Align glutamate-tRNAGln ligase (EC 6.1.1.24) (characterized)
to candidate WP_013430673.1 CALKRO_RS08745 glutamate--tRNA ligase
Query= BRENDA::Q9X2I8 (487 letters) >NCBI__GCF_000166775.1:WP_013430673.1 Length = 480 Score = 433 bits (1114), Expect = e-126 Identities = 219/478 (45%), Positives = 311/478 (65%), Gaps = 20/478 (4%) Query: 24 LVRVRFAPSPTGHLHVGGARTALFNWMFARKEGGKFILRIEDTDTERSSREYEQQILESL 83 +VRVRFAPSPTG LH+GGARTALFN++FA+K GKFILRIEDTD ERS E+ + I+ SL Sbjct: 1 MVRVRFAPSPTGQLHIGGARTALFNYLFAKKHNGKFILRIEDTDLERSREEWAKGIMRSL 60 Query: 84 RWCGLDWDEGPDIGGDFGPYRQSERLEIYREYAEKLVEDKRAYYVVYDKE--DPSKELFT 141 RW G++WDEGPD+GGDFGPY QS+R EIY EY +KL+E+ +AYY +E + +E+ Sbjct: 61 RWLGIEWDEGPDVGGDFGPYFQSQRKEIYLEYIKKLLEEGKAYYCFCTQEEIEREREIAR 120 Query: 142 TYEYPHEYKEK---------------GHPVTIKFKV-LPGKTSFEDLLKGYMEFDNSTLE 185 + P++Y +K G ++ K + G T D+++G +EF N L+ Sbjct: 121 QQKIPYKYSKKCRNISLEEAKKRIKNGEKAVVRIKAPVEGTTVVHDIIRGDVEFSNDQLD 180 Query: 186 DFIIMKSNGFPTYNFAVVVDDHLMRISHVFRGEDHLSNTPKQLMIYEAFGWEAPVFMHIP 245 DFII+KS+G PTYNF V+DD+LM+ISHV R E+HLSNTPKQL+IYEA + P F H+P Sbjct: 181 DFIILKSDGNPTYNFVCVIDDYLMKISHVIRAEEHLSNTPKQLIIYEALNIQPPQFAHVP 240 Query: 246 LILGSDRTPLSKRHGATSVEHFRREGILSRALMNYLALLGWRVEGDE-IFTIEEKLQSFD 304 +IL DR+ LSKRHGATSVE F G L A++NYL LLGW D I +++E +Q F+ Sbjct: 241 MILAPDRSKLSKRHGATSVEEFFENGYLKEAIVNYLLLLGWSPGEDRTIISLDEAIQKFE 300 Query: 305 PKDISNKGVIFDYQKLEWVNGKHMRRIDLEDLKREFIEWAKYAGKEIPSVDERYFSETLR 364 +++S I+D KL W+NG +++ ID++DL + G +I S D+ Y L+ Sbjct: 301 LENVSKNAAIYDINKLTWINGYYLKEIDIDDLYERMKYFYSKNGIDISSFDKEYVKSVLK 360 Query: 365 ICREKVNTLSQLYDIMYPFMNDDYEYEKDYVEKFLKREEAERVLEEAKKAFKDLNSWNME 424 + REKV TL+++ F + +YEYE+ VEK+ + + L+ K++ ++ E Sbjct: 361 LVREKVKTLAEVVSASSYFFDSNYEYEQKGVEKYFTADNL-KYLQLLLNDLKNVQPFSAE 419 Query: 425 EIEKTLRDLSEKGLASKKVVFQLIRGAVTGKLVTPGLFETIEVLGKERTLKRLERTLQ 482 EIEK +R +E+ + IR ++G+ VTPGLFE +EVLGK+ + R+E+TL+ Sbjct: 420 EIEKLVRSKAEEFNTKAANLIHTIRMCISGRTVTPGLFEMMEVLGKDEVINRIEKTLK 477 Lambda K H 0.320 0.139 0.416 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: 708 Number of extensions: 36 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: 487 Length of database: 480 Length adjustment: 34 Effective length of query: 453 Effective length of database: 446 Effective search space: 202038 Effective search space used: 202038 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 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