Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate WP_011383647.1 AMB_RS06270 glutamate--tRNA ligase 1
Query= SwissProt::Q8DLI5 (485 letters) >NCBI__GCF_000009985.1:WP_011383647.1 Length = 444 Score = 253 bits (645), Expect = 1e-71 Identities = 176/453 (38%), Positives = 232/453 (51%), Gaps = 35/453 (7%) Query: 5 VRLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEGLQWL 64 VR APSPTG LH+G AR A+ N L+A+ GG FILR++DTD ERSRPE+ E IL+ L+WL Sbjct: 6 VRFAPSPTGLLHVGNARVALLNRLFAKAHGGSFILRLDDTDLERSRPEFAEAILDDLRWL 65 Query: 65 GLTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQAPRYDNR 124 GL WD QS RLD Y A + L G Y CY TP+ELE R Q +G P YD Sbjct: 66 GLDWDRLER-QSARLDAYAAAAERLKVSGRVYACYETPDELELRRKVQLGRGLPPVYDRA 124 Query: 125 HRHLTPEEQAAFEAAGRTPVIRFKIEDDRQIEWQDLVRGRVSWQGADLGGDMVIARAAPR 184 L P+E A EA GR P RFK+E + + W D VRG + G +L ++I R Sbjct: 125 ALKLAPDEIARLEAEGRRPHWRFKLELE-DVRWDDCVRGPSHYHGGNLSDPVLI-----R 178 Query: 185 GEIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGATPPNFAHTPLILNS 244 G+ G LY L VVDDI G+T +IRGEDH+ NT QI L++ALGA PP FAH PL+ + Sbjct: 179 GD-GSFLYTLPSVVDDIEFGVTHIIRGEDHVTNTAPQIQLFQALGAVPPAFAHLPLLTGA 237 Query: 245 TGQKLSKRDGVTSISDFRAMGYLAPALANYMTLLGWSPPEGVGELFTLDLAAKHFSFERI 304 TG+ LSKR G S+ D RA G AL + + LG S + + TL F++++ Sbjct: 238 TGEGLSKRLGSGSLKDLRATGIHPMALNSLLAKLGSS--DAIDIRHTLAELEAEFAWDKF 295 Query: 305 NKAGARFDWDKLNWLNRQYIQQLEPEEFLAELIPLWQGAGYAFDEERDRPWLFDLAQLLQ 364 + +FD +L L+ + + E L D + WL ++ Sbjct: 296 GRGTPKFDSAELERLDARLMHTASFAEVRDRL---------GIDGADEEFWL-----AVR 341 Query: 365 PGLNTLREAIDQGAVFFIPSVTFDSEAMAQLGQPQSATILAYLLEHLPAEPALTVAMGQQ 424 P LN L EA A+ D + + G+ A L + A A Sbjct: 342 PNLNHLAEAEAWWAI-----CRQDLTPVIEDGEFTRAAAA------LLPDGAWDHATWGA 390 Query: 425 LIQQAAKAAGVKKGATMRTLRAALTGAVHGPDL 457 + +A G K A LR ALTG +GP+L Sbjct: 391 WTETVKQATGRKGKALFHPLRLALTGRENGPEL 423 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: 566 Number of extensions: 30 Number of successful extensions: 5 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: 444 Length adjustment: 33 Effective length of query: 452 Effective length of database: 411 Effective search space: 185772 Effective search space used: 185772 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