Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate Ga0059261_1809 Ga0059261_1809 tRNA synthetases class I (E and Q), catalytic domain
Query= reanno::Caulo:CCNA_01982 (470 letters) >FitnessBrowser__Korea:Ga0059261_1809 Length = 280 Score = 141 bits (355), Expect = 3e-38 Identities = 89/255 (34%), Positives = 125/255 (49%), Gaps = 6/255 (2%) Query: 9 VVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEGLD 68 +VTRFAPSPTG LH+G A +A+ +AR G+FL+R+ED D RS V I L+ Sbjct: 2 IVTRFAPSPTGRLHLGHAFSAIRAHDFARERNGRFLVRIEDIDGTRSRPEHVETILRDLE 61 Query: 69 WLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARA-EGRAIRS 127 WLGL D EV+FQ R R+ + L A G Y C+ + ++ + EG Sbjct: 62 WLGLGWDGEVVFQSQRLARYEAALDRLRAAGLLYPCFCTRADIAASVSAPHGPEGPVYPG 121 Query: 128 PWRDAPEGDLSAPHVIRFKGPLDGETLVNDLV-----KGPVTFKNIELDDLVLLRADGAP 182 R DLS PH R T+ L +G V + D+VL R D Sbjct: 122 TCRALVSPDLSRPHCWRIDMAKALATVSTPLTFEEGGRGRVEADPLSHGDVVLARKDAPA 181 Query: 183 TYNLAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKLS 242 +Y+LAV +DD VT ++RG+D + L+ + VP + H L+ G DG +L+ Sbjct: 182 SYHLAVTIDDAAQQVTDIVRGEDLIAATHVHRLLQALLGLPVPRYHHHALLTGADGERLA 241 Query: 243 KRHGAQAVGEFADLG 257 KRHGA + + G Sbjct: 242 KRHGAPTLAALREAG 256 Lambda K H 0.319 0.135 0.405 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: 421 Number of extensions: 17 Number of successful extensions: 2 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: 470 Length of database: 280 Length adjustment: 29 Effective length of query: 441 Effective length of database: 251 Effective search space: 110691 Effective search space used: 110691 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 (21.7 bits) S2: 49 (23.5 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