Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate WP_020175249.1 A3OQ_RS0110020 glutamate--tRNA ligase
Query= SwissProt::Q8DLI5 (485 letters) >NCBI__GCF_000385335.1:WP_020175249.1 Length = 446 Score = 223 bits (567), Expect = 1e-62 Identities = 170/459 (37%), Positives = 230/459 (50%), Gaps = 36/459 (7%) Query: 1 MTVRVRLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEG 60 MT+ VR APSPTG +H+G ARTA+ N+L+ + G F+LR +DTD ERS+ EY +I Sbjct: 1 MTI-VRFAPSPTGRIHLGNARTALLNYLFTKAHNGLFLLRFDDTDLERSKEEYALDIEVD 59 Query: 61 LQWLGLTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQAPR 120 L WLG+ D QS R LY +A + L G Y CY T +EL+ R Q+AKGQ P Sbjct: 60 LAWLGVKPDL-VLRQSQRFALYHEAAERLRAAGRLYPCYETADELDRKRKRQQAKGQPPV 118 Query: 121 YDNRHRHLTPEEQAAFEAAGRTPVIRFKIEDDRQIEWQDLVRGRVSWQGADLGGDMVIAR 180 YD LTP+++AA EA GR P RF +E R + W DLVRG A L D V+ R Sbjct: 119 YDRAALALTPDDRAALEAQGRKPHWRFLLEH-RTVHWNDLVRGESHIDSASLS-DPVLLR 176 Query: 181 AAPRGEIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGATPPNFAHTPL 240 E G LY L VVDD+ IT VIRGEDH+ NT QI L+EALG T P FAH L Sbjct: 177 -----EDGSYLYTLPSVVDDLDQKITHVIRGEDHVTNTAVQIELFEALGGTAPVFAHHNL 231 Query: 241 ILNSTGQKLSKRDGVTSISDFRAMGYLAPALANYMTLLGWSPPEGVGELFTLDLAAKHFS 300 +++ +G+ LSKR G SI R + A+A L G S V + +L+ K Sbjct: 232 LVSESGEGLSKRSGALSIGGLRDQDIESLAVAALAVLTGTS--HAVHAVTSLEELGKDLE 289 Query: 301 FERINKAGARFDWDKLNWLNRQYIQQLEPEEFLAELIPLWQGAGYAFDEERDRPWLFDLA 360 I++ A+FD +L L+ + + L P E + + + GY + + WL Sbjct: 290 PSHISRTPAKFDPAELAGLSARTLHAL-PFETVRDRLAAHDILGY----KAEAFWL---- 340 Query: 361 QLLQPGLNTLREAIDQGAVF--FIPSVTFDSEAMAQLGQPQSATILAYLLEHLPAEPALT 418 ++ L+T + + + I V D + + + G+ LP EP Sbjct: 341 -AVRGNLSTFLDVVTWWRIIEGEIEPVREDLDYLEEAGRA------------LPEEPWDE 387 Query: 419 VAMGQQLIQQAAKAAGVKKGATMRTLRAALTGAVHGPDL 457 A + G K A LR ALTG GP+L Sbjct: 388 NAWA-AWTEVLKSRTGRKGRALFHPLRLALTGREQGPEL 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: 583 Number of extensions: 38 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: 446 Length adjustment: 33 Effective length of query: 452 Effective length of database: 413 Effective search space: 186676 Effective search space used: 186676 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