Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate GFF2602 PGA1_c26430 glutamyl-tRNA synthetase GltX
Query= SwissProt::Q8DLI5 (485 letters) >FitnessBrowser__Phaeo:GFF2602 Length = 441 Score = 221 bits (564), Expect = 3e-62 Identities = 166/467 (35%), Positives = 230/467 (49%), Gaps = 34/467 (7%) Query: 6 RLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEGLQWLG 65 R APSPTG +H+G RTA+ N+L AR GG FILRI+DTD ERS+ EY + I + L+WLG Sbjct: 5 RFAPSPTGYIHVGNLRTALMNYLIARKAGGSFILRIDDTDPERSKEEYVDAIKQDLEWLG 64 Query: 66 LTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQAPRYDNRH 125 L WD QS+RL+ Y A L + G Y + TP EL+ R +Q G+ P YD Sbjct: 65 LGWDRVER-QSERLERYVAAADKLREIGRFYEAFETPVELDLKRKKQLNMGKPPVYDRAA 123 Query: 126 RHLTPEEQAAFEAAGRTPVIRFKIEDDRQIEWQDLVRGRVSWQGADLGGDMVIARAAPRG 185 L+ +E+AA A V RFK+ D ++IEW D + G +S A + ++I RG Sbjct: 124 LALSDDEKAALRAERGDGVWRFKL-DQQRIEWADGILGDISIDAASVSDPVLI-----RG 177 Query: 186 EIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGATPPNFAHTPLILNST 245 + G LY L VVDD MG+T V+RG DH+ NT QI + EALG T P+FAH L+ Sbjct: 178 D-GQFLYTLASVVDDTEMGVTHVVRGSDHVTNTATQIQIIEALGGTVPSFAHHSLLTGPQ 236 Query: 246 GQKLSKRDGVTSISDFRAMGYLAPALANYMTLLGWSPPEGV-GELFTLDLAAKHFSFERI 304 G+ LSKR G ++ D R G AL + M LG S P + E+ L F R Sbjct: 237 GEALSKRLGTLALRDLREAGVQPMALLSMMARLGSSDPVEIRSEMAEL---IDGFDINRF 293 Query: 305 NKAGARFDWDKLNWLNRQYIQQLEPEEFLAELIPLWQGAGYAFDEERDRPWLFDLAQLLQ 364 A +FD + L L +Y+Q L + + L A E++ W + + Sbjct: 294 GAAPTKFDVEDLYPLTARYLQSLSLADVQTHVDALGVPA-----EKQAAFW-----DVAK 343 Query: 365 PGLNTLREAIDQGAVFFIPSVTFDSEAMAQLGQPQSATILAYLLEHLPAEPALTVAMGQQ 424 ++TL+ D G + + L + +A + LP P + G+ Sbjct: 344 ENISTLK---DLGGWW-----ELCRDGAEPLIAEEDTAFIAEAMALLPEGPYDGESWGKW 395 Query: 425 LIQQAAKAAGVKKGATMRTLRAALTGAVHGPD---LMAAWQILHQRG 468 K KG M LR A+TG GPD L+A + + RG Sbjct: 396 TAAVKEKTGRKGKGLFM-PLRKAVTGMERGPDMSALLALMETVRARG 441 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: 508 Number of extensions: 20 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: 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 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