Align glutamate-tRNAGln ligase (EC 6.1.1.24) (characterized)
to candidate WP_012101848.1 CKL_RS07170 glutamate--tRNA ligase
Query= BRENDA::Q9X2I8 (487 letters) >NCBI__GCF_000016505.1:WP_012101848.1 Length = 487 Score = 332 bits (850), Expect = 2e-95 Identities = 196/484 (40%), Positives = 290/484 (59%), Gaps = 29/484 (5%) Query: 25 VRVRFAPSPTGHLHVGGARTALFNWMFARKEGGKFILRIEDTDTERSSREYEQQILESLR 84 VR RFAPSPTG++HVG RTAL+ ++ A+ +GG FILRIEDTD ER I +L Sbjct: 4 VRTRFAPSPTGYMHVGNLRTALYTYLIAKHDGGDFILRIEDTDQERFVEGALDIIYHTLE 63 Query: 85 WCGLDWDEGPDIGGDFGPYRQSERLEIYREYAEKLVEDKRAYYV---------VYDKEDP 135 GL DEGPDIGG GPY QS+R +IY EYA++L++ +AYY + +K+D Sbjct: 64 ITGLKHDEGPDIGGPVGPYIQSQRTDIYLEYAKELIDKGKAYYCFCTKERMDSLKNKDDE 123 Query: 136 SKELFTTYEY-----PHEYKEK---GHPVTIKFK-VLPGKTSFEDLLKGYMEFDNSTLED 186 KE + ++ E EK P I+ G T+F D + G + DNS L+D Sbjct: 124 EKEFYKYDKHCLKLSKEEINEKLASNIPYVIRQNNPESGFTTFHDEIYGDISVDNSELDD 183 Query: 187 FIIMKSNGFPTYNFAVVVDDHLMRISHVFRGEDHLSNTPKQLMIYEAFGWEAPVFMHIPL 246 I++KS+G+PTYNFA VVDDHLM I+HV RG ++LS+ PK +Y+AFGWE P+++H P Sbjct: 184 MILIKSDGYPTYNFANVVDDHLMGITHVVRGSEYLSSAPKYNRLYDAFGWEVPIYIHCPP 243 Query: 247 ILGSDRTPLSKRHGATSVEHFRREGILSRALMNYLALLGWRVEGD-EIFTIEEKLQSFDP 305 I+ LSKR+G S + +G L A++NY+ALLGW + EIF ++E ++ F+ Sbjct: 244 IMKDAHQKLSKRNGDASFQDLIEKGYLKEAVLNYIALLGWNPGNEKEIFDLDELVELFNY 303 Query: 306 KDISNKGVIFDYQKLEWVNGKHMRRIDLEDLKREFIEWAKYAGKEIPSVDERYFSETLRI 365 K+I+ IFD KL+W+NG++M+++ LE+ + + + K + ++D SE L+I Sbjct: 304 KNINKSPAIFDNVKLKWMNGEYMKKLPLEEFNKMALPYYKKVISK--NLDFLKISELLKI 361 Query: 366 CREKVNTLSQLYDIMYPFMNDDYEYEKD-YVEKFLKR--EEAERVLEEAKKAFKDLNSWN 422 +V LS++ D M F N+ EY + Y+ K +K E + LE+ FK+L+ W Sbjct: 362 ---RVEILSEIPD-MLDFFNELPEYSTEIYIHKKMKTNLENSLFTLEKILPKFKELSPWT 417 Query: 423 MEEIEKTLRDLSEKGLASKKVVFQLIRGAVTGKLVTP-GLFETIEVLGKERTLKRLERTL 481 +E IEK DL + +V +R A++GK TP G FE +++GK+ +LKR+E + Sbjct: 418 LENIEKCCMDLISELQVKNGIVLWPVRIALSGKKSTPGGAFEIADIIGKDESLKRIEYGI 477 Query: 482 QFLK 485 + LK Sbjct: 478 KKLK 481 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: 688 Number of extensions: 37 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: 487 Length of database: 487 Length adjustment: 34 Effective length of query: 453 Effective length of database: 453 Effective search space: 205209 Effective search space used: 205209 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 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