Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate WP_041466348.1 CPAR_RS08795 glutamate--tRNA ligase
Query= metacyc::MONOMER-13959 (483 letters) >NCBI__GCF_000020505.1:WP_041466348.1 Length = 503 Score = 388 bits (996), Expect = e-112 Identities = 197/491 (40%), Positives = 308/491 (62%), Gaps = 14/491 (2%) Query: 2 GNEVRVRYAPSPTGHLHIGNARTALFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQLN 61 G VR R+APSPTG+LH+G RTAL+NYLFA+ G+F+IR+EDTD+ R +E E++ ++ Sbjct: 3 GQRVRTRFAPSPTGYLHVGGLRTALYNYLFAKRMNGEFVIRIEDTDQSRKVEDAEKNLIS 62 Query: 62 YLKWLGIDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEELEKEREE 121 L+W GI DES GG YGPY QS+R DIYK Y ++LL+ AY C+ T EELE+ R+ Sbjct: 63 TLEWAGIIADESPMHGGNYGPYVQSQRLDIYKKYCQQLLDDKNAYYCFSTSEELEENRQL 122 Query: 122 QIARGEMPRYSGK------HRDLTQEEQEKFIAEGRKPSIRFRVPEGKVIAFNDIVKGEI 175 Q+ +G P+Y+ K + Q E +K + EG +R +VP+ + F D+++G I Sbjct: 123 QLKQGLQPKYNRKWLPEDMGGSMPQSEIKKKLDEGVPYVVRMKVPDYVSVWFEDVIRGPI 182 Query: 176 SFESDGIGDFVIVKKDGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAFGWD 235 F+S I D V++K DG PTY+FA IDD+LM+ TH++RGE+ + + PK +++Y+ FGW+ Sbjct: 183 EFDSATIDDQVLMKSDGFPTYHFASVIDDHLMEFTHIIRGEEWLPSMPKHLLLYEFFGWE 242 Query: 236 IPQFGHMTLIVNESRKKLSKRDESIIQFIEQYKELGYLPEALFNFIGLLGWS--PVGEEE 293 P+F H+ L++N R KLSKR + +E Y GY EA+ NF+ LLGW+ E+E Sbjct: 243 PPKFAHLPLLLNPDRSKLSKRQGDVA--VEDYVRKGYSSEAIVNFVALLGWNEGEGSEQE 300 Query: 294 LFTKEQFIEIFDVNRLSKSPALFDMHKLKWVNNQYVKKLDLDQVVELTLPHLQKA-GKVG 352 +F+ ++ IE F + R+ K+ A+F++ KL W+ QY+K +D +VE P L +A + Sbjct: 301 VFSMDELIEKFSLERVGKAGAVFNVDKLSWLEKQYIKTRPVDVIVEGIKPVLNEALAQRS 360 Query: 353 TELSAE---EQEWVRKLISLYHEQLSYGAEIVELTDLFFTDEIEYNQEAKAVLEEEQVPE 409 E+S E +++ K++ L E++++ E V + FF + Y ++A A +PE Sbjct: 361 PEMSVEWITSDDYLAKVVDLMRERVNFEHEFVTFSSYFFFEPESYEEDAVAKRWRPDMPE 420 Query: 410 VLSTFAAKLEELEEFTPDNIKASIKAVQKETGHKGKKLFMPIRVAVTGQTHGPELPQSIE 469 +L F+ LE ++FT +NI+A +KA G K + P+R+ V+G + GP L +E Sbjct: 421 LLGEFSKLLEANDDFTAENIEAELKAFVAPKGLKPAVIIHPLRLVVSGVSFGPSLYHMLE 480 Query: 470 LIGKETAIQRL 480 ++GKET ++R+ Sbjct: 481 VLGKETVLRRI 491 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: 706 Number of extensions: 52 Number of successful extensions: 6 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: 503 Length adjustment: 34 Effective length of query: 449 Effective length of database: 469 Effective search space: 210581 Effective search space used: 210581 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