Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate WP_011444626.1 SARO_RS04830 glutamate--tRNA ligase 1
Query= SwissProt::Q8DLI5 (485 letters) >NCBI__GCF_000013325.1:WP_011444626.1 Length = 442 Score = 261 bits (667), Expect = 3e-74 Identities = 192/470 (40%), Positives = 242/470 (51%), Gaps = 41/470 (8%) Query: 1 MTVRVRLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEG 60 M R APSPTG LH+G RTA+ NWL A+ GG+F+LRI+DTD ERSR EY E+I Sbjct: 1 MATVTRFAPSPTGKLHVGNVRTALHNWLLAKKTGGRFLLRIDDTDAERSREEYVESIRAD 60 Query: 61 LQWLGLTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQAPR 120 LQWLGL D G QS R +LY + Q L++ G Y Y T +EL+ R +G P Sbjct: 61 LQWLGLIPD-GEERQSLRTELYEREFQRLVEAGRIYRAYETAQELDLKRKILLGRGLPPI 119 Query: 121 YDNRHRHLTPEEQAAFEAAGRTPVIRFKIEDDRQIEWQDLVRGRVSWQGADLGGDMVIAR 180 YD LT + AA AAG P RF ++ D+ I W D +RG S+ + D VI R Sbjct: 120 YDRAALKLTEADHAAKAAAGERPHWRFLLDHDQPITWDDGIRGPQSFDPRQM-SDPVIRR 178 Query: 181 AAPRGEIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGATPPNFAHTPL 240 A G LY L +DDIAMGITDV+RGEDH+ NT QI ++ ALGA PP FAH L Sbjct: 179 AD-----GSWLYMLPSAIDDIAMGITDVLRGEDHVSNTATQIQMFTALGAEPPRFAHEAL 233 Query: 241 ILNSTGQKLSKRDGVTSISDFRAMGYLAPALANYMTLLGWSPPEGVGELFTLDLAAKHFS 300 + S G KLSKR G ++DFR G A+ + LG S P LD AA S Sbjct: 234 LTGSEG-KLSKRLGALGMADFREQGIEPEAIVALLARLGTSDPVDA----ALDAAALATS 288 Query: 301 FE--RINKAGARFDWDKLNWLNRQYIQQLEPEEFLAELIPLWQGAGYAFDEERDRPWLFD 358 F+ R +A ARFD L+ +N Q + +L P +A L+P QG G A W Sbjct: 289 FDLSRFGRAPARFDEADLHRVNAQIVHRL-PYARVAHLLP--QGMGEA-------AW--- 335 Query: 359 LAQLLQPGLNTLREAIDQGAVFFIP--SVTFDSEAMAQLGQPQSATILAYLLEHLPAEPA 416 + ++P L + EA D V P + TFD E A L Q+A A L A Sbjct: 336 --EAIRPNLAHIDEARDWWNVVTGPVTAPTFDDETRAFLA--QAAKTAASLDWSADPWRA 391 Query: 417 LTVAMGQQLIQQAAKAAGVKKGATMRTLRAALTGAVHGPDLMAAWQILHQ 466 LT + G K A LR ALTG HGP++ A ++ Q Sbjct: 392 LTATL--------KDGTGRKGKALFLPLRQALTGHDHGPEMAALLPLIAQ 433 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: 607 Number of extensions: 29 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: 442 Length adjustment: 33 Effective length of query: 452 Effective length of database: 409 Effective search space: 184868 Effective search space used: 184868 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 10 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