Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate WP_081662653.1 G579_RS0107000 glutamate--tRNA ligase
Query= metacyc::MONOMER-13959 (483 letters) >NCBI__GCF_000423825.1:WP_081662653.1 Length = 519 Score = 333 bits (853), Expect = 1e-95 Identities = 195/476 (40%), Positives = 274/476 (57%), Gaps = 18/476 (3%) Query: 8 RYAPSPTGHLHIGNARTALFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQLNYLKWLG 67 R+APSPTG +H+GN RTALF++L A G+FI+R+EDTD +R+ + + L+WLG Sbjct: 57 RFAPSPTGLIHLGNVRTALFSWLAAHRGQGRFILRIEDTDAERSRPEYVAALMADLRWLG 116 Query: 68 IDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEELEKEREEQIARGE 127 + W+E + GG +GPY QSER +Y YY EL + AY C+C+ EELE R+ Q+++G Sbjct: 117 LHWEEGPEAGGPHGPYHQSERGAVYARYYHELEAQAFAYPCFCSPEELELSRKLQLSQGR 176 Query: 128 MPRYSGKHRDLTQEEQEKFIAEGRKPSIRFRVPEGKVIAFNDIVKGEISFESDGIGDFVI 187 PRY+G R L+ E+ + G +P++RFRVPEG+ + F D+V+G F+SD IGDF+I Sbjct: 177 APRYAGACRRLSAAERAARLEAGHQPTLRFRVPEGQTVEFTDVVRGPQRFQSDDIGDFII 236 Query: 188 VKKDGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAFGWDIPQFGHMTLIVN 247 + DGTP + F AIDD LM+++ VLRGEDH++NTP+QI++ QA G +P +GHM LIV Sbjct: 237 RRADGTPAFFFCNAIDDALMEVSLVLRGEDHLTNTPRQILLLQALGLPVPGYGHMALIVG 296 Query: 248 ESRKKLSKRDESIIQFIEQYKELGYLPEALFNFIGLLGWSPVGEEELFTKEQFIEIFDVN 307 + + LSKR+ S + + + +E GY PEA+ N++ LG S + + L FD Sbjct: 297 DDGQPLSKRNGS--RNVAELREAGYFPEAVDNYLARLGHS-LDSDALLDLAGLAARFDAA 353 Query: 308 RLSKSPALFDMHKLKWVNNQYVKKLDLDQVVELTLPHLQKAGKVGTELSAEEQEWVRKLI 367 L +SPA FD +L Q + LTLP + + L+ E R+ Sbjct: 354 HLGRSPARFDPQQLDHWQRQAL----------LTLPWERIWAWLADYLATPVPESRREAF 403 Query: 368 SLYHEQLSYGAEIVELTDLFFTDEIEYNQEAKAVLEEEQVPEVLSTFAAKLEELEEFTPD 427 G E EL + A AV+ PE L + A L L+ D Sbjct: 404 VTAVRANLNGPEEAELWAAACFGDAPLEPGAHAVI--AGAPEAL--WPAALAALDTHGTD 459 Query: 428 NIKASIKAVQKETGHKGKKLFMPIRVAVTGQTHGPELPQSIELIGKETAIQRLKNI 483 KA + G KGK+LFMP+R A+TGQTHGPEL Q + LIG E A RL+ I Sbjct: 460 -FKALAAQAGQAAGLKGKQLFMPLRAALTGQTHGPELAQLLPLIGPERARARLQRI 514 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: 587 Number of extensions: 15 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: 519 Length adjustment: 34 Effective length of query: 449 Effective length of database: 485 Effective search space: 217765 Effective search space used: 217765 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: 52 (24.6 bits)
This GapMind analysis is from Apr 10 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