gaps = 44/464 (9%) Query: 1 MTVRVRLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEG 60 MTV R APSPTG LH+G RTA+ NW++AR +GG+F+LRI+DTD ERSR E+ +I + Sbjct: 1 MTVVTRFAPSPTGRLHVGNIRTALHNWMWARKQGGRFLLRIDDTDGERSREEHVLSIRDD 60 Query: 61 LQWLGLTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQAPR 120 L WLGL D G QS R DLY + L G Y Y T +EL+ R +G P Sbjct: 61 LAWLGLVPD-GEARQSQRFDLYERRFAELAAAGRVYPAYETQQELDLKRKILLGRGLPPV 119 Query: 121 YDNRHRHLTPEEQAAFEAAGRTPVIRFKIEDDRQIEWQDLVRGRVSWQGADLGGDMVIAR 180 YD L ++A EA G P RF+++ IEW DL+RG + A + D V+ R Sbjct: 120 YDRAALALADADRARLEAEGVRPHWRFRLDHSAAIEWHDLIRGPQRFDPATM-SDPVVRR 178 Query: 181 AAPRGEIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGATPPNFAHTPL 240 A G LY L V+DDI MGIT V+RGEDH+ NT Q+ +++ALGATPP FAH L Sbjct: 179 AD-----GSWLYLLPSVIDDIDMGITHVVRGEDHVSNTAAQLQMFDALGATPPAFAHEAL 233 Query: 241 ILNSTGQKLSKRDGVTSISDFRAMGYLAPALANYMTLLGWSPP-EGVGELFTLDLAAKHF 299 + S G KLSKR G FR G A+ + LG S P E + L LA F Sbjct: 234 LTGSEG-KLSKRLGSLGADHFRNAGIEPQAIVALLARLGTSDPVEPQADPAPL-LAT--F 289 Query: 300 SFERINKAGARFDWDKLNWLNRQYIQQLEPEEFLAELIPLWQGAGYAFDEERDRPWLFDL 359 F R +A ARFD +L LN + + QL+ E + L AG+ Sbjct: 290 DFARFGRAPARFDEAELAQLNARILHQLDYETVASRLPAGMDEAGW-------------- 335 Query: 360 AQLLQPGLNTLREAIDQGAVFFIPSVTF----DSEAMAQLGQPQSATILAYLLEHLPAEP 415 ++P L+TL EA D V P DS +AQ Q + + H Sbjct: 336 -DAVRPNLSTLAEAADWWQVVEGPVDAVRDPGDSAFLAQAAQAAAGLDWSDDPWH----- 389 Query: 416 ALTVAMGQQLIQQAAKAAGVKKGATMRTLRAALTGAVHGPDLMA 459 ALT A+ A G K A LR ALTG GPD+ A Sbjct: 390 ALTNAL--------KDATGRKGKALFLPLRRALTGRDSGPDMAA 425 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: 573 Number of extensions: 31 Number of successful extensions: 5 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: 441 Length adjustment: 33 Effective length of query: 452 Effective length of database: 408 Effective search space: 184416 Effective search space used: 184416 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: 51 (24.3 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