Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate WP_106716146.1 CU100_RS08350 glutamate--tRNA ligase
Query= metacyc::MONOMER-13959 (483 letters) >NCBI__GCF_003010935.1:WP_106716146.1 Length = 457 Score = 225 bits (573), Expect = 3e-63 Identities = 162/486 (33%), Positives = 246/486 (50%), Gaps = 44/486 (9%) Query: 5 VRVRYAPSPTGHLHIGNARTALFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQLNYLK 64 + VR+APSPTG++HIGN R ALFN+LFA G+FI+R +DTD R+ + + L Sbjct: 3 ITVRFAPSPTGYIHIGNTRIALFNWLFALKNNGQFILRFDDTDTVRSKTEYADATIADLD 62 Query: 65 WLGIDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEELEKEREEQIA 124 WLGI+ EY QS+R +Y E L G+ Y CY T EELE++R+ ++A Sbjct: 63 WLGIE-----PARIEY----QSKRIPVYDAAAERLKAAGVLYPCYETSEELERKRKLRLA 113 Query: 125 RGEMPRYSGKHRDLTQEEQEKFIAEGRKPSIRFRVPEGK---------VIAFNDIVKGEI 175 R P Y LT ++EK AEGR+P RF +P K + +ND+V+ Sbjct: 114 RRLPPIYGRDALKLTAADREKLEAEGRQPHWRFLLPNFKDDPFAIERTEVHWNDLVRDRE 173 Query: 176 SFESDGIGDFVIVKKDGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAFGWD 235 + + + D V+V++DGT Y F +DD M+++H++RG DHI+N+ QI I +A G Sbjct: 174 TVDLASLSDPVLVREDGTYLYTFTSVVDDIDMEISHIIRGNDHITNSGVQIAIIEALGAK 233 Query: 236 IPQFGHMTLIVNESRKKLSKRDESIIQFIEQYKELGYLPEALFNFIGLLGWSPVGEEELF 295 +P GH+ L+ S + +SKR ++ I + GY P A+ + L+G S + Sbjct: 234 VPDLGHINLLTTASGEGISKRTGAL--SIGSLRRDGYEPMAVASLAVLIGTSE-NVTAVP 290 Query: 296 TKEQFIEIFDVNRLSKSPALFDMHKLKWVNNQYVKKLDLDQVVELTLPHLQKAGKVGTEL 355 +IFD SKS + FD +L +N + + Q + + +G E Sbjct: 291 DMATLADIFDPAATSKSASKFDPAELDALNRALIHAMPYAQAKD-------RLAALGIEG 343 Query: 356 SAEEQEW--VRKLISLYHEQLSYGAEIVELTDLFFTDEIEYNQEAKAVLEEEQVPEVLST 413 E+ W VR +S + + I D TDE L +E V + Sbjct: 344 ERAEEFWLAVRGNLSRISDAAGWWKII---KDGPATDE---------QLADEDRDFVRTA 391 Query: 414 FAAKLEELEEFTPDNIKASIKAVQKETGHKGKKLFMPIRVAVTGQTHGPELPQSIELIGK 473 F L E ++ + K AV+ ++G KGK LFMP+R+A+TG + GPEL + L+G+ Sbjct: 392 F--DLLPREPWSRETWKLWTDAVKIQSGRKGKPLFMPLRIALTGLSSGPELADLLPLLGR 449 Query: 474 ETAIQR 479 E + R Sbjct: 450 EGTLAR 455 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: 466 Number of extensions: 25 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: 483 Length of database: 457 Length adjustment: 33 Effective length of query: 450 Effective length of database: 424 Effective search space: 190800 Effective search space used: 190800 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: 51 (24.3 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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