Align Glutamyl-tRNA(Gln) amidotransferase subunit D; Glu-ADT subunit D; EC 6.3.5.- (uncharacterized)
to candidate 350054 BT0526 L-asparaginase I (NCBI ptt file)
Query= curated2:A5UK11 (436 letters) >FitnessBrowser__Btheta:350054 Length = 346 Score = 164 bits (416), Expect = 3e-45 Identities = 116/344 (33%), Positives = 176/344 (51%), Gaps = 13/344 (3%) Query: 92 NISIISTGGTVSSIIDYRTGAVHPKFTAADLIKANPELLDYANYNVKALY---NILSENM 148 ++ +I TGGT+ I + TGA+ F L+K PEL + NY + + + S +M Sbjct: 7 SVLLIYTGGTIGMIENPETGALE-NFNFDHLLKHVPELKRF-NYRISSYQFDPPLDSSDM 64 Query: 149 QPKYWVEAAESIANDISDGSDGIVIAHGTDTLHYTAAALSFMLKT-PVPIVITGAQRSSD 207 +P YW + + I N D DG VI HGTDT+ YTA+ALSFML+ P+++TG+Q Sbjct: 65 EPAYWAKLVK-IINYNYDYFDGFVILHGTDTMAYTASALSFMLENLSKPVILTGSQLPIG 123 Query: 208 RPSSDANMNLIDSVVAAKSDIAEVSVCMHGSLNDSYTYLHKGTKVRKMHTSRRDTFRSIN 267 +D NLI ++ A + + + + +L +G + K++ + FRS N Sbjct: 124 TLRTDGKENLITAIEIAAAKNPDGTAIVPEVCIFFENHLMRGNRTTKINAENFNAFRSFN 183 Query: 268 YEPIAKIENHSVDINPNYRYTKRNENELEVNSAVEEKVGLIKSFPGICEELIE--YHIDK 325 Y P+A++ H + PN + L+ + + V ++ FPGI EE+I H+ Sbjct: 184 YPPLARVGIH-IKYEPNLIRKPDPDKPLKPHYLFDTNVVILTLFPGIQEEIIHSLLHVP- 241 Query: 326 GYKGLVIEGTGLGHVPDK--LITPLARAHDENIPVVMTSQCLYGRVNMNVYSTGREILNA 383 G K +V++ G G+ P K I L A D I +V +QC G V M Y TG +L A Sbjct: 242 GLKAVVMKTFGSGNAPQKEWFIRELKEATDRGIIIVNITQCASGAVEMGRYETGMHLLEA 301 Query: 384 GVISGRDMTPETAYVKLSWVLGQTNDIGEVAKLMNKNIAGEFNE 427 GVISG D TPE A KL ++LG ++ MN + GE + Sbjct: 302 GVISGYDSTPECAVTKLMFLLGHGLSNKDIRYKMNSCLIGEITK 345 Lambda K H 0.313 0.132 0.373 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: 416 Number of extensions: 27 Number of successful extensions: 5 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: 436 Length of database: 346 Length adjustment: 30 Effective length of query: 406 Effective length of database: 316 Effective search space: 128296 Effective search space used: 128296 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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