Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate 5210702 Shew_3130 glutamate--tRNA ligase (RefSeq)
Query= reanno::Caulo:CCNA_01982 (470 letters) >FitnessBrowser__PV4:5210702 Length = 319 Score = 125 bits (315), Expect = 2e-33 Identities = 97/289 (33%), Positives = 150/289 (51%), Gaps = 19/289 (6%) Query: 10 VTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEGLDW 69 V RFAPSP+G LH G AL ++L AR G++L+R+ED D R + A I + L+ Sbjct: 34 VGRFAPSPSGPLHFGSLIAALGSYLRARAEQGQWLVRIEDIDPPREVKGASDLILKTLEA 93 Query: 70 LGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGR-AIRSP 128 GL D V++Q +R + ++ LLA+ +AY C + ++++ +GR AIR+ Sbjct: 94 YGLHWDGAVLYQSSRLDDYQARLNSLLAEDKAYYCQCTRKQIQAM--GGTYDGRCAIRTA 151 Query: 129 WRDAPEGDLSAPHVIRFKGPLDGETLVNDLVKGPVTFK-NIELDDLVLLRADGAPTYNLA 187 A IR + L + ++L+ GP+ + +D ++ R DG Y LA Sbjct: 152 KHTA--------GAIRIRNTLAIDHFDDELL-GPIRVEPEFAAEDFIIKRRDGLYAYQLA 202 Query: 188 VVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKLSKRHGA 247 VV+DD G+T V+RG D L ++ARQ ++ D P + H+PL G KLSK++ A Sbjct: 203 VVMDDAFQGITEVVRGADLLTSSARQATLFNLFDDNAPKWLHLPLACAEPGMKLSKQNHA 262 Query: 248 QAVGEFADLGYIPEGMRNYLARLGWGHGD-DEVFTD-EQAISWFDVADV 294 A+ DL + LA LG D D V T QA+S F+++ + Sbjct: 263 PAI----DLKAPQASINAALAFLGQAPCDIDSVKTMLAQAVSQFELSRI 307 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: 394 Number of extensions: 24 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: 319 Length adjustment: 30 Effective length of query: 440 Effective length of database: 289 Effective search space: 127160 Effective search space used: 127160 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: 50 (23.9 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