Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate WP_012283802.1 HM1_RS12680 tRNA glutamyl-Q(34) synthetase GluQRS
Query= metacyc::MONOMER-13959 (483 letters) >NCBI__GCF_000019165.1:WP_012283802.1 Length = 338 Score = 209 bits (531), Expect = 2e-58 Identities = 120/308 (38%), Positives = 169/308 (54%), Gaps = 6/308 (1%) Query: 8 RYAPSPTGHLHIGNARTALFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQLNYLKWLG 67 RYAPSPTG LH+GNARTAL +L R GG+FI+R+ED D R++ + L L+WLG Sbjct: 16 RYAPSPTGQLHLGNARTALLAWLQIRRLGGRFILRLEDLDPARSVAAYARQILADLRWLG 75 Query: 68 IDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEEL-EKEREEQIARG 126 +DWDE DVGG GPY QS R Y + G + C C+ ++L E R Sbjct: 76 LDWDEGPDVGGPCGPYEQSRRQAFYDAAVDLFRRSGRIFPCACSRKDLAELARAPHGQNE 135 Query: 127 EMPRYSGKHRDLTQEEQEKFIAEGRKPSIRFRVPEGKVIAFNDIVKGEISFE-SDGIGDF 185 E P Y G R+LT E + + + + RF+VPEG ++F D V G IS +GDF Sbjct: 136 EGPPYPGICRNLTPAAWEAKLRQKGQCAYRFQVPEGS-LSFVDAVAGPISQNVRQAVGDF 194 Query: 186 VIVKKDGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAFGWDIPQFGHMTLI 245 V+ + DG Y AV +DD LM +THVLRG+D +++TP+QI++Y A +P F H+ L+ Sbjct: 195 VVRRADGVTAYQLAVVVDDALMGVTHVLRGDDLLASTPRQILLYHALDMPVPHFCHVPLV 254 Query: 246 VNESRKKLSKRDESIIQFIEQYKELGYLPEALFNFIGLLGWSPVGEEELFTKEQFIEIFD 305 + +LSKR I +E G PE + F+ + E E ++ I +F Sbjct: 255 LGPDGARLSKRHGGTA--ISALQEQGIAPEKVIGFLAYTA-GLLPEPEPVRPQELIPLFA 311 Query: 306 VNRLSKSP 313 +L + P Sbjct: 312 EAKLPRHP 319 Lambda K H 0.316 0.137 0.394 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: 414 Number of extensions: 15 Number of successful extensions: 3 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: 483 Length of database: 338 Length adjustment: 31 Effective length of query: 452 Effective length of database: 307 Effective search space: 138764 Effective search space used: 138764 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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