Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate WP_085773695.1 B1812_RS12630 glutamate--tRNA ligase
Query= reanno::Caulo:CCNA_01982 (470 letters) >NCBI__GCF_002117405.1:WP_085773695.1 Length = 474 Score = 468 bits (1205), Expect = e-136 Identities = 250/466 (53%), Positives = 306/466 (65%), Gaps = 10/466 (2%) Query: 9 VVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEGLD 68 V+TRFAPSPTGFLHIG ARTALFNWLYAR GGK L+R+EDTDRERST+AA+ AI +G+ Sbjct: 5 VITRFAPSPTGFLHIGSARTALFNWLYARKHGGKMLLRIEDTDRERSTQAAIEAILDGMR 64 Query: 69 WLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIR-- 126 WLGL D + I+Q RAPRH EV ELLAKG+AYRC+ + ELE REKARAEGR R Sbjct: 65 WLGLDWDGDAIYQFARAPRHREVAEELLAKGKAYRCFATAAELEEMREKARAEGRPPRYD 124 Query: 127 SPWRDAP--EGDLSAPHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRADGAPTY 184 WRD E A V+R K P +GET+V D V+G V F N +LDD VLLR+DG PTY Sbjct: 125 GRWRDRDPSEAPAGASSVVRLKAPREGETIVGDAVQGRVAFPNKDLDDFVLLRSDGTPTY 184 Query: 185 NLAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKLSKR 244 LAVVVDDHDMGVT +IRGDDH NAARQT IYQAM W +PAFAHIPLIHG DGAKLSKR Sbjct: 185 MLAVVVDDHDMGVTQIIRGDDHFTNAARQTHIYQAMGWDIPAFAHIPLIHGADGAKLSKR 244 Query: 245 HGAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPARLDWA 304 HGA V + LGY+P +RNYLARLGW GD E FT ++ I FD+A V ++PAR D+ Sbjct: 245 HGALGVDAYRALGYLPIALRNYLARLGWSQGDKEFFTPDELIQAFDIAQVHRSPARFDFV 304 Query: 305 KLNHINAQHLR-KADDARLTALALAAAETRGEP-----LPADAAERIARTVPEVKEGAKT 358 KL ++N +R AD+ L AL +G P L ++ + +K AKT Sbjct: 305 KLENMNGHFMRAMADEELLLALIDTLPYLKGGPEALTKLDERKRAQLLAAMSGLKARAKT 364 Query: 359 ILELVDHCAFALKTRPLALEEKTQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLKSF 418 + EL+D AF RPLA +EK + LTE+ RL L +LAA P++ AAT E ++ Sbjct: 365 LNELLDGAAFLFAERPLAPDEKAKSLLTEQGKARLAALAKRLAALPEWSAATSEAAVRET 424 Query: 419 AESEGVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDD 464 A + G LR LTG +P + + M L R+E++ R+ D Sbjct: 425 ANELSLKLGDLAQPLRAALTGRGVSPPIFEVMEILGREESLARIAD 470 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: 667 Number of extensions: 31 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: 474 Length adjustment: 33 Effective length of query: 437 Effective length of database: 441 Effective search space: 192717 Effective search space used: 192717 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 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