Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate 3609363 Dshi_2748 glutamyl-tRNA synthetase (RefSeq)
Query= SwissProt::Q8DLI5 (485 letters) >FitnessBrowser__Dino:3609363 Length = 440 Score = 223 bits (568), Expect = 1e-62 Identities = 162/462 (35%), Positives = 222/462 (48%), Gaps = 29/462 (6%) Query: 6 RLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEGLQWLG 65 R APSPTG LH+G RTA+FN++ AR GG FILRI+DTD ERS+PEY + I E L WLG Sbjct: 5 RFAPSPTGYLHVGNLRTALFNYMIARKAGGTFILRIDDTDPERSKPEYVDAIQEDLTWLG 64 Query: 66 LTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQAPRYDNRH 125 LTWD Y QS RLD Y +A L G Y + TP EL+ R +Q G+ P YD Sbjct: 65 LTWDRIEY-QSRRLDRYAEAADALRAAGRFYEAFETPTELDLKRKKQLNMGRPPVYDRAA 123 Query: 126 RHLTPEEQAAFEAAGRTPVIRFKIEDDRQIEWQDLVRGRVSWQGADLGGDMVIARAAPRG 185 L+ +E+AA A V RFK++ +R I W D + G +S A + ++I RG Sbjct: 124 LALSEDEKAALRAERGQGVWRFKLDHER-ITWTDGILGDISIDAASVSDPVLI-----RG 177 Query: 186 EIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGATPPNFAHTPLILNST 245 + G LY + VVDD MG+T V+RG DH+ NT QI + ALG P FAH L+ Sbjct: 178 D-GQVLYTIASVVDDTEMGVTHVVRGSDHVTNTATQIQIMAALGHGHPEFAHHSLLTGPQ 236 Query: 246 GQKLSKRDGVTSISDFRAMGYLAPALANYMTLLGWSPPEGVGELFTLDLAAKHFSFERIN 305 G+ LSKR G ++ D RA G AL + M LG S P V +L+ + F Sbjct: 237 GEALSKRLGTLALRDLRAEGIEPMALLSLMARLGSSQPVEVAG--SLEALIEGFDLSTFG 294 Query: 306 KAGARFDWDKLNWLNRQYIQQLEPEEFLAELIPLWQGAGYAFDEERDRPWLFDLAQLLQP 365 A +FD L L + + E E+ L A A + W ++ + Sbjct: 295 AAPTKFDRADLFPLTARLLHATPFAEVADEIAALGVPAAQA-----ELFW-----EVARA 344 Query: 366 GLNTLREAIDQGAVFFIPSVTFDSEAMAQLGQPQSATILAYLLEHLPAEPALTVAMGQQL 425 + T + +F + A L + +A LP P G Sbjct: 345 NITTRADLAGWWQLF--------RDGGAPLVAEEDRAFVADAFARLPEPPYGPETWGAWT 396 Query: 426 IQQAAKAAGVKKGATMRTLRAALTGAVHGPDLMAAWQILHQR 467 + A A+G K LR A+TG GP++ ++L ++ Sbjct: 397 AEVKA-ASGRKGKGLFMPLRKAVTGLERGPEMADVMRLLQKK 437 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: 561 Number of extensions: 24 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 485 Length of database: 440 Length adjustment: 33 Effective length of query: 452 Effective length of database: 407 Effective search space: 183964 Effective search space used: 183964 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