Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate GFF1424 PGA1_c14410 putative glutamyl-tRNA synthetase
Query= reanno::Caulo:CCNA_01982 (470 letters) >FitnessBrowser__Phaeo:GFF1424 Length = 291 Score = 130 bits (328), Expect = 4e-35 Identities = 90/276 (32%), Positives = 129/276 (46%), Gaps = 26/276 (9%) Query: 11 TRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEGLDWL 70 TRFAPSPTG LH+G A +AL A+ GG+FL+R+ED D RS I+E L WL Sbjct: 5 TRFAPSPTGPLHLGHAYSALLAHDMAQANGGRFLLRIEDIDTARSRPHWEQQIYEDLTWL 64 Query: 71 GLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKAR-------AEGR 123 GL V+ Q R PR+ + +L A G Y C + ++E A + +GR Sbjct: 65 GLNWPQPVMRQSQRLPRYRATLDQLTAMGLTYPCRCNRRDIEAAAGAPQEGVPQFGPDGR 124 Query: 124 AIRSPWRDAPEGDLSAPHVIRFKGPLDGETLVNDLVKGPVTFKN---------------I 168 R+ P + A VIR L+ E+ VN P T Sbjct: 125 IYPGTCRNRPMAEAGAEDVIR----LNMESAVNAARLRPFTETGETYNGQHPMDARRLIT 180 Query: 169 ELDDLVLLRADGAPTYNLAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFA 228 + D++L+R Y+L+VVVDD D +THV+RG D L+ + P + Sbjct: 181 TVGDIILVRRGMGSAYHLSVVVDDADQHITHVVRGADLFEATQIHVLLQALLGLPTPTYH 240 Query: 229 HIPLIHGPDGAKLSKRHGAQAVGEFADLGYIPEGMR 264 H LI G +L+KR A+A+ ++ G P+ +R Sbjct: 241 HHNLIRDEQGKRLAKRDDARAIAKYRAEGATPQDIR 276 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: 370 Number of extensions: 13 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: 291 Length adjustment: 30 Effective length of query: 440 Effective length of database: 261 Effective search space: 114840 Effective search space used: 114840 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