Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate 208049 DVU2552 glutamyl-tRNA synthetase
Query= reanno::Caulo:CCNA_01982 (470 letters) >MicrobesOnline__882:208049 Length = 463 Score = 366 bits (940), Expect = e-106 Identities = 208/469 (44%), Positives = 273/469 (58%), Gaps = 16/469 (3%) Query: 7 TGVVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEG 66 + VVTRFAPSPTG LHIGGARTA+FNWL ARH GG+F++R+EDTD ERS + +I Sbjct: 2 SNVVTRFAPSPTGHLHIGGARTAIFNWLLARHFGGRFVLRIEDTDTERSKQEYTDSILAS 61 Query: 67 LDWLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIR 126 + WLGL D ++I+Q R + + LL G AY C +E+E RE+ARA+G R Sbjct: 62 MKWLGLDWDGDLIYQSERFDIYNSYIDRLLESGHAYWCECPPDEVEKMREEARAKGLKPR 121 Query: 127 SPWR----DAPEGDLSAPHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRADGAP 182 R D GD V+R K P +G + +DLVKG V F ELDD+VL R+DGAP Sbjct: 122 YNGRCRSRDLGPGD---GRVVRLKAPAEGRIVFDDLVKGTVAFDVAELDDMVLRRSDGAP 178 Query: 183 TYNLAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKLS 242 TYNLAVVVDD MGVTHV+RGDDHL+N +Q L+YQA+ + +P F H+P+I GPD KLS Sbjct: 179 TYNLAVVVDDATMGVTHVLRGDDHLSNTPKQILLYQALGFDLPRFGHVPMILGPDRKKLS 238 Query: 243 KRHGAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPARLD 302 KRHGA+AV E+ G +P+ + NYL RLGW HGD E+F E+ + F ++ + A D Sbjct: 239 KRHGAKAVIEYEQYGLLPQALVNYLVRLGWSHGDQEIFALEELVEKFGTENLNSSAAGFD 298 Query: 303 WAKLNHINAQHLRKADDARLTALALAAAETRGEPLPADAAERIARTVPEVKEGAKTILEL 362 KL +N +LR+ L L L G + A R+A+ VP +E A ++EL Sbjct: 299 PDKLEWLNGHYLRETSPEELARLVLPFVAAEGFDVD---ASRLAQLVPLFRERANNLVEL 355 Query: 363 VDHCAFALKTRPLALEE----KTQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLKSF 418 F L P A E K LTEE + +R+ LAA FD E + + Sbjct: 356 ARVMRFMLV--PAAEVEYDAAAVAKALTEEGRRHVAGVREALAALGTFDREGCEKAIHDY 413 Query: 419 AESEGVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDALA 467 E G+ F + PA+R + G P L MA L RD+ + RLD A+A Sbjct: 414 VEGNGLKFKQVAPAVRVAVVGAMGGPGLPDMMALLGRDDVLARLDRAVA 462 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: 669 Number of extensions: 35 Number of successful extensions: 3 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: 463 Length adjustment: 33 Effective length of query: 437 Effective length of database: 430 Effective search space: 187910 Effective search space used: 187910 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: 51 (24.3 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