Align glutamate-tRNAGln ligase (EC 6.1.1.24) (characterized)
to candidate WP_011868351.1 MMARC5_RS02955 glutamate--tRNA ligase
Query= BRENDA::Q9X2I8 (487 letters) >NCBI__GCF_000016125.1:WP_011868351.1 Length = 555 Score = 143 bits (360), Expect = 2e-38 Identities = 125/402 (31%), Positives = 191/402 (47%), Gaps = 54/402 (13%) Query: 25 VRVRFAPSPTGHLHVGGARTALFNWMFARKEGGKFILRIEDTDTERSSREYEQQILESLR 84 V +RFAP+P+G LH+G AR ++ N F +K GK +LR+EDTD +R E + I E L+ Sbjct: 94 VVMRFAPNPSGPLHIGHARASVLNDFFTKKYNGKLVLRLEDTDAKRVLPEAYEMIQEDLK 153 Query: 85 WCGLDWDEGPDIGGDFGPYRQSERLEIYREYAEKLVEDKRAYYVVYDKED--PSKELFTT 142 W G+ DE QSERLE Y EY KL+E +AY D ++ +E T Sbjct: 154 WLGVKVDE---------VIVQSERLETYYEYGRKLIEMGQAYVCDCDADEFRTLREQGTL 204 Query: 143 YEYPHEYKEKGHPVTIKFKVLPGK-TSFEDLLKGYMEFDNSTLEDFIIMK-------SNG 194 + E+ + + K+L G+ + LK + N ++ DF I + NG Sbjct: 205 CKCRDTIPEEN--LKLWEKMLAGELDNVAVRLKTDIAHKNPSIRDFPIFRIERTPHPKNG 262 Query: 195 -----FPTYNFAVVVDDHLMRISHVFRGEDHLSNTPKQLMIYEAFGWEAPVFMHIPLI-L 248 +P N +V VDDHL+ ++HV RG+DH+ NT KQ IY FGWE P ++H ++ + Sbjct: 263 IKYHVYPLMNLSVTVDDHLLGMTHVLRGKDHIVNTEKQEYIYNYFGWEIPEYVHYGILKI 322 Query: 249 GSDRTPLSKRH-GATSVEH-------------FRREGILSRALMNYLALLGWRVEGDEIF 294 SK H G S E+ R+ GI AL + +G + + D F Sbjct: 323 EGPVLSTSKMHAGILSGEYSGWDDARLGTLRALRKRGIRPEALYKLMVEIGIK-QADVRF 381 Query: 295 TIEEKLQSFDPKDISNKGV----IFDYQKLEWVNGKHMRRIDLEDLKREFIEWAKYAGKE 350 E + KDI +K + K ++G R+IDL R + ++ +E Sbjct: 382 AWENLYAA--NKDIIDKDARRFFFVESPKKLVISGADSRKIDL----RMHPDRSELGNRE 435 Query: 351 IPSVDERYFSETLRICREKVNTLSQLYDIMYPFMNDDYEYEK 392 + E Y S+ L K+ L +L++I+ + +D Y K Sbjct: 436 LLFDGEIYVSDDLE--AGKMYRLMELFNIVVEKVENDILYAK 475 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: 725 Number of extensions: 40 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 487 Length of database: 555 Length adjustment: 35 Effective length of query: 452 Effective length of database: 520 Effective search space: 235040 Effective search space used: 235040 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 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