Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate CA265_RS21610 CA265_RS21610 glutamate--tRNA ligase
Query= metacyc::MONOMER-13959 (483 letters) >FitnessBrowser__Pedo557:CA265_RS21610 Length = 502 Score = 311 bits (797), Expect = 3e-89 Identities = 174/493 (35%), Positives = 277/493 (56%), Gaps = 29/493 (5%) Query: 1 MGNEVRVRYAPSPTGHLHIGNARTALFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQL 60 M +VRVR+APSPTG LH+G RTALFNYLFA+ G F++RVEDTD+ R +EG EQ + Sbjct: 1 MDKKVRVRFAPSPTGGLHLGGVRTALFNYLFAKRNNGTFVLRVEDTDQNRFVEGAEQYIV 60 Query: 61 NYLKWLGIDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEELEKERE 120 N L W GI DES D G YGPYRQSER Y+ + E+L+ G AY + T E+L+ +R+ Sbjct: 61 NCLDWCGITPDESPDNPGAYGPYRQSERKPSYRKFAEQLISDGYAYYAFDTPEDLDAKRK 120 Query: 121 E--QIARGEMPRYSGKHR-DLTQEEQEKFIAEGRKPSIRFRVPEGKVIAFNDIVKGEISF 177 E G+ R ++ LT E E+ +A IR +VP +++ FND+++G++SF Sbjct: 121 EIPNFQYGQATRMQMRNSLTLTISEVEELLAAKTPHVIRIKVPADEIVHFNDLIRGDVSF 180 Query: 178 ESDGIGDFVIVKKDGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAFGW--D 235 E+ + D V++K DG PTY+ AV +DD M++TH RGE+ + + P I++++ GW D Sbjct: 181 ETSLVDDKVLLKADGMPTYHLAVVVDDKAMEITHAFRGEEWLPSAPVHILLWKYLGWEAD 240 Query: 236 IPQFGHMTLIVN-ESRKKLSKRDESIIQF---------------IEQYKELGYLPEALFN 279 +P + H+ LI+ + KLSKRD + F + +KE+G++PEA N Sbjct: 241 MPAWAHLPLILKPDGHGKLSKRDGDRLGFPVYAMNWTDPKTGDVTKGFKEMGFMPEAFIN 300 Query: 280 FIGLLGWSPVGEEELFTKEQFIEIFDVNRLSKSPALFDMHKLKWVNNQYVKKLDLDQVVE 339 + LLGW+ ++ELF+ ++ E F + R+SK+ A FD K KW N++++K +++ Sbjct: 301 MLALLGWNDGTDQELFSLKELEEKFSIERISKAGAKFDFEKAKWYNHEWIKSQGAERLAP 360 Query: 340 LTLPHLQKAGKVGTELSAEEQEWVRKLISLYHEQLSYGAEIVELTDLFFTDEIEYNQEAK 399 L+KAG + + ++ +I L ++ + + V + FF Y+ + Sbjct: 361 TVKEELEKAG-----IEVNDHAFLNTVIDLIKDRCTLLPDFVAQSSYFFASPEVYDVNS- 414 Query: 400 AVLEEEQVPEVLSTFAAKLEELEEFTPDNIKASIKAVQKETGHKGKKLFMPIRVAVTGQT 459 ++ + E F A + L + +A+ KA+ +E G K +L +P R+ + G Sbjct: 415 --VKPKWTVEKADFFNAFADGLTLTDAVSAEAAFKALAEEKGFKPGELMLPFRIMLVGGK 472 Query: 460 HGPELPQSIELIG 472 GP + L+G Sbjct: 473 FGPGVFDIAVLLG 485 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: 687 Number of extensions: 32 Number of successful extensions: 4 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: 502 Length adjustment: 34 Effective length of query: 449 Effective length of database: 468 Effective search space: 210132 Effective search space used: 210132 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 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