Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate BWI76_RS05010 BWI76_RS05010 tRNA glutamyl-Q synthetase
Query= metacyc::MONOMER-13959 (483 letters) >FitnessBrowser__Koxy:BWI76_RS05010 Length = 293 Score = 133 bits (335), Expect = 7e-36 Identities = 87/253 (34%), Positives = 128/253 (50%), Gaps = 27/253 (10%) Query: 8 RYAPSPTGHLHIGNARTALFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQLNYLKWLG 67 R+APSP+G LH G+ AL +YL AR Q G + +R+ED D R + G + L L+ G Sbjct: 9 RFAPSPSGELHFGSLIAALGSYLQARAQNGIWRVRIEDIDPPREVPGAADTILRQLERYG 68 Query: 68 IDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEELEKEREEQIARGE 127 + WD V QS+R++ Y+ + L E+ L Y C CT + G Sbjct: 69 LHWDGEV--------LWQSKRHEAYREHLAWLREQDLCYYCTCTRARIH---------GI 111 Query: 128 MPRYSGKHRDLTQEEQEKFIAEGRKPSIRFRVPEGKVIAFNDIVKGEI-SFESDGIGDFV 186 Y G RDL + AE +R P V+ F D ++G I + E DF+ Sbjct: 112 GGIYDGHCRDL------RLGAENAALRLRQTRP---VLEFYDRLRGTIVADEPLAREDFI 162 Query: 187 IVKKDGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAFGWDIPQFGHMTLIV 246 I ++DG YN AV +DD+ ++ ++RG D I T +QI +YQ FGW P + H+ L + Sbjct: 163 IHRRDGLFAYNLAVVVDDHFQGVSEIVRGADLIEPTVRQISLYQHFGWQAPDYIHLPLAL 222 Query: 247 NESRKKLSKRDES 259 N KLSK++ + Sbjct: 223 NAQGNKLSKQNHA 235 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: 307 Number of extensions: 9 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: 293 Length adjustment: 30 Effective length of query: 453 Effective length of database: 263 Effective search space: 119139 Effective search space used: 119139 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