Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate WP_078429462.1 BK574_RS17620 glutamate--tRNA ligase
Query= metacyc::MONOMER-13959 (483 letters) >NCBI__GCF_002019605.1:WP_078429462.1 Length = 487 Score = 668 bits (1723), Expect = 0.0 Identities = 306/480 (63%), Positives = 398/480 (82%) Query: 1 MGNEVRVRYAPSPTGHLHIGNARTALFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQL 60 M NEVRVR+APSPTGHLHIG AR+ALFNYL+ARNQGGKFI+R+EDTD+ RN+E ++ L Sbjct: 1 MSNEVRVRFAPSPTGHLHIGGARSALFNYLYARNQGGKFILRIEDTDQARNVENAKEKLL 60 Query: 61 NYLKWLGIDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEELEKERE 120 LKWL IDWDESVD+GGEYGPY ER DIY+ Y ++L+++ AY CY TEEELE ERE Sbjct: 61 ESLKWLQIDWDESVDIGGEYGPYSCMERLDIYEKYLQQLIDEKKAYYCYMTEEELEAERE 120 Query: 121 EQIARGEMPRYSGKHRDLTQEEQEKFIAEGRKPSIRFRVPEGKVIAFNDIVKGEISFESD 180 QIARGE P+YSG+ RDLT+E+++ + +G KP +RFRV E K +D V+G++SFESD Sbjct: 121 AQIARGENPKYSGRDRDLTEEQRKVYEEKGLKPVVRFRVQEDKTYIIDDAVRGQVSFESD 180 Query: 181 GIGDFVIVKKDGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAFGWDIPQFG 240 GIGDFVI +KDG P YNFAV +DD+LMK+TH++RGE+H+SNTP+Q M+Y+AFGW++P+F Sbjct: 181 GIGDFVIARKDGIPMYNFAVVVDDHLMKITHIIRGEEHLSNTPRQAMLYEAFGWEVPKFA 240 Query: 241 HMTLIVNESRKKLSKRDESIIQFIEQYKELGYLPEALFNFIGLLGWSPVGEEELFTKEQF 300 H +LI+N R+K+SKRDESIIQF+EQY++LGYLPEA+ NF+ LLGWSPVGEEE+FTK + Sbjct: 241 HASLILNPDRQKMSKRDESIIQFVEQYRDLGYLPEAIVNFLALLGWSPVGEEEVFTKAEL 300 Query: 301 IEIFDVNRLSKSPALFDMHKLKWVNNQYVKKLDLDQVVELTLPHLQKAGKVGTELSAEEQ 360 IE FD++R++K+PA+FD KL W+NNQY+K+ DLD+VVEL LPHL +AG++ +S E++ Sbjct: 301 IEQFDLDRVAKAPAVFDTDKLAWMNNQYMKEADLDRVVELALPHLVRAGRLSESMSTEQK 360 Query: 361 EWVRKLISLYHEQLSYGAEIVELTDLFFTDEIEYNQEAKAVLEEEQVPEVLSTFAAKLEE 420 +W ++LI LY EQ+SYGAEIVELT+LFF EI+YN+EAK +L E+QVPEVL+ F ++LE+ Sbjct: 361 DWAKRLIGLYQEQMSYGAEIVELTELFFKLEIDYNEEAKQILTEDQVPEVLNQFMSELEQ 420 Query: 421 LEEFTPDNIKASIKAVQKETGHKGKKLFMPIRVAVTGQTHGPELPQSIELIGKETAIQRL 480 +E FT +NI ++KA QK TG KGKKLFMPIRVA TGQTHG +LP ++EL+GK+ QRL Sbjct: 421 IETFTAENINKAMKATQKATGQKGKKLFMPIRVATTGQTHGRDLPDTLELLGKDLVNQRL 480 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: 784 Number of extensions: 19 Number of successful extensions: 1 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: 487 Length adjustment: 34 Effective length of query: 449 Effective length of database: 453 Effective search space: 203397 Effective search space used: 203397 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