Align Glutamyl-tRNA(Gln) amidotransferase subunit D; Glu-ADT subunit D; EC 6.3.5.- (uncharacterized)
to candidate 5209470 Shew_1940 cytoplasmic asparaginase I (RefSeq)
Query= curated2:A5UK11 (436 letters) >FitnessBrowser__PV4:5209470 Length = 337 Score = 156 bits (395), Expect = 8e-43 Identities = 113/348 (32%), Positives = 179/348 (51%), Gaps = 24/348 (6%) Query: 90 KQNISIISTGGTVSSIIDYRTGAVHPKFTAADLIKANPELL--DYANYNVKALYNIL-SE 146 K +I + TGGT+ A P F D +KA PE + ++ + ++ S Sbjct: 3 KPSIYVAYTGGTIGMQKTDNGFAPVPGFLT-DCVKAMPEFFHQEMPDFVISEYCPLIDSS 61 Query: 147 NMQPKYWVEAAESIANDIS---DGSDGIVIAHGTDTLHYTAAALSFMLK-TPVPIVITGA 202 NM P W + IA+DI D DG VI HGTDT+ +TA+ALSFML+ P+++TG+ Sbjct: 62 NMAPTDW----QMIADDIKANYDKYDGFVILHGTDTMAFTASALSFMLQGLTKPVIVTGS 117 Query: 203 QRSSDRPSSDANMNLIDSV-VAAKSDIAEVSVCMHGSLNDSYTYLHKGTKVRKMHTSRRD 261 Q + SD NL++++ +AA +AEV + + L +G + K H D Sbjct: 118 QIPLAQLRSDGQTNLLNALYIAANYPVAEVCLFFNNKL-------FRGNRTTKAHADGFD 170 Query: 262 TFRSINYEPIAKIENHSVDINPNYRYTKRNENELEVNSAVEEKVGLIKSFPGICEELIEY 321 F S N+ PI + + R ++ N L VN + +G++ +PGI E+I+ Sbjct: 171 AFASPNF-PILLEAGIKIRLKAG-RISESKANTLTVNKISPQPIGVVTLYPGITTEIIDN 228 Query: 322 HIDKGYKGLVIEGTGLGHVPD--KLITPLARAHDENIPVVMTSQCLYGRVNMNVYSTGRE 379 + + K L++ G+G+ P +L+ L +A++ I +V +QCL G+VNM Y+TG Sbjct: 229 ILQQPVKALILLTYGVGNAPQNPELLECLRKANERGIILVNLTQCLQGKVNMGGYATGNA 288 Query: 380 ILNAGVISGRDMTPETAYVKLSWVLGQTNDIGEVAKLMNKNIAGEFNE 427 + AGVISG DMT E A KL ++L ++ M +++ GE E Sbjct: 289 LAKAGVISGFDMTTEAALTKLHYLLSTELSPSDIRVQMQQDLCGELTE 336 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: 338 Number of extensions: 19 Number of successful extensions: 4 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: 337 Length adjustment: 30 Effective length of query: 406 Effective length of database: 307 Effective search space: 124642 Effective search space used: 124642 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