Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate WP_011841679.1 RSPH17029_RS12390 glutamate--tRNA ligase
Query= SwissProt::Q8DLI5 (485 letters) >NCBI__GCF_000015985.1:WP_011841679.1 Length = 441 Score = 240 bits (612), Expect = 8e-68 Identities = 172/467 (36%), Positives = 229/467 (49%), Gaps = 32/467 (6%) Query: 1 MTVRVRLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEG 60 MT R APSPTG +H+G RTA+ NW AR GG FILR++DTDRERS+ EY++ I+E Sbjct: 1 MTTVTRFAPSPTGYIHVGNLRTALMNWAIARKSGGTFILRLDDTDRERSKQEYSDGIMED 60 Query: 61 LQWLGLTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQAPR 120 L+WLGLTWD QSDRLD Y +A L G Y C+ +P EL+ R + G+ P Sbjct: 61 LEWLGLTWDRLER-QSDRLDRYAEAADELRRAGRFYECFESPTELDLKRKKLLNMGKPPV 119 Query: 121 YDNRHRHLTPEEQAAFEAAGRTPVIRFKIEDDRQIEWQDLVRGRVSWQGADLGGDMVIAR 180 YD L+ EE+A A R RF ++ +R IEW D + G +S A + D V+ R Sbjct: 120 YDRAALKLSDEERARLRAE-RGGYWRFLLDQER-IEWTDGILGPISIDAASV-SDPVLIR 176 Query: 181 AAPRGEIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGATPPNFAHTPL 240 A G LY VDDI MG+T ++RG DH+ NT QI + +ALG TPP+FAH L Sbjct: 177 AD-----GQVLYTFASSVDDIDMGVTFIVRGGDHVTNTATQIQIMQALGGTPPSFAHHSL 231 Query: 241 ILNSTGQKLSKRDGVTSISDFRAMGYLAPALANYMTLLGWSPPEGVGELF-TLDLAAKHF 299 + + G+ LSKR G S+ D RA G AL + M LG S P ELF T + F Sbjct: 232 LTGAQGEALSKRLGTLSLRDLRARGVEPMALLSLMARLGSSQPV---ELFRTHEELLAGF 288 Query: 300 SFERINKAGARFDWDKLNWLNRQYIQQLEPEEFLAELIPLWQGAGYAFDEERDRPWLFDL 359 A +FD + L L R Y+Q L E + L D+ + W Sbjct: 289 DVSTFGAAPTKFDAEDLFPLTRHYVQGLPFEAVRGRIAALG-----VPDDLAEPFW---- 339 Query: 360 AQLLQPGLNTLREAIDQGAVFFIPSVTFDSEAMAQLGQPQSATILAYLLEHLPAEPALTV 419 ++ + + L D G + T SE P+ + + LP P Sbjct: 340 -RVAKDNIGVLE---DLGGWW-----TLFSEGAEPQIDPEDEDFIRQAMTLLPPPPYGPE 390 Query: 420 AMGQQLIQQAAKAAGVKKGATMRTLRAALTGAVHGPDLMAAWQILHQ 466 + Q +A G K LR ALTG HGPD+ +L + Sbjct: 391 SWA-QFTAAVKEATGRKGKGLFMPLRKALTGQAHGPDMSEVMPLLQK 436 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: 574 Number of extensions: 29 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: 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 16 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